Term
| Peptide bond: _______ bond linking two amino acids together |
|
Definition
|
|
Term
| Average polypeptide chain length: approximately _____ amino acids |
|
Definition
|
|
Term
| 4 substituents of an amino acid: _________ |
|
Definition
| α-amino group, α-carboxy group, H atom & R (residue) group. |
|
|
Term
| Central α-carbon atom: center of ________. |
|
Definition
|
|
Term
Except for ______, amino acids
are all chiral |
|
Definition
|
|
Term
| L & D-______ isomers are _____ images of each other |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Majority of amino acids are L or D isomers |
|
Definition
|
|
Term
| Ionization: ability to become _____ via _____ or _____ |
|
Definition
charged
protonation (H+) or deprotonation |
|
|
Term
| Zwitterion: possesses ______ |
|
Definition
| the positive and negative charges simultaneously |
|
|
Term
| Zwitterion is between ____ form & ____ form. |
|
Definition
|
|
Term
| Zwitterion is at the _____ point of an amino acid. |
|
Definition
| Isoeletric (charged but electrically neutral) |
|
|
Term
|
Definition
| 50% is protonated and 50% is deprotonated |
|
|
Term
| Optimal buffering or a resistance to change of pH occurs at the _____. |
|
Definition
|
|
Term
| pI: (or _______): pH at which the net electrical charge is _____. |
|
Definition
|
|
Term
| Aspartate is an acidic amino acid that has _____ protonation states |
|
Definition
|
|
Term
| Lysine is a ____ amino acid with ____ protonation states. |
|
Definition
|
|
Term
| R-groups are typically _____ or _____. |
|
Definition
|
|
Term
| Two general classes of amino acids: ____ & ______ |
|
Definition
|
|
Term
Hydrophilic R-groups generally have
_________ atoms |
|
Definition
|
|
Term
| Three Hydrophilic subgroups: _____ |
|
Definition
Acidic (Negative)
Basic (Positive)
Neutral |
|
|
Term
| Hydrophilic Basic (positive) have ____ atoms. |
|
Definition
|
|
Term
| Hydrophilic Acidic (negative) |
|
Definition
|
|
Term
| Cys and Met are weakly ______ |
|
Definition
| Hydrophilic (Neutral subgroup as well) |
|
|
Term
| Disulfide linkages are formed between ____ |
|
Definition
|
|
Term
Cysteine frequently pairs with another Cys in a disulfide linkage (-S-S-),
usually in the ____ of a protein; so it becomes more _____. |
|
Definition
|
|
Term
Hydrophobic R-groups have straight,
_____ or _____ carbon structures. |
|
Definition
|
|
Term
| Aliphatic ______ carbon structure. |
|
Definition
|
|
Term
| Aromatic _____ carbon structure. |
|
Definition
|
|
Term
| Aromatic amino acids: ______ |
|
Definition
Phenylalanine
Tyrosine
Tryptophan |
|
|
Term
| Phenylalanine has a _____ ring |
|
Definition
|
|
Term
| Tyrosine has a _____ ring |
|
Definition
|
|
Term
| Tryptophan has a _____ ring |
|
Definition
|
|
Term
Although proline has a ring, it is technically _____, because the side chain is initially straight, but this side
chain subsequently cyclizes with the ____. |
|
Definition
|
|
Term
| Proline has a distinctive R-group, which has an _____ group (_____) as part of the aliphatic ring structure as a result of the side chain cyclizing. |
|
Definition
|
|
Term
| Aromatic saturated or unsaturated? |
|
Definition
|
|
Term
| Aliphatic saturated or unsaturated? |
|
Definition
|
|
Term
| When pH = pK ____ protonated _____ deprotonated |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| The equivalent point _____ |
|
Definition
| pH = pK 1:1 deprotonated protonated |
|
|
Term
α-carbon group ionization: occurs for the carboxyl & amino groups with
their pKs about ____ and _____, respectively, for the free amino acids. |
|
Definition
|
|
Term
Side chain group ionization: at physiological pH of ~ 7.3 all the acidic
and all the basic side chain groups are ______. |
|
Definition
|
|
Term
| Noncovalent ____ kcal/mole per bond |
|
Definition
|
|
Term
| Covalent _____ kcal/mole per bond |
|
Definition
|
|
Term
| Noncovalent bonds of protein structure: ______ |
|
Definition
H-bonds
Hydrophobic interactions
Electrostatic interactions (ionic or "salt" bonds)
van der Waals interactions |
|
|
Term
| Disulfide bonds are ____ of two adjacent S-H R groups from Cys |
|
Definition
|
|
Term
| Primary structure stabilized by ______ |
|
Definition
| covalent peptide (amide) bonds |
|
|
Term
| Secondary structure stabilized by ______ |
|
Definition
|
|
Term
| R groups of α-helix & β-pleated sheets ______ |
|
Definition
|
|
Term
| Tertiary structure stabilized by ______ |
|
Definition
| hydrophobic interactions of R-groups |
|
|
Term
| ____ side chains form the core of the protein |
|
Definition
|
|
Term
| _____ side chains are solvent exposed |
|
Definition
|
|
Term
| Which structures are based on just the protein itself |
|
Definition
| primary, secondary, tertiary |
|
|
Term
| Quaternary: protein of associated multiple polypeptides, each in their final shape; mostly stabilized by ______ |
|
Definition
| multiple weak noncovalent bond interactions,but may also be stabilized by disulfide bonds between polypeptide subunits |
|
|
Term
| _____ bond facilitates polymerization of the primary structure of proteins |
|
Definition
|
|
Term
| Mechanism of Peptide Bond formation ____ |
|
Definition
|
|
Term
| Peptide Polymers Formed: ________ |
|
Definition
| dipeptides, oligopeptides and polypeptides |
|
|
Term
| Unblocked amino and carboxy termini are ____ at physiological pH = 7.3. |
|
Definition
|
|
Term
| ____ group can be added to the terminal amino end |
|
Definition
acetyl group
acetylated amino terminus |
|
|
Term
| _____ group can be added to the terminal amino end |
|
Definition
| amide to form a carboxamide a amidated carboxy terminus |
|
|
Term
| ____ controls disulfide bond editing when necessary. |
|
Definition
| PDI (protein disulfide isomerase) |
|
|
Term
| Cystine: a _____ acid of 2 cysteines resulting after ______. |
|
Definition
diamino
proteolytic digestion |
|
|
Term
| Does the peptide bond allow for rotation? |
|
Definition
|
|
Term
| There is no rotation around a peptide bond, because we have a ___ bond structure in the ______ form that predominates. |
|
Definition
| bond and half bond structure in the trans form |
|
|
Term
| There is a partial positive charge on the ____ atom of the peptide bond and a partial negative charge on the ____ atom, this allows for _______ |
|
Definition
|
|
Term
| Fibrous proteins are typically soluble or insoluble? |
|
Definition
|
|
Term
| The _____________ Are the Three Most Common Types of Secondary Structures. |
|
Definition
| The α-Helix, β-Pleated Sheet and β-Turn |
|
|
Term
| All secondary structure formations are stabilized by ______ |
|
Definition
|
|
Term
| The R groups in an alpha helix are joined by a single bond so they are able to _____ and also are found ______ |
|
Definition
rotate
pointing away fromthe helice |
|
|
Term
| Most alpha helices are ____ handed. |
|
Definition
|
|
Term
| By having the R groups point out ____ is minimized. |
|
Definition
|
|
Term
| β-pleated sheet structures have ______ and ______ forms |
|
Definition
|
|
Term
| Alignment in Beta Sheets can be ____ or _____. |
|
Definition
|
|
Term
β-turns facilitate a change in direction of the ______ backbone
to assist in _____ folding. |
|
Definition
|
|
Term
| ____ bonds are found at the extreme ends of beta turns. |
|
Definition
|
|
Term
| _______ are the principal forces stabilizing Tertiary Structure |
|
Definition
|
|
Term
| _____ Core results from side chain packing in _____ proteins. |
|
Definition
|
|
Term
| Domains are distinct ______ units, resulting from hydrophobic side chain packing and assembling of all secondary structures. |
|
Definition
|
|
Term
| Tertiary structures may have more than one ______. |
|
Definition
|
|
Term
| Quaternary structure are protein assemblies containing _______. |
|
Definition
| more than just one polypeptide chain |
|
|
Term
| Higher order structure forms when? |
|
Definition
| while the peptide is synthesized. |
|
|
Term
| Chaperones may assist in ______ and _____. |
|
Definition
| folding and correcting minor folding mistakes |
|
|
Term
| Correct folding is _____ with instructions in ____ structure. |
|
Definition
|
|
Term
| Irreversibly folded polypeptides are _______. |
|
Definition
| degraded back to amino acids |
|
|
Term
Formation of additional covalent bonds: the post-translational modifications
occur _______. |
|
Definition
|
|
Term
| Which amino acids can form phosphate bonds? |
|
Definition
|
|
Term
| ____ amino acids can form O-glycosidic bonds in glycoproteins. (O-Linked Glycoslation) |
|
Definition
|
|
Term
| _____ amino acid can form N-glycosidic bond in glycoproteins. (N-linked Carbohydrates) |
|
Definition
|
|
Term
| Forms in which Asn can form a N-glycosidic bond? |
|
Definition
Asn - X - Ser
Asn - X - Thr
X can be anything but proline |
|
|
Term
| As a coenzyme the prosthetic group participates in ______ |
|
Definition
|
|
Term
| Biotin (Vitamin H) can only be covalently bound to which amino acid? |
|
Definition
|
|
Term
| Denaturation is the loss of ______ bonds |
|
Definition
| weak noncovalent , but not the covalent |
|
|
Term
| Denaturation results in loss of _____ structures |
|
Definition
|
|
Term
| Heat denaturation occurs for most proteins between ____ and ____ degrees Celsius. |
|
Definition
|
|
Term
| Eventual outcome of Heat denaturation is ______. |
|
Definition
| progressive unfolding that eventually results in a random coil |
|
|
Term
| If the protein is denatured what happens to function? |
|
Definition
|
|
Term
| Detergents and organic solvents denature proteins by _________. |
|
Definition
| dissipating hydrophobic interactions |
|
|
Term
| With Detergents and Organic Solvents the core of the folded polypeptide is disrupted by interfering with ______ interactions of ______ amino acids. |
|
Definition
|
|
Term
| Strong acids and bases denature proteins because they ______. |
|
Definition
| change the charge patterns |
|
|
Term
| Strong acids and bases cause denaturing by resulting in loss of all ______ charges with acids and _____ charges with bases. |
|
Definition
|
|
Term
| Strong acids and bases eliminate any stabilizing ____ bonds. |
|
Definition
|
|
Term
| 8M urea and 6M guanidine hydrochloride are _____ agents that have high _____ potential. |
|
Definition
Hydrophilic
Hydrogen Bonding |
|
|
Term
| 8M urea and 6M guanidine hydrochloride denature by disrupting ________. |
|
Definition
| any interactions stabilized by hydrogen bonding. |
|
|
Term
| Heavy metals, such as lead, cadmium, mercury, etc., denature proteins by _______ |
|
Definition
| binding to carboxylate groups, sulfur side chains, etc. |
|
|
Term
| Disulfide bond reactivity are affected by ______ agents. |
|
Definition
| reducing and oxidizing agents |
|
|
Term
| Heavy metals interact with the ____ and then the _____ in carboxyls. |
|
Definition
|
|
Term
| Protein modifications generally occur when? |
|
Definition
|
|
Term
| _____ of a disulfide bond is irreversible. |
|
Definition
|
|
Term
| reduction of a disulfide bond is irreversible or reversible? |
|
Definition
|
|
Term
| Protein solubility in distilled water is ____ because of _______. |
|
Definition
|
|
Term
| _____ occurs of protein molecules in distilled water. |
|
Definition
|
|
Term
| With the Salt Effect, a ____ amount of salt enhances solubility (salting _____), while a ___ amount of salt causes the protein to participate out (salting _____) |
|
Definition
moderate .5-5% NaCl
salting in
>33% (NH4)2SO4
salting out |
|
|
Term
| Salting in results in ___ between protein molecules. |
|
Definition
|
|
Term
| In salting out the salt ties up ____ reducing protein solubility. |
|
Definition
|
|
Term
| Does solubility depend on pH? |
|
Definition
|
|
Term
| When is a protein least soluble? |
|
Definition
| pH of solution = pI of protein |
|
|
Term
| At a low pH the protein charges are predominately _____ and therefore _____ solubility. |
|
Definition
positive
increase (repulsion of like charges between the side chains) |
|
|
Term
| At a high pH the protein charges are predominately _____ and therefore ______ solubility. |
|
Definition
| Negative (repulsion of like charges between the side chains) |
|
|
Term
| At the pI the net charge = _____ |
|
Definition
|
|
Term
| Proteins can be separated by ____ and ____ differences. |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Proteins with a size above the cutoff will _____ in dialysis |
|
Definition
| remain in the dialysis bag while the proteins below the cutoff size will diffuse out into the dialysis solution |
|
|
Term
| Anode is the ____ charged end and is where the _____ will migrate towards. |
|
Definition
|
|
Term
| Cathode is the _____ charged end and is where the _____ will migrate towards. |
|
Definition
|
|
Term
| The pH of the solution in electrophoresis is typically set at _____, because most proteins at this pH will have a net ___ charge. |
|
Definition
|
|
Term
| Electrophoresis with a polyacrylamide gel separates based on _____ |
|
Definition
|
|
Term
| With electrophoresis with a polyacrylamide gel and separating based on size, the proteins are denatured with _____ in order to eliminate shape influences. |
|
Definition
|
|
Term
| Control the pore size in Electrophoresis with a polyacrylamide gel by adjusting _____ |
|
Definition
| % of polyacrylamide in the gel, higher % leads to smaller pores |
|
|
Term
| Protein solubility is a function of the R groups ______. |
|
Definition
|
|
Term
| When determining the primary structure, Amino acid composition is determined by _____ |
|
Definition
| complete digest in 6 N HCl at 100oC overnight |
|
|
Term
|
Definition
| on C-terminal side of Lys or Arg. |
|
|
Term
| Chymotrypsin cuts _______ |
|
Definition
| on C-terminal side of bulky hydrophobic amino acids |
|
|
Term
| Cyanogen Bromide (CNBr) hydrolyzes ______ |
|
Definition
| on C-terminal side of Met. |
|
|
Term
| Edman degradation provides for the discrete ordering of amino acids in peptide fragments by using _______, which covalently attaches to the ____ amino acid of a peptide. |
|
Definition
phenylisothiocyanate
N-terminal |
|
|
Term
| In Edman Degradation phenylisothiocyanate, which covalently attaches to the N-terminal amino acid of a peptide and this modified amino acid is removed as a ____ derivative and the corresponding amino acid identified. |
|
Definition
| phenylthiohydantoin (PTH) |
|
|
Term
The cycle of Edman Degradation can be repeated up to _____ times per peptide, advancing sequentially one amino acid from
the _____ end for each cycle. |
|
Definition
|
|
Term
| Methods for analyzing secondary structure: ______ |
|
Definition
1. Circular dichroism (CD) -- a specialized spectroscopic method.
2. Optical rotary dispersion (ORD) -- a specialized spectroscopic method. |
|
|
Term
| Methods for analyzing Tertiary and Quaternary structures: ______ |
|
Definition
1. X-ray diffraction of proteins crystals (x-ray crystallography) -- any size.
2. NMR (nuclear magnetic resonance spectroscopy) -- about 50 kDal max. |
|
|
Term
| Max size for NMR is _____ |
|
Definition
|
|
Term
| Max size for X-ray diffraction of proteins crystals? |
|
Definition
|
|
Term
| Malfolded proteins can result in _____ Disorders. |
|
Definition
| Neurodegenerative Disorders: |
|
|
Term
| Three common neurodegenerative diseases associated with malfolded proteins: _______ |
|
Definition
1. Prion diseases (protein infection – originally thought to result form a “slow”
virus infection)
2. Alzheimers disease
3. Parkinsons disease |
|
|
Term
| Alzheimers disease & Parkinsons disease are a result of ____ of proteins. |
|
Definition
|
|
Term
| With Human Prions only the _____ is the infectious particle not _______. |
|
Definition
|
|
Term
| Normal prion is ____ amino acids |
|
Definition
|
|
Term
| Human prions exist on the ______ and their function is unknown. |
|
Definition
|
|
Term
| Prions remain in the ______ |
|
Definition
|
|
Term
| With human prions disease etiology is a consequence of _______. |
|
Definition
| conformational change to normal protein |
|
|
Term
| Conformational change induced by Human Prions is a decrease in ______ content, while ____ content increases. |
|
Definition
|
|
Term
| Prions have abnormal resistance to ____ |
|
Definition
|
|
Term
| With Human Prions, β-sheet ______, because it is ________. |
|
Definition
aggregates
much less soluble than α-helical form |
|
|
Term
| Abnormal prion proteins are more stable, that is much more _______. |
|
Definition
|
|
Term
| Neurotoxic amyloid results in _____ |
|
Definition
| brain cell apoptosis and patient death |
|
|
Term
| Normal prions can spontaneously convert to abnormal form (_____ frequency). |
|
Definition
|
|
Term
Conversion of normal to abnormal prion proteins ______ over time, since abnormal prion “seed” concentration.
increases |
|
Definition
|
|
Term
| Identity of amino acids ___ and _____ are of critical importance for prion proteins. |
|
Definition
|
|
Term
| Variants of amino acid 129 must be either ____ or ____ for prion disease. |
|
Definition
|
|
Term
| Codon 178 has a ____ transition mutation, which changes ____ to ____. |
|
Definition
| purine (GA, changes asp to asn) |
|
|
Term
| Creutzfeldt-Jacob disease results from a _____ combination of 128 and 178. |
|
Definition
|
|
Term
| Fatal familial insomnia disease results from a ____ combination of 128 and 178. |
|
Definition
|
|
Term
| Potential Therapy for Prion Diseases... long as shit and for fun. |
|
Definition
from atomic level structure data engineer a small molecular
weight compound that might facilitate greater stability for the α-helical rich
form versus the abnormal β-sheet form, thus minimizing the probability of
normal prion protein conformational conversion to the abnormal form. |
|
|
Term
| The first law of thermodynamics: _____ |
|
Definition
|
|
Term
| The second law of thermodynamics: _____ |
|
Definition
| Entropy (S) tends to Increase |
|
|
Term
|
Definition
|
|
Term
|
Definition
| ΔG = ΔGo + RT ln([C][D]/[A][B]) |
|
|
Term
|
Definition
|
|
Term
| At equilibrium ΔG = 0, ΔGo’ = _____ |
|
Definition
ΔGo’ = - RT ln [C][D]/[A][B]
ΔGo’ = - RT ln K’equ |
|
|
Term
| Kinetics: measures ______ |
|
Definition
| rates of chemical reactions |
|
|
Term
| Enzyme kinetics: measures ____ |
|
Definition
rates of chemical
reactions catalyzed by enzymes. |
|
|
Term
| Enzymes do not change the ___ of a chemical reaction but lower the ______. |
|
Definition
equilibrium
energy of the transition state, |
|
|
Term
Standard conditions:
- pH is _____
-temperature is ____ |
|
Definition
|
|
Term
| The substrate has to bind to the enzyme to form a ____ bonded enzyme-substrate complex |
|
Definition
|
|
Term
Enzymes do not change the _____ of substrates and products at equilibrium (i.e. ____) but they decrease
the ____ required to reach equilibrium |
|
Definition
|
|
Term
| Cofactors float into the ____ and out again |
|
Definition
|
|
Term
| Coenzymes are cofactors that are _____ |
|
Definition
|
|
Term
| Prostetic group: cofactor that _____ |
|
Definition
| remains stably bound to the enzyme |
|
|
Term
| The heme in in hemoglobin is an example of a ______ |
|
Definition
|
|
Term
| ATP requires ____ cofactor. |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Lineweaver-Burk plot: 1/V= |
|
Definition
| 1/V = 1/Vmax + Km/Vmax x 1/[S] |
|
|
Term
|
Definition
| substrate concentration required to reach 1/2Vmax |
|
|
Term
| V is a measurement of _____ |
|
Definition
|
|
Term
| At low [S] velocity increases _____ with [S]. |
|
Definition
|
|
Term
| At high [S] velocity is dependent on the ____, e.g. all enzymes are ______. |
|
Definition
[E]
occupied with substrate. |
|
|
Term
| Basic principle of enzyme regulation is controlling ____ of substrate |
|
Definition
|
|
Term
| Km tells us the _____ of an enzyme for a substrate. |
|
Definition
|
|
Term
| Maximum velocity is reached when _____ |
|
Definition
|
|
Term
|
Definition
| half the sites are filled |
|
|
Term
| Km is a measure for the _____ of an enzyme for a particular substrate |
|
Definition
|
|
Term
|
Definition
| weak bonding of the enzymne to substrate |
|
|
Term
| Vmax reveals the _____ which is also called _____. |
|
Definition
|
|
Term
| ______ is a measure for catalytic efficiency. |
|
Definition
|
|
Term
|
Definition
| micro mol product formed /min/mg enzyme |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Km is a measure of affinity for the ______ of an enzyme |
|
Definition
|
|
Term
| What is the fastest enzyme _____ |
|
Definition
|
|
Term
| Kinetic Perfection: _____ |
|
Definition
| the turnover rate (Kcat/Km) is close to the diffusion rate ~10^8-10^9 s^-1 M^-1 |
|
|
Term
| First order kinetics: ____ substrate, reaction rate is ______ to the substrate concentration which ____ over time because ____________. |
|
Definition
one
directly proportional
declines
less and less substrate is available. |
|
|
Term
Second order kinetics: ____ substrates,
reaction rate depends on _______. |
|
Definition
two
concentration of both substrates |
|
|
Term
| Zero order kinetics: reaction rate is ______ |
|
Definition
| independent of the concentration of substrate |
|
|
Term
| Drug metabolism (liver) usually follows _____order kinetics (_____). T1/2 = _____. |
|
Definition
first
[S] < Km
half of S is consumed. |
|
|
Term
| Metabolism of alcohol is limited by _____ which becomes rapidly _____ after initial ingestion (_____ order kinetics) . |
|
Definition
alcohol dehydrogenase
oversaturated
zero |
|
|
Term
| Hemoglobin is regulated by _____ |
|
Definition
|
|
Term
| Noncompetitive inhibitors bind to ____ |
|
Definition
|
|
Term
| uncompetitive inhibitors bind to ______ |
|
Definition
|
|
Term
| Presence of a competitive inhibitor _____ Km and ____ Vmax |
|
Definition
Increases Km
Doesn't affect Vmax |
|
|
Term
| Presence of a competitive inhibitor decreases Km, which ____ the affinity of the enzyme for the substrate. |
|
Definition
|
|
Term
| In addition to ethanol, ____ is also a substrate for ADH. |
|
Definition
|
|
Term
| Methanol is an example of a _____ inhibitor for ADH. |
|
Definition
|
|
Term
| Toxic product of methanol metabolism by ADH. |
|
Definition
| Fromaldehyde and therefore Formic acid |
|
|
Term
| Dihydrofolate Reductase plays a role in the synthesis of ________ |
|
Definition
|
|
Term
| Dihydrofolate Reductase's typical substrate is Dihydrofolate and _____ which is similar in structure to it can act as a competitive inhibitor. |
|
Definition
|
|
Term
| Presence of a noncompetitive inhibitor _____ Km and _____ Vmax |
|
Definition
|
|
Term
| noncompetitive inhibitors bind at ______ |
|
Definition
|
|
Term
| The HIV drug that uses a protease inhibitor is an example of a _____ inhibitor. |
|
Definition
|
|
Term
| HIV protease inhibitor is called _____, which mimics a ______, but binds with ______. |
|
Definition
Crixivan
peptide substrate
very tightly to the active site |
|
|
Term
| Crixivan inhibits the HIV protease by specifically interacting with two ____ at the bottom of the active site of the protease. |
|
Definition
|
|
Term
| Irreversible enzyme inhibition by _____ |
|
Definition
|
|
Term
| Sarin Nerve gas is an example of an ____ inhibitor. |
|
Definition
|
|
Term
| Sarin Nerve gas acts an irreversible inhibitor by binding to a -______ group of _____ on the enzyme ____________. |
|
Definition
-OH of a Ser
Acetylcholinesterase |
|
|
Term
| Penicillin irreversibly inhibits ______ |
|
Definition
| glycopeptide transpeptidase |
|
|
Term
| By Penicillin irreversibly inhibiting glycopeptide transpeptidase, the bacteria can no longer properly ______ |
|
Definition
|
|
Term
| Glycopeptide Transpeptidase is irreversibly inhibited by Penicillin, by it forming a bond with the -____ group of ____, rendering the enzyme inactive. |
|
Definition
|
|
Term
| Need _____ to phosphorylate enzymes. |
|
Definition
|
|
Term
|
Definition
| Marks protein for destruction by protesomes. |
|
|
Term
| Enzymes are phosphorylated by _______. |
|
Definition
|
|
Term
| Protein Kinases phosphorylate proteins through _____. |
|
Definition
|
|
Term
| Can a Kinase reverse its phosphorylation? |
|
Definition
| No, you need a phosphatase to hydrolyze off the phosphate group. |
|
|
Term
| ___ phosphate is from ATP to: _____ amino acid residues. |
|
Definition
|
|
Term
| Phosphorylation - dephosphorylation is not a ____ process |
|
Definition
|
|
Term
| Phosphorylation - dephosphorylation is not a reverse process, ______ are required and in both reactions ____ is generated |
|
Definition
two different enzymes
free energy |
|
|
Term
| _________ ensure unidirectional P -transfer in Phosphorylation & dephosphorylation. |
|
Definition
| Highly favorable free energy changes |
|
|
Term
| Phosphorylation controls the activity of the target proteins by addiing ____ charges. |
|
Definition
|
|
Term
| Phosphorylation controls the activity of the target proteins by giving a phosphate group that can form _____ |
|
Definition
|
|
Term
| In phosphorylation of a protein half of the ΔG (-12 kcal/mol) goes into ____ and the other half is _____. |
|
Definition
| the P-Bond and the other half is conserved in the protein |
|
|
Term
| _____ links the energy status of the cell to the phosphorylation |
|
Definition
|
|
Term
Secretion of ____ by an acinar cell of
the pancreas. |
|
Definition
|
|
Term
Proenzymes are synthesized and stored in granules, the granules accumulate at the
apex of the ____ cell and are released into the lumen. The proezymes are then activated by small amounts of ____ on release into the duodenum |
|
Definition
|
|
Term
| Proenzyme is an ____ form that requires some modification to become _____. |
|
Definition
|
|
Term
| Digestive Enzymes use enzyme activation by specific _________. |
|
Definition
Digestive Enzymes
proteolytic cleavage |
|
|
Term
In Blood clotting a cascade of _____ ensure
rapid and amplified response |
|
Definition
|
|
Term
| Insulin requires activation by ____ |
|
Definition
| specific proteolytic cleavage |
|
|
Term
| ADH is an example of a ____ class of enzymes that perform ____ reactions. |
|
Definition
Oxidoreductases
Oxidation-reduction |
|
|
Term
| ATP synthase and Kinases are an example of a ____ class of enzymes that perform ____ reactions. |
|
Definition
Transferases
Group Transfer |
|
|
Term
| Chymotrypsin is an example of a ____ class of enzymes that perform ____ reactions. |
|
Definition
|
|
Term
| Lyases is a class of enzymes that catalyzes ____ types of reactions. |
|
Definition
Addition or removal of groups
to form double bonds |
|
|
Term
|
Definition
| intramolecular group transfer |
|
|
Term
| Ligases catalyze ___ types of reactions. |
|
Definition
Ligation of two substrates at
the expense of ATP hydrolysis |
|
|
Term
| Chymotrypsin cleaves at the ________ |
|
Definition
| carboxyl terminus of aromatic or large hydrophobic amino acids |
|
|
Term
| Carbonyl carbon of a peptide bond has partial double bond character, and is therefore ____________ |
|
Definition
| less susceptible to nucleophilic attack |
|
|
Term
| Electronegativity describes the ability of an atom to ________ |
|
Definition
| attract electron density towards itself in a covalent bond. |
|
|
Term
| Chymotrypsin is a ______. |
|
Definition
|
|
Term
| The catalytic triangle of Chymotrypsin is composed of: ________. |
|
Definition
|
|
Term
| Serine 195's function in the catalytic triangle of Chymotrypsin? |
|
Definition
| Donates H from its -OH group to His 57 |
|
|
Term
| Histidine 57's function in the catalytic triangle of Chymotrypsin? |
|
Definition
| Accepts the H from the -OH group of Ser 195 in order to become protonated. |
|
|
Term
| Aspartate 102's function in the catalytic triangle of Chymotrypsin? |
|
Definition
| Stabilizes the positive His 57 after it becomes protonated by Ser 195 |
|
|
Term
| The oxyanion hole at Glycine 193 in Chymotrypsin stabilizes ______ through ____ bonds from backbone ____-groups stabilize the oxyanion |
|
Definition
Tetrahedral intermediate formed on Ser 195
Hydrogen
NH2 |
|
|
Term
| ATP Synthase has 3 catalytic sites mainly on the _____ subunits and 3 noncatalytic sites mainly on the _____ subunits. |
|
Definition
|
|
Term
| Daily need of oxygen: ____ g. |
|
Definition
|
|
Term
| Myoglobin function is to _____ |
|
Definition
| Store oxygen for strenuous exercise. |
|
|
Term
|
Definition
|
|
Term
| Oxygenation is reversible: oxygen is bound when _____ and released when ____. |
|
Definition
|
|
Term
Hemeproteins are specialized proteins that
contain heme as a ________. |
|
Definition
| tightly bound prosthetic group |
|
|
Term
| The heme group is the ______ site. |
|
Definition
|
|
Term
| Heme consists of _____ chelating a _____ iron (Fe__+) in the center. |
|
Definition
|
|
Term
| A heme consists of 4 pyrrole rings, held together by _____ bridges decorated with 2 ____ groups on the top, and 4 ___, & 2 _____ groups. |
|
Definition
methine
2 propionate groups on top
4 methyl and 2 vinyl groups |
|
|
Term
| The vinyl groups are part of the _____ in a heme. |
|
Definition
| conjugated double bond system |
|
|
Term
| The system of _______ of a heme is responsible for the color of blood. |
|
Definition
|
|
Term
| Fe2+ is bonded to ___ in the center of the plane of a heme. |
|
Definition
|
|
Term
| Deoxygenated hemoglobin is _____. |
|
Definition
|
|
Term
| Oxygenated hemoglobin is _____. |
|
Definition
|
|
Term
| Iron is ____ to oxygen binding in hemes. |
|
Definition
|
|
Term
| The Proximal His is important in the _____ heme protein, but not in the ____ heme protein. |
|
Definition
Important in hemoglobin
not important in myoglobin |
|
|
Term
| The 5th Coordinate is _____ |
|
Definition
| The N from the proximal His |
|
|
Term
| Fe2+ is held in place (coordinated) by the N of the ______,and by the _______. |
|
Definition
4 pyrrole rings
proximal His (F8). |
|
|
Term
| Oxygen (O2) can bind to the ____ coordinate. |
|
Definition
|
|
Term
| Fe2+ in heme is _____ not ______. |
|
Definition
|
|
Term
| Myoglobin contains 153 amino acids (aa) which form __________. |
|
Definition
| eight alpha helices (A-H) |
|
|
Term
| The heme group in myoglobin is tucked between ______. |
|
Definition
|
|
Term
| The proximal His is residue #8 in helix ______ of myoglobin. |
|
Definition
|
|
Term
| _____ of myoglobin of the structure is alpha helical. |
|
Definition
|
|
Term
| _____ are the major stabilizing forces for Myoglobin |
|
Definition
| Hydrophobic interactions of non-polar side chains |
|
|
Term
| Hydrophilic aa are on the surface of Myoglobin and make it a ______ |
|
Definition
|
|
Term
| Hemoglobin is enclosed within ______ |
|
Definition
|
|
Term
| Erythrocytes are released from bone marrow and circulate for ____ days |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Do RBCs consume any of the oxygen they are transporting? |
|
Definition
|
|
Term
| Erythrocytes are “bags” filled with ____ dissolved in the cytoplasm |
|
Definition
|
|
Term
|
Definition
| Volume of hemoglobin when you spin it down |
|
|
Term
| Hematocrit levels for Males & Females? |
|
Definition
Males 42-53%
Females 38-46% |
|
|
Term
| Hemoglobin In Whole Blood for Males and Females? |
|
Definition
Males 14-17%
Females 12-15% |
|
|
Term
| Patients with abnormally low hemoglobin concentrations are ____. |
|
Definition
|
|
Term
| Hemoglobin is a _____ of two ____ and two “_____” chains |
|
Definition
tetramer
two alpha chains and two "non alpha" chains |
|
|
Term
| Fetal Hemoglobin is composed of ____ subunits |
|
Definition
|
|
Term
| 2 Hemoglobin dimers: ____ |
|
Definition
alpha 1 beta 1 dimer
alpha 2 beta 2 dimer |
|
|
Term
| In hemoglobin _____ enhances oxygen delivery. |
|
Definition
|
|
Term
| Hemoglobin is ____ shifted compared to myoglobin. |
|
Definition
|
|
Term
| The steepest part of the oxygen saturation curve of hemoglobin is located at the partial pressure of _______ |
|
Definition
|
|
Term
| In the lungs _____ of the oxygen binding sites of hemoglobin are occupied. |
|
Definition
|
|
Term
| p50 of Hemoglobin is _____ |
|
Definition
|
|
Term
| Hemoglobin oxygen saturation curve is marked _____, and with its steep slope is an indicator of ______. |
|
Definition
|
|
Term
| What unloads faster, myoglobin or hemoglobin? |
|
Definition
|
|
Term
| Hemoglobin posses _____ binding sites with _____ states. |
|
Definition
|
|
Term
| ____ conformation of hemoglobin is taken in absence of Oxygen |
|
Definition
|
|
Term
| _____ conformation of hemoglobin is the fully oxygenated form. |
|
Definition
|
|
Term
| R binds oxygen _____x tighter than that of T. |
|
Definition
|
|
Term
| Hemoglobin participates in positive or negative cooperativity? |
|
Definition
|
|
Term
|
Definition
Transition from T to R:
Binding of O2 to the first heme increases the affinity of the neighboring
heme, which increases the affinity of the next neighbor |
|
|
Term
| Deoxyhemoglobin the Fe2+ is _____ |
|
Definition
is slightly too large to fit and lies below
the plane |
|
|
Term
| Oxygen (O2) binds to 6th coordination, and _____ away from Fe2+, and iron can now fit into the tetrapyrrole ring. |
|
Definition
|
|
Term
| O2 binding pulls the Fe2+ into the plane and moves the ____ up, which is part of the _ alpha helix that moves with it. |
|
Definition
|
|
Term
| The COOH terminus of the F alpha helix lies in the ____ leading to _____ rearrangements. |
|
Definition
interface between the two dimers
quaternary |
|
|
Term
O2 binding to heme pulls the ____ into the plane of the pyrrole ring and with it the ______.
and its -helix leading to large conformational changes in the hemoglobin tetramer |
|
Definition
|
|
Term
| Transition from T to R state; one pair of _____ |
|
Definition
| alpha beta subunits rotates by 15o |
|
|
Term
| Cooperativity enhances _____ |
|
Definition
|
|
Term
| The oxygen binding/dissociation curve is steepest at the oxygen concentrations that occur in the ___. This permits oxygen delivery to respond to ______ |
|
Definition
tissue
small changes in pO2. |
|
|
Term
| Myoglobin has ___ affinity for oxygen than hemoglobin in the tissues. |
|
Definition
|
|
Term
| Who binds oxygen tighter, hemoglobin or myoglobin? |
|
Definition
|
|
Term
| Hemoglobin binds and releases O2 with positive ______ |
|
Definition
|
|
Term
| Concentration of BPG in red blood cells is ___ mM |
|
Definition
|
|
Term
| 2,3-BPG is a _____ effector |
|
Definition
|
|
Term
| 2,3-BPG is a negative allosteric effector and therefore binds to a _____ and acts through ______. |
|
Definition
site different than O2,
and acts through confrontational changes. |
|
|
Term
| 2,3-BPG dramatically ______ affinity of ____ for O2 |
|
Definition
|
|
Term
| 2,3-BPG binds to the center cavity of ______ ONLY and shifts the equilibrium to the _ state effectively ____ the O2 affinity. |
|
Definition
deoxyhemoglobin
T
reducing |
|
|
Term
| ____ charged residues in each ___ chain are involved in binding of 2,3-BPG. |
|
Definition
Three positively (His)
Beta |
|
|
Term
| The binding of 2,3-BPG causes a ___ shift, leading to a much more effective _____. |
|
Definition
right
loss of the 3rd or possibly 4th oxygens |
|
|
Term
| 2,3-BPG binds the ____ state. |
|
Definition
|
|
Term
| What can lead to an increase in 2,3-BPG? |
|
Definition
| Exercise, altitude, and chronic anemia (sickle cell) |
|
|
Term
| BPG enhances ____ of oxygen in the tissues whose oxygen partial pressure are in the ____ part of the oxygen binding curve. |
|
Definition
|
|
Term
Fetal hemoglobin binds BPG _____, thus facilitating transfer of O2 from
the maternal to the fetal blood. |
|
Definition
|
|
Term
| His143 in beta-chains in adult hemoglobin is _____ in fetal gamma-chains, this removes _______. |
|
Definition
Ser
2 charges from the BPG binding site. |
|
|
Term
| _____ chains have much lower affinity for 2,3-BPG |
|
Definition
|
|
Term
| In fetal hemoglobin His143 (on γ hemoglobin) is substituted by a Ser reducing the affinity for ______. |
|
Definition
|
|
Term
| Protons (low pH) ____ the O2 binding affinity of hemoglobin and favor _____ of O2. |
|
Definition
|
|
Term
| In the Bohr Effect, protons are involved in ______ in the T form |
|
Definition
|
|
Term
|
Definition
| Increases delivery of O2 in tissue |
|
|
Term
Carbon dioxide (CO2), the product of oxidative metabolism, ____ O2
affinity of hemoglobin. |
|
Definition
|
|
Term
| Carbon dioxide (CO2) binds to _____ groups of the alpha and beta chains resulting in ______. |
|
Definition
N-terminal
carbamino-hemoglobin (a carbamate) |
|
|
Term
| pH and CO2 ensure that oxygen is released preferentially in _____ tissue where it is most needed. |
|
Definition
|
|
Term
| ____% of CO2 is transported by hemoglobin |
|
Definition
|
|
Term
| In addition to Hemoglobin, CO2 is transported in the blood as _______. |
|
Definition
|
|
Term
| Bohr Effect causes the curve to shift ____. |
|
Definition
|
|
Term
| Under Low Oxygen conditions it is the right thing to do |
|
Definition
|
|
Term
| At ____ pH caused by increase in protons (as in the Bohr Effect) salt bridge stabilizes quaternary structure of ______. |
|
Definition
|
|
Term
| A decrease in pH causes a ____ shift. |
|
Definition
|
|
Term
| Heterotropic effectors of Hemeglobin |
|
Definition
| Hydrogen ions and CO2 promote release of oxygen (negative allosteric effectors). |
|
|
Term
| H+ and CO2 are ____ effectors of hemoglobin |
|
Definition
| negative allosteric effectors |
|
|
Term
| Bohr effect: lower pH and high CO2 concentrations increase ____ interactions and shift the enzyme to the _-state, which in turn facilitates _____ binding to the center cavity and further shifts the equilibrium to the _ state effectively ____ the O2 affinity. |
|
Definition
subunit
T
2,3-BPG
T
reducing (Right Shift) |
|
|
Term
| _____ is produced when combusting glucose. |
|
Definition
|
|
Term
|
Definition
|
|
Term
| ~80% of CO2 is transported as inorganic bicarbonate, other as _______. |
|
Definition
|
|
Term
In the RBC CO2 is hydrated to _____ by _____, leaves the cell in exchange for
____ ion, and is transported back to the
lungs dissolved in plasma. |
|
Definition
carbonic acid
carbonic anhydrase
chloride |
|
|
Term
| In the lungs bicarbonate is adsorbed back into the RBC and dehydrated into CO2 and released into the lungs. |
|
Definition
|
|
Term
| By hydrating CO2 into bicarbonate you have now made it ______. |
|
Definition
| soluble and able to dissolve in the plasma |
|
|
Term
| Carbonic anhydrase catalyzes at ______ |
|
Definition
| near catalytic perfection (diffusion limit) |
|
|
Term
| Carbonic Anhydrase has a ___ cofactor |
|
Definition
|
|
Term
| The catalytic site of Carbonic Anhydrase is made up of ______ |
|
Definition
| Three His that coordinate to the Zn2+ cofactor |
|
|
Term
Role of Zn2+ in Carbonic Anhydrase?
Role of H2O in Carbonic Anhydrase? |
|
Definition
Activates H2O, allowing to lose a H+ and then become a strong nucleophile to attack CO2
Zn2+ also stabilizes the negative charge (of the transition state) formed on the O of CO2 following the nucleophilic attack |
|
|
Term
| If a patient has carbon monoxide poisoning they will have arterial blood gas that shows ______. |
|
Definition
| elevated carboxyhemoglobin |
|
|
Term
| CO is a byproduct of _____ |
|
Definition
|
|
Term
| CO is a _____ for O2 and its binding to heme groups. |
|
Definition
| competitive antagonist (Comp inhibitor) |
|
|
Term
| CO binds to _____, with a ____ times greater affinity than O2. |
|
Definition
|
|
Term
| Throbbing, headache, confusion, fainting occur when ____% of the hemes are occupied by CO, ____% is fatal. |
|
Definition
|
|
Term
| CO poisoning can be treated with ______. |
|
Definition
| hyperbaric oxygen, O2 will slowly replace CO |
|
|
Term
| CO-hemoglobin has a _____ color |
|
Definition
| cherry-red (not cyanosed) |
|
|
Term
| The binding of carbon monoxide at one of the four sites ____ the oxygen affinity of the remaining three sites, which causes the hemoglobin molecule to ______. |
|
Definition
increases
retain oxygen that would otherwise be delivered to the tissue. |
|
|
Term
| CO shifts the Oxygen Saturation Curve to the _____. |
|
Definition
| Left (increases affinity) |
|
|
Term
Because of the increased affinity between
hemoglobin and oxygen during carbon monoxide poisoning, the blood oxygen content is ______. |
|
Definition
|
|
Term
The problem in Carbon Monoxide poisoning is that because all the oxygen stays in the ______, none is delivered to the
_____. This leads to a ____ injury. |
|
Definition
hemoglobin
tissues
Hypoxic Tissue injury |
|
|
Term
| Hemoglobin acquires a ____ color when converted into carboxyhemoglobin, so poisoned patients have been described as looking pink-cheeked and healthy. |
|
Definition
|
|
Term
| Methemoglobin is the _____ form and is ____ colored. |
|
Definition
|
|
Term
Methemoglobin contains the oxidized form of ____ iron (____) which is useless as an
oxygen transporter |
|
Definition
|
|
Term
| Oxidizing chemicals like aniline dyes, aromatic nitro compounds, and inorganic or organic nitrites cause _____ formation. |
|
Definition
|
|
Term
| Natural protection against oxidation of hemeglobin include, erythrocytes containing ____ & ____ as reducing agents |
|
Definition
| ascorbic acid and glutathion |
|
|
Term
| ______ reduces methemoglobin back to normal hemoglobin. |
|
Definition
|
|
Term
| Methemoglobinemia is treated with _____ which reduces ferric iron back to ferrous iron. |
|
Definition
|
|
Term
| Hemoglobin chain imbalance: ______ |
|
Definition
|
|
Term
| Sickle Cell Hemoglobin is caused by |
|
Definition
| Mutations in the alpha or beta chains |
|
|
Term
| Deoxyhemoglobin the Fe2+ is _____ |
|
Definition
is slightly too large to fit and lies below
the plane |
|
|
Term
| Oxygen (O2) binds to 6th coordination, and _____ away from Fe2+, and iron can now fit into the tetrapyrrole ring. |
|
Definition
|
|
Term
| O2 binding pulls the Fe2+ into the plane and moves the ____ up, which is part of the _ alpha helix that moves with it. |
|
Definition
|
|
Term
| The COOH terminus of the F alpha helix lies in the ____ leading to _____ rearrangements. |
|
Definition
interface between the two dimers
quaternary |
|
|
Term
O2 binding to heme pulls the ____ into the plane of the pyrrole ring and with it the ______.
and its -helix leading to large conformational changes in the hemoglobin tetramer |
|
Definition
|
|
Term
| Transition from T to R state; one pair of _____ |
|
Definition
| alpha beta subunits rotates by 15o |
|
|
Term
| Cooperativity enhances _____ |
|
Definition
|
|
Term
| The oxygen binding/dissociation curve is steepest at the oxygen concentrations that occur in the ___. This permits oxygen delivery to respond to ______ |
|
Definition
tissue
small changes in pO2. |
|
|
Term
| Myoglobin has ___ affinity for oxygen than hemoglobin in the tissues. |
|
Definition
|
|
Term
| Who binds oxygen tighter, hemoglobin or myoglobin? |
|
Definition
|
|
Term
| Hemoglobin binds and releases O2 with positive ______ |
|
Definition
|
|
Term
| Concentration of BPG in red blood cells is ___ mM |
|
Definition
|
|
Term
| 2,3-BPG is a _____ effector |
|
Definition
|
|
Term
| 2,3-BPG is a negative allosteric effector and therefore binds to a _____ and acts through ______. |
|
Definition
site different than O2,
and acts through confrontational changes. |
|
|
Term
| 2,3-BPG dramatically ______ affinity of ____ for O2 |
|
Definition
|
|
Term
| 2,3-BPG binds to the center cavity of ______ ONLY and shifts the equilibrium to the _ state effectively ____ the O2 affinity. |
|
Definition
deoxyhemoglobin
T
reducing |
|
|
Term
| ____ charged residues in each ___ chain are involved in binding of 2,3-BPG. |
|
Definition
Three positively (His)
Beta |
|
|
Term
| The binding of 2,3-BPG causes a ___ shift, leading to a much more effective _____. |
|
Definition
right
loss of the 3rd or possibly 4th oxygens |
|
|
Term
| 2,3-BPG binds the ____ state. |
|
Definition
|
|
Term
| What can lead to an increase in 2,3-BPG? |
|
Definition
| Exercise, altitude, and chronic anemia (sickle cell) |
|
|
Term
| BPG enhances ____ of oxygen in the tissues whose oxygen partial pressure are in the ____ part of the oxygen binding curve. |
|
Definition
|
|
Term
Fetal hemoglobin binds BPG _____, thus facilitating transfer of O2 from
the maternal to the fetal blood. |
|
Definition
|
|
Term
| His143 in beta-chains in adult hemoglobin is _____ in fetal gamma-chains, this removes _______. |
|
Definition
Ser
2 charges from the BPG binding site. |
|
|
Term
| _____ chains have much lower affinity for 2,3-BPG |
|
Definition
|
|
Term
| In fetal hemoglobin His143 (on γ hemoglobin) is substituted by a Ser reducing the affinity for ______. |
|
Definition
|
|
Term
| Protons (low pH) ____ the O2 binding affinity of hemoglobin and favor _____ of O2. |
|
Definition
|
|
Term
| In the Bohr Effect, protons are involved in ______ in the T form |
|
Definition
|
|
Term
|
Definition
| Increases delivery of O2 in tissue |
|
|
Term
Carbon dioxide (CO2), the product of oxidative metabolism, ____ O2
affinity of hemoglobin. |
|
Definition
|
|
Term
| Carbon dioxide (CO2) binds to _____ groups of the alpha and beta chains resulting in ______. |
|
Definition
N-terminal
carbamino-hemoglobin (a carbamate) |
|
|
Term
| pH and CO2 ensure that oxygen is released preferentially in _____ tissue where it is most needed. |
|
Definition
|
|
Term
| ____% of CO2 is transported by hemoglobin |
|
Definition
|
|
Term
| In addition to Hemoglobin, CO2 is transported in the blood as _______. |
|
Definition
|
|
Term
| Bohr Effect causes the curve to shift ____. |
|
Definition
|
|
Term
| Under Low Oxygen conditions it is the right thing to do |
|
Definition
|
|
Term
| At ____ pH caused by increase in protons (as in the Bohr Effect) salt bridge stabilizes quaternary structure of ______. |
|
Definition
|
|
Term
| A decrease in pH causes a ____ shift. |
|
Definition
|
|
Term
| Heterotropic effectors of Hemeglobin |
|
Definition
| Hydrogen ions and CO2 promote release of oxygen (negative allosteric effectors). |
|
|
Term
| H+ and CO2 are ____ effectors of hemoglobin |
|
Definition
| negative allosteric effectors |
|
|
Term
| _______, mutation causes hydrophobic patch interacts with beta Phe85 and beata Leu88, leading to sickle cell anemia. |
|
Definition
|
|
Term
| Light Microscope resolution |
|
Definition
|
|
Term
| Light Microscope lenses are made up of ____ |
|
Definition
|
|
Term
| Light Microscope Filament _____ |
|
Definition
|
|
Term
| In transmission electron microscopy the sectioning results in ____ thick sections. |
|
Definition
|
|
Term
| Transmission Electron Microscope (TEM) filament _____ |
|
Definition
|
|
Term
| Transmission Electron Microscope (TEM) Resolution |
|
Definition
|
|
Term
| In Transmission Electron Microscope (TEM) the condenser is a _____ instead of _____. |
|
Definition
|
|
Term
| The Objective Magnet in Transmission Electron Microscope (TEM) magnifies _________. |
|
Definition
|
|
Term
| Three magnets found in Transmission Electron Microscope (TEM)? |
|
Definition
| Condenser, Objective, & Projection Magnets |
|
|
Term
| Scanning Electron Microscope (SEM) Filament _____ |
|
Definition
|
|
Term
| Scanning Electron Microscope (SEM) Condenser ______ |
|
Definition
|
|
Term
| Magnets in Scanning Electron Microscope (SEM)? |
|
Definition
| Condenser and Scanning Magnets |
|
|
Term
| Scanning Electron Microscope (SEM) shows a ____ structure with ____ resolution. |
|
Definition
|
|
Term
| The nuclear lamina is fibrous layer of ____ & ______. |
|
Definition
| intermediate filaments and nuclear lamins |
|
|
Term
| Within the nucleus, DNA in chromosomes is complexed with proteins to form ______. |
|
Definition
|
|
Term
| Each extraordinarily long chromosome can be compacted _____ during interphase and _____ more during mitosis. |
|
Definition
|
|
Term
|
Definition
| Interphase is the phase of the cell cycle in which the cell spends the majority of its time and performs the majority of its purposes including preparation for cell division. |
|
|
Term
| Interphase chromosomes contain both _____ staining heterochromatin that is highly condensed and transcriptionally ____ and more _____ staining euchromatin that is less condensed and more and transcriptionally _____ |
|
Definition
darkly
inactive
lightly
active |
|
|
Term
| The nuclear envelope consists of inner and outer membranes separated by a ______ space which is continuous with the _____ space of the rough endoplasmic reticulum (rER). |
|
Definition
perinuclear cisternal space
cisternal |
|
|
Term
| The outer nuclear membrane is continuous with _____ and is studded with ______ |
|
Definition
| the rER and is studded with ribosomes. |
|
|
Term
| A rigid and fibrous structure called the ______ supports the inner nuclear membrane. |
|
Definition
|
|
Term
| The nuclear lamina is a meshwork of ______ that lies just beneath and supports the inner nuclear membrane. |
|
Definition
| intermediate filaments (e.g. nuclear lamins and associated proteins) |
|
|
Term
| Unlike most other intermediate filaments, lamins __________. |
|
Definition
| disassociate and reassemble during mitosis (open mitosis). |
|
|
Term
| The nuclear lamina is intimately involved in the regulation of ________ & _______. |
|
Definition
| DNA replication and transcription. |
|
|
Term
| Impairment of nuclear lamina architecture (_______) is at the heart of several genetic diseases. |
|
Definition
|
|
Term
| Hereditary Emery-Dreifuss muscular dystrophy (EDMD) is a disease of _______, involving impairments of the _______. |
|
Definition
muscle wasting and cardiomyopathy.
nuclear lamina |
|
|
Term
| An autosomal dominant form of EDMD is caused by mutations in ________. While the X-linked recessive form is caused by mutations in the _______. |
|
Definition
lamins A and C.
lamin receptor emerin. |
|
|
Term
| The rare genetic disease progeria is another example of a disease resulting from impairment of the nuclear lamina, in which it causes _______ and is caused by a __________. |
|
Definition
rapidly accelerated aging in young children
point mutation in the lamin A gene. |
|
|
Term
|
Definition
| Cardiomyopathy (literally "heart muscle disease") is the measurable deterioration of the function of the myocardium (the heart muscle) for any reason, usually leading to heart failure |
|
|
Term
| The nuclear pore complex (NPC) is very large (~125 x 106 daltons) and contains more than 50 different ______. |
|
Definition
|
|
Term
| Eukaryotic cells contain _____ NPCs per nucleus |
|
Definition
|
|
Term
| The central framework of the NPC forms a cylinder lined by ___ protein subunits. |
|
Definition
|
|
Term
| A ______ & _____ anchors the central framework of the NPC in the nuclear membrane. |
|
Definition
| cytoplasmic and nucleoplasmic ring |
|
|
Term
| The cytoplasmic ring of the NPC is decorated with protein ____ while a nuclear basket and terminal ring extends into the nucleus |
|
Definition
|
|
Term
| The NPC transports ______ sized macromolecules |
|
Definition
|
|
Term
| Large proteins or complexes are dependent upon ______ to direct them to the _______ for transport which is actively driven via a ____-dependent mechanism. |
|
Definition
nuclear localization signals (NLS)
nuclear import receptor importin
GTP |
|
|
Term
| Nuclear export of RNA and protein depends upon ______ to direct them to ____ for transport out of the nucleus also via a ____-dependent mechanism. |
|
Definition
nuclear export sequences (NES)
exportin
GTP |
|
|
Term
| Small molecules (< ____ daltons) cross the NPC by diffusion. |
|
Definition
|
|
Term
| The nucleolus is a condensed ____ region that is the primary site of ____ transcription and _____ biogenesis. |
|
Definition
heterochromatic
rRNA transcription
ribosome |
|
|
Term
| The nucleolus consists of the non-random localization of _____ called______ from the __ arms of five _____ chromosomes: _____ |
|
Definition
>200 rRNA gene clusters called nuclear organizing regions (NORs)
p (short arms)
acrocentric (centromere shifted towards the end of the chromosome)
13,14,15,21, and 22. |
|
|
Term
| The nucleolus is not contained by a membrane but instead consists of the non-random localization of >200 rRNA gene clusters called nuclear organizing regions (NORs) from the p arms (short arm) of five acrocentric chromosomes (centromere shifted towards the end of the chromosome) 13,14,15,21, and 22. |
|
Definition
|
|
Term
Metacentric – centromere in the middle of the chromosome
· Submetacentric – centromere divides the chromosome into 1/3 and 2/3
· Acrocentric – centromere near the end of the chromosome |
|
Definition
|
|
Term
| The nucleolus is a unique eukaryotic organelle: It is the site where RNA Pol I transcribes the ____transcript, which is the pre-rRNA transcript that codes for _____. |
|
Definition
45S
28S, 18S, and 5.8S rRNAs. |
|
|
Term
| The 5S subunit is transcribed by Pol ___ in ______ |
|
Definition
|
|
Term
| The nucleolus (plural nucleoli) Wiki |
|
Definition
|
|
Term
| Nucleoli are more frequently found in ____ cells |
|
Definition
| active cells (e.g. cells growing and proliferating or non-proliferating cells with high rates of biosynthesis).) |
|
|
Term
| Clinical correlates: The p53 tumor suppressor and the protein subunit of telomerase (hTERT) are known to localize to the ______. |
|
Definition
|
|
Term
| The number and makeup of chromosomes in a given nucleus is called a _____. |
|
Definition
|
|
Term
| The 46 chromosomes contain ____ base pairs that code for ____ genes. |
|
Definition
|
|
Term
| Polymorphism[1] {WIKI} in biology occurs when two or more clearly different phenotypes exist in the same population of a species |
|
Definition
|
|
Term
| In addition to normal polymorphisms, individuals can vary genetically in the ____ of genes in their genome. |
|
Definition
|
|
Term
| Normally, all genes present on autosomes (non-sex chromosomes) are present in ____ copies. |
|
Definition
|
|
Term
| _____ are a widespread source of genetic differences, in which individuals have a differing number of copies of genes (something other than 2) |
|
Definition
| copy number variations (CNVs) |
|
|
Term
| Each chromosome consists of two paired ____ that join together at a ____. |
|
Definition
|
|
Term
| The ends of chromosomes are called telomeres and consist of ________ repeats of the sequence _____. |
|
Definition
| 3-20 kb repeats of the sequence TTAGGG. |
|
|
Term
| The short arm of a chromosome is called the _-arm |
|
Definition
|
|
Term
| long arm is called the _-arm |
|
Definition
|
|
Term
| chromosomes occupy ____ locations in the nucleus |
|
Definition
|
|
Term
|
Definition
| overall structure and linkage maps of chromosomes has revealed that large blocks of genomic sequence is conserved between organisms. |
|
|
Term
| Clinical correlates: Telomere length is regulated by an enzyme called _____. |
|
Definition
|
|
Term
| Clinical correlates: Most ____ cells lack telomerase, and therefore, their telomeres shorten slightly with each ______. |
|
Definition
|
|
Term
| Clinical correlates: Loss of telomere function is believed to be a cause of _____ |
|
Definition
|
|
Term
| Clinical correlates: over-expression of telomerase is associated with _____ |
|
Definition
|
|
Term
| The average human nucleus is _____ and contains ___ meters of DNA. |
|
Definition
|
|
Term
| ~25% of our DNA is found in _____ regions |
|
Definition
|
|
Term
| Cells contain ___ types of histones: _____ |
|
Definition
5
H1, H2a, H2b, H3, and H4. |
|
|
Term
| In general, chromatin is an ~_:_ complex of DNA and proteins. |
|
Definition
|
|
Term
| Two pairs of four of the histones (_______) come together to form an ____ histone core which wraps up ___ bp of DNA. |
|
Definition
H2a, H2b, H3, and H4
octameric
146 |
|
|
Term
| Octameric histone core wraps up 146 bp of DNA, these structures are called ______ or _____ |
|
Definition
| 11 nm fibers or “beads on a string.” |
|
|
Term
| Histone H1 binds the “____” between these cores to further condense these ____ into 30 nm fibers. |
|
Definition
|
|
Term
|
Definition
| A nucleosome is the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around four histone protein cores.[1] This structure is often compared to thread wrapped around a spool.[2] |
|
|
Term
| Very tightly packed chromatin is called _______ and sometimes in extreme cases can be seen extruded from the nucleus as in the situation with _____ in neutrophils |
|
Definition
heterochromatin
Barr bodies (condensed and repressed X-chromosomes) |
|
|
Term
| DNA is a ______-handed helix that exists in at least 3 different forms |
|
Definition
|
|
Term
| Normal physiological DNA is said to be in _-form where __- base pairs are found in each helical turn. |
|
Definition
|
|
Term
| Dehydrated DNA is referred to as the _-form with ___ base pairs in each helical turn. |
|
Definition
|
|
Term
| Sometimes DNA is found in a left-handed helix called _-DNA with ~__ bp per helical turn. |
|
Definition
|
|
Term
| Each base pair is ___ angstroms in height, so a turn of B-DNA is completed every ___ angstroms to reveal both minor and major grooves which facilitate the binding of ______. |
|
Definition
3.4
34
important regulatory proteins like transcription factors. |
|
|
Term
| In humans, replication origins found every _____ bp mediate DNA replication. |
|
Definition
|
|
Term
| Irwin Chargaff discovered that in all organisms the ______. This is known as Chargaff’s rule. |
|
Definition
|
|
Term
| The ____ is the primary site of rRNA transcription and ribosome biogenesis. |
|
Definition
|
|
Term
| Nuclear organizing regions are located on the _____. |
|
Definition
| short arms of five acrocentric chromosomes. |
|
|
Term
Nucleotides have five functions in human
physiology: ______ |
|
Definition
| Energetics, Intracellular signaling, Metabolism/co-enzymes, Oligosaccharide structure, Genetics |
|
|
Term
| Nucleotides have function in Intracellular Signalling through ____ and ____ primarily. |
|
Definition
cAMP
GDP and Gprotein couple receptors |
|
|
Term
| RNA and DNA are called nucleic acids because, they are most prevalent in the ____ & stain with ______ chemical stains |
|
Definition
cellular nucleus
basic (as in acid/base) |
|
|
Term
| _____ are polymers of nucleotides |
|
Definition
|
|
Term
| Two types of nucleic acids: _____ |
|
Definition
|
|
Term
| Nucleotides are composed of a ____ & _____ |
|
Definition
| Pentose sugar backbone and a purine or pyrimidine base |
|
|
Term
| Nucleotides have 1–3 phosphate groups (PO4) attached to their ____ ends |
|
Definition
|
|
Term
| Nucleosides are nucleotides that _____ |
|
Definition
| lack the phosphate groups (which are replaced with a 5' hydroxyl) |
|
|
Term
Nucleotides have five functions in human
physiology: ______ |
|
Definition
| Energetics, Intracellular signaling, Metabolism/co-enzymes, Oligosaccharide structure, Genetics |
|
|
Term
| Inosine & pseudouridine are examples of _____ |
|
Definition
| Modified RNA nucleotide bases |
|
|
Term
| Certain bases in transfer RNA (tRNA) are always ________. |
|
Definition
|
|
Term
| The ____ position in the ribose sugar is modified in eukaryotic mRNA capping |
|
Definition
|
|
Term
| DNA bases are sometimes modified by ____ in chromatin |
|
Definition
|
|
Term
| Nucleic acids (both RNA and DNA) are long, linear _____ |
|
Definition
|
|
Term
| Nucleic acids have a built-in ______. |
|
Definition
|
|
Term
| "DNA is usually ____-stranded |
|
Definition
|
|
Term
| RNA is usually _____-stranded |
|
Definition
|
|
Term
| RNA is usually a copy of a _____ |
|
Definition
|
|
Term
| DNA is the genetic material found in the _____ and _____. |
|
Definition
| cell nucleus and in mitochondria |
|
|
Term
|
Definition
|
|
Term
|
Definition
1. structural (i. e., ribosomal RNA)
2. informational (i. e., messenger RNA)
3. adaptational (i. e., transfer RNA)
4. regulatory (i. e., micro RNA) |
|
|
Term
1. 5!-GGATCCCTT-3!
2. pGpGpApTpCpCpCpTpT
a. “p” stands for “5' phosphate group,”
emphasizing phosphate backbone
3. p-GGATCCCTT-OH
a. “OH” stands for “3' hydroxyl group”
4. pppGpGpApUpCpCpCpUpU
a. Triphosphate remaining at 5' end, normal
monophosphate backbone |
|
Definition
|
|
Term
| 5' triphosphate is a hallmark of _____ |
|
Definition
| the first nucleotide of a newly synthesized RNA (or DNA) chain |
|
|
Term
| GMP is synonymous with pG or Gp? |
|
Definition
|
|
Term
| GMP "pG" is a common product of enzymatic digestion of _____ |
|
Definition
|
|
Term
| “Gp”—guanine 3' phosphate is usually, a product of enzymatic _____ |
|
Definition
|
|
Term
| With “Gp”—guanine 3' phosphate, the phosphate was originally on the _____ |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| A purine always basepairs with a _____ |
|
Definition
|
|
Term
| Basepaired DNA strands are antiparallel or parallel? |
|
Definition
|
|
Term
| A single-stranded RNA can form _______ called secondary structure |
|
Definition
|
|
Term
| Regions of an RNA molecule can be complementary to _____ |
|
Definition
|
|
Term
| Complementary RNA regions will form ______, which are called ______ |
|
Definition
| intramolecular (within the same molecule) basepairs called secondary structure |
|
|
Term
| Secondary structure can be critically important to an RNA molecule’s _____ (such as with _____ or ____) |
|
Definition
|
|
Term
| tRNA has to base pair with the _____ |
|
Definition
|
|
Term
| Supercoils can either be _____ or ___. |
|
Definition
|
|
Term
| negative super coils are ______ handed and tend to _____ the double-helix |
|
Definition
|
|
Term
| positive are _____ handed supercoils that tend to _____ the double-helix |
|
Definition
|
|
Term
| Any net increase in the positive or negative supercoiling requires the input of ________ |
|
Definition
| energy in the form of ATP hydrolysis |
|
|
Term
| Relaxed DNA has no _______ |
|
Definition
| net negative or positive supercoils |
|
|
Term
DNA that is nicked (one strand is missing a
________) |
|
Definition
|
|
Term
DNA that is cut (____ strands have
missing phosphodiester bonds) |
|
Definition
|
|
Term
| DNA that is nicked (one strand is missing a phosphodiester bond) or cut (both strands have missing phosphodiester bonds) will tend to ______ |
|
Definition
| “unravel” to a relaxed state |
|
|
Term
| Topoisomerases are enzymes that _____ |
|
Definition
|
|
Term
| Topoisomerases are also called ____ or ____ |
|
Definition
|
|
Term
| Bacterial topoisomerase is called ____. |
|
Definition
|
|
Term
| Eukaryotic cells have ____ types of topoisomerases |
|
Definition
|
|
Term
| Type I topoisomerase (Eukaryotic) function? |
|
Definition
| nicks and reseals one DNA strand at a time |
|
|
Term
| Type II topoisomerase (Eukaryotic ) function? |
|
Definition
| cuts and reseals both DNA strands at the same time |
|
|
Term
| Topoisomerases require ____ to increase supercoiling |
|
Definition
|
|
Term
| In the absence of ATP, topoisomerases will ______ |
|
Definition
|
|
Term
| Another way to twist DNA is to wind it around a central core— this is how _____ work |
|
Definition
|
|
Term
| Clinical: Two drugs that affect bacterial gyrase but not eukaryotic topoisomerases are _______ and ______. |
|
Definition
| nalidixic acid and ciprofloxacin |
|
|
Term
| Nalidixic acid and ciprofloxacin which only affect bacterial gyrase but not eukaryotic topoisomerases are used in the treatment of ______ |
|
Definition
Used in treatment of urinary tract and other
bacterial infections |
|
|
Term
| DNA can be denatured and _____ |
|
Definition
|
|
Term
| Renaturation is also called _____ |
|
Definition
|
|
Term
| Denaturation and renaturation require ____ conditions |
|
Definition
|
|
Term
| Denaturation of DNA occurs at ____ temperatures. |
|
Definition
| High temperatures (often 70–100°C) |
|
|
Term
| Temperature at which _____ is known as the Tm |
|
Definition
| 50% of a particular DNA is denatured |
|
|
Term
| Denaturation of DNA occurs at ____ salt concentrations. |
|
Definition
Low salt concentration (often less than 10 mM NaCl or similar cations)
i. Physiological salt concentration is 150 mM NaCl—too high to allow most DNA to melt |
|
|
Term
| Denaturation of DNA occurs with _____ content. |
|
Definition
Low GC content (less than, say, 25% of total
basepairs) |
|
|
Term
| We can calculate the Tm from the ____ content |
|
Definition
|
|
Term
Unlike renaturation, denaturation can happen
_____. |
|
Definition
|
|
Term
| What adsorbs light more readily, single or double stranded? |
|
Definition
|
|
Term
| Renaturation (or hybridization) is favored by ____ temperatures. |
|
Definition
| Lower temperatures, Must be below the Tm (~5°C below the Tm is optimal) |
|
|
Term
| At temperatures too much below the ____, the individual strands of DNA will often ______; this strand will no longer be able to hybridize to its proper complementary strand |
|
Definition
Tm
“snap-back” on themselves and form basepairs within the same
strand |
|
|
Term
| Renaturation (or hybridization) is favored by _____ salt concentrations. |
|
Definition
Higher salt concentrations
Physiological salt (150 mM NaCl) is a good
starting point |
|
|
Term
| Renaturation (or hybridization) is favored by ____ content. |
|
Definition
Higher GC content
DNA with very high GC content (say, greater than 75%) can be very hard to denature |
|
|
Term
Thermophilic organisms usually have DNA with
high ______. |
|
Definition
|
|
Term
| Renaturation (or hybridization) is favored by ____ time. |
|
Definition
|
|
Term
| Renaturation is measured as ____ |
|
Definition
| Cot, or [initial DNA concentration] ✕ time |
|
|
Term
| Sequences that are more frequent will renature ___ than those that are less frequent |
|
Definition
|
|
Term
| Semiconservative means both parent strands _____, while both child strands _____. |
|
Definition
|
|
Term
In conservative replication both parent
strands ______. |
|
Definition
| remain together after making child strands |
|
|
Term
dispersive replication both parent
strands ______. |
|
Definition
| both parental strands disappear and two new strands are made |
|
|
Term
| Each strand in the double helix is the _____ of the other strand |
|
Definition
|
|
Term
| Coding Strand aka "______" |
|
Definition
|
|
Term
| Template Strand aka "______" |
|
Definition
|
|
Term
| By convention, the strand that is ________ is called “sense.” |
|
Definition
| the same as the mRNA encoded by that DNA |
|
|
Term
| An _____ piece of DNA can be used as a probe to find a sense piece of DNA or RNA by hybridization or to make PCR primers |
|
Definition
|
|
Term
| As the replication bubble expands _____ is introduced. |
|
Definition
|
|
Term
| DNA can be either ____ and double-stranded or _____ and double-stranded |
|
Definition
|
|
Term
| Bacterial chromosomes are _____; eukaryotic chromosomes are _____. |
|
Definition
|
|
Term
| With Eukaryotic origins of replication each replication fork moves ______ than bacteria |
|
Definition
|
|
Term
| Bacteria have _____ replication origins for for their whole circular chromosome |
|
Definition
|
|
Term
| Mitochondria are cytoplasmic organelles with their own _______. |
|
Definition
| Plasma Membrane, DNA, polymerases, tRNAs, rRNAs, mRNAs |
|
|
Term
| Mitochondria resemble _____ in many ways |
|
Definition
|
|
Term
| Structure of Mitochondrian DNA? |
|
Definition
| Like bacteria, they have their own circular, doublestandard DNA genome |
|
|
Term
| Mitochondria are _____ inherited. |
|
Definition
|
|
Term
| DNA (and RNA) can only be made in a ______ direction |
|
Definition
|
|
Term
| DNA is composed of two antiparallel strands—therefore, replication must occur in ________. |
|
Definition
|
|
Term
| Cannot join a 3" end to an existing 5" end, without help from an enzyme called ______. |
|
Definition
|
|
Term
| _____ polymerases Have proofreading activity |
|
Definition
|
|
Term
| _____ polymerases Tend to be highly accurate |
|
Definition
|
|
Term
| _____ polymerases Are very processive |
|
Definition
|
|
Term
| DNA polymerases require a ____ |
|
Definition
|
|
Term
|
Definition
| primer—a preexisting nucleic acid fragment from which new DNA can “grow” |
|
|
Term
| _____ polymerases Do not have proofreading |
|
Definition
|
|
Term
| _____ polymerases Tend to be error-prone |
|
Definition
|
|
Term
| _____ polymerases Are not very processive |
|
Definition
|
|
Term
| _____ polymerases Do not require a primer |
|
Definition
|
|
Term
| The first step in DNA replication is strand separation creating the ______ |
|
Definition
|
|
Term
| The DNA is already in a state of _____ supercoiling before the replication fork is formd. |
|
Definition
|
|
Term
| Gyrase introduces _____ supercoils ahead of the replicating fork |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Helicase (or dnaB) unwinds the ______, which ______ from the DNA strands. |
|
Definition
two parent strands
negative supercoils (or introduces positive supercoils) from the DNA strands |
|
|
Term
| Helicase is required because supercoiling creates _______ |
|
Definition
| an energy barrier to DNA replication |
|
|
Term
| The strands are stabilized (held apart) by ________ |
|
Definition
| helix destabilizing proteins (also known as single-strand binding [SSB] proteins) |
|
|
Term
| helix destabilizing proteins (also known as single-strand binding [SSB] proteins) prevent ______ |
|
Definition
| Hydrogen Bonding from forming between the newly separated Strands. |
|
|
Term
| Helicase does the _____ and requires. |
|
Definition
| opening up and requires ATP hydrolysis |
|
|
Term
| topisomerases introduce _____ supercoils |
|
Definition
|
|
Term
| _______ polymerase for prokaryotes does leading and lagging strand synthesis. |
|
Definition
|
|
Term
| Helicase (dnaB) in the primosome does what? |
|
Definition
| opens up the replication fork |
|
|
Term
| WIKI In molecular biology, a primosome is a protein complex responsible for creating RNA primers on single stranded DNA during DNA replication. |
|
Definition
|
|
Term
| _______ (for prokaryotes) “reads” the parent strand and inserts a complementary deoxyribonucleotide |
|
Definition
|
|
Term
| DNA polymerase (III?) catalyzes formation of a ______bond between the ___ end of the existing child strand and the _____ end of the new nucleotide. |
|
Definition
|
|
Term
| In DNA replication ___ of the three phosphate groups from the deoxyribonucleotide are removed, which provides ______ |
|
Definition
two
the energy to drive this reaction forward |
|
|
Term
| For lagging strand DNA synthesis, small DNA fragments (_____) grow from ____ that serve as temporary primers. |
|
Definition
Okazaki fragments
small RNAs |
|
|
Term
For the Lagging Strand Synthesis short RNA fragments are made in the new growing fork
by the _____ |
|
Definition
|
|
Term
| RNA polymerases do not require a ____ or an existing _____. |
|
Definition
|
|
Term
| The short RNA fragments created for Lagging Strand synthesis provide the necessary _____ required by DNA polymerase _____ to make a true DNA strand |
|
Definition
|
|
Term
| The enzyme responsible for making the RNA primers is called ______. |
|
Definition
| primase (dnaG in E. coli) |
|
|
Term
| The short RNA segments used as primers for DNA polymerase III must be excised, either by an enzyme called ____ (in eukaryotes) or by ________ (in prokaryotes) |
|
Definition
| RNase H (in eukaryotes) or by DNA polymerase I (in prokaryotes) |
|
|
Term
| The short RNA segments must be excised, either by an enzyme called RNase H (in eukaryotes) or by DNA polymerase I (in prokaryotes). The junction between the two DNA strands is sealed by ______. |
|
Definition
|
|
Term
| ______ makes tiny RNA primers for DNA Pol ____ |
|
Definition
|
|
Term
| dna_ (____) opens up the replication fork. |
|
Definition
|
|
Term
| Okazaki Fragments are composed of _____ |
|
Definition
|
|
Term
| _____ erases the RNA primer and fills it in. |
|
Definition
|
|
Term
| ______ connects loose ends on the lagging strand. |
|
Definition
|
|
Term
| Mutations are inherited changes in DNA—since, they are inherited, they must require ______. |
|
Definition
|
|
Term
| Clinical: Xeroderma pigmentosum, is an inherited disease that results from lack of ______. These patients are extremely prone to _____, especially ______. |
|
Definition
DNA repair
cancers
skin cancer |
|
|
Term
|
Definition
| a change in a single basepair of DNA |
|
|
Term
|
Definition
| a point mutation in which a purine is replaced by another purine, or a pyrimidine by a pyrimidine IN THE SAME DNA STRAND |
|
|
Term
|
Definition
a purine is replaced by a pyrimidine, or
vice versa |
|
|
Term
|
Definition
| transfer of a segment of DNA (short or long) from one position in the DNA to another; can also mean transfer from a different piece of DNA |
|
|
Term
|
Definition
| addition of one or more nucleotide basepairs (sometimes, though not always due to a translocation) |
|
|
Term
|
Definition
| removal of one or more nucleotide basepairs |
|
|
Term
|
Definition
| removal and reinsertion of sequences in the opposite orientation |
|
|
Term
| Mutations can have several possible outcomes: _______ |
|
Definition
1. Silent mutations
2. Nonsense mutations
3. Frameshift mutations
4. Missense mutations |
|
|
Term
| Silent mutations— _______ |
|
Definition
| do not change the amino acid sequence of the encoded protein or are otherwise without effect on phenotype |
|
|
Term
| Nonsense mutations— ________ |
|
Definition
| insert a premature stop codon in the protein coding region |
|
|
Term
| Frameshift mutations— _______ |
|
Definition
| insertions or deletions that alter the reading frame of the encoded protein |
|
|
Term
| Missense mutations— _______ |
|
Definition
| mutations that change one codon to a different amino acid |
|
|
Term
| Tautomeric shift is a ______ chemical changes by which rare electronic shifts in DNA bases can make one nucleotide _______ |
|
Definition
spontaneous
mimic another |
|
|
Term
| Examples of Ionizing radiation: ______ |
|
Definition
| X-rays, radioactivity, gamma rays |
|
|
Term
| Ionizing radiation can cause Radiation induced mutations with high energy radiation that can _______ in DNA bases, causing chemical shifts; can occasionally _______. |
|
Definition
displace electrons
sever the phosphodiester bond |
|
|
Term
| Ultraviolet light is non ______ and can cause Radiation induced mutations, because UV light wavelengths interact greatly with DNA or RNA, photoactivating ____, especially ______. |
|
Definition
|
|
Term
| Photoactivated thymine is especially prone to producing _______ |
|
Definition
|
|
Term
| Examples of Chemical mutagens: |
|
Definition
a. Base analogs
b. Alkylating agents
c. Deaminating agents
d. Intercalating agents |
|
|
Term
| Base analogs are an example of chemical mutagens that substitute for _____, but ______ |
|
Definition
| normal DNA bases, but pair with different bases. |
|
|
Term
| Bromouracil is an example of a ______ that causes _____. |
|
Definition
Base analog
chemical mutations |
|
|
Term
| Bromouracil can replace ______, but often basepairs with _______ instead of _____. |
|
Definition
thymine,
guanine instead of adenine |
|
|
Term
| Alkylating agents react with _______. |
|
Definition
| amino groups in bases (including ethylene oxide, methyl bromide) |
|
|
Term
| Deaminating agents remove ______ |
|
Definition
|
|
Term
| Deaminating agents remove amino groups, which for instance could change a cytosine to a ______. |
|
Definition
|
|
Term
| Intercalating agents are ____ or ____ structures that insert between adjacent basepairs in DNA, causing _______. |
|
Definition
planar phenolic or multiple ring structures
temporary frame-shifts. |
|
|
Term
| DNA polymerases have three activities: ____ |
|
Definition
DNA polymerization (5' to 3')
3' to 5' exonuclease activity
5' to 3' exonuclease activity |
|
|
Term
| 3' to 5' exonuclease activity is required for _____. If an unmatched base is inserted, the 3' to 5' exonuclease activity causes DNA polymerase to __________. |
|
Definition
Required for proofreading
“back up,” remove the offending base, and reinsert a correct nucleotide. |
|
|
Term
| 5ʹ to 3ʹ exonuclease activity acts in the ____ direction of replication. |
|
Definition
|
|
Term
| 5ʹ to 3ʹ exonuclease activity, function is to _______ & ________. |
|
Definition
Removes RNA primer (Okazaki fragments) from DNA
Removes damaged DNA |
|
|
Term
| Not all eukaryotic DNA polymerases have all ______, while some have addition. |
|
Definition
| All three activities of DNA polymerase |
|
|
Term
| DNA polymerase alpha has built-in _____ activity. |
|
Definition
| primase activity- an RNA Polymerase |
|
|
Term
| Thymine dimers are repaired by _____ |
|
Definition
|
|
Term
| Clinical: If a mutation compromises XPA, XPG, etc. than what condition results? |
|
Definition
| Xeroderma Pigmentosum, DNA repair (espicially excision repair) is impaired, which means thymine dimers created by UV light cannot be excised. |
|
|
Term
| If C becomes deaminated it becomes _____ |
|
Definition
|
|
Term
| Repair of Depurination (Apurinic site) steps: _____ |
|
Definition
| Following Depurination, AP endonuclease DNA polymerase Beta ligate the strand at this missing purine, DNA Polymerase Beta then fills in the missing purine, DNA ligase then connects the strands back together. |
|
|
Term
| Repair of Cytidine Deamination Sites Steps: _______ |
|
Definition
| Following deamination of Cytidine into Uracil, DNA Glycosylase removes the uracil, AP endonuclease DNA polymerase Beta cuts the strand and then fills in the Cytidine, DNA ligase then connects the strands back together. |
|
|
Term
|
Definition
| is an enzyme that is involved in the DNA base excision repair pathway (BER). Its main role in the repair of damaged or mismatched nucleotides in DNA is to create a nick in the phosphodiester backbone of the AP site created when DNA glycosylase removes the damaged base. |
|
|
Term
| _____ are the ends of chromosomes. |
|
Definition
|
|
Term
| Telomeres consist of ~250–1500 repeats of ________ and associated proteins at the ends of eukaryotic chromosomes |
|
Definition
|
|
Term
| Telomerase is a specialized _____ that requires an ____ component and a protein component |
|
Definition
|
|
Term
| Without telomerase, _______ with each chromosome replication, this process is called ______. |
|
Definition
grow shorter (by ~100–200bp) with each chromosome replication
replicative cell senescence |
|
|
Term
| The number of cell divisions before a cell will senesce and die is called the ________. |
|
Definition
|
|
Term
| Cells that maintain very active telomerases? |
|
Definition
| Germ Cells (Cells producing eggs and sperm), stem cells, and cancer cells. |
|
|
Term
| In cancer cells, a second mechanism of telomere ______ called ______ is sometimes active. |
|
Definition
lengthening
alternative lengthening of telomeres (ALT |
|
|
Term
| Telomerase activity requires both _____ & _____ |
|
Definition
| telomerase reverse transcriptase (TERT) and telomerase RNA component (TERC) |
|
|
Term
| TERC (telomerase RNA component) acts as ______. |
|
Definition
| both a template and a primer |
|
|
Term
| The protein component of Telomerase is ______ and the RNA component serves as ______. |
|
Definition
Reverse Transcriptase
Template |
|
|
Term
| Following the binding of Telomerase to the telomeres, what are the subsequent repeating steps? |
|
Definition
| Elongation, Translocation, Elongation, Translocation. |
|
|
Term
| What happens during elongation by Telomerase? |
|
Definition
| New bases are added to the chromosome. |
|
|
Term
| Thymine dimers result from ______ |
|
Definition
|
|
Term
| Leading Strand Synthesis in Prokaryotes is done by ______? |
|
Definition
|
|
Term
| Which DNA pol erases the primer and fills in on the lagging strand (Prokaryotes)? |
|
Definition
|
|
Term
| Who unwinds the replication fork? (Prokaryotes) |
|
Definition
|
|
Term
| What DNA polymerase has both a protein and RNA component? |
|
Definition
|
|
Term
| What enzyme increases negative supercoiling? |
|
Definition
|
|
Term
| What is the primase in Prokaryotes? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| DNA through transcription produces hnRNA then through mRNA processing it becomes mRNA, it is then transported across the nuclear membrane into the cytoplasm by nuclear-cytoplasmic transportation where it is translated into proteins |
|
|
Term
|
Definition
|
|
Term
|
Definition
| Double-Stranded DNA Template, an RNA Polymerase (Which Doesn't Require Primer), and All Four Ribonucleotide Triphosphates (NTPs) |
|
|
Term
|
Definition
|
|
Term
| RNA polymerase I creates a single large rRNA precursor that is subsequently ______ |
|
Definition
| processed into two smaller subunits (18S and 28S) |
|
|
Term
| 18S is the RNA component of the ______ |
|
Definition
| small ribosomal subunit (40S) |
|
|
Term
| 28S is the RNA component of the ______ |
|
Definition
| large ribosomal subunit (“60S”) |
|
|
Term
| The Whole Ribosome, small + large subunit is _____S. |
|
Definition
| 40S small and 60S large, 80S Whole |
|
|
Term
| RNA polymerase I is found _______. |
|
Definition
| exclusively in nucleoli within the nucleus |
|
|
Term
| rRNA created by RNA polymerase I does not have ______ |
|
Definition
|
|
Term
| RNA polymerase II makes _____ |
|
Definition
Makes heterogeneous nuclear RNA (hnRNA) that is processed to become messenger RNA (mRNA)— RNAs that encode proteins
Makes small nuclear RNAs (snRNAs, involved in splicing and other RNA processing events)
Micro RNAs (miRNA), telomerase RNA, etc. |
|
|
Term
|
Definition
|
|
Term
|
Definition
| splicing and other RNA processing |
|
|
Term
| heterogeneous nuclear RNA (hnRNA) is processed into ______ |
|
Definition
|
|
Term
|
Definition
|
|
Term
| RNA polymerase III makes? |
|
Definition
|
|
Term
| tRNA and 5S rRNA created by RNA polymerase III have or don't have caps? |
|
Definition
|
|
Term
| Where are the caps located? |
|
Definition
|
|
Term
| Which RNA Pol(s) make RNA with caps? |
|
Definition
|
|
Term
| Because RNA made by RNA pol I & III do not have 5' caps, what do they have at their 5' end? |
|
Definition
|
|
Term
| What are the structural RNA Pol(s)? |
|
Definition
| RNA pol I and RNA pol III |
|
|
Term
| What are the protein encoding RNA Pol(s)? |
|
Definition
|
|
Term
| RNA Pol I is located in the ______ |
|
Definition
|
|
Term
| RNA Pol II is located in the _____ |
|
Definition
|
|
Term
| RNA Pol III is located in the _____ |
|
Definition
|
|
Term
| Types of Eukaryotic RNA polymerase: ______ |
|
Definition
| RNA pol I, II, III, Mitochondrial, DNA pol alpha ("Primase"), Poly(A) polymerase. |
|
|
Term
| All the Eukaryotic RNA polymerases are located in the nucleus except? |
|
Definition
| RNA pol I (Nucleolus) and Mitochondrial (MT) |
|
|
Term
| What are the three kinds of regulatory elements in the DNA? |
|
Definition
| Promoters, Enhancers, Silencers/repressors |
|
|
Term
| Promoters—core DNA elements required for ____ |
|
Definition
|
|
Term
| Promoters are found near _____ |
|
Definition
| the start site of mRNA transcription |
|
|
Term
| Promoters sequence is _____ at ______ & _____ at ______ |
|
Definition
TATA box at -25 to -30
“CCAAT” box at about –40 to –110 |
|
|
Term
| Some promoters lack the TATA box and are called _____ |
|
Definition
|
|
Term
| “Housekeeping genes” are genes that are _____ |
|
Definition
| essential genes and expressed in nearly every cell |
|
|
Term
| “Housekeeping genes” often have “___” boxes at about ______, and do not have ____ |
|
Definition
|
|
Term
| Enhancers are DNA elements required for _____ positive control (increase) of expression |
|
Definition
|
|
Term
Enhancers are Orientation-_____ and distance
______ |
|
Definition
|
|
Term
| Where can enhancers be found? |
|
Definition
| nearby or at great distances upstream of transcription start site and even occasionally downstream of or within the gene |
|
|
Term
| Enhancers can be ______ and still retain their function |
|
Definition
|
|
Term
| Silencers/repressors are DNA elements required for _____ negative control (decrease) of expression |
|
Definition
|
|
Term
| Silencers/repressors are Orientation-_____ and distance ______ |
|
Definition
|
|
Term
| The TATA Box is bound by ____ protein |
|
Definition
| TFIID (which includes the TATA binding protein TBP) |
|
|
Term
|
Definition
| common proteins found in every cell and tissue, and are essential elements for all transcription |
|
|
Term
| Enhancers and repressors bind ______ |
|
Definition
| tissue-specific proteins (though some are found in many tissues) |
|
|
Term
| Enhancers and repressors are distance ______ |
|
Definition
|
|
Term
| Transcriptional regulation is the combination of activities of ____ & ____ with ______ elements |
|
Definition
positive and negative transcription factors
basal promoter |
|
|
Term
| The proteins that bind the promoter are found ______, but whether or not they bind the promoter is ______. |
|
Definition
In every cell
tissue specific |
|
|
Term
| The regulatory elements of DNA transcription are specifically recognized and bound by ______. |
|
Definition
|
|
Term
| RNA Pol ____ has a large number of accessory proteins required for its function |
|
Definition
|
|
Term
| Pol II plus the accessory proteins is called the _____ or ______. |
|
Definition
| “RNA polymerase holoenzyme” or the “pol II complex” |
|
|
Term
| Accessory proteins named ______. |
|
Definition
“TFIIA” (transcription factor IIA), “TFIIB,” "TFIIC,” "TFIID,”
“TAFs” (transcription accessory factors), etc. |
|
|
Term
| An essential subunit of TFIID (of the RNA Pol II Complex) is the _____, which ______. |
|
Definition
| “TATAbinding protein” (TBP), which binds to DNA at the TATA box |
|
|
Term
TBP is required for ______
transcription |
|
Definition
|
|
Term
| Some pol II promoters lack the TATA box—these still require ____, even though it does not directly bind the DNA. |
|
Definition
|
|
Term
| Enhancer-binding proteins (and repressor-binding proteins) Serve to recruit _____ & _____ to the transcriptional start site |
|
Definition
| basal transcription factors and promoter-binding factors |
|
|
Term
| Enhancer-binding proteins (and repressor-binding proteins) each have an essential protein-protein interaction _____ to interact with other factors |
|
Definition
|
|
Term
| Enhancer-binding proteins and repressor-binding proteins usually bind DNA as _____ |
|
Definition
| dimers— two similar proteins must interact with each other before they can bind DNA |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Some enhancer-binding proteins must be ______ before binding |
|
Definition
|
|
Term
| Many hormone-responsive transcription factors like steroid hormone receptors must bind their ______ before they bind DNA |
|
Definition
| ligand (e. g. estrogen, retinoic acid, testosterone) |
|
|
Term
Many transcription factors must be
______ and others must be ______ before they bind DNA |
|
Definition
phosphorylated
dephosphorylated |
|
|
Term
| Repressor-binding proteins are thought to behave in similar ways as enhancer-binding proteins, but _______. |
|
Definition
| block access of other factors to important sites on the DNA |
|
|
Term
| Histones are concentrated in “_____” regions of chromatin that are transcriptionally _____ |
|
Definition
|
|
Term
| Two forms of chromatin: ______ |
|
Definition
Heterochromatin
Euchromatin |
|
|
Term
| Who contains less histones, heterochromatin or euchromatin? |
|
Definition
|
|
Term
| The presence of histones around a promoter will _______. |
|
Definition
| inhibit transcription of that gene |
|
|
Term
| One of the roles _____ & _____ is to displace histones from the start site for transcription |
|
Definition
| of promoter- and enhancer-binding proteins |
|
|
Term
|
Definition
| epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence |
|
|
Term
| ____ and ____ are ways to mark DNA and histones. |
|
Definition
| Acetylation of histones & Methylation of DNA |
|
|
Term
| Acetylases and deacetylases for histones are associated with ______. |
|
Definition
|
|
Term
| An increase in the level of acetylation of histones will _____ transcription |
|
Definition
|
|
Term
| A decrease in the level of acetylation of histones will ______ transcription |
|
Definition
|
|
Term
| Acetylation modification can be ______ from cell division to cell division (______) |
|
Definition
“remembered” or inherited
epigenetics |
|
|
Term
| Methylation of DNA will _____ transcription |
|
Definition
|
|
Term
| An increase in methylation of DNA will _____ transcription |
|
Definition
|
|
Term
| A decrease in methylation of DNA will _____ transcription |
|
Definition
|
|
Term
| Methylation of DNA occurs at the ____ residue of the sequence _______. |
|
Definition
|
|
Term
| Cells use methylation as a way of marking an _____ |
|
Definition
|
|
Term
| The )_____ during DNA replication is methylated (____ strands are not methylated) |
|
Definition
|
|
Term
| The ____-inherited chromosome can be methylated —“genomic imprinting” |
|
Definition
|
|
Term
| Alteration of transcriptional pathways in cancer will change the _______. |
|
Definition
|
|
Term
| The normal role of the retinoblastoma protein (pRb) is to _______. |
|
Definition
| suppress entry into the cell cycle |
|
|
Term
| Mutation or inactivation of pRB will allow ______ of many cell cycle proteins, including ______. |
|
Definition
|
|
Term
| The normal role of the ____-specific cyclin D1 is to allow the controlled transition of cells from _____ to ____ phase |
|
Definition
|
|
Term
| ____-expression of cyclin D1 is common in many cancers, leading to uncontrolled growth |
|
Definition
|
|
Term
| pRB is ___ in many cancers |
|
Definition
|
|
Term
| Cyclin D1 is ____ in cancer. |
|
Definition
|
|
Term
|
Definition
|
|
Term
| what makes mRNAs and miRNAs? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Makes primers for DNA replication |
|
Definition
Eukaryotes- DNA polymerase Alpha
Prokaryotes- dnaG |
|
|
Term
| Most affected by alpha-amanitin |
|
Definition
|
|
Term
| __________ are required for any mRNA to be exported from the nucleus |
|
Definition
| Correct capping, polyadenylation and splicing |
|
|
Term
| There are four major mRNA processing events that affect most EUKARYOTIC mRNAs: _____ |
|
Definition
A. 5′ end capping
B. 3′ end polyadenylation
C. Intron splicing
D. Cap and internal nucleotide methylation |
|
|
Term
| UTR does not _____, but gets _____. |
|
Definition
(UTR- Untranslated Region)
Does not code for the protein (so does not get translated), but does get transcribed and survives splicing. |
|
|
Term
| _____ is where miRNA binds. |
|
Definition
|
|
Term
| Where does the ORF (open reading frame) begin? |
|
Definition
| at the start of the coding region, past the 5' UTR |
|
|
Term
| Where is the stop codon located? |
|
Definition
|
|
Term
| Poly A tail is attached to the _____ |
|
Definition
|
|
Term
| Caps are required for the initiation of ______ |
|
Definition
|
|
Term
| A capped mRNA has a _____ linkage for its cap. |
|
Definition
|
|
Term
| Is there a free 3' OH group on the 5' cap? |
|
Definition
|
|
Term
| Nucleotides near the 5ʹ cap are ______. |
|
Definition
|
|
Term
| 3′ end polyadenylation 3 Steps: _____ |
|
Definition
Three steps:
1. Recognition of the correct site of polyadenylation
2. Cleavage of the pre-mRNA at the correct site,
leaving a 3! hydroxyl group
3. Addition of about 250 adenosine residues (“poly(A)”) at the 3' end |
|
|
Term
| 3ʹ end polyadenylation Requires the sequence “____” within ____ nucleotides upstream of the site of cleavage (“polyadenylation signal”), which acts as a “Upstream sequence element” (USE) |
|
Definition
|
|
Term
_____ or _____ sequence about 10–24 nt
downstream of the cleavage site act as the “Downstream sequence element” (DSE) required for 3ʹ end polyadenylation |
|
Definition
|
|
Term
| “Upstream sequence element” (USE) for 3ʹ end polyadenylation is _______ |
|
Definition
| AAUAAA within 12–35 nucleotides of the site of cleavage (“polyadenylation signal”) |
|
|
Term
| “Downstream sequence element” (DSE) for 3ʹ end polyadenylation is _______ |
|
Definition
| U-rich or GU-rich sequence about 10–24 nt downstream of the cleavage site |
|
|
Term
| Polyadenylation function in cells is necessary for transcriptional ______. |
|
Definition
|
|
Term
| Polyadenylation function in cells is necessary for correct _____ of the mRNA from __________. |
|
Definition
export
the nucleus to the cytoplasm |
|
|
Term
| Polyadenylation function in cells is necessary for mRNA ____ & _____. |
|
Definition
| Translation and stability |
|
|
Term
| What happens to the U-rich or GU-rich sequence about 10–24 nt downstream of the cleavage site? |
|
Definition
|
|
Term
| Intron splicing involves precise removal of intron sequences from the ______ |
|
Definition
|
|
Term
| Intron splicing involves chemical steps called ______. |
|
Definition
|
|
Term
| Intron splicing requires _____. |
|
Definition
| snRNPs (small nuclear ribonucleoproteins) |
|
|
Term
| snRNPs which are required for intron splicing have an RNA component called ______. |
|
Definition
|
|
Term
| Intron splicing Involves an intermediate called the ______ having a large loop of the intron RNA attached with an unusual _____ bond |
|
Definition
|
|
Term
| Introns require ____ at the 5' end and ____ at the 3' end of the intron and a “___” at lariat attachment point |
|
Definition
|
|
Term
| Transesterficatioin I results in _____ |
|
Definition
| G at the 5' end of the intron becomes attached to the A at the lariat attachment point, through a 5' (G) to 2' (A) |
|
|
Term
| Transesterficatioin II results in _____ |
|
Definition
| The bonding of the two adjacent exons and the expulsion of the “intron lariat” |
|
|
Term
| Capping, Splicing, and Polyadenylation are Coupled with ______. |
|
Definition
|
|
Term
| Splicing and polyadenylation can change the mRNA, and therefore the ______. |
|
Definition
|
|
Term
| By including or excluding exons, different _____ (and therefore _____) can be made in different _____. |
|
Definition
|
|
Term
| Polyadenylation can also alter the 3' ____ region and reveal _______. |
|
Definition
untranslated
regulatory sequences |
|
|
Term
| Some mRNAs do not have introns, many of the genes that code for them arose as _____ |
|
Definition
|
|
Term
|
Definition
| Retrotransposons (also called transposons via RNA intermediates) are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon. |
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|
Term
| _____ mRNAs are not polyadenylated |
|
Definition
|
|
Term
| Histone mRNAs are not polyadenylated, instead, there is a special method for histone mRNA 3′ end formation, creating a special _______ in the histone mRNA 3' ends. |
|
Definition
| “hairpin loop” in the histone mRNA 3ʹ' ends |
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|
Term
| In some cells, poly(A) is removed temporarily from the 3′ end to inhibit _____; this occurs in the _____, not in the _____. |
|
Definition
translation
cytoplasm
nucleus |
|
|
Term
| Micro RNAs (miRNAs, a type of non-coding RNA) are processed extensively in the _____ |
|
Definition
|
|
Term
| G residues in ______ regions of mRNA are modified to become inosine (“I”)—this is thought to _____ |
|
Definition
double-stranded
inosine
protect against certain viral infections |
|
|
Term
| Can 3' end polyadenylation result in changes to the protein coding region (ORF)? |
|
Definition
|
|
Term
| Characteristics of the Genetic Code |
|
Definition
Colinear
Degenerate
Unambiguous
Non- overlapping
Non-punctuated
Universal |
|
|
Term
|
Definition
| Amino acid in proteins from the amino terminus (NH2) to the carboxyl (COOH) terminus corresponds to the 5' end of the messenger RNA to the 3' end. This refers to the coding sequence in the mRNA, excluding the un-translated (UTR) regions of the messenger RNA. |
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|
Term
|
Definition
| More than one codon codes for the same amino acids |
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|
Term
| Wobble base in messenger RNA is directly related to the ______. |
|
Definition
| degeneracy of the genetic code. |
|
|
Term
|
Definition
| Each codon refers to only one amino acid (UUU is always phenylalanine). |
|
|
Term
|
Definition
| Codon refer to 3 bases that are read as a unit. No nucleotides of one codon is a part of another codon. |
|
|
Term
|
Definition
| The mRNA is translated in successive triplet codon until a stop is reached |
|
|
Term
| Universal (nearly but not absolute)- |
|
Definition
| The same codon denotes the same amino acids in all organisms. |
|
|
Term
| What mechanism is used to "translate " nucleotide sequence in mRNA into amino acids in protein? |
|
Definition
| Aminoacyl tRNA Synthetase |
|
|
Term
| Aminoacyl tRNA Synthetase has _____ substrates, which are _____. |
|
Definition
| amino acid and transfer RNA. |
|
|
Term
| Aminoacyl tRNA Synthetase catalyzes the first ______ step in protein synthesis. |
|
Definition
|
|
Term
| Aminoacyl tRNA Synthetase is absolutely required for the ____ of protein synthesis |
|
Definition
|
|
Term
| Aminoacyl tRNA Synthetase recognizes the specific amino acid by:_____ |
|
Definition
| size, charge and free energy |
|
|
Term
| Aminoacyl tRNA Synthetase recognizes the specific transfer RNA by _____ recognition sites. |
|
Definition
|
|
Term
| Aminoacyl tRNA Synthetase Contains a catalytic editing site that is ______ dependent which is used to "proof read" the _____ that is bound in order to assure it is the correct one. |
|
Definition
|
|
Term
| Linkage of the tRNA occurs through _____ and results in a high energy bond between ____ & ____. |
|
Definition
ATP hydroylsis
the tRNA and the Carboxyl Group |
|
|
Term
| _____ the transfer RNA with the amino acid is prerequisite Step for Protein Synthesis |
|
Definition
|
|
Term
| First step in protein synthesis is "charging" the tRNAs witht he correct amino acid by ______. |
|
Definition
| amino acyl tRNA synthetases |
|
|
Term
| The process of charging a tRNA with an amino acid requires ______. |
|
Definition
| hydrolyzes of 1 ATP/amino acid |
|
|
Term
| The process of charging a tRNA with an amino acid requires hydrolyzes of 1 ATP/amino acid. This reaction results in the formation of a high energy bond (____ bond) contained in the amino acid. |
|
Definition
|
|
Term
| The high ester energy bond created following hydrolysis of ATP and joining of tRNA to the amino acid will be used in the _____ step in the _____ phase of protein synthesis: which is the _______ |
|
Definition
second
elongation
formation of the peptide bond between aminoacyl tRNA and the growing peptide. |
|
|
Term
| The Amino Acid acceptor stem of tRNA is located at the ____ end and is composed of _____ nucleotides. |
|
Definition
|
|
Term
| Variable Loop accounts for _____ |
|
Definition
|
|
Term
| Anticodon loop does what? |
|
Definition
|
|
Term
| The Gm nucleotide in the anticodon loop binds to _____ |
|
Definition
|
|
Term
| There is _____ binding between the tRNA and the mRNA |
|
Definition
|
|
Term
| Transfer RNAs are synthesized as precursor molecules by ______. |
|
Definition
|
|
Term
| The precursor of tRNA is processed at both the 5' and 3' end of the molecule. _____ acts on the 5' end of the transfer RNA resulting in a mono- phosphate. |
|
Definition
| RNase P a ribozyme (RNA that is an enzyme) |
|
|
Term
|
Definition
|
|
Term
| The 3' end of all "active" transfer RNAs contain the sequence ______ |
|
Definition
|
|
Term
| The CCA end of tRNA is a ______ step. Meaning that the CCA is ______ |
|
Definition
post transcriptional
CCA is not part of the transcribed RNA. |
|
|
Term
| The CCA end of tRNA is where _____ |
|
Definition
| the amino acid is put by the aminoacyl tRNA synthetase. |
|
|
Term
| The CCA is added to the 3' end of tRNA by the enzyme _______. |
|
Definition
|
|
Term
| If the tRNA is not "charged with an amino acid it is susceptible to removal by the enzyme _______. |
|
Definition
|
|
Term
| What is more stable, tRNA or mRNA? |
|
Definition
|
|
Term
| Transfer RNAs are stable compared to mRNAs, because of the ____ structure and base pairing which prevents ______ activity. |
|
Definition
|
|
Term
| The modified and unique bases of tRNA are recognition sites for their _______. |
|
Definition
| specific aminoacyl tRNA synthetase. |
|
|
Term
| Ribosomes: Organelle for _______. |
|
Definition
|
|
Term
| Ribosomes are made up of a _____ and _____ subunit composed of _____ and _____ components. |
|
Definition
large and small
RNA and protein |
|
|
Term
| The _____ subunit of the ribosome is involved in the first step in the initiation process of protein synthesis. |
|
Definition
|
|
Term
| Ribosomal RNA – _____ & _____ (prokaryotes) _____ & ____(eukaryotes). |
|
Definition
|
|
Term
| Ribosomal RNA, 18 S and 28S (eukaryotes) is Transcribed by _____ in the ______ of eukaryotes. |
|
Definition
RNA polymerase I
nucleolus |
|
|
Term
| 5S RNA both prokaryotes and eukaryotes of ribosomes is transcribed by ______ |
|
Definition
|
|
Term
| The protein component of Ribosomes consists of _____ proteins with _____ charge binds to the ribosomal RNA, _____ charged due to _____. |
|
Definition
Basic
positive
negatively
phosphates |
|
|
Term
| Ribosomal proteins are considered to be _____ proteins involved in maintaining the integrity of the RNA by protecting the RNA from ____ activity. |
|
Definition
|
|
Term
| In addition to their role in protecting the integrity of RNA ribosomal proteins also play a role in maintaining the active sites for ______ binding. |
|
Definition
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