Term
|
Definition
| cytoskeletal fibers built from small globular protein subunits--used as reinforcing in the cell |
|
|
Term
| Basic structural unit of microtubule |
|
Definition
|
|
Term
|
Definition
a) alpha-tubulin + beta-tubulin = dimer
b) dimer + dimer = protofilament (pair of coiled coils)
c) 13 protofilaments wrap into a hollow tube |
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|
Term
| Which end of microtubule grows and dissembles faster? |
|
Definition
|
|
Term
Best known intermediate filaments
What are some examples? |
|
Definition
alpha-keratin
skin, hair and claws |
|
|
Term
| Intermediate filaments are exclusively what type of protein |
|
Definition
|
|
Term
| How many intermediate filaments are in the human body |
|
Definition
|
|
Term
| Basic structure of intermediate filaments |
|
Definition
a) a dimer of alpha-hilices that wind into a coil
b) 7-residue repeating unit with hydrophobic residues in contact
c) 16-32 polypeptides in cross-section
d) anti-parallel and cross-linked thru disulfide bonds |
|
|
Term
| Most abundant animal protein |
|
Definition
|
|
Term
| Major structural role of collagen |
|
Definition
| Supporting animal's weight |
|
|
Term
| Ever 3rd amino acid of collagen is: |
|
Definition
|
|
Term
| There are least _ types of collagens |
|
Definition
|
|
Term
| What form does collagen take? |
|
Definition
| three polypeptides form a right-handed triple helix |
|
|
Term
| How is collagen stabilized? |
|
Definition
|
|
Term
| What are the collagen cross-links? |
|
Definition
| Covalent bonds between side chains. The # of cross-links increases with age. |
|
|
Term
|
Definition
Cys (C)
N-terminus
Tyr (Y)
Lys (K)
Arg (R) |
|
|
Term
| Relationship between pK and Ka |
|
Definition
|
|
Term
| What do covalent bonds do? |
|
Definition
| Hold atoms together to form molecules |
|
|
Term
| What do non-covalent bonds do? |
|
Definition
| Govern 3-D shape of molecules & how they interact with each other |
|
|
Term
| Which are stronger: ionic or hydrogen bonds? |
|
Definition
|
|
Term
| What is a compound without polar groups called? |
|
Definition
|
|
Term
| What is the hydrophobic effect? |
|
Definition
| the exclusion of nonpolar substances from an aqueous solution |
|
|
Term
|
Definition
| Having both hydrophobic and hydrophilic portions |
|
|
Term
| What are the three forms for amphiphilic structures? |
|
Definition
a) micelle: snail shell
b) Bilayers: two-layered sheets with polar head and non-polar tail
c) Vesicle: formed by lipid-bilayer--traps some of the aqueous solution and polar solutes tend to remain |
|
|
Term
|
Definition
| 10^-14, which means [H][OH] = (10^-7)(10^-7) |
|
|
Term
|
Definition
|
|
Term
| What is the pH of human blood? |
|
Definition
|
|
Term
| Definition of acid and base |
|
Definition
acid: Donates a proton
base: Accepts a proton |
|
|
Term
| What is the definition of pK? |
|
Definition
| an acid's tendency to ionize |
|
|
Term
| Relationship between Ka and pKa |
|
Definition
|
|
Term
| The higher the Ka, the __ likely acid is to ionize. |
|
Definition
|
|
Term
| Henderson-Hasselbalch equation |
|
Definition
|
|
Term
| When adding a strong acid to pure H2O, all of the acid goes towards ____ |
|
Definition
|
|
Term
The pK of an acid is the pH where:
a)
b) |
|
Definition
a) acid is half-dissociated
b) concentration of acid & conjugate base is equal |
|
|
Term
| What is the effective buffering capacity of an acid? |
|
Definition
| Within one pH unit of its pK |
|
|
Term
| Water has a high Dielectric Constant. What is this? |
|
Definition
| ability to surround ions in dipole interactions and diminish their attraction for one another (D) |
|
|
Term
|
Definition
| Cage-like structure that is formed by water molecules surrounding a hydrophobic solute |
|
|
Term
| What are the colligative properties of water? |
|
Definition
freezing point depression
boiling point elevation
vapor pressure lowering
osmotic pressure |
|
|
Term
| Name the two important buffer systems and what systems they are important to |
|
Definition
1) Phosphate system: intercellular fluid
2) Carbonate system: blood plasma |
|
|
Term
|
Definition
| Cytosine, thymine and uracil |
|
|
Term
|
Definition
|
|
Term
|
Definition
a base bonded to a sugar
Example: adenosine |
|
|
Term
|
Definition
1-3 phosphate groups bonded to nucleosides, usually at C'5
Example: adenosine 5'-monophosphate (AMP) |
|
|
Term
| Which N of purines and pyrimidines is linked to the sugar? |
|
Definition
|
|
Term
| What are the two differences between RNA and DNA? |
|
Definition
1) DNA contains deoxyribose instead of ribose. Ribose has an OH at C'2, where deoxyribose has only H.
2) DNA contains thymine instead of uracil. |
|
|
Term
| How many bonds link A&T? G&C? |
|
Definition
|
|
Term
| What are the backbones of DNA? |
|
Definition
|
|
Term
| The double helix has a repeating space of ___ |
|
Definition
|
|
Term
| Are the two strands of DNA in a double helix parallel or anti-parallel? |
|
Definition
|
|
Term
| Diameter of double helix is: |
|
Definition
|
|
Term
| A turn of the double helix is completed every _ base pairs |
|
Definition
|
|
Term
| What part of the double helix is exposed to the solvent? |
|
Definition
| Sugar and phosphate backbone |
|
|
Term
| Define mRNA, rRNA and tRNA |
|
Definition
mRNA: carries message of template DNA to the ribosome
rRNA: major component of ribosome
tRNA: carries amino acids to ribosome where they are assembled into polypeptide chain |
|
|
Term
|
Definition
| Set of 3 bases recognized by tRNA in the mRNA through complementary base pairing. The ribosome covalently links the amino acids to form a protein. |
|
|
Term
| Difference in DNA & RNA roles |
|
Definition
DNA: long-term storage of genetic info
RNA: more active role in genetic info expression |
|
|
Term
|
Definition
| DNA that has base-paired with RNA to form a RNA-DNA hybrid double helix |
|
|
Term
| What are the stacking interactions that provide double helix stability? |
|
Definition
| van der Waals interaction between adjacent base pairs |
|
|
Term
| Which base pairs are stronger? |
|
Definition
|
|
Term
| Which base pairs of a higher melting point? |
|
Definition
|
|
Term
|
Definition
| The midpont of the danaturation melting curve |
|
|
Term
| How can you renature DNA? |
|
Definition
|
|
Term
| Short segments of DNA renature __ than long segments |
|
Definition
|
|
Term
| What are the two types of supercoils? |
|
Definition
negative: underwound double helix
positive: overwound double helix |
|
|
Term
|
Definition
| circular or linear DNA with fixed ends |
|
|
Term
| What is a linking number? |
|
Definition
L = T + W
T= twist, the number of helical turns
W= writhe, the # of times the dbl helix crosses over itself |
|
|
Term
|
Definition
| The combo of DNA, RNA and protein that makes up chromosomes and is found in nuclei |
|
|
Term
|
Definition
| The chief component of chromatin--the spools around which DNA winds |
|
|
Term
| What is the structural entirety of chromatin called? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| What is the form chromatin takes and its size? |
|
Definition
| "Beads on a string", 11 nm |
|
|
Term
| Six nucleosomes/turn equals a ___. What is its size? |
|
Definition
|
|
Term
| What are the 3 steps of the central dogma? |
|
Definition
1) DNA is replicated
2) a portion of DNA is transcribed to produce a complementary strand of RNA
3) RNA is translated into a protein |
|
|
Term
|
Definition
| An organism's complete set of genetic info |
|
|
Term
|
Definition
| The correspondence between amino acids & mRNA codons |
|
|
Term
|
Definition
|
|
Term
| What are 3 of the codons? |
|
Definition
"Stop" signals that terminate translation
The other 61 represent the 20 standard amino acids found in proteins |
|
|
Term
| What do dideoxy nucleotides lack? |
|
Definition
| both 2' and 3' hydroxyl groups |
|
|
Term
| 4444 bases = how many codons and amino acids? |
|
Definition
|
|
Term
| Define restriction enzymes |
|
Definition
| catalyze the breakage of bonds at or near specific nucleotide sequences |
|
|
Term
| Restriction enzymes create two types of ends: |
|
Definition
|
|
Term
| What will happen if fragments treated with the same restriction enzyme are mixed together? |
|
Definition
| The sticky ends may find their complements and re-form base pairs. A DNA ligase can form bonds between these adjacent nucleotides. |
|
|
Term
|
Definition
| a DNA ligase forming bonds between two DNA fragments that have been treated with the same restriction enzyme and have identical sticky ends |
|
|
Term
|
Definition
| small, circular DNA molecules capable of replicating independent of the chromosomal DNA. They carry genes for specialized functions |
|
|
Term
| What is the method of identifying bacterial cells containing plasmids using blue-dye called? |
|
Definition
|
|
Term
| What are the 4 ingredients of PCR (polymerase chain reaction) |
|
Definition
1) DNA sample
2) DNA polymerase
3) All 4 deoxynucleotides
4) 2 oligonucleotide primers |
|
|
Term
| What does a DNA polymerase do? |
|
Definition
| "Reads" an intact DNA strand as a template and uses it to synthesize the new strand. |
|
|
Term
| What is it called when a primer in PCR contains an error? |
|
Definition
| site-directed mutagenesis |
|
|
Term
| The target DNA ___ in concentration with each PCR cycle |
|
Definition
|
|
Term
| What is a method of cloning large amounts of DNA |
|
Definition
|
|
Term
| What are the steps of PCR? |
|
Definition
1) sample is heated to separate DNA strands
2) Temp is lowered and primers hybridize w/ DNA strands
3) temp is increased and the DNA polymerase synthesizes new DNA by extending the primers |
|
|
Term
| What is the relationship between non-coding DNA and organism complexity? |
|
Definition
| The more complex the organism, the higher the proportion of non-coding DNA |
|
|
Term
| What percentage non-coding DNA is found in yeast? In humans? |
|
Definition
|
|
Term
| Explain why certain large genomes include low #'s of genes |
|
Definition
| much non-coding DNA consists of repeating sequences with no known function |
|
|
Term
| Define transposable elements |
|
Definition
| Short segments of DNA that are copies many times and inserted randomly into chromosomes |
|
|
Term
|
Definition
| Sections of reassembled sequence, separated by gaps of highly repetitive DNA |
|
|
Term
| What is a gene with no known function? |
|
Definition
|
|
Term
| There are 3 million of these scattered throughout human base pairs...locations where the nucleotide sequence varies. |
|
Definition
| single-nucleotide polymorphisms |
|
|
Term
| In general, the genomes of two individuals differ about every ___ base pairs |
|
Definition
|
|
Term
| How many base pairs are in the human genome? |
|
Definition
|
|
Term
|
Definition
| gene humans share with another organism like a mouse, yeast or nematode that has similar sequences & functions and is derived from a common ancestor |
|
|
Term
| Where is foreign DNA placed in RNA Expression Construction? |
|
Definition
1) polylinker cloning site
2) promoter site |
|
|
Term
| Where is foreign DNA placed in Protein Expression Construction? |
|
Definition
1) promoter site
2) ribosome-binding site |
|
|
Term
|
Definition
| site of RNA polymerase binding |
|
|
Term
| Which cloning vector has the larger max. insert size, the yeast artificial chromosome or plasmid? |
|
Definition
|
|
Term
| Define sequence similarities |
|
Definition
| genes with similar functions in different species often resemble each other |
|
|
Term
| 3 steps to preparing the genomic library |
|
Definition
1) isolating total chromosomal DNA
2) digesting this DNA to produce fragments of a suitable size
3) cloning DNA fragments into a cloning vector |
|
|
Term
|
Definition
| DNA copies of mRNA molecules |
|
|
Term
| How are "open reading frames" (ORFs) identified? |
|
Definition
| DNA is matched with corresponding mRNA stop codons |
|
|
Term
|
Definition
| a set of cloned chromosomal DNA fragments representing the entire genome of an organism |
|
|
Term
| What does blotting allow? |
|
Definition
| Specific DNA, RNA or proteins to be detected in mixtures of these molecules |
|
|
Term
| Blotting technique for DNA, RNA and protein |
|
Definition
DNA: Southern
RNA: Northern
Protein: Western (separated by gel and detected with antibodies) |
|
|
Term
| Define human gene therapy |
|
Definition
| introduction of a functional version of a defective gene into cells to correct damage caused by mutant gene |
|
|
Term
|
Definition
| Intracellular protein that gives vertebrate muscles their red color |
|
|
Term
| What is the major protein of red blood cells? |
|
Definition
|
|
Term
| Which group of amino acids can act as an acid or base? Why? |
|
Definition
| Polar group: can ionize at physiological pH levels |
|
|
Term
| What is the function of regulatory proteins? |
|
Definition
| Regulate the ability of other proteins to carry out their functions. |
|
|
Term
| What is the function of contractile and motile proteins? |
|
Definition
| Produce cel movement in processes such as cell division, muscle contraction and cell motility |
|
|
Term
| Define size exclusion chromatography |
|
Definition
| purification technique using gel beads used to separate particles based on their size |
|
|
Term
| Define affinity purification |
|
Definition
| Uses ligands--makes use of specific interactions of proteins |
|
|
Term
| What is used for separation of DNA, RNA or protein using an electric current? |
|
Definition
|
|
Term
| How many residues are in an oligiopeptide? |
|
Definition
|
|
Term
| Most polypeptides contain between __ and ___ amino acid residues |
|
Definition
|
|
Term
| Where are the hydrophobic and hydrophilic amino acids located in globular proteins |
|
Definition
| hydrophobic in interior, hydrophilic are on the outside |
|
|
Term
| The folded hydrophobic core of a globular protein is called a: |
|
Definition
|
|
Term
| What are oriented outward in a membrane protein? |
|
Definition
| hydrophobic amino acid side chains |
|
|
Term
| What are the specific bonds of the alpha-helix? |
|
Definition
|
|
Term
| Most alpha-helix are __ residues long |
|
Definition
|
|
Term
| Most beta-sheets have _ to _ polypeptide strands, with an average of __. |
|
Definition
| 2 to 12, with an average of 6 |
|
|
Term
| 3 types of secondary structures |
|
Definition
alpha-helix
beta-sheet
irregular |
|
|
Term
| What amino acid occurs frequently in beta-turns? |
|
Definition
|
|
Term
| Give example of Type 1, 2 and 3 kinds of collagen |
|
Definition
1: bones, skin, tendons
2: cartilage
3; blood vessels |
|
|
Term
|
Definition
| when a charged residue occurs in the protein interior, it is almost always located near a residue w/ the opposite charge |
|
|
Term
| How much more stable is a protein fully-folded than in its unfolded form? |
|
Definition
|
|
Term
| What is the largest governing force in protein folding? |
|
Definition
|
|
Term
| What is the basic structural unit of collagen? |
|
Definition
| Tropocollagen, which consists of 3 intertwined polypeptide chains |
|
|
Term
| What happens in the heme of myoglobin? What type of protein is myoglobin? |
|
Definition
1) proteins bind
2) globular |
|
|
Term
| What is the main amino acid of collagen? |
|
Definition
|
|
Term
| What element is a stabilizing force of proteins? |
|
Definition
|
|
Term
|
Definition
| cross-links of 20-60 residues w/ 1-2 Zn ions |
|
|
Term
|
Definition
| cross-links of 20-60 residues w/ 1-2 Zn ions |
|
|
Term
|
Definition
| cross-links of 20-60 residues w/ 1-2 Zn ions |
|
|
