Term
| What are the most abundant atoms found in living systems? |
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Definition
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Term
| Living organisms are ______-based |
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Definition
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Term
| 4 Major types of biomolecules |
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Definition
| amino acids, carbohydrates, nucleotides, lipids |
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Definition
| proteins, nucleic acids, polysaccharides |
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Term
| General structure of amino acid |
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Definition
| There's an alpha carbon that has a negatively carboxyl group (COO-), a positively charged amine group (H3N+), a hydrogen, and an R side chain attached to it |
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Definition
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Definition
think of this as either OR
ROR |
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Definition
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Term
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Definition
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Term
| General structure of carbohydrates |
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Definition
Are sugars so think of the glucose structure
Has the general formula (CH2O)n where n is the number of carbons |
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Term
| General structure of nucleotides |
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Definition
| 5 carbon suger, nitrogen containing ring and one or more phosphate groups |
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Term
| General structure of lipids |
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Definition
| Very hydrophobic so will most likely have a ton of CH sequences |
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Term
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Definition
| joins polymers of nucleotides |
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Term
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Definition
| joins polymers of carbohydrates |
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Term
| Lipids don't form polymers. Why? |
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Definition
| Are hydrophobic and basically have nothing to bind to. |
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Definition
the energy relevant to biochemical systems.
Equation: deltaG = deltaH - deltaTS |
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Definition
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Term
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Definition
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Term
Under what conditions would ΔG always
be a negative value? |
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Definition
| Low enthalpy, high entropy |
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Term
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Definition
| refers to deltaG (the change in energy). If a system is endergonic, then that it means it absorbed energy and this is a nonspontaneous process. If a system is exergonic, it released energy and that means the system is nonspontaneous |
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Term
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Definition
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Term
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Definition
| Loss of electrons, loss of hydrogens, gain of oxygens |
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Term
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Definition
| Gain of electrons, gain of hydrogens, loss of oxygens |
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Term
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Definition
| Bacteria, Archaea, Eukaryotes |
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Term
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Definition
| Similar in structure to bacteria, live in extreme environments |
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Term
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Definition
| The strongest bond there is. Is an intramolecular force meaning it binds atoms of a molecule |
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Term
| Basic principle of a hydrogen bond |
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Definition
| Electronegative element has to be covalently bonded to a H. This electronegative atom can then bind to another hydrogen |
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Term
| Strong H-bond vs a weak one? |
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Definition
| A linear bond is stronger because it is not constrained |
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Term
| What makes water a polar molecule? |
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Definition
| It's tetrahedral shape allows for an uneven distribution of charge |
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Term
| H-bonds formation in liquid water |
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Definition
| Each hydrogen bond doesn't last long and so the structure of water constantly reorients itself |
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Term
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Definition
| each water molecule forms 4 hydrogen (the max) bonds with other water molecules |
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Term
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Definition
| it's ability to form hydrogen bonds makes it very cohesive |
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Term
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Definition
| The H atom that is bonded to an electronegative atom |
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Term
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Definition
| The atom that is electronegative and has a lone pair |
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Term
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Definition
| Covalent > Ionic > Hydrogen > Van der Waals (dipole-dipole > London dispersion) |
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Term
| van der waal interaction between two polar molecules |
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Definition
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Term
| van der waal interaction between two nonpolar molecules |
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Definition
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Term
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Definition
a measure of a solvent's ability to dissociate ions from each other, ie how good can this solvent dissolve a solute?
A solvent's dielectric constant is directly proportional to how polar it is. |
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Term
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Definition
Nonpolar substances will not dissolve in water and will shield itself to get away from as much of the water as possible.
Is related to entropy. When a hydrophobic molecule is placed in water, the water molecules have to align themselves with their polar ends away from the nonpolar molecules. This is an unfavorable condition and thus results in a drop of entropy. Because this orientation prevents the "constrained" water molecules from forming hydrogen bonds |
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Term
| How the hydrophobic effect drives spontaneous associations based on polarity |
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Definition
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Term
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Definition
| Caused by the hydrophobic effect. It is a spherical structure where the hydrophobic tails of the lipids aggregate and the polar heads are exposed to the solvent water |
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Term
Benefits of lipid associations into
membranes |
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Definition
| Acts as a barrier that can prevent the spontaneous diffusion of ions and molecules down their concentration gradients. This allows the membrane bound organelle to maintain its interior concentration |
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Term
| What type of molecules can pass through the lipid bilayer? |
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Definition
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Term
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Definition
a measure of how much the acid dissociates. A large Ka means the acid will dissociate more
Concentration of the products/concentrations of the reactants |
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Term
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Definition
-log(Ka)
Also corresponds to the pH at which the acid is half ionized. This is because pH = pKa when [HA] = [A-]
At half-ionization, [HA] = [A-] since half of the concentration of HA becomes [A-] |
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Term
| Henderson Hasselbach equation |
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Definition
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Term
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Definition
| acid is protonated (there exists more hydrogen ions because it's more acidic) |
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Term
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Definition
| acidic and conjugate base form exist at equal concentrations |
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Term
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Definition
| acid is deprotonated (there exists less hydrogen ions because it's more basic) |
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Term
| Converting log into a regular number |
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Definition
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Term
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Definition
| Protons jumps rapidly through a network of hydrogen-bonded water molecules (like crowd surfing). Free protons never exist |
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Term
| Ionization constant of water |
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Definition
To get this equation, just arrange the dissociation of water into an equation:
H20 <-> H+ + OH-
You know K is always equal to products/reactants:
K= [H+][OH-]/[H2O]
Kw = K[H2O] = [H+][OH-]
Kw = 10^-14 because [H+] = 10^-7 and [OH-] = 10^-7 in water |
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Term
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Definition
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Term
| pH scale 10 fold difference |
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Definition
| a difference of 1 pH unit is the equivalent of a difference of 10 times the amount of concentration |
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Term
| How to determine [H+] from pH |
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Definition
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Term
| Relationship between pKa and acid strength |
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Definition
| Just think of pKa like pH. The smaller the pKa, the greater the acid strength and the greater the tendency to donate H+ |
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Term
| Effect of adding a weak acid/base to water |
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Definition
| It only half dissociates so when you do the problems, you have to consider Kw of water? Initial value [H+] = 10^-7? |
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Term
| Effect of adding strong acid/base to water |
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Definition
It fully dissociates so all the [H+] comes from the acid
Initial value [H+] = 0? |
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Term
| Effect of adding a strong acid/base to a weak acid/base |
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Definition
This is the principle of buffers.
To use acid as an example, when you add a strong acid to a weak acid (with its conjugate base) the pH only slightly changes. This is because the conjugate base can accept some protons which neutralizes the acid. The reason there is a conjugate base is because the weak acid doesn't fully dissociate?
Same concept with a base |
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Term
| Effective buffering range |
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Definition
| the pH that is +- the pKa of the acid |
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Term
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Definition
| Usually a strong acid with a conjugate base or a strong base with a conjugate acid |
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Term
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Definition
Adenine and Guanine
Is a two cyclic structure |
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Term
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Definition
Cytosine, Thymine, Uracil
Is a 1 cyclic structure |
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Term
| Designation of carbon atoms in the sugars of nucleotides |
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Definition
The carbon that is connected to the base is labeled 1 and the labeling continues in a clockwise direction
The 3' carbon is the one that forms the phosphodiester bond with another nucleotide.
The 5' carbon is the one that is connected to the phosphate group |
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Term
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Definition
| In deoxyribose, the 2' carbon on the sugar is connected to just Hydrogen instead of OH |
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Term
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Definition
A nucleoside is just the sugar + base
Nucleotide is the sugar + base + phosphate groups |
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Term
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Definition
2 anti-parallel strands
Sugar-phosphate backbones are solvent-exposed (hydrophilic)
Bases are hydrophobic so they are packed inside perpendicular to the backbone
Is a right-handed twist |
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Term
| Directionality of DNA strands |
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Definition
| 5' to 3' pairs with 3' to 5' in order to form H bonds |
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Term
| How 2 DNA strands bind to each other |
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Definition
| DNA double helix is stabilized by van der waals, base stacking and the hydrophobic effect |
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Term
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Definition
| Allows hydrogen bonding to occur between its base pairs and it's the only way they can fit with each other |
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Term
| Major vs minor groove of DNA |
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Definition
| Major groove is when the backbones are far apart while a minor groove occurs when they are close together. This results because of the twisting of the DNA ladder into a helix |
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Term
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Definition
| purine always binds to pyrimidines |
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Term
| G-C H bonds vs A-T H bonds |
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Definition
G-C has 3 H bonds
A-T has 2 H bonds |
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Term
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Definition
single stranded
Forms secondary structure by intramolecular base pairing |
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Term
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Definition
| makes up ribosomes along with proteins |
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Term
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Definition
| carries amino acids to ribosome by codon pairing |
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Term
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Definition
| transcribed RNA, carries the genetic info from nucleus to cytoplasm where the ribosomes are located |
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Term
| Why are G-C bonds harder to separate? |
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Definition
| Base stacking differences instead of # of hydrogen bonds |
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Term
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Definition
| temp at which half of DNA is melted |
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Term
| What happens if you cool DNA too fast after it has been denatured? |
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Definition
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Term
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Definition
| Replication forms DNA which is transcribed into RNA which is translated into Protein |
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Term
| Coding vs template strand |
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Definition
| The template strand is the strand that a replicating strand is basing its code on. This replicating strand will exactly match the other strand which is called the coding strand because this will be what the mRNA bases its sequence on |
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Term
| DNA is replicated in what direction? |
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Definition
| reads 3' to 5' and adds 5' to 3' |
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Term
| Everything is read 3' to 5' and added 5' to 3' |
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Definition
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Term
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Definition
| Coding DNA codes for proteins while noncoding genes don't |
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Term
| Repetitive DNA sequences as it relates to the human genome |
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Definition
| A lot of the human genome is filled with repetitive DNA sequences which explains why our genome is so large |
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Term
| Two ways genes can be identified |
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Definition
Look for an open reading frame. Finds the start codon first?
Another method is to compare sequences to known genes |
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Term
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Definition
| A protein is the functional product of 1 or more polypeptide chains and a polypeptide chain is just a sequence of amino acids |
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Term
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Definition
| All amino acids found in proteins are the L enantiomers |
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Term
| Where are hydrophobic/hydrophilic residues found in proteins? |
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Definition
hydrophobic - inside
hydrophilic - outside |
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Term
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Definition
joins amino acids together
is formed between the amine group of acid and the carboxyl group of another. Results in the release of water
side chains are in the trans conformation
no free rotation around peptide bond
very stable bond, short length |
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Term
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Definition
isoelectric point, this is the pH where the net charge on the entire molecule is 0 (zwitterionic form)
pI = (pk1+pk2)/2
pI is important because it influences separations of proteins based on charge |
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Term
| Why are the pK's of carboxy and amine termini 1 pH unit closer to neutral in a peptide compared to those of free amino acid? |
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Definition
| In a protein, the terminal sides are farther apart |
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Term
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Definition
| actual amino acid sequence, peptide bonds |
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Term
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Definition
| localized folding of the polypeptide due to hydrogen bonding of the backbone. Forms alpha helices and beta sheets |
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Term
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Definition
3D structure of an entire polypeptide
Forms due to a combo of H-bonds, ionic bonds, disulfide bonds, van der waals |
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Term
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Definition
the spatial arrangement of multiple chains, has subunits
Forms due to a combo of H-bonds, ionic bonds, van der waals, disulfide bonds |
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Term
| So tertiary and quaternary structure forms because of the same type of bonds. secondary structure forms only because of hydrogen bonds |
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Definition
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Term
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Definition
right handed helix formed by hydrogen bonds. R groups radiate outward
There's a H bond with every 4th AA, which keeps the hydrogen bond linear (stronger) |
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Term
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Definition
linear extended ZIG ZAG pleated sheet
formed by hydrogen bonds between chains which can be in parallel and antiparallel formations. The antiparallel is more stable because it forms linear hydrogen bonds |
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Term
| Hydrophobic effect has most to do with protein folding |
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Definition
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Term
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Definition
| in denaturation, enzyme loses tertiary structure, then secondary. Can be denatured by pH, temp, ionic strength, solubility |
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Term
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Definition
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Term
| Protein domain vs protein subunit |
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Definition
| Domain is in 1 polypeptide chain and subunits are multiple polypeptide chains |
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Term
| Protein structure is determined by |
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Definition
| amino acid sequence and chaperones |
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Term
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Definition
| proteins that assist in the folding of a protein. Makes sure they fold properly so as to not to lead to disease |
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Term
| Processing after protein synthesis |
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Definition
| Some of protein is clipped off, chemical groups are added |
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Term
| Size exclusion chromatography |
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Definition
| With this technique, proteins are separated by size. Small molecules will get stuck inside porous beads allowing for larger proteins to elute first |
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Term
| Ion exchange chromatography |
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Definition
With this technique, separation is based on charge. Usually the matrix contains positive DEAE groups or negatively charged CM groups.
When the mixture of proteins are added, they will bind to the opposite charge of the matrix while uncharged and like-charged proteins will flow to the bottom |
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Term
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Definition
| In this method, the N-terminus side of a peptide is cleaved off and identified one by one. It does this by reaction with PITC |
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Term
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Definition
only determines primary structure
With this method, a protein is sent through a capillary tube where it forms ions. The first instrument sorts the ions and allows only 1 out at a time. It will then go through another instrument where the mass-to-charge ratio is measured. This is done for every ion and the sequence is determined by comparing the masses of increasingly larger fragments |
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Term
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Definition
| crystallize protein and then bombard it with X-rays. This will give you a 3D map of electron density which can be converted into a 3D model |
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Term
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Definition
| proteins are coated with a negative charged and then put in a gel matrix where they move toward the positive electrode. Smaller MW proteins move the fastest |
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Term
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Definition
is a porphyrin ring
has an iron atom in the middle which is bound to 4 nitrogen atoms and can bind to an oxygen
Is coordinated with Histine residues
The His E7 is above the ring (distal) and forms a hydrogen bond with oxygen
The His F8 is below the ring (distal)
Is not a good oxygen carrier by itself, needs iron |
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Term
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Definition
made up of just 1 heme group
is a monomer, mostly alpha-helical |
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Term
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Definition
aka relaxed form, when oxygen binds, the iron is pulled into the plane of the ring
h bonds form with His E7, His F8 is pulled toward heme which changes quaternary structure of protein
histidine on beta chain shifts between 2 threonine residues of the alpha chain |
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Term
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Definition
| aka terse form, heme is slightly bowed down, His F8 further from ring |
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Term
| As binding affinity for oxygen of myoglobin goes up |
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Definition
| the dissociation constant (Kd) goes down. This makes sense because Kd is a measure of how easily myoglobin and oxygen dissociate |
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Term
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Definition
the proportion of the total myoglobin molecules that have bound O2
It depends on the concentration of oxygen available and the affinity for myoglob
Y = pO2/K + pO2 |
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Term
| Plot of myoglobin saturation |
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Definition
is a hyperbolic shape
binding increases rapidly until most molecules saturated |
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Term
| How to determine p50 from graph |
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Definition
| K = p50 and it's the value where Mb is half saturated |
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Term
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Definition
tertiary structure is similar to myoglobin, though primary structure isn't that similar to myoglobin (only 18%)
has 4 heme groups |
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Term
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Definition
| residues that are identical in all globins, are essential for the structure and/or function of the proteins |
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Term
| Conservative substitutions |
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Definition
| when an amino acid can be substituted out with another similar amino acid and the function won't be altered |
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Term
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Definition
| residues that can be switched out with any ol amino acid and the function won't changed |
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Term
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Definition
graph is sigmoidal, indicates cooperative and allosteric binding
p50 is a lot higher than with Mb
at low pO2, Hb is reluctant to bind O2 but the affinity increases as pO2 increases until it levels off |
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Term
| Affinity of Hb for O2 in tissues vs lungs |
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Definition
low in tissues, high in lungs
This is so the Hb can drop off the oxygen in tissues and pick up oxygen from lungs
In the tissues, Mb takes up this released oxygen from Hb |
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Term
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Definition
high pH (low H+ concentration) favors binding, low pH (high H+ concentration) favors release
tissues release CO2 as they consume O2. this CO2 enters red blood cells where it is converted into bicarbonate which releases H+. this will cause for the release of O2
in the lungs, hemoglobin binds more O2, releasing the protons, combines with bicarbonate to form Co2 which is breathed out |
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Term
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Definition
when it binds to Hb, it converts it into the T state which decreases the affinity for oxygen
this allows oxygen to transfer from mother to fetus. mother has BPG binded to her hemoglobin (more willing to give uo O2). baby has Hb that binds BPG less well and so it has a higher affinity for oxygen. it snatches up the oxygen that the mother releases |
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Term
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Definition
| body produces more BPG, lower affinity for O2 in Hb and so more O2 in tissues |
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Term
| 3 main classes of structural proteins |
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Definition
| microfilaments, intermediate filaments, microtubules |
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Term
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Definition
is globular and monomeric
converts to F-actin when it polymerizes several monomers |
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Term
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Definition
grows faster at rapid end (+)
driven by ATP hydrolysis
newly formed subunit binds to ATP
ATP hydrolysis occurs after the subunit adds |
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Term
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Definition
| ATP binding cleft is at the - end |
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Term
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Definition
| breaks a high energy phosphate bond in ATP. this energy drives a lot of reactions |
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Term
| Actin polymerization/depolymerization |
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Definition
| polymerization of actin is reversible as actin grows and shrinks over time |
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Term
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Definition
| when addition of actin subunits equals the subtraction of actin subunits |
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Term
| Structure of tubulin protofilament |
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Definition
| is a dimer that contains beta and alpha tubulin (beta on top) |
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Term
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Definition
dimers of tubulin forms hollow cylinder
requires GTP hydrolysis. the GTP on the alpha tubulin is blocked but solvent exposed on the beta end so this is the one that gets hydrolyzes
protofilaments line up side by side to form tube
+ side is faster at addition and disassembly |
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Term
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Definition
| construct cilia and flagella, align and separate chromosomes |
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Term
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Definition
a dimer of coiled alpha helices
has a 7 residue repeat where #1 and #4 are nonpolar
held together by hydrophobic interactions |
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Term
| How keratin forms an intermediate filament |
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Definition
| monomer -> dimer -> tetramer -> octamer -> intermediate filament |
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Term
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Definition
a left handed helix that has many repeating Gly-Pro-Hyp residue. 3 of these helices combine to form a right handed twiple helix
Every 3rd residue is Gly |
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Term
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Definition
| animal bones and tendon, part of connective tissue |
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Term
| Why is Gly so important in collagen |
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Definition
no other residue will fit in center of helix and it allows for h bonding
Note: H bonding also occurs between Hyp residues |
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Term
| How is collagen processed after formation? |
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Definition
| is secreted from cell and trimmed by proteases |
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Term
| Importance of Lys residues in collagen |
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Definition
|
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Term
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Definition
| 2 polypeptides that form 2 heads and a coiled tail |
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Term
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Definition
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Term
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Definition
also has 2 heads and a coiled tail
light chains are at end of tail which carry the "cargo", shorter neck than myosin |
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Term
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Definition
|
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Term
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Definition
| contains ATP binding site and a binding site for actin |
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Term
|
Definition
| has 2 light chains wrapped around it |
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Term
| Total number of chains for myosin |
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Definition
| 6: 2 main polypeptide chains, 2 light chains on each of the necks |
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Term
| How myosin forms thick filaments |
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Definition
| the tails of the myosin form the thick filaments while the heads interact with thin filaments (actin) |
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Term
| Movement sequence of sequence |
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Definition
remember that the heads can't be bound to both ATP and actin at the same time.
head starts out bound to actin
an ATP binds that cocks the head back and makes it let go of the actin
ATP hydrolyzes to ADP + P which gives the head energy to cock forward
head attaches to actin on down
this causes ADP + P to be released which makes the head return to its original position. this rubs against the thin filament which causes it to move (power stroke) |
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Term
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Definition
driven by ATP hydrolysis
think of the heads as feet
leading head is bound to protofilament of tubulin
trailing head is bound to ADP
leading head binds to ATP and the neck retracts
this swings the trailing head forward (force generating step)
new leading head binds tubulin and releases ADP which moves the cargo forward
new trailing head hydrolyzes ATP and is now bound to ADP
rinse and repeat
only one head is bound at a time |
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