Biochemistry Exam 1

enantiomer

molecules that are mirror images of each other

pKa

pH where the buffer is 50% WA and 50% CB

Condensation

forms a peptide bond

conjugated proteins

proteins that contain permanently associated chemical components

what is the highest level of folding observed in myoglobin?

tertiary

Which amino acid doesn’t participate in an alpha helix formation?

Glycine

What amino acids belong to the polar uncharged groups?

serine, threonine, cysteine, aspartagine, glutamine

What amino acids belong to the nonpolar groups?

glycine, alanine, proline, valine, leucine, isoleucine, methionine

What amino acids belong to the positively charged groups?

lysine, histidine, arginine

What amino acids belong to the negatively charged groups?

aspartate and glutamate

What amino acids belong to the aromatic groups?

phenylalanine, tryptophan, tyrosine

what type of catalyst utilizes a metal ion to stabilize charge and mediate redox reactions?

metal ion catalysis

Addition of this type of allosteric modulator of an enzyme causes K0.5 to shift to the left?

activator

Addition of this type of allosteric modulator of an enzyme causes K0.5 to shift to the right?

inhibitor

Bohr Effect

when pH is low, there’s a decrease in oxygen binding affinity due to a conformational change to the T state. (O2 leaves, CO2 binds)

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when pH is high, there’s an increase in oxygen binding affinity for the R state (O2 binds, CO2 leaves)

what are the major components of cells?

C, H, O, N

which functional group contains sulfur?

thioester

what is largely responsible for the unusual properties of water?

hydrogen bonding

a cell present in a _____ solution causes the cell to shrink due to net movement of water out of the cell.

hypertonic

T/F? According to the concerted model of cooperative binding, all binding sites in an allosteric protein will change conformation upon the binding site of at least one ligand.

True

T/F? One way addition of an irreversible inhibitor into an enzyme-catalyzed reaction can inhibit the reaction is by destroying a functional group essential for enzyme activity.

True

T/F? Enzymes are complementary to the substrate

False - not always

T/F? Osmotic pressure depends on the number and size of the solute particles in a given amount of solvent.

False - doesn’t affect size

T/F? The Km of an enzyme-catalyzed reaction is essentially a measure of affinity.

False - Km is not always the measure of affinity

T/F? A noncompetitive inhibitor does not compete with the substrate for the active site on the enzyme, and results in a decrease of Km and Vmax. Its also characterized by a=1 and a’>1.

False - its UNcompetitive

T/F? It is known that the following polypeptide forms an alpha helix. There is hydrogen bonding between Ala and Thr.

Ala-Phe-Val-Ser-Thr-His

True

T/F? Translocases are enzymes involved in transferring a functional group to the other molecules.

False - its movement of molecules or ions across membranes

T/F? The pre-steady state of an enzyme catalyzed reaction is characterized by the rapid increase in free enzyme and rapid decrease in enzyme-substrate complex.

False

T/f? A protein with a higher Kd has a higher affinity for the ligand.

False - higher affinity for the release of the ligand

Free amino acids all assume this form at a pH=7 and have both (+) and (-) ions in the same molecule

Zwitterion formation

Organelles that are found in animal cells but not in plants

lysosome

organelles found in plant cells but not animal cells

chloroplasts

Which is the weaker acid, pK2 = 4.76 or pK1 = 9.60?

pK1 = 9.60 because its more basic than 4.76

how many stereoisomers are possible for a molecule containing 5 chiral carbons?

2^5 = 32

an increase in ____ is mostly responsible for the ease of dissolving salts in water.

entropy

the delta G of a given reaction is 15kcal/mol. what type of reaction is this?

endergonic

the clustering together of hydrophobic regions in aqueous solutions

micelle

phospholipids are an example of a(n) _____ molecule.

amphipathic

which domain of life is capable of inhabiting extreme environments?

archaea

stereospecificity

the ability to distinguish between stereoisomers

phototrophs

use sunlight

chemotropohs

derive energy from the oxidation of a chemical fuel

autotrophs

use CO2

heterotrophs

require organic nutrients

What are humans/animals considered?

chemoheterotrophs

what are plants considered?

photoautotrophs

first law of thermodynamics

total amount of energy in the universe remains constant

second law of thermodynamics

total entropy (randomness) of the universe is continually increasing

Gibbs Free Energy

G = H - TS

* s = entropy (randomness)
* H = enthalpy
* T = temp in kelvin

Spontaneity

ΔG = ΔH - TΔS

* Endergonic = + ΔG
* Exergonic = - ΔG

what drives the hydrophobic effect?

entropy

osmolarity

the measure of a solute in a solvent (NOT SIZE)

colligative properties that are altered by solutes

vapor pressure, osmotic pressure, boiling point, melting and freezing point

Equilibrium constant equation

Keq = \[C\]\[D\] / \[A\]\[B\]

Equilibrium constant of water

Kw = \[H+\]\[OH-\] / \[H2O\]

* Kw = 1.8 x 1-^-16 M
* in pure H2O at 25C → \[H+\]=\[OH-\]=10^-7M

pH

pH = -log\[H+\]

pKa

pKa = -logKa

* Keq = \[H+\]\[A-\]/\[HA\] = Ka

buffering region

\+/- 1 of the pKa

Henderson-Hasselbalch Equation

pH = pKa + log \[B/A\]

optimum pH

the characteristic pH at which enzymes typically show maximum catalytic activity (transition state on a graph)

which is the only amino acid that is achiral?

glycine

which amino acid groups can contribute to the hydrophobic effect?

aromatic

what are the essential amino acids?

phenylalanine, valine, tryptohan, threonine, isoleucine, methionine, histidine, arginine, leucine, lysine

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(PVT TIM HALL)

What are the non essential amino acids?

alanine, arginine, glutamine, glycine, proline, serine, tyrosine

isoelectric point (pl)

the pH at which the net electric charge is zero

if pH < pKa …

protonated

if pH > pKa …

deprotonated

hydrolysis

breaks a peptide

dipeptide

2 amino acids, 1 peptide bond

tripeptide

3 amino acids, 2 peptide bonds

oligopeptide

a **FEW** amino acids

* N-terminal (pk2)
* C-terminal (pk1)

polypeptide

**MANY** amino acids

protein

thousands of amino acids; multiple polypeptide chains

prosthetic group

the non-amino acid part of a conjugated protein

lipoprotein

contains lipids

glycoproteins

contain sugars (carbohydrates)

metalloproteins

contain specific metals

phosphoproteins

contain phosphate groups

hemoproteins

contain heme (iron)

flavoproteins

contain flavin nucleotides

alpha helix

simplest arrangement, maximum number of hydrogen bonds

intrahelical hydrogen bonds

every n+4 residue

* confers significant stability

stabilizing alpha helix

formation of ion pairs and hydrophobic effect

destabilizing alpha helix

charge, size, and shape of R chains

what is found at the N-terminus?

NH3+, negatively charged amino acids

What is found at the C-terminus?

COO-, positively charged amino acids

which is most likely to not form an alpha helix?

proline & glycine

beta-strand

single protein segment

beta conformation

polypeptide backbone extends into a zigzag

beta sheet

several strands in beta conformation side by side

anitparallel

opposite orientation; beta turns highly favorable

parallel

same orientaiton; unfavorable

beta turns

connect ends of two adjacent segments of antiparallel beta sheets

* Gly (residue 3) & Pro (residue 2)

what is the highest level of protein folding in hemoglobin?

quaternary

fibrous proteins

arranged in long strands or sheets

globular proteins

folded into spherical or globular shapes

membrane proteins

embedded into hydrophobic lipid membranes

intrinsically disordered proteins

(don’t fit in any other group)

lacking stable tertiary structures

often lack a hydrophobic core

high densities of charged residues

facilitates a protein to interact with multiple binding partners

alpha-keratin turns which way?

right handed alpha helix

repeating a-keratin residues

ala, val, leu, Ile, Met, Phe