biochem exam 1

what are characteristics of a beta-pleated sheet

• the polypeptide chain is almost fully extended

• there are hydrogen bonds perpendicular to the direction of the polypeptide chain

• the polypeptide chains may be hydrogen bonded together in parallel or anti-parallel orientation

which functional groups of a peptide can form hydrogen bonds with water

both the amino group and the carbonyl group

why does a decrease in pH alter/disrupt the tertiary structure of an enzyme

it disrupts ions/salt bridges

what is a domain

a folded segment of polypeptide with a separate hydrophobic core

what are quaternary structures stabilized by

the same types of non-covalent interactions as tertiary structure

what do amyloid fibers consist of

stacked beta strands

what disease has been linked to protein misfolding

creutzfeldt-jakob disease

structurally myoglobin and hemoglobin, are very similar proteins. in what level of structure do they differ most?

quaternary structure

what triggers the transition from T state to R state (low to high affinity) in hemoglobin

oxygen binding

what do bone and tendons contain

collagen

what do hair and nails contain

keratin

what functional groups could NOT act as a hydrogen bond donor

aldehyde and ester

rank bond/interaction distances correctly in order from shortest to longest

covalent bond, hydrogen bond, van der waals interactions

what is the conjugate acid of H2PO4-

H3PO4

molecules such as methanol and ethanol are very soluble in water because

they contain O-H groups that can form multiple H-bonds with water

a molecule that has both a polar and nonpolar region

amphiphilic

in a water molecule, what are hydrogens partially charged

positive

in a water molecule, what are oxygens partially charged

negative

the pK of acidic acid is 4.76. what is the effective buffering range

pH: 3.76-5.76

what statement best explains why buffers are best made when the desired pH is within one unit of the corresponding weak acids pK

solutions typically resist changes in pH up to the point where the molar concentrations of weak acid and conjugate base are within a factor of 10

what is the pH characteristic of a buffer solution

pH is unaffected upon dilution

what is a reaction coordinate diagram

illustrates the change in free energy between the reactants and products as well as the activation energy required to meet the transition state

what are the 20 amino acid constituents of proteins differentiated by

the chemical properties of their side chains, which can be roughly classified as hydrophobic, polar, or charged

what are amino acids linked by

peptide bonds to form a polypeptide

what does the protein secondary structure include

the a helix and b sheet in which hydrogen bonds form between backbone carbonyl and amino groups

what is a globular protein

it has a hydrophobic core and is stabilized primarily by the hydrophobic effect

oxygen binding affinity to hemoglobin decreases with

hypoventilation

the formation of a dipeptide from two amino acids require

loss of water

what is a coenzyme

an organic molecule that is tightly bound to an enzyme and participates in an enzyme catalyzed reaction

what is change in enthalpy

the heat content of a system

what is hydrophobic effect

used to describe the exclusion of nonpolar substances from an aqueous solution

when a peptide bond forms, what reacts with a carboxyl group

amine

what level of protein structure is characterized by the three dimensional structure of an entire polypeptide including all amino acid side chains

tertiary

alpha-helices and beta-sheets comprise what structure

secondary

what is the most critical for maintaining the tertiary structure of a protein

hydrophobic interactions

what is the prominent type of secondary structure observed in myoglobin

alpha helices

what is cooperativity

the idea that binding of one molecule of oxygen to hemoglobin enhances further binding of oxygen to hemoglobin

chymotrypsin catalyzes the hydrolysis of a peptide bond and is therefore categorized as what

hydrolase

the ability for an enzyme to pick out one particular substrate from the myriad of molecules floating around its environment is an example of

specificity

what does the transition state represent

the highest point in a reaction coordinate diagram

how does a catalyst increase the rate of a reaction

it allows reacting molecules to more easily form the transition state

what is a prosthetic group

an organic molecule that is tightly bound to an enzyme and participates in an enzyme catalyzed reaction

an enzyme that forms a covalent bond with its substrate during the course of a reaction is considered to undergo what

covalent catalysis

the ability for an enzyme to change its shape upon substrate binding represents the concept of

induced fit

why are zymogens not enzymatically active

their active sites are covered or distorted and incapable of enzymatic activity

what is a competitive inhibitor

an inhibitor that binds to the active site only in the absence of a substrate and in a reversible fashion

what does the KI for a competitive inhibitor mean

lower KI values mean tighter binding to the enzyme

what is a noncompetitive inhibitor

a reversible inhibitor that binds to a site other than the active site regardless of whether or not the substrate is bound

what do irreversible enzyme inhibitors do

innactivate the enzyme

the overlap of chemistry and biology is considered to have first occured with

the discovery and synthesis of urea

how can a eukaryote be distinguished from a prokaryote

presence of a nucleus

the presence of a continuous membrane studded with ribosomes is a characteristic of what

rough endoplasmic reticulum

what is the largest chiral amino acid

molecule called tryptophan

as proteins are commonly written, the beginning on the left, NOT the end on the right, is called

N-terminus

the term ∆G° describes what

the energy difference between reactants/substrates and product

how can pH be altered

• by adding a base or acid to shift the balance between [H+] and [OH-]

• adding an acid increases the concentration of [H+] and decreases pH; adding a base has the opposite effect

what is a buffer

a weak acid whose pH resists change upon addition of either more acid or more base

• a buffer consists of a weak acid and its conjugate base

how do buffers resist change in pH

• binding H+ when an acid is added

• releasing H+ when a base is added

how does the number of protons on the acid get affected by the pH and pKa value

• if the pH is BELOW the pKa, more protons are ON the acid

• if the pH is ABOVE the pKa, more protons are OFF the acid

what does the Henderson-Hasselbalch Equation determine

the pH if one knows the pKa and the amount of acid and conjugate base

what does the Henderson-Hasselbalch equation tell us

• if the concentration of [A-] is higher than [HA], the pH is higher than the pKa

• if the concentration of [A-] is lower than [HA], the pH is lower than the pKa

when is a buffer effective

in a range of about 1 pH unit above or below the pKa of the weak acid

what is the principal buffer in cells

H2PO4-/HPO42-

what is hyperventilation

can result in increased blood pH (and potential blackout)

what is hypoventilation

can result in decreased blood pH

what do amino acids contain

• a-carboxyl group

• a-amino group

• an intervening a-carbon

are amino acids chiral or non-chiral

• MOST are chiral

• have two stereoisomers (L and D)

what is an amino acid R group

• what distinguishes one amino acid from another

• protein folding and function depends on the number and order of R groups

what is the most common difference between amino acids

their side chains

what amino acids have non-polar side chains

• Ala

• Val

• Leu

• Ile

• Pro

• Phe

• Trp

• Met

what amino acids have neutral polar side chains

• Ser

• Tyr

• Thr

• Cys

• Gln

• Asn

what amino acid groups are acidic

• carboxyl groups (COOH) donate protons (therefore are acidic)

• when this happens, groups become negatively charged

what amino acid groups are basic

• the nitrogen groups (amine groups) in the side chain can accept a proton at neutral pH (pH 7)

• each amine group is positively charge

what is the ionization of amino acids

• all amino acids have at least 2 pKas

• the amino pKa is about 9.5

• the carboxylic acid groups pKa is about 2

how does the titration curve work

when an amino acid is titrated, the curve represents the reaction of each functional group with the hydroxide ion

what is the c-terminus

end, or right end, of peptide or protein, free carboxyl terminus

what is the primary structure of a protein

amino acid sequence

what is the secondary structure of a protein

the localized arrangement in space of the peptide backbone of a protein

what is the tertiary structure of a protein

final 3-D arrangement of all amino acids

what is the quaternary structure of a protein

arrangement of separate peptide chains with each other to form an active protein (enzyme)

what is bond 1 in secondary protein structure

between alpha-C and the carboxyl C of the same residue

• termed: psi

what is bond 2 in secondary protein structure

between alpha-C and amino N of the same residue

• termed: phi