Biochem Exam 1

Glycine (Gly)

Cysteine (Cys)

alanine (Ala)

methionine (Met)

valine (Val)

asparagine (Asn)

isoleucine (ile)

glutamic acid (Glu)

leucine (Leu)

aspartic acid (Asp)

phenylalanine (Phe)

glutamine (Gln)

proline (Pro)

threonine (Thr)

tryptophan (Trp)

arginine (Arg)

tyrosine (Tyr)

lysine (Lys)

histidine (His)

serine (Ser)

Hydrophilic subfamily

serine, threonine, cysteine, asparagine, glutamine

charged subfamily

aspartic acid, glutamic acid, lysine, arginine, histidine

hydrophobic subfamily

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

aromatic subfamily

phe, tyr, trp

Why do unfolded proteins tend to aggregate?

Hydrophobic regions on the exterior of misfolded proteins interact and form large complexes

adenine

guanine

cytosine

thymine

a patient presents with metabolic acidosis. Based on carbonic-acid bicarbonate buffering system and physiological adaptation, which response most directly helps raise blood pH toward normal?

increase breathing rate to lower CO2 and reduce H2CO3, with reduced renal excretion of HCO3-

Which statement explains structural changes in the DNA molecule during transcription?

Supercoils form to conserve the linking number while accommodating unwinding.

B-form conformation of DNA

most stable

A-form conformation of DNA

squished version; not natural

Z-form confromation of DNA

left-handed helix; considered unnatural

Paralogs

genes that share similar sequence in species

orthologs

genes conserved across species

First law of thermodynamics

energy cannot be created nor destroyed, only transformed

neg change in H

exothermic

pos change in H

endothermic

Second law of thermodynamics

in any spontaneous process, total entropy of an isolated system always increases, and heat cannot spontaneously flow from colder to hotter body

neg change in G

favorable

pos change in G

unfavorable

Keq > 1

reaction proceeds spontaneously; change in G expected <0; exergonic

Keq < 1

reaction favors formation of A & B; change in G expected > 0; endergonic

Hierarchical strucutre (smallest to largest)

elements and functional groups, biomolecules, macromolecules, metabolism, cells, organisms, ecosystems

Q

mass action ratio

phi torsional angle

rotation around the N-Ca bond

psi torsional angle

rotation around the Ca-C bond

primary structure

amino acid sequence

secondary structure

local arrangement of the polypeptide backbone into regular repeating conformations of which there are three primary types: beta strands, alpha helices, beta turns

tertiary structure

complete arrangement of all the atoms in the polypeptide chain; stabilized by weak noncovalent interactions and disulfide bridges between cysteine residues or metal ions

quaternary structure

number and organization of protein subunits within a protein complex; consist of two or more protein subunits that can be identical or different

Christian Anfinsen demonstrated

RNaseA could be denatured by urea and then folded to regain enzymatic activity, showing that the primary amino acid sequence is all that is required for folding

Hsp70 uses

Atp to bind/release unfolded proteins

specific activity

ration of protein activity units to total amount of protein in sample

multifold increase

new specific activity divided by last specific activity

nucleoside

base attached to a sugar

nulceotide

phosphorylated nucleoside

nonhomologous end joining

rejoins broken ends and often introduces random insertions or deletions resulting in gene knockout

homology-directed repair

uses a donor DNA template that shares sequence homology with the regions flanking the cut site, allowing the cell to copy the donor sequence precisely into the genome, leading to a precise gene knock-in

Taq polymerase is used rather than a typical mammalian DNA polymerase, why?

it remains functional after repeated exposure to the high denaturation temps used in each cycle

four regions connected to an amino acid central alpha carbon

amino group, carboxyl group, hydrogen atom, and R group

peptide bond

forms through a condensation reaction between the carboxyl group of one amino acid and the amino group of a second amino acid, releasing H20

which arrangement of beta strands is described as producing the more stable sheet and why?

antiparallel strands because their hydrogen bonds are more directly and linearly aligned

Four helix bundle

heme placed into a hydrophobic pocket formed by interactions between hydrophobic side chains

greek key fold

tertiary protein consisting of four or more beta sheets

rossmann fold

two regions of alternating alpha helices and beta strands that form together

TIM barrel fold

alternating alpha helix/beta strand structure that has parallel beta sheets that are surrounded by alpha helices

examples of tertiary structures

four helix bundle, greek key fold, rossman fold, TIM barrel fold

examples of secondary structures

beta strands, alpha helices, beta turns

examples of quaternary structures

fibrous proteins (keratin), collagen, globular proteins