BIO 3232 Exam 2 Study Guide

Nucleotide

base + sugar + phosphate

Nucleoside

base + sugar

DNA

deoxyribose nucleic acid with A T G C

What does the x intercept represent in a Lineweaver Burk plot?

1/-Km

What does the y intercept represent in a lineweaver burk plot?

1/Vmax

What does the slope of the lineweaver burk plot represent?

Km/V

RNA

ribose nucleic acid with A U G C

Purines

adenine and guanine

Pyrimidines

cytosine thymine uracil

N‑glycosidic bond

bond between base and sugar

Phosphodiester bond

bond linking 5′ phosphate to 3′ hydroxyl

Primary structure nucleic acids

nucleotide sequence

Secondary structure nucleic acids

double helix or RNA hairpins

Watson‑Crick pairing

A–T (2 H‑bonds) and G–C (3 H‑bonds)

Major groove

wide DNA groove formed by base pairing geometry

Minor groove

narrow DNA groove formed by base pairing geometry

A‑form DNA

right‑handed helix with 11 bp per turn - large and small gaps

B‑form DNA

right‑handed helix with 10.5 bp per turn Watson and Crick model with

Z‑form DNA

left‑handed helix with 12 bp per turn

Palindrome DNA

sequence identical forward and backward on opposite strands

Hairpin

single‑stranded fold forming base‑paired stem and loop

Cruciform

double‑stranded structure formed from palindromic DNA

mRNA

RNA carrying genetic information to ribosome

Monocistronic mRNA

encodes one polypeptide

Polycistronic mRNA

encodes multiple polypeptides

ATP

primary cellular energy carrier

NAD⁺

adenine‑containing redox cofactor

FAD

adenine‑containing redox cofactor

CoA

adenine‑containing acyl‑group carrier

cAMP

nucleotide second messenger

cGMP

nucleotide second messenger

ppGpp

nucleotide regulating bacterial stress response

Epimer

diastereomer differing at one chiral center

Diastereomer

stereoisomer not a mirror image

Enantiomer

mirror‑image stereoisomer

Anomer

isomer differing at anomeric carbon

Anomeric carbon

former carbonyl carbon that becomes new chiral center

Aldose

sugar with aldehyde group

Ketose

sugar with ketone group

Monosaccharide

single polyhydroxy aldehyde or ketone

Disaccharide

two monosaccharides linked by glycosidic bond

Polysaccharide

polymer of monosaccharides

Fischer to Haworth rule

right = down

Reducing sugar

sugar with free anomeric carbon

Nonreducing sugar

sugar with anomeric carbons in glycosidic bond

Glycosidic linkage

bond between anomeric carbon and hydroxyl group

Homopolysaccharide

polymer of one type of monosaccharide

Heteropolysaccharide

polymer of multiple types of monosaccharides

Amylose

linear α(1→4) glucose polymer

Amylopectin

branched α(1→4) with α(1→6) branches

Glycogen

highly branched α(1→4) with α(1→6) branches every 8–12 residues

Cellulose

β(1→4) glucose polymer

Chitin

β(1→4) N‑acetylglucosamine polymer

Agarose

heteropolysaccharide used for DNA electrophoresis

Enzyme

biological catalyst that lowers activation energy

Cofactor

inorganic ion required for enzyme activity

Coenzyme

organic molecule that carries functional groups

Prosthetic group

tightly bound cofactor essential for activity

Holoenzyme

active enzyme with all cofactors

Apoenzyme

enzyme protein without cofactors

Active site

pocket where substrate binds and reaction occurs

Substrate

molecule acted on by an enzyme

Ground state

starting energy level of substrate or product

Transition state

high‑energy state between substrate and product

Activation energy ΔG‡

energy required to reach transition state

Binding energy ΔGB

energy released from enzyme‑substrate interactions

Induced fit

enzyme changes shape to stabilize transition state

Specificity

enzyme’s ability to select specific substrates

Reaction intermediate

species with finite lifetime between substrate and product

Rate‑limiting step

slowest step with highest activation energy

Saturation

condition where all active sites are filled

Pre‑steady state

initial transient phase before ES stabilizes

Steady state

ES formation equals ES breakdown

Initial velocity V₀

reaction rate at time zero

Vmax

maximum reaction velocity at saturation

Km

substrate concentration at ½ Vmax

kcat

turnover number; substrate molecules converted per second

Michaelis‑Menten equation

V₀ = Vmax[S] / (Km + [S])

Lineweaver‑Burk equation

1/V₀ = (Km/Vmax)(1/[S]) + 1/Vmax

Sequential mechanism

both substrates bind before products release

Ping‑pong mechanism

one substrate binds and product releases before second binds

Competitive inhibition

inhibitor competes with substrate for active site

Uncompetitive inhibition

inhibitor binds only to ES complex

Mixed inhibition

inhibitor binds to E or ES at separate site

Irreversible inhibition

inhibitor covalently inactivates enzyme

Regulatory enzyme

enzyme whose activity changes with signals

Allosteric regulation

modulators alter enzyme activity

Covalent modification

regulation via phosphorylation or similar changes

Proteolytic activation

cleavage of zymogen to activate enzyme

Ligand

molecule bound reversibly by a protein

Binding site

region on a protein complementary to the ligand

Induced fit

conformational change in a protein upon ligand binding

Allosteric protein

protein where ligand binding at one site affects another site

Homotropic modulator

modulator is the same molecule as the ligand

Heterotropic modulator

modulator is a different molecule than the ligand

Cooperativity

ligand binding at one subunit affects binding at other subunits

Prosthetic group

non‑amino‑acid component essential for protein function

Association constant Ka

measure of ligand affinity; higher Ka = higher affinity

Dissociation constant Kd

reciprocal of Ka; lower Kd = higher affinity

Fractional saturation θ

fraction of binding sites occupied