Biochem Exam 2

Competitive Inhibition

Km increases, Vmax reduced, slope changes, y-intercept same

Uncompetitive Inhibition

Km reduced, Vmax reduced, slope same, y-intercept changes

Noncompetitive Inhibition

Km unaffected, Vmax reduced, slope changes, y-intercept changes

Covalent catalysis

Forms temporary covalent enzyme–substrate bond

General acid–base catalysis

Donates or accepts H⁺

Metal-Ion Catalysis

Stabilizes charges, activates water, or facilitates electron transfer

Proximity/orientation Catalysis

Positions reactants correctly

Electrostatic catalysis

Stabilized charged transition states

Histidine (proton donor/acceptor)

Example/role for General acid–base catalysis

Serine (can form a temporary covalent intermediate)

Example/role for covalent catalysis

Allosteric Regulation

Effector binds a regulatory site, changing enzyme activity

Feedback Inhibition

Pathway's end product inhibits an earlier enzyme

Covalent modification

Chemical modification, such as phosphorylation, alters activity

Proteolytic activation

Inactive zymogen is cleaved to become active

Enzyme concentration

Synthesis or degradation changes the amount of enzyme

Km

Concentration when V0 = 1/2Vmax

Kcat

turnover number

higher affinity

Lower Kcat =

greater catalytic efficiency

higher Kcat/Km =

velocity proportional to [S]

[S] < Km

V0 = Vmax, enzyme approaches saturation

[S] > Km

Nitrogenous Base

Purine or pyrimidine

Nucleoside

Base + pentose sugar

Nucleotide

Base + sugar + phosphate(s)

Purines

Adenine (A), Guanine (G) — 2 rings

Pyrimidines

Cytosine (C), Thymine (T), Uracil (U) — 1 ring

Phosphodiester Bond

Covalent bond linking nucleotides in the sugar–phosphate backbone through 3′ and 5′ positions.

N-glycosidic bond

Connects nitrogenous base to sugar.

tRNA charging

Amino acid attaches to tRNA through an ester bond.

Codon

Three mRNA nucleotides specifying amino acid or stop

Anticodon

Complementary three-base sequence on tRNA

Degenerate

Multiple codons can encode the same amino acid

Unambiguous

Each codon specifies one amino acid or stop signal

AUG (Met)

What is the start Codon

UAA, UAG, UGA

What are the stop codons

Helices

Unwinds and separates DNA strands

SSB proteins

Keep separated DNA strands from reannealing

Topoisomerase

Relieves torsional stress and supercoiling

primase

Produces RNA primers

DNA polymerase

Extends new DNA strands

DNA ligase

Seals nicks in the DNA backbone

A-T (2 bonds), G-C (3 bonds)

H-bond base pairing:

Processivity

the average number of nucleotides a polymerase adds before dissociating from its template

Initiation

RNA polymerase recognizes the promoter and locally unwinds DNA.

Elongation

RNA polymerase reads template DNA 3′→5′, producing RNA 5′→3′.

Termination

RNA transcript is released and transcription stops.

Promotor

DNA region where transcription machinery assembles; helps determine initiation site and transcription direction.

Sigma Factor

Helps RNA polymerase recognize promoters.

Rho Factor

ATP-dependent protein that terminates certain transcripts.

Transcription Bubble

Locally unwound region of DNA within RNA polymerase.

mRNA

Carries genetic information to ribosomes

tRNA

Delivers amino acids using anticodon recognition

rRNA

Structural and catalytic component of ribosomes

snRNA

Participates in pre-mRNA splicing

miRNA

Helps regulate gene expression

Introns

Sequences removed from pre-mRNA during splicing.

Exons

Sequences retained in mature RNA (can include untranslated regions).