cell biology exam 1

cellular membrane

allow the cytoplasm to maintain compartments with distinct environments

n terminus

starting end of a protein or polypeptide chain, defined by a free amine group (-NH2)

c terminus

end of a protein or polypeptide chain that terminates with a free carboxyl group (-COOH)

side chain

r group

polar side chain

side chain that has an -O or -SH

acidic (-) / basic (+) side chain

side chain that has a positive or negative charge

nonpolar side chain

side chain that is neither acidic / basic nor polar

primary structure

order of amino acids (ex. Met Ala Tyr Pro)

secondary structure

alpha helix (tightly coiled) and beta sheets (wavy) throughout protein

tertiary structure

overall shape of protein

quaternary structure

multi-subunit complex

first law of thermodynamics

enthalpy (change in heat / ∆H)

• translation (movement through space)

• vibration

• rotation

second law of thermodynamics

entropy is a measure of disorder or randomness (∆S = change in entropy)

gibbs free energy

∆G = ∆H - T∆S

reaction dynamics

exergonic reaction

endergonic reaction

two ways that cells control reactions

enzymes and concentration

-ase

indicates an enzyme

-omics

studying the entire thing in a cell in opposition to just one (ex. genomics, metabolomics, proteomics)

oxidative phosphorylation

final common pathway converting electron
energy to ATP

krebs cycle

glycolysis

fatty acid oxidaiton

major pathway of aerobic energy production

• fatty acids enter krebs cycle as acetyl coa

dna polymerase

synthesize dna strands from 5’ to 3’ (dna replication)

proofreading

dna polymerase

dna polyerase error rate

error rate: 1 per 10,000

w/ proofreading: 1 per 1,000,000

w/ mismatch repair: < 1 per 100,000,000

proteins required for replication

• dna polymerase

• dna ligase

• rna primer

• dna primase

• okazaki fragment

• sliding clamp

• helicase

• single-strand binding proteins

• topoisomerase

primase (rna polymerase)

provide a 3’-OH end to dna polymerase so that it can initiate dna synthesis

clamp loader

use the energy of ATP hydrolysis for assembly of sliding clamps

helicase

separates the 2 strands of DNA ahead of the advancing replication fork using energy from ATP hydrolysis

• multimeric

multimeric

composed of multiple monomers that are linked together

fixing double-strand breaks

homologous recombination

CRISPR

Homologous Recombination to replace areas of the genome with new DNA

replication

1. origin of recognition (ORC) binds eukaryotic origins

2. ORC recruits Cdc6, which recruits Cdt1 and the MCM helicase

3. Cdc6 is degraded or exported after origin firing, which prevents reinitiation

genome

complete set of genetic material carried by an organism

• each gene is a sequence of DNA that codes for at least one RNA or protein as its final product

nucleotides

consist of nucleoside and phosphate

nucleosides

5-carbon sugar and purine / pyrimidine (sugar + nitrogenous base)

nucleic acid

nucleotide polymer (connecting together)

nitrogenous bases

cytosine, uracil, thymine, adenine, guanine

hydrogen-bonding

hold the two complementary strands of a DNA double helix together by connecting the nitrogenous bases in the center

van der waahl forces

help stabilize the three-dimensional structure of DNA by acting between the flat, stacked base pairs in the core of the double helix

rna secondary structure

types of dna damage

activators and receptors

regulate transcription initiation by binding to DNA sequences proximal or distal to the basal initiation complex at the core promoter region

5’ cap

protects the 5’ end from enzymatic degradation and it a binding site for both proteins involved in mRNA export from the nucleus to the cytoplasm and translation initiation factors in the cytoplasm

poly-a tail

protects the 3’ end from degradation and modulates the efficiency of translation initiation

intron

spliced out of pre-mRNA