unit 6: molecular genetics (up to topic 5)

RNA (function)

genetic code; protein synthesis; regulation; energy; structure

mRNA/tRNA (function)

protein synthesis

mRNA

carries the genetic signal from nucleus to ribosomes

rRNA

physical structure of ribosome

tRNA (function)

pulls amino acids into ribosome; to be synthesized by mRNA

microRNA

regulates mRNA translation and breakdown; post-transcriptional regulation

rRNA (function)

protein synthesis; structure

DNA (function)

genetic code

nucleotide (structure)

nitrogen base; 5 carbon sugar; phosphate group

nitrogen bases

pyrimidines; purines

pyrimidines

single ring; Cytosine, Thymine, Uracil

purines

double ring; Adenine, Guanine

two hydrogen bond

Adenine to Thymine; Adenine to Uracil

three hydrogen bond

Guanine to Cytosine

nucleoside (structure)

nitrogen base; 5 carbon sugar

DNA (structure)

phosphate; complementary nitrogen bases; double helix

DNA (synthesized)

dna; from 5’ to 3’

transcription (conversion)

from dna to rna

translation (conversion)

from rna to protein

DNA replication

unwind; unzip; prime; copy; replace; conjoin; proofreading

unwind

involves topoisomerase

topoisomerase

unwinds DNA; relaxes supercoiling

unzip

involves helicase and SSBs

single-stranded DNA binding protein (SSB)

binds to single strand DNA; prevents reconnections

helicase

breaks hydrogen bonds between template stands

prime

involves primase

primase

adds an RNA primer where replication starts

RNA primer

provides DNA polymerase III starting points

copy

involves DNA polymerase III

DNA polymerase III

creates a complementary DNA strand behind it

leading strand

dna; grows from 5’ to 3’; grows continuously

lagging strand

dna; grows from 3’ to 5’; grows in okazaki fragments

okazaki fragments

dna; 5’ to 3’ fragments

replace

involves DNA polymerase I

DNA polymerase I

replaces RNA primers with DNA

conjoin

involves DNA ligase

DNA ligase

connects disjointed ends of okazaki fragments

proofreading

involves DNA polymerase II

DNA polymerase II

used for proofreading

prokaryote replication

two replication forks; one replication bubble

eukaryote replication

many replication forks; many replication bubbles

replisome

molecular machinery at the replication fork

plasmid

circular DNA; distinct from chromosomal DNA

transcription (steps)

initiation; elongation; termination; post-transcriptional modifications

initiation (transcription)

unzips; RNA polymerase binds to promoter

promoter

recognition sites called TATA boxes; in eukaryotes and archaebacteria

elongation (transcription)

RNA polymerase reads template strand; creates pre-mRNA

pre-mRNA

rna; made in complement to template strand

template strand

rna; from 3’ to 5’

coding strand

rna; from 5’ to 3’

termination (transcription)

RNA polymerase transcribes the terminator signal; pre-RNA separates from template strand

rho independent termination

eukaryotes or prokaryotes; termination by a hairpin loop in mRNA

rho dependent termination

only prokaryotes

post-transcriptional modifications (transcription)

cap and tail; spicing

5’ cap and 3’ poly-A tail

eukaryotes; protect mRNA from exonucleases

RNA splicing

only eukaryotes and archaebacteria; removes introns; pre-mRNA to mature-mRNA

intron

stay in nucleus; removed from pre-mRNA

extron

exit nucleus; remain in pre-mRNA

alternate splicing

region of DNA can code for multiple proteins by using different exons

translation (prokaryotes)

occurs simultaneously with transcription; no post-transcriptional modifications

translation (eukaryotes)

occurs after RNA exits nucleus; undergoes post-transcriptional modifications

codon

three nucleotides; start, amino acid, stop

start codon

AUG; methionine

stop codon

UAA; UAG; UGA

ribosome

made of large and small subunits; APE sites for tRNA

APE sites

aminoacyl; peptidyl; exit

tRNA (parts)

anticodon; d loop; t loop; amino acid attachment site

anticodon

nucleotides that are complementary to a codon

amino acid attachment site

only the amino acid that matches the codon can bind

wobble pairing

last nucleotide in anticodon doesn’t match codon

translation (steps)

initiation; elongation; termination

initiation (translation)

ribosome assembles around start codon

initiation (translation / prokaryotes)

initiation complex around start codon with Shine-Dalgarno sequence; large subunit joins with tRNA in P site

initiation (translation / eukaryotes)

initiation complex around 5’ cap until start codon; large subunit joins with tRNA in P site

initiation complex

assembly of small subunit + first tRNA

elongation (translation)

amino acids added to polypeptide chain; goes through APE sites

A site

tRNA enters; peptide bond between A and P amino acids

P site

peptide bond between A and P amino acids; tRNA in P site releases amino acid; ribosome shifts over one codon

E site

ribosome shifts over one codon; tRNA here released

termination (translation)

release factor binds to stop codon; ribosome complex breaks apart + releases polypeptide

stop codons

do not have complementary tRNA

release factor

protein; recognizes + binds to stop codon

modRNA (definition)

synthetic mRNA made with nucleotide analogues

modRNA (function)

used to trick the cell into coding for a specific protein; read as A,U,C, or G (but not actually)

gene expression (transcriptional)

activators; inhibitors/repressors; histones; methylation

gene expression (post-transcriptional)

microRNA; alternate splicing

promoter

region where RNA polymerase bind

regulatory sequence (definition)

noncoding region of DNA; influences gene expression

regulatory sequence (types)

promoter; operator; enhancer; silencers

regulatory gene (definition)

coding region of DNA; influences gene expression

transcription factor (definition)

protein; influences gene expression by binding regulatory sequences

activator

turns on/promotes transcription

repressor

turns off/decreases transcription; blocks RNA polymerase

operon (definition)

series of related genes; transcription initiated by one promoter

operon (product)

one mRNA; multiple proteins

inducible operator

transcription “turned off”; until inducer binds to the repressor

inducer

releases the repressor from operator

activator

bind to enhancer; guides RNA polymerase onto the promoter

repressible operator

transcription “turned on”; until co-repressor binds to the repressor

corepressor

enables the repressor to bind to the operator