Molecular Biology

how do genes work

-Instructions for building and maintaining an organism

-made of DNA

-most code for proteins

Central dogma

of molecular biology

information flows from

DNA->RNA-> protein

DNA-> RNA process

=transcription

RNA-> protein process

=translation

genotype

sequence of DNA bases

phenotype

physical characteristics determined by proteins

alleles

-specific DNA sequences of a gene

different alleles usually produce

different proteins, thus different phenotypes

codon

3 bases in RNA that code for a single amino acid

genetic code redundancy

some amino acids coded for by more than 1 codon

special codons

start and stop

if DNA sequence is known

then you can predict the RNA and protein sequence

DNA>RNA

base pairing rules

RNA> protein

codon rules

permanent change in DNA

-changes genotype

-can change phenotype

point mutation

-single base change

-often result from DNA replication errors

silent

change in nucleotide sequence that does not change the amino acid specified by a codon

-no change in phenotype

-neutral

missense

change in nucleotide sequence that changes the amino acid specified by codon

-change in primary structure of protein

-may be beneficial or neutral

nonsense

change in nucleotide sequence that results in an early stop codon

-leads to mRNA breakdown or a shortened polypeptide

-deleterious

frameshift

addition or deletion of a nucleotide

-reading frame is shifted, altering the meaning of all subsequent codons

-almost always deleterious

transcription

RNA made from base pairing with DNA template strand

3 steps

initiation, elongation and termination

holoenzyme

core enzyme+ regulatory factor

core enzyme (RNA polymerase)

forms phosphodiester bonds

sigma

regulatory factor

transcription initiation 1

-promoter

-DNA region upstream of transcription start

-contains -10 box and -35 box

-bound by sigma

transcription initiation 2

-sigma opens DNA helix

transcription begins (ribonucleotides base pair with template strand)

transcription initiation 3 and elongation

-sigma releases

-transcription proceeds-elongation of RNA polymer (synthesizes RNA in the 5'->3' direction)

transcription termination

-RNA forms hairpin

-weak A-U pairs within enzyme are easy to separate

-RNA, RNA polymerase, and DNA separate

Eukaryotic Transcription

-differences from bacterial transcription

-occurs in the nucleus

-3 types of RNA polymerases

Transcription factors

instead of bacterial sigma

TATA box in promoters

instead of bacterial -10 and -35 boxes

RNA porcessing

-splicing

-cap and tail

exons

coding regions of eukaryotic genes (will be part of the final mRNA product)

introns

intervening noncoding sequences (not in the final mRNA)

RNA splicing

-removal of introns

-occurs in nucleus

spliceosome

-complex of small nuclear ribonucleoproteins (snRNPs)

-catlyzzes the splicing reaction

mRNA

modified at both ends

5' cap

recognition signal for translation

poly(A) tail

-100s of adenine nucleotides added to the 3' end

stabilizes mRNA against degradation

protein synthesized

based on mRNA sequence

bacteria

same time as transcription

eukaryotes

separated from transcription (translation in cytosol)

ribosome

enzyme that forms peptide bonds

tRNA

adaptor between mRNA codon and amino acid

3' end CCA

binds amino acid

anticodon

base pairs with mRNA codon

enzyme

adds correct amino acid to tRNA

many different tRNAs

each with a specific amino acid

contains proteins and ribosomal RNA

rRNA

2 parts

large subunit and small subunit

3 binding sites

tRNA

A site

acceptor site

P site

peptide bond forms

E site

exit site

ribosome binding site

sequence on mRNA complementary to rRNA in small subunit

Initiation factors

"help" interaction between mRNA and ribosome

Aminoacyl tRNA binds to

start codon

translation initiation

ribosome large subunits binds

translation elongation 1

-aminoacyl tRNA binds to the codon in the A site

-peptide bond formation between amino acids on the tRNAs in theP and A sites

ribosome moves down mRNA (A site now empty)

translation elongation 2

-new aminoacyl tRNA binds to the A site

-peptide bond formation between amino acids on the tRNAs in theP and A sites

-ribosome moves down mRNA (A site now empty)

-E site tRNA ejected

translation termination

a site comes to a stop codon

release factor

-binds to stop codon A site

-hydrolyzes (breaks) down between peptide chain and P site tRNA

-peptide chain (protein) and tRNAs released

polyribosomes

-string of ribosomes along single mRNA

-increase rate of protein synthesis

-occurs in prokaryotes and eukaryotes