Bio 183 dna rep/protein synthesis

genetic material

1)contain info to construct entire organism

2)pass parent to offspring/cell to cell during division

3)accurately copied

4)account for known variation between species

Frederick Griffith

earliest, study 2 strands bacteria (phenomena), infected mice with strains to understand difference

S strain

sick

R strain

harmless

results of S strain

killed mouse

results of R strain

did not kill mouse

results with Heat and R strain

killed S strain but NOT mouse

Results with heat killed S and R strain

transformed R into S called transformation; mouse dead

process of genetic materials throughout the years

-late 1800s, inherited substance (some biochem material)

-discovered chromosomes

-100 years ago thought proteins passed genetic materials b/c seemed more complicated biochemically

Avery, MacLeod, McCarty

repeat grittiths experiment using purified cell extracts; Discovered: DNA was the transforming material (biochem material actually dna)

Hersey & Chase

make sure its dna; investigated bacteriophages: virus species specific infect bacteria composed of only dna and protein

Hersey & Chase experiement

only viral bacteria became radioactive, sheared off virus from bacteria, radio labeled protein not in pellet (not part of cell) gives evidence dna is transforming material

dna structure

dna nucleic acid; building blocks are nucleotides; composed of deoxyribose (5-carbon sugar). phosphate group (PO4), nitrogenous base

does a double ring always bind to a single?

yes

Rosalind Franklin

studying dna by taking x-ray pics; researched helped watson and crick

James watson & francis crick

double helix dna, very readable, digestible popular magnesium, wider audience, took all credit and didn’t reference anyone

double helix

2 sugar phosphate backbones, nitrogenous bases toward interior of molecule, bases form hydrogen bonds with complementing bases on opposite sugar-phosphate backbone

why can’t bind C to A

bond formation

2 stands antiparallel to eachother

one runs 5’ to 3’ while other runs 3’ to 5’

is dna stable?

very; double helix makes structure very stable

is rna stable?

no; very fragile (just the messenger)

dna replication

dna strands antiparallel to each other; leading strand copied in continuous line (same direction as replication fork); lagging strand copied little pieces (okazaki fragments)

conservation

take molecule as whole and copy whole thing at once (no one heavy; becomes old)

semiconservation

copy 1 side and then copy other side, figure out how to merge (heavy band as templates)

dispersive

chop it all up with enzymes, copy those little pieces, somehow shuffle all back together (heavy mix every strand)

how does dna copy?

semiconservation

problems with dna coping conservation/semiconservation

takes too much ATP (energy)

problems with dna being copied as dispersive

takes ATP and more likely to generate errors

replication includes

initiation, elongation, termination

initiation

replication begins at origin of replication

elongation

new strands dna synthesized by dna polymerase (enzyme)

termination

replication terminated differently in prokaryotic/eukaryotic

dna replication prokaryotics

polymerase and replication can go around both directions to produce new circular chromosomes (origin travel 2 diff directions and produce 2 circular pieces of dna)

DNA helicase

binds to dna and travels 5’ to 3’ using ATP to separate strand and move fork forward

DNA Topoisomerase

reveals additional coiling ahead of replicated fork (go ahead to relieve tension)

Single-Strand Binding Proteins (SSBP)

hold 2 pieces of dna apart, they want to pop back together (have to take helix and unwind so theres room for enzymes to come in)

dna polymerase

binds to 1 piece (template strand) reads A will bring T and drop it on there

pull dna apart using 2 enzymes and SSBP

1) locate origin and bind rna primer—→ later polymerase will replace rna with dna

2)polymerase bind to 3’ piece of dna and add new nucleotides in 5’ to 3’ direction going to antiparallel

polymerase one way moving

5’ to 3’

leading strand

dna primase makes 1 rna primer

polymerase attaches nucleotides 5’ to 3’ direction

lagging strand

polymerase travels opposite direction, okazaki fragments, dna primase lays down rna, polymerase lay down dna while removing rna primers and fill in with dna

need what to join DNA fragments

DNA ligase; because pieces connect to template and not each other

Beadle & Tatum

looked for fungal cells lacking specific enzymes, identified mutant deficient in each enzyme pathway

what we determined from beadle and tatum enzymes

after identifying mutants able to figure out where mutation is and determine enzyme was coded for by a different gene/DNA

Beadle and Tatum proposed

1 gene & 1 polypeptide enzyme hypothesis= each piece dna code specifically for a specific enzyme

central dogma of molecular biology states

DNA (transcription) RNA (translation) Protein

bacteria DNA

circular DNA string transcribe into RNA, translate protein, all in cytoplasm

eukaryotic DNA

dna replicated in nucleus, transcript—> translation

codon

set 3 nucleotides (ex:ATT, GAT)

reading frame

read in sets of 3 BUT harder to read when add letter (messed up reading frame)

what must you have to make functional proteins

specific stop and end point

stop codon

3 codons (UUA, UGA, UAG) stop translation

start codon

AUG signifying start translation

template strand

what is read to make RNA

coding strand

complementary to template (what RNA polymerase will bind to and read)

RNA polymerase

bind to DNA and read it to produce RNA

transcription proceeds thru

initiation, elongation, termination

initiation (transcription)

RNA polymerase identifies were to begin

Elongation (transcription)

elongate and produce RNA

Termination (transcription)

stop transcription, drops off DNA producing RNA for particular protein

translation proceeds thru

Initiation, elongation, termination (same process but RNA)

Initiation (translation)

mRNA, tRNA, ribosomes come together

elongation (translation)

tRNA being amino acids to ribosomes for incorporation into polypeptides

termination (translation)

ribosomes encounter stop codon and release polypeptides

simplified translation RNA

bind to rna, make longer, stop, string amino acid into protein

messanger RNA (mRNA)

carries info from DNA that encodes for proteins

ribosomal RNA (rRNA)

reads RNA strands, structural component of ribosomes

transer RNA (tRNA)

carries amino acids to ribosomes for translation (read codon make sure it corresponds to appropriate amino acid)

gene expression step1

double strand dna unwinds

gene expression step 2&3

recognize promotor and sigma says start here

gene expression step 4 & 5

RNA polymerase binds and travel along template strand DNA

gene expression step 6 & 7

RNA binds to DNA elongation piece and find terminator and unbind mRMNA (becomes template for protein) and polymerase

gene expression steps (shorter)

-RNA polymerase binds 3’ template strand DNA

-mRNA is produced in 5’ to 3’

-after bind produced complementary piece of RNA can read either direction

-template and coding can sometimes not be the same all the way thru

eukarotif pre-mRNA splicing 3 process mechanisms

5’ cap and 3’ poly-A tail (add to ends to stabilized)

removal non-coding sequences (introns)

removal non-coding sequences (introns)

nucleotides in DNA there for stability but when time to produce protein don’t need those sections so enzymes cut them up

5’ cap

sequence G’s which help make stable

3’ poly-A tail

sequence A’s

what to do to a piece of mRNA to get it ready to make a protein?

capping, splicing, tailing

aminoacyl

tRNA synthetases add amino acids to acceptor arm for tRNA

anticodon loop

contains 3 nucleotides complementary to mRNA codons

A site

tRNA binds amino acid to growing chain

P site

amino acid attracts to protein

E site

uncharged tRNA needs to leave and recharge

tRNA charging

-enzyme reads codon (aminoacyl-tRNA synthesis)

-uncharged b/c no amino acid yet

-once amino acid binds it becomes charged

tRNA charging steps 1&2

1) found start codon

2) tRNA comes in and brings amino acids too

tRNA charging steps 3 & 4

3) as moving along its gonna grow polypeptide chain

4) A site bring amino acid and adds to chain

tRNA charging steps 5 & 6

5) then able to exit uncharged (E site)

6) polypeptide finishes so all uncharged tRNA fall away

tRNA charging step 7

polypeptide disengaged from ribosomes

translation

elongation continues till ribosome encounters stop codon (UGA); recognize and everything release

ER role

-helps process proteins, before ER js string of proteins

-as polypeptide being provided ribosomal unit migrates to ER

-pores in ER that protein can funnel into eventually process/folded into functional protein

point mutations

alter single base (not a terrible thing) could create stop codon which stop production of protein

nonsense mutations

create stop codon

frameshift mutations

insertion/deletion of a single base (devastating)

reading coding strands

5’—>3’, T—>U, read backwards

coding strand 3’ - CGT TAG ACG - 5’

5’ - GCA GAU UGC - 3’

reading template strands

3’ to 5’, read normally, replace opposite letters

reading template ex: 3’ - TAG ACG - 5”

5’ - AUG UGC - 3’