difference btwn NTPs and dNTPs

NTPs have a hydroxyl group on the 2'carbon

Template strand

strand that is read by the enzyme

nontemplate/coding strande

sequence matches the sequence of the RNA that is transcribed from the template strande and codes for a polypeptide

DNA polymerase

RNA poly performs a template-directed synthesis in the 5' 3' direction

RNA poly does NOT require a primer to begin translation

RNA Poly I

produces genes that code for rNA molecules found in ribosoes

RNA Poly II

produces protein coding genes that produce mRNA's 

processing and regulating of mRNA

Poly III

produces gens that code for tRNAs

sigma

-bacterial RNA polymerase detachable protein subunit

-must bind to the polymerase before transcription can occur

BACTERIA

Holoenzyme

multipart enzyme consisting of a core enzyme along with other required proteins

Core enzyme

-responsible for catalysis in a multi part holoenzyme

contains active site for catlysis

promoters

-short nucleotide sequence in DNA that binds RNA poly enabling transcription ot begin

prokaryotic promoters vs eukaryotic promoters

-prokaryotic DNA-single promoter often associated with several continguous genes

-eukaryotic DNA-each gene generally has its own promoter

Downstream

DNA that is located in the direction RNA polymerase moves during transcription

upstream

DNA located in the opposite direction RNA polymerase moves during transcription

 TATA box

inque sequence centered about 20 base pairs upstream

eukaryotic promoter

sigma

regulatory protein

tells RNA poly where and when to start synthesizing

the type of sigma protein in th RNA poly holoenzyme determines which type of genes will be transcribed

basal transcription factor

eukaryotes-RNA poly does nto bind directly to promoter seqences by itself

-proteins that initiate eukaryotic transcription by binding the appropriate promoster region in the DNA

Elongation

RNA poly moves DNA template 3'5' direction synthesising 5'3'

rudder

inter of the enzyme

aa that helps steer the template and nontemplate strands throught the cannels inside the enzyme

Enzymes Active site

catalyzes the addition of nucleotides to the 3' end of the growing RNA molecule

enzyme' zipper

group of a.a. that helps separate the newly synthesized RNA from the DNA template

Termination of Transcription

-transcription stops wehn RNA poly reaches DNA sequence that functions as a transcriptional termination signal

-hairpin of RNA forms and causes it to separate from RNA poly

primary transcript 

pre-mRNA

when a eukaryotic gene is transcribed, the product is this

have to go throught a series of steps before they can be translated

Length of DNA sequences in bacteria versus eukaryotic cells

-eukaryotic genes do not consist of one continuous DNA sequence that codes for a product (BACTERIAL genes DO!)

-instead the regions in eukaryotic gene that code for proteins are intermitenly disrupted by stretches of bases

Splicing

introns are removed from the growing mRNA strand

small nuclear RNAs

(snRNAs)

-catalyzes splicing 

-complex of proteins and specialized RNA

small nuclear ribonucleoproteins

snRNPs

snRNAs (proteins) plus RNA complesxes

5' cap

-molecule 7 methyl guanylate and 3 phosphate groups

as soon as 5' end of eukaryotic RNA emperges from RNA poly enzymes add this

Poly (A) tail

-an enzyme cleaves the 3' end of most RNAs once transcription is complete and other enzymes add long rows of 100-250 adenine nucleotides

mature mRNA

-cap and tail and splicing is completed

prossessing of the primary RNA transcriptio is complete this is the product

purpose of caps and tails

to protect from degradation by ribonucleases 

and enhance efficiency of translation

RNA processing

any modification  needed to convert a primary transcript into a mature RNA

-bacteria: robosomes attach to mRNAs and begin synthesizing proteins even before transcription complete

*occur simultaneously!!!!!*

-mult ribosomes attach to each mRNA 

poyribose

mult ribosomes attach to each mRNA (bacteria)

-many copies of aprotein can be produced from a single mRNA

why can transcription and tranlation occur simultaneously?

-no nuclear envelope to separate the 2 process

-physically connected

Translation in eukaryotes

-primary transcripts processed in nucleus to form mature mRNA 

-mRNA then exported to cytosol

-once mRNA outside nucleus ribosomes attach to them and begin translation

what happens when mRNA interacts w/a ribosome

hereditary instruction endcoded in nucleic acids are tranlated into a different chemical language

tRNA

anticodon on one end and a.a. binding site on the other

-each picks up a specific a.a. and binds to the corresponding codon in mRNA during tranlation

aminoacyl tRNA synthetases

catalyze the addition of a.a. to tRNAs

-for each of the 20 major a.a. there is a different aminoacyl tRNA synthetase and one or monre tRNAs

aminoacyl tRNA

combination of tRNA molecule COVALENTLY liked to a.a. (fit TIGHTLY together)

CCA sequenct at the 3' end of tRNA

then anticodon on loop

offers a binding for a.a.

triplet on loop serves an anticodon-pairs w/mRNA

Wobble Hypothesis

(1) many a.a. are specified by more than one codon

(2) codons for the same a.a. tend to have the same nucleotides in the 1st and 2nd positions but a different nucleotide in the 3rd

Wobble in the 3rd position allows what

allows just 40 or so tRNAs to bind to all 61 mRNA codons

Covernsion of mRNA codon complete when...

a pepetide bond forms btween the tRNA's a.a. and the growing polypeptide chain

ribosomal RNA

small subunit-hols mRNA in place duirng translation

large subunit- peptid bond formation takes place

A site

acceptor 

tRNA carries its a.a. into the ribosome and places it here

P site

tRNA that holds the growing polypeptide chain

*peptide formation*

E Site

tRNA that no longer has an a.a. attached and is about to leave the ribosome

Step 1 protein synthesis in ribosome

-an amino acyl tRNA diffuses into the A site --> its anticodon binds to a codon in mRNA

Step 2 protein synthesis in ribosome

a peptide bond forms btwn the a.a. held by the aminoacyl tRNA in the A site and the growing polypeptide which is held by a tRNA in the P site

Step 3 protein synthesis in ribosome

the ribosome moves ahead and all 3 tRNAs move on one position down the lin

A-->P-->E

ribosome binding site

-section of rRNA in a small ribosomal subunt that binds to a complementary sequence on the mRNA

initiation factors

mediates initial interaction btwn the small subunit and the message

3 steps of initiating translation

(1) mRNA binds to a small ribosomal subunit

(2) initiator aminoacyl tRNA bearing f-met binds to the start codon (AUG)

(3) large ribosomal subunit binds, completeing the complex

6 steps of elongation

(1) Incoming aminoacyl tRNA-new tRNA to A site; anticodon base pairs w/mRNA codon

(2)  Peptide bond formation-a.a. attached to tRNA in the P site transferred to tRNA in the A site

(3) translocation

repeat

elongation factors

move  the mRNA so that it ratchets through the ribosome in the 5'--3' direction

allows for a new codon to be in the A section to bind to new tRNA

release factor

when translocation opens the A site and expression one of the stop codon proteins called_________

-do not carry a.a. instead rxn occurs that frees the polypeptide

2 types of post translational modification

-proteins are not fully formed and fucntionl when termination occurs so....

(1) Folding

(2) chemical modification

Folding-post translational control

protein function depends on how it is fold

fold spontaneously (sped up by molecular chaperones)

molecular chaperones

speed up the process of folding proteins

chemical modification (post translational)

small chemical groups may be added to protien (sugar/lipid)

phosphorylation / dephosphorylation

change chem reactivity of proteins