mod 9 translation genetics

what is the start/stop codon for mRNA in translation?

start- N-terminus

stop-C-terminus

are 5’ and 3’ UTRs found inside or outside of mRNA ?

outside

explain the orientation of translation

mRNA is read 5’-3’ by ribosome

has N-terminus+ C-terminus

Explain codons

• 4 bases (AUCG) x 3 bases per codon results = 64 codons

• never overlaps + essentially universal

Code is redundant and not ambiguous

whats start codon and stop codons of genetic code

Start: AUG

Stop: UAG, UGA, UAA

what is tRNA synthetase?

what’s a large molecule that contacts several points on the tRNA in the recognition process

Explain process of aminoacetyl tRNA synthetase

1. amino site attaches to active site using ATP hydrolysis

2. tRNA attaches to other active site and joins with amino acid

3. tRNA is charged by enzyme

What’s third base wobble?

occurs through flexible pairing at 3’-most nucleotide of codon and 5’ most nucleotide of anticodon

synonymous codons can be grouped into pairs that differ in only third base

pyrimidines still base-pair with purines

Ribosomal subunit structures

30-50-70 bact.

16s rRNA

40-60-80 euk.

18s rRNA

explain 2-D electrophoresis

unpacking ribosomes
-separated in gel in one dimension by electrical charge by pH gradient

-proteins denatured by SDS separated by size

67-74 ribosomal proteins in humans,rats, and chickens

explain important regions of ribosomes

Aminoacetyl site (A)- binds new tRNA containing an amino acid to be added to the chain

peptidyl site (P)- holds the tRNA to wich the polypeptide is attached

exit site (E)- provides avenue/exit for uncharged tRNA

explain bact. translational initiation

1. preinitiation complex- 16s rRNSs pairs with Shine-Dalgarno sequence on mRNA

2. initiator tRNA binds to start codon, tRNA^fMet; ssuRNA, mRNA, and initiator tRNA form 30S initation complex

3. larger 50s subunit joins small 30s subunit to form intact ribosome; create 70s initiation complex

explain euk. translational initiation

small (40s) subunit complexes with eLF proteins and initiator tRNA^Met to form preinitiation complex

mRNA joins to form initation complex

scanning moves small subunit along 5’ UTR to find start codon

90% of eukaryotic mRNAs use first ___ as start codon which is embedded in which sequence

AUG; kozak

recruitment of large (60s) subunit to complex uses energy from __ and dissociation of

GTP hydrolysis ; eLF proteins

Elongation begins with recruitment of __ proteins that use _ _ to:

elongation factor (EF); GTP hydrolysis

1. recruit charged tRNAs to A site

2. forms peptide bonds between sequential amino acids

3. translocate the ribosome in 3’ direction along mRNA

Peptidyl transferase

catalyzes peptide bond formation between amino acids at P + A sites, elongating the polypeptide + transfering tRNA at A site

steps of elongation

1. tRNA from P site exits through E site

2. EF-G translocates the ribosome, moving it 3 nucleotides toward 3’ end of mRNA

3. moves tRNA at A site to P site + opens A site for next charged tRNA carrying correct anticodon

what are release factors used for in translation

bind stop codon in A site

what are the release factors in bact, euk, and archaea

bact. RF1, RF2, and RF3

euk. aRF1

archaea eRF1

why are R groups important?

side chain groups that attach to alpha carbon + give each amino acid its chem properties

largely influence 3D shape of protein

What’s the levels of proteins

1. primary- sequence of amino acids held by peptide bonds

2. secondary-alpha helices + beta pleated sheets by hydrogen bonds

3. tertiary- 3D shape of 1 polypeptide by R group + backbone interactions

4. quarternary- multiple polypeptide chains by interactions between chains

how does variation in amino acid sequences affect protein function + ex?

sequences differ between species but protein function can stay the same

ex. pax6 in eye development