Genetics - chapter 9

what is the structure of amino acids?

a carboxyl group (COOH), an amino group (NH2), and an R group bound to a central carbon atom

what is the importance of the R group?

it varies so it confers specific chemical properties

how many amino acids are there in humans?

20 basic amino acids

what are the four types of amino acids?

nonpolar (hydrophobic), polar (hydrophillic), polar (positively charged and basic), and polar (negatively charged and acidic)

what are the three polar, positively charged, and basic proteins?

lysine (Lys), Arginine (Arg), and Histidine (His)

how is a peptide bond formed?

forms by a dehydration reaction between the carboxyl group of one amino acid and the amino group of another (removes H2O to make bonds)

what is the primary structure of proteins?

it happens immediately out of the ribosome. it is a linear structure with peptide bonds. the amino end is positive and the carboxyl end is negative

what is the secondary structure of proteins?

hydrogen bonds between adjacent amino and carboxyl groups. can be alpha helix or pleated sheets

what is the tertiary structure?

interactions between the R groups. it is the folding of secondary structures. bonds can include hydrogen, ionic, hydrophobic interactions, disulfide bridges)

what is the quarternary structure?

composed of two or more separate folding polypeptides

in the mRNA, triplet codons specify for what?

one amino acid

what is the main characteristic of the code?

nonoverlapping!

what does it mean by degenerate?

more than one codon is in many cases assigned to a single amino acid

what is the start codon?

AUG - MET

what are the stop codons?

UAA, UGA, UAG

what does transfer RNA do?

it brings amino acids to ribosomes. 

where are tRNAs made?

in the nucleus by RNAP III

what is the D loop of tRNA?

it is for stability (dihydrouridine)

what is the anticodon loop?

it binds to codons of mRNA

what is the variable loop of mRNA?

it interacts with aminoacyl-tRNA synthetase

what is the T loop?

interacts with the ribosome. it contains thymidine (weird its RNA)!

what is the acceptor step of the tRNA?

it is where the amino acid is added

what are aminoacyl-tRNA synthetases?

have binding sites for tRNA and amino acid

how many aminoacyl-tRNA synthetases are there?

20! one for every amino acid

what must happen before translation can proceed?

tRNA molecules must be chemically linked to their respective amino acid (charged by aminoacyl tRNA synthetase)

what is the prokaryotic ribosome?

70S (50S and 30S)

what does the 50S ribosomal unit breakdown into?

23S rRNA, 5S rRNA, and 31 proteins

what does the 30S ribosomal unit break into and what is it?

decoding center (makes sure codon matches anticodon). 16S rRNA and 21 proteins

what is the eukaryotic ribosome?

80S ribosome (60S and 40S)

what does the 60S ribosomal subunit breakdown into?

28S rRNA, 5.8S rRNA, 5S rRNA, and 49 proteins

what does the 40S ribosomal subunit breakdown into?

it is the decoding center and it breaks into 18S rRNA and 33 proteins

what is the makeup of the typical prokaryote ribosome?

60% RNA and 40% protein

what is the makeup of the typical eukaryote ribosome?

50% RNA and 50% proteins

what is the decoding center?

the part of the ribosome on the small ribosomal unit where an incoming tRNA is matched with a messenger RNA codon

what is the peptidyl-transferase center?

located on the larger subunit of the ribosome. involved in catalyzing peptide bond formation and peptide release

what are the three key sites in the ribosome?

A site, P site, and E site

what is the A site?

it bings an incoming aminoacyl-tRNA whose anticodon matches the codon in the A site of 30S subunit

what is the P site?

tRNA in this position binds the growing peptide chain

what is the E site?

exit site! it contains tRNA lacking an amino acid (deacylated)

how is translation carried out?

by the ribosomes moving along the mRNA in the 5’ to 3’ direction

what do tRNAs do?

bring the amino acids to the ribosomes and their anticodons base pair to the mRNA codons

what are the three parts of translation?

initiation, elongation, termination

what does initiation involve?

placing the first aminoacyl-tRNA in the P-site of the ribosome and establishing the correct reading frame of the mRNA

in most prokaryotes and eukaryotes, what is the first amino acid in any newly synthesized polypeptide?

methionine (codon AUG)

how is MET inserted?

by a special tRNA called initiator (tRNAMeti)

In bacteria, what is added?

a formyl group is added to the methionine while the amino acid is attached to the initiator, forming N-formylmethionine

what are initation codons preceded by?

special sequences called Shine-dalgarno sequences that pair with the 3’ end of an rRNA (16S rRNA), in the 30S ribosomal subunit

what is the shine-dalgarno sequence?

AGGAGGU

what is the importance of the 16S rRNA here?

it is compliment to Shine-Dalgarno sequence. So when shine binds to the 16S, the start codon falls onto the P site. this base pairing correctly positions the AUG in the P site where the initiator tRNA will bind

where is the shine dalgarno sequence?

in the 5’ UTR

what is another name for the shine dalgarno sequence?

ribosome binding site

in bacteria what is needed to assemble an active 70S ribosome?

initiation factors IF1, IF2, and IF3

what is the first step for initiation in prokaryotes?

IF1 blocks the A site and IF3 prevents premature action between large and small subunits (keeps large subunit away)

what is the second step for initiation in prokaryotes?

the shine-dalgarno sequence helps start codon bind to P site with the help of the 16S rRNA

what is the third step for initiation?

IF2 brings initiator tRNA to the P-site. Attached to IF2 is GTP (GTPase activity = energy)

what is the fourth step of initiation?

break down of GTP for energy and IFs go away

what is the fifth step of initiation?

50S subunit attaches to create fully functional ribosome

what is the 30S preinitiation complex?

it is right before 50S joins. contains IF1, IF2, and IF3

what are the two elongation factors in prokaryotes?

EF-Tu and EF-G

what is the peptidyltransferase center?

it makes peptide bonds between amino acids

what is the first step of elongation?

EF-Tu brings in next tRNA

what is the second step of elongation?

peptide bond is formed between the two amino acids

what is the third step of elongation?

first amino acid is cut off from the first tRNA

what is the fourth step of elongation?

EF-G moves first tRNA to E-site and second tRNA to P site

what is the fifth step of elongation?

EF-Tu brings in next tRNA

what is the sixth step of elongation?

the tRNA on E just falls off as soon as new tRNA is brought to A

what is the seventh step of elongation?

peptide bonds form between the two amino acids

what is the 8th step?

the second amino acid is cut off from the second tRNA

what is the 9th step?

EF-G moves the tRNA to E site and third tRNA to P site

what are the three termination factors in prokaryotes?

RF1, RF2, and RF3

when does elongation stop?

when the codon in the A site is one of the 3 stop codons

what do the release factors do?

they recognize the stop codons

what does RF1 recognize?

UAA and UAG

what does RF2 recognize?

UAA and UGA

what is the first step of translation termination in prokaryotes?

RF1 recognizes UAA on A site

what is the 2nd step of translation termination in prokaryotes?

RF3 brings RF1 to the A site

what is the 3rd step of translation termination in prokaryotes?

polypeptide chain is cleaved off by GTPase activity of RF3 + addition of H2O

what is the 4th step of translation termination in prokaryotes?

RRF, EF-G, and IF3 break everything apart. IF3 is recruited here again to keep large subunit away from binding to small subunit

what is RRF?

ribosome recycling factor

so what does RF3 do?

brings the release factors that recognize the stop codon to the A site

where is the polypeptide chain growing?

on the P site

what is the first step of initiation in eukaryotes?

tRNA is brought in first

what is the reason for the 5’ to 3’ scanning?

looking for AUG- start codon

what are the initiation factors in eukaryote?

eIF1A, eIF1, eIF3, eIF2, eIF5, and eIF5B

what does eIF1A do?

blocks the A site

what do eIF1 and eIF3 do?

prevent premature interaction between large and small subunits

what do eIF2 and eIF5 do?

help position and bring tRNA to the P site

what does eIF5B do?

helps promote binding of large and small subunits

what is the capping complex eIF4F made up of?

eIF4A, eIF4G, and eIF4E (AGE)

what is eIF4A

it has ATPase helicase activity. the ATPase breaks down ATP. the helicase is built in just in case G and C are there during scanning that want to build secondary structures

what is eIF4G?

it interacts with polyA tail

what is eIF4E?

it interacts with the cap

what is the purpose of the capping complex?

to circulate mRNA to make many copies of mRNA (loop)

what is the kozak sequence?

GCCGCCRCCAUGG

the R is a purine (A or G but usually A)

what is the role of the Kozak sequence?

helps ribosomes bind to and identify the correct start codon, facilitating the initiation of protein synthesis

what are the elongation factors in eukaryotes?

eEF1a and eEF2

what does eEF1A do?

brings incoming tRNA

what does eEF2 do?

translocation

what are the termination factors in eukaryotes?

eRF1 and erF3

what does eRF1 do?

recognizes all 3 stop codons