Genetics Chapter 15: The Genetic Code and Translation

ascomycete fungus Neurospora

what did Beadle and Tatum use to show that genes encode enzymes?

one gene, one polypeptide

the one gene, one enzyme hypothesis was eventually revised to be ...

mutagenesis using X-rays produced auxotrophs, identified mutations that lacked enzymes needed for synthesis of amino acids by transferring to tubes with minimal media + one amino acid

briefly describe Beadle and Tatum's experiment

precursor --> ornithine --> citrulline --> arginine

what did Srb and Horowitz propose the pathway for arginine synthesis was?

20

how many amino acids are found in proteins?

amino acids

proteins are polymers composed of ___ ___

a central carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and an R group

what does every amino acid consist of?

peptide bonds

how are amino acids in proteins linked?

one end has a free amino group and the other end has a free carboxyl group

describe the polarity of polypeptides

the sequence of amino acids

what is the primary structure of proteins?

a structure with twists and folds produced through interactions between neighboring amino acids

what is the secondary structure of protein?

beta pleated sheet and alpha helix

what are the common secondary structures found in proteins?

the overall, three-dimensional shape of the protein

what is the tertiary structure of a protein?

primary structure

the secondary and tertiary structures of a protein are largely determined by the ___ of the protein

two or more polypeptide chains associating together

what is the quaternary structure of a protein?

3 nucleotides in a codon would be enough to produce 20 amino acids (parsimony)

how did researchers determine that 3 nucleotides were in a codon?

triplet

the genetic code is a ___ code

RNA molecules consisting of a single type of nucleotide

what are homopolymers?

homopolymers, random copolymers, and ribosome bound tRNAs

what was used to determine the genetic code?

synthetic RNAs that contain random mixtures of 2 or 3 bases

what are random copolymers?

short mRNAs with a single codon were added to ribosomes and tRNAs with amino acids, isolated tRNAs bound to mRNAs and ribosomes and determined the amino acid present

how were tRNAs used to determine the genetic code?

64

how many possible codons are there?

61

how many sense codons are ther?

3

how many stop codons are there?

one that encodes for an amino acid

what is a sense codon?

it is redundant, the code contains more information than is needed to specify the amino acids

the genetic code is degenerate. what does that mean?

codons that specify the same amino acid

what are synonymous codons?

some amino acids are carried by more than one tRNA

there are 30-50 tRNAs in most organisms, meaning ...

different tRNAs that accept the same amino acid but have different anticodons

what are isoaccepting tRNAs?

30 to 50

how many different tRNAs are in most organisms?

one anticodon can pair with different codons through flexibility in base pairing at the third position of the codon

why are there more codons than anticodons?

some nonstandard pairings of bases could take place at the third position of a codon

what is the wobble hypothesis?

wobble

some codons are synonymous though ___

first, third

specific flexibility occurs with base pairing between the ___ position of the anticodon and the ___ position of the codon

no

do all organisms use the same genetic code?

no, one nucleotide is generally not a part of more than one codon

is the genetic code overlapping?

AUG

what is the most common initiation codon?

termination and nonsense codons

what are a couple other names for stop codons?

there are no tRNAs that have anticodons that pair with them

how do nonsense codons stop translation?

mostly, but not completely

is the genetic code universal?

mitochondrial genes, nuclear genes of some protozoans and bacterial DNA

where are the most common places to find nonuniversal codons?

the conversion of the genetic information of the mRNA into an amino acid polymer

what is translation?

ribosomes

translation takes place on ___

tRNA charging, initiation, elongation, termination

what are the stages of translation?

the sequence CCA at the 3' end

what is common among all tRNAs?

the carboxyl group of the amino acid is attached to the adenine nucleotide at the 3' end of the tRNA

how is an amino acid attached to a tRNA?

aminoacyl-tRNA synthetases

what is the key to specificity between an amino acid and its tRNA?

20, one for each amino acid

how many aminoacyl-tRNA synthetases does a cell have?

recognize a particular amino acid as well as all the tRNAs that accept that amino acid

what do aminoacyl-tRNA synthase enzymes do?

the attachment of a tRNA to its appropriate amino acid

what is tRNA charging?

ATP

where does the energy for tRNA charging come from?

all components necessary for protein synthesis: mRNA, small and large subunits of the ribosome, initiation factors, initiator tRNA, and GTP

what components must assemble during initiation of translation?

two subunits: small 30S subunit and large 50S subunit

what does the ribosome of bacteria consist of?

binds to the small ribosomal subunit and prevents the large subunit from binding during initiation

what does initiation factor 3 (IF-3) do?

a consensus sequence that is complementary to a sequence of nucleotides at the 3' end of the 16S rRNA (part of the small ribosomal subunit)

what is the Shine-Dalgarno sequence?

nucleotides in the sequence pair with their complementary nucleotides in the 16S rRNA, allowing the small ribosomal subunit to attach to the mRNA and positioning the ribosome directly over the initiation codon

what does the Sine-Dalgarno sequence do during initiation?

methionine tRNA and more initiation factors

what bind with GTP during initiation?

IF-3 dissociates from the small subunit, allowing the large ribosomal subunit to join the initiation complex, makes the 70S initiation complex

what is the final step of initiation?

amino acids are joined to create a polypeptide chain

what happens during elongation?

the 70S initiation complex made during initiation, charged tRNAS, several elongation factors, GTP

what does elongation require?

aminoacyl (A) site, peptidyl (P) site, exit (E) site

what are the sites in a ribosome that can be occupied by tRNAs?

P site

what site does the met-tRNA occupy in elongation?

a charged tRNA binds to the A site, done when tRNA makes a complex with elongation factor Tu (EF-Tu) and GTP

what is the first step of elongation?

GTP forms GDP, the EF-Tu-GDP complex is released

what happens after a charged tRNA binds to the A site?

the formation of a peptide bond between the amino acids that are attached to tRNAs in the P and A sites

what is the second step of elongation?

within the large ribosomal subunit (the rRNA acts as a ribozyme)

where does peptide bond formation occur during elongation?

the release of the amino acid in the P site from its tRNA

what does the formation of a peptide bond during elongation cause?

translocation

what is the third step of elongation?

GTP is hydrolyzed and elongation factor G (EF-G) enters to drive ribosome movement to the next codon

how does translocation occur?

the ribosome moves to the next codon, the tRNA in the P site moves to the E site and is ejected, the tRNA in the A site is moved to the P site, leaving the A site open

what happens during translocation?

cytoplasm --> A site --> P site --> E site --> cytoplasm

what is the path of tRNA progression during elongation?

the secondary structures are unwound by helicase activity located in the small ribosomal subunit

what happens to secondary structures on mRNA as the ribosome moves along?

when the ribosome translocates to a termination codon

when does protein synthesis end?

release factors enter A site (instead of tRNA) and RF-3-GTP associates with this complex; polypeptide, ribosomal subunits, tRNA, and RFs are released

what happens during termination?

GTP hydrolysis

what powers the release of the polypeptide, ribosomal subunits, tRNA, and RFs during termination?

stabilizes tRNAs and amino acids

what is the function of the 50S subunit during initiation?

binds GTP and charged tRNA, delivers charged tRNA to A site

what is the function of elongation factor Tu?

stimulates translocation of ribosome to next codon

what is the function of elongation factor G?

GTP

what provides energy during elongation?