Understanding Gene Expression: Translation and the Genetic Code, Study notes of Genetics

Download Understanding Gene Expression: Translation and the Genetic Code and more Study notes Genetics in PDF only on Docsity!

Gene Expression: Translation

Reminder

• Genes that encode proteins are transcribed and the transcript is processed to make mRNA.
• Next the base sequence in the mRNA must be translated into amino acid sequences in a polypeptide.
• Once polypeptides are formed, they fold up and combine with other molecules, but this is the realm of biochemistry, not genetics. Review structure of polypeptides; a protein consists of one or more polypeptides.

Important The 20 Amino Acids

features:

• Differ only in side chains
• Each has three- letter and one- letter abbreviations You should understand that the sequence of amino acids in a polypeptide (protein) can be written two ways: Arg Thr Ser Ser R T S S Polypeptides have an N- and a C-terminal AA You don’t have to memorize these but you do have to know there are 20 and recognize amino acid sequences.

The Genetic Code

The code is:

• Written in RNA because

it is the mRNA sequence

that is read.

• Universal (almost) Exceptions (small): Vertebrate mitochondria Invertebrate mitochondria Chloroplasts Ciliate nuclear Mycoplasma nuclear Candida nuclear etc.
• Triplet
• Nonoverlapping
• Commaless
• Degenerate

The Genetic Code

CACCAUGGUGCACCUGACUCCUGAG…CACUAAGCU

Met Val His Leu Thr Pro Glu …. His Stop

Start

UAA, UAG, and UGA are

nonsense codons; they do not

code for any amino acid and

hence are stop or

termination codons.

All the rest are sense codons.

AUG is the start codon and

codes for methionine (Met,

M).

(only one to memorize)

Open Reading Frames

CACCAUGGUGCACCUGACUCCUGAG…CACUAAGCU

Met Val His Leu Thr Pro Glu …. His Stop

Start

An open reading frame (ORF) is a string of sense codons starting with the start codon ATG and flanked at the 3’ end by a stop codon. All genes that code for proteins must have an ORF.

Using Open Reading Frames to Find Genes

A computer program can search a sequence of bases for open reading

frames. These are candidates for genes encoding proteins.

Problems:

• A gene can be on either strand, but the sequence is only written for one strand. Solution: search both complementary sequences.
• A random sequence of bases can have an ORF. Partial solutions: look for long ORFs starting with ATG.
• Introns can interrupt ORFs. The introns are spliced out of the mRNA leaving only the exons which form a continuous ORF; but DNA sequences will still have the introns. Partial solution: look for sequences that often flank introns. Designing computer programs to seach complete genome sequences is a major problem in bioinformatics.

The Mechanics of Translation

1. Translation requires:

• Small ribosomal subunit = SSUrRNA + ribosomal proteins
• Large ribosomal subunit = LSUrRNA + ribosomal proteins + 5SrRNA (eukaryotes)
• (Small and large subunits also have S names: 16S, 18S, 23S, etc. S is for Svedberg units describing how fast something moves in a centrifugal field.)
• Aminoacyl tRNAs = transfer RNAs + amino acids
• **Accessory proteins that promote various steps

2. mRNA is translated 5’ to 3’
3. Polypeptide is made N-terminal to C-terminal**

Making Aminoacyl tRNAs

Each tRNA has a specific base sequence, including an anticodon that can base pair with a codon.

A A A A A U

U U U U U A

Lys Asn

A A A A A U

U U U U U A

Lys Asn

A A A A A U

U U U

Asn Lys Asn U U A An aminoacyl tRNA synthase recognizes a U U A tRNA and its corresponding amino acid and joins them. The anticodon on the aminoacyl tRNA base- pairs with its codon on the mRNA. A new peptide bond is formed to join the amino acids.

Translation in More Detail than You Wanted or Need to Know (see text Figure 10.17 for a better diagram) $$ ribosome small subunit

Ribosome Binding, Translation Initiation, and

Termination Signals on mRNAs

Prokaryotes: a special sequence (the “Shine-Delgarno sequence”) is the ribosome binding site. Eukaryotes: the 5’ end of the mRNA is modified to form the “5’ cap” that initiates ribosome binding. Prokaryotes and eukaryotes: the AUG start codon is the signal to initiate translation; the nonsense stop codon binds no tRNA and this stops translation.

Unique Features of Translation in Prokaryotes

One mRNA can encode more than one polypeptide. ≥ 2

Unique Features of Translation in Prokaryotes

Translation of an mRNA can begin before transcription is complete, because these processes are not separated by a nuclear membrane.