Protein and synthesis

Translation

Process of protein synthesis from mRNA

Purpose of translation

Converts the linear sequence of codons in mRNA into a linear sequence of amino acids

Two major RNA classes involved in translation

mRNA and functional RNA

Function of mRNA

Serves as the template for protein synthesis

Functional RNAs involved in translation

tRNA and rRNA

Most abundant RNAs in cells

rRNA and tRNA

Percentage of total RNA represented by rRNA and tRNA

Approximately 95%

Protein

A polymer composed of amino acid monomers

Polypeptide

Another name for a protein chain

Number of naturally occurring amino acids in proteins

20

R group

The unique side chain that gives each amino acid its properties

Four components of an amino acid

Amino group, carboxyl group, hydrogen, and R group

Peptide bond

Covalent bond linking amino acids

How is a peptide bond formed?

Between the amino group of one amino acid and the carboxyl group of another

What molecule is removed during peptide bond formation?

Water

Primary protein structure

The linear sequence of amino acids

Secondary protein structure

Local folding caused by hydrogen bonds

Two examples of secondary structure

Alpha helix and beta pleated sheet

Scientists associated with secondary structure

Linus Pauling and Robert Corey

Silk protein structure

Beta pleated sheet

Tertiary protein structure

Folding of secondary structure due to side chain interactions

Forces involved in tertiary structure

Salt bridges and disulfide bonds

Salt bridge

Interaction between acidic and basic side chains

Disulfide bond

Covalent bond formed between cysteine residues

Quaternary protein structure

Interaction of two or more polypeptide subunits

Globular proteins

Compact proteins such as enzymes and antibodies

Fibrous proteins

Linear proteins found in skin, hair, and tendons

Active site

Region of a protein where substrate binding occurs

Protein domain

Region of a protein with a specific function

Genetic code

Rules that translate nucleotide sequences into amino acid sequences

RNA Tie Club

Group founded to help solve the genetic code

Founder of the RNA Tie Club

James Watson

Co-founder of the RNA Tie Club

George Gamow

Scientists awarded the 1968 Nobel Prize for decoding the genetic code

Khorana, Holley, and Nirenberg

Codon

A sequence of three nucleotides specifying an amino acid or stop signal

Length of a codon

Three nucleotides

Stop codons

UAA, UAG, and UGA

UAA mnemonic

U Are Away

UAG mnemonic

U Are Gone

UGA mnemonic

U Go Away

Why can't a one-base code work?

Too few combinations to encode all amino acids

Why can't a two-base code work?

Only 16 combinations are possible

Genetic code property: nonoverlapping

Each nucleotide belongs to only one codon

Reading frame

One possible grouping of nucleotides into codons

Number of possible reading frames

Three

Degenerate genetic code

Multiple codons can specify the same amino acid

Example of degeneracy

GAA and GAG both code for glutamic acid

Ordered genetic code

Related amino acids often have similar codons

Start codon

AUG

AUG codes for

Methionine

Adapter molecule in translation

tRNA

Function of tRNA

Interprets codons and brings the correct amino acid

Anticodon

Three-base sequence on tRNA complementary to an mRNA codon

Structure of tRNA

Cloverleaf structure with stems and loops

Location of anticodon

On the middle loop of tRNA

Aminoacyl-tRNA synthetase

Enzyme that attaches amino acids to tRNAs

Number of aminoacyl-tRNA synthetases

20

Wobble

Flexible pairing at the third codon position

Benefit of wobble

Allows one tRNA to recognize multiple codons

Ribosome

Large cellular machine responsible for protein synthesis

Components of ribosomes

rRNA and proteins

Ribosome subunits

Large and small subunit

Function of rRNA

Structural and catalytic component of ribosomes

Svedberg unit (S)

Measurement of sedimentation rate during centrifugation

How does rRNA fold?

Through intramolecular base pairing

Ribosomal A site

Binds incoming aminoacyl-tRNA

Ribosomal P site

Holds the growing polypeptide chain

Ribosomal E site

Exit site for deacylated tRNA

Decoding center

Ensures correct codon-anticodon pairing

Peptidyltransferase center

Site of peptide bond formation

Catalytic molecule in peptidyltransferase center

rRNA

2009 Nobel Prize significance

Showed rRNA performs catalytic activity in the ribosome

Three stages of translation

Initiation, elongation, and termination

Major components required for translation

Ribosomes, mRNA, tRNA, and translation factors

Goal of initiation

Place the first aminoacyl-tRNA in the P site

First amino acid in most proteins

Methionine

Initiator tRNA

tRNAMet

5' UTR

Region between transcription and translation start sites

Function of the 5' UTR

Helps position the ribosome for translation

Shine-Dalgarno sequence

Ribosome binding site in bacterial mRNA

Function of Shine-Dalgarno sequence

Positions the start codon in the P site

Bacterial small ribosomal subunit

30S

Bacterial large ribosomal subunit

50S

Initiation factor IF1

Helps proper initiation

Initiation factor IF2

Ensures initiator tRNA enters P site

Initiation factor IF3

Keeps 30S separate from 50S

Translation and transcription in prokaryotes

Coupled processes

Transcription and translation in eukaryotes

Occur in separate compartments

Location of transcription in eukaryotes

Nucleus

Location of translation in eukaryotes

Cytoplasm

Eukaryotic initiation factors that remove RNA secondary structure

IF4A, IF4B, and IF4G

Site recognized during eukaryotic initiation

5' cap

Elongation factor EF-Tu

Binds aminoacyl-tRNA and delivers it to the ribosome

Elongation factor EF-G

Promotes translocation during elongation

Termination signal in translation

A stop codon enters the A site

Stop codons recognized during termination

UAA, UAG, and UGA

Why doesn't a tRNA bind stop codons?

No tRNA carries a complementary anticodon

Release factors

Proteins that recognize stop codons

Bacterial release factors

RF1, RF2, and RF3

Function of release factors

Terminate translation and release the protein