1 Translation of RNA The Genetic Code and Protein Metabolism The Process of Protein Synthesis The Three Stages of Protein Synthesis Post-translational.

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Translation of RNAThe Genetic Code and Protein Metabolism

Translation of RNAThe Genetic Code and Protein Metabolism

The Process of Protein Synthesis

The Three Stages of Protein Synthesis

Post-translational Processing of Protein

Regulation of Protein Synthesis

The Process of Protein Synthesis

The Three Stages of Protein Synthesis

Post-translational Processing of Protein

Regulation of Protein Synthesis

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Characteristics of protein synthesis

Characteristics of protein synthesis

Occurs on a ribosomeribosome - a complex of ribosomal RNA and proteins.

Made of two subunitsMade of two subunits• largelarge - three rRNA and about 49 proteins• smallsmall - one rRNA and about 33 proteins• Together they provide a platform for

synthesis

You can think of a ribosome like a tape player, where the tape is mRNA.

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RibosomesRibosomes

Two ribosomal subunits join to form a polysome.

large subunit small subunit

synthesisplatform

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Where protein synthesis beginsWhere protein synthesis begins

It has been verified that protein synthesis begins at the amino terminus.

N N H

C H

R

COO - H2N C H

R'

COO -+

N N H

C H

R

C N H

C H

R'

COO -

O

growing chain

growing chain

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Role of tRNARole of tRNATransfer RNATransfer RNA

• Serves as an adapter molecule to translate the 4 letter language of mRNA into 20 amino acids.

• Binds to a single amino acid at one end.

• Serves to bring the proper amino acid to the right spot on the mRNA-ribosome complex.

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tRNAtRNAA

C

C

A

C

C

U

C

G

U

CU

U

C

G

G

G

G

G

CC GGG

CC GG

A CGG

CC GGU

C

C

C

C

U

C

A

U

G

G

A

G

G

G

G

GU

U

CC G

U

C GC

AU

G

G

C

U

AG U

A GU

G

GC

HO-

Site of aminoacid attachment

Site of aminoacid attachment

Three base anticodon site

Three base anticodon site

Point ofattachmentto mRNA

Point ofattachmentto mRNA

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Attachment of amino acidsAttachment of amino acids

Amino acids are linked to tRNAs by aminoacyl-tRNA synthetases.

These enzymes are able to recognize both the correct tRNA and amino acid.

amino acid + ATP aminoacyl adenylate + PPi

aminoacyl adenylate + tRNA aminoacyl-tRNA + AMP

PPi + H2O 2Pi

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Attachment of an amino acidAttachment of an amino acid

A

C

C

A

C

C

U

C

G

U

CU

U

C

G

G

G

G

G

CC GGG

CC GG

A CGG

CC GGU

C

C

C

C

U

C

A

U

G

G

A

G

G

G

G

GU

U

CC G

U

C GC

AU

G

G

C

U

AG U

A GU

G

GC

HO-C O

O

CH

NH3+amino acyl group

R

ester bond

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Genetic code, mRNAand protein amino acids


Important termsImportant terms

TripletTripletA set of three nucleotide bases on mRNA for one amino acid.

NonoverlappingNonoverlappingA set of three adjacent bases are treated as a complete group - codoncodon.

No punctuation.No punctuation. There are no intervening bases between triplets.

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Important termsImportant terms

DegenerateDegenerateA single amino acid may have more than one triplet code. There is usually a sequential relationship between these codes.

UniversalUniversalThe same genetic code is used by all organisms except mitochondria and some algae.

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Amino acid codonsAmino acid codons

alanine GCA, GCC, GCGGCU, AGA, AGG

arginine AGA, AGG, CGACGC, CGG, CGU

asparagine AAC, AAUaspartate GAC, GAU cysteine UGC, UGUglutamate GAA, GAGglutamine CAA, CAGglycine GAA, GCC, GGG

GGUhistidine CAC, CAUisoleucine AUA, AUC, AUUleucine CUA, CUC, CUG

CUU, UUA, UUG

lysine AAA, AAGmethionine AUGphenylalanine UUC, UUUproline CCA, CCC

CCG, CCUserine UCA, UCC

UCG, UCU AGC, AGU

threonine ACA, ACC ACG, ACU

tryptophan UGGtyrosine UCA, UCUvaline GUA, GUC

GUG, GUU

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Three stages of protein synthesis

Three stages of protein synthesis

Production of a protein requires several players.

aminoacyl - tRNAaminoacyl - tRNAsource of amino acids

mRNAmRNAthe information source for construction of the protein sequence

RibosomesRibosomesplatform for synthesis - rRNA and protein.

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Steps in protein synthesisSteps in protein synthesis

Step One - InitiationStep One - InitiationA special protein is required to bring the ribosome parts and mRNA together.

It recognizes the initiation (STARTSTART) codon (AUG).

Once formed, the ribosome complex will- hold the mRNA in place.- provide binding sites for the growing protein and incoming amino acids.

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Step Two - Chain elongationStep Two - Chain elongation

Amino acid is added sequentially to the peptide chain.

An enzyme, peptidyl transferase, is used to move the ribosome down the mRNA strand - translocationtranslocation.

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Step Three - TerminationStep Three - TerminationWhen one of three codons (UAA, UAG or UGA) is encountered, there is no tRNA that matches.

Protein synthesis stops.

A releasing factor is attracted to the site.

This results in the growing protein being released from the ribosome.

The ribosome complex then falls apart into the original subcomplexes.

Protein synthesisProtein synthesis

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Protein synthesis and energyProtein synthesis and energy

The energy requirements for synthesis are quite high.

• Two anhydride bonds in ATP are cleaved on activation of each amino acid and synthesis of an aminoacyl-tRNA.

• One GTP is required for entry of each amino acid into the ribosomal unit.

• One GTP is required during each translocation step.

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Post-translationalprocessing of proteins

Post-translationalprocessing of proteins

Protein synthesis establishes the primary structure for a protein.

Additional processing is required to convert it to it’s biologically active form.

This may include:This may include:

foldingfolding

chemical modificationchemical modification

attachment of other groupsattachment of other groups

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Protein foldingProtein folding

Results from interaction of side chains.

Proteins called chaperones act as catalysts to guide this process.

Possible side chain interactions:Possible side chain interactions:

• Similar solubilities

• Ionic attractions

• Attraction between + and - side chains

• Covalent bonding

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- S - S -

Salt bridge

DisulfideCrosslink

Hydrogenbonding

Hydrophobicinteraction

-COO- H3N -

-O \

H

-O \

H

+

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Side chain interactionsSide chain interactions Help maintain specific structure.

Oxidation of cystine - crosslink formation. O ||

HO-C-CH-CH2-SH

|

NH2

O ||

HS-CH2-CH-C-OH

|

NH2 O ||

HO-C-CH-CH2-S -S -

|

NH2

O ||

SS-CH2-CH-C-OH +H2O

|

NH2

oxidation [O]

covalentdisulfide

bond

covalentdisulfide

bond

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An example of how a S-SAn example of how a S-Scrosslink can affect foldingcrosslink can affect folding

20 glycines - cysteine

20 glycines - cysteine

40 glycin

es

crosslink

- helix structure

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Biochemical modificationBiochemical modification

Proteolytic cleavageProteolytic cleavage

About half of all proteins require the removal of their N-terminus amino acid to become active.

In addition, many enzymes are produced in an inactive form - zymogenszymogens. They require that one or several specific bonds be cleaved to produce the active form.

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Amino acid modificationAmino acid modification

PhosphorylationPhosphorylationSerine, threonine and tyrosine residues may be modified by transfer of a phosphoryl group.

HydroxylationHydroxylationProline and lysine may be converted to hydroxyproline or hydroxylysine.

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Attachment of carbohydratesAttachment of carbohydratesThis process is used for the production of glycoproteins.

Attachment of prosthetic groups.Attachment of prosthetic groups.The addition of small organic, inorganic or organometallic groups - heme, FAD, biotin, ...

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Protein targetingProtein targeting

Most proteins are synthesized by the ribosomes in the cytoplasm.

However, they may be required in other cellular regions and organelles

Protein targeting deals with the process of sorting out and moving proteins to where they are needed.

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Protein targetingProtein targeting

• In general, proteins that must be transported are produced with an extra sequence of 15-36 amino acids - at the amino terminus.

• The sequence marks it for transport.

• The sequence is removed by hydrolysis upon arrival.

• Proteins sent to the nucleus use an internal sequence that is not cleaved.

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Protein degradationProtein degradation

After a protein has served it’s purpose or becomes damaged, it is marked for destruction.

The turnover rate varies by protein.

Protein half-lifeRat liver RNA polymerase I 1.5 minRat liver cytochrome c 150 minHuman hemoglobin 100 days

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Protein degradationProtein degradation

Ubiquitin pathwayUbiquitin pathwayImportant route for protein labeling and degradation in eukaryotic cells.

UbiquitinUbiquitin

• A small protein with 76 amino acid residues.

• It is highly conserved.

• Yeast and human ubiquitin differ at only 3 of the 76 residues.

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UbiquitinUbiquitin

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Ubiquitin pathwayUbiquitin pathway

• Ubiquitin is covalently attached via a peptide bond to lysine residues.

• Several ubiquitin molecules are often attached to a single protein.

• Degradation then occurs via proteolytic action.

N

Lys

C

O

H

ubiquitin C N protein

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Regulation of protein synthesisRegulation of protein synthesis

• A typical bacterial cell has about 4000 genes in its DNA genome.

• The human genome has an estimated 100,000 to 150,000

• Only a small fraction of these genes is used by a cell at any given time, if at all.

• The amount of each protein generated must be carefully regulated to account for the needs of the cell.

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Regulation of gene expressionRegulation of gene expression

There are many steps that can be regulated.• transcription• post-transcriptional processing• mRNA degradation• protein synthesis• post-translational processing• protein degradation

Most gene expression is controlled at the level of transcription initiation.

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Aminoacids

Nucleotidesprotein

degradationmRNA

degradation

transcription translation

post-translationalprocessing

post-transcriptional

processing

DNAprimary

transcri ptmatureRNA

inactiveprotein

Activeprotein

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Two fundamental types of gene expression.

Expression of constitutive genes.Expression of constitutive genes.Continuous transcription which produces a constant level of certain proteins.

Expression of inducible or repressible genes.Expression of inducible or repressible genes.Genes that can be activated (induced) or deactivated (repressed). This allows for varied levels of RNA. They are regulated by RNA polymers and molecular signals.

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Principles of regulatinggene expression


In many prokaryotic cells, genes for proteins of related function are clustered in units. The components in these units are:

• Structural genes - the gene which is to be transcribed & translated.

• Promoter region - responsible for RNA polymerase binding to the initiation site.

• Binding site for inducers.

• Binding site for repressors - called operators.

All structural genes are regulated by nucleotide sequences upstream from the start site (+1).

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RNA polymeraseRNA polymerase

• The key participant in transcription.

• It initiates transcription by binding to a DNA promoter region.

• The sequences in each promoter region determines the affinity for its binding.

• For inducible or repressible genes, other levels of control are superimposed - regulatory proteins and other signals.

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Eukaryotic gene regulation is a more complicated process.

• Complex sets of regulatory elements are present in promoter regions.

• Three classes of RNA polymerase using different modes of regulation are present.

• The DNA is much more complex in both size and structure.

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RNA polymerase activity is mediated by regulatory proteins of two major types.

Activators.Activators. Bind to promoter regions and assist the binding of RNA polymerase to the adjacent promoter.

Repressors.Repressors. Bind to specific base sequences in the promoter region and prevent RNA polymerase in gaining access.

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Most regulatory process can be classified into one of four mechanistic types.

Positive regulationPositive regulationTranscribes until a molecular signal is

sent.Transcribes after a signal is sent.

Negative regulationNegative regulationBlocks transcription until a signal is sent.Stops transcription when the signal is

sent.

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Positive regulationPositive regulation

activator RNA polymerase

molecularsignal

Binding of molecularsignalcauses dissociation ofactivator from DNA

Binding of molecular

signalcauses strong

binding of of activator to

DNA

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Negative regulationNegative regulation

operator

Binding ofthe molecularrecognitionsignal causes dissociation of the operatorfrom the DNA

Binding ofthe molecular

recognitionsignal causes

strongerbinding of the

operator to DNA

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Regulatory proteins have common, discrete binding domains.

• 20-100 amino acid residues.

• They bind because the domain is an exact fit for the outer edge of the DNA helix.

• Held together by hydrogen bonding that is not disruptive to DNA.

• Lysine, arginine, glutamate, asparagine and glutamine form the hydrogen bonds.

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Classes of regulatory proteinsClasses of regulatory proteins

Helix-turn-helix motifHelix-turn-helix motifAbout 20 amino acid residues, in two helical regions and a turn.

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Zinc finger motifZinc finger motifOnly found in eukaryotic regulatory proteins.

ZnCys

His

Cys

His

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Leucine zipper motifLeucine zipper motifFeatures an -helix region of approximately 30 residues. Leucine occurs as every seventh one. This allows two molecules of the protein to form a zipper like region.

1 Translation of RNA The Genetic Code and Protein Metabolism The Process of Protein Synthesis The Three Stages of Protein Synthesis Post-translational.

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