Proteinsby Sakvinder S Khalsa

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• WE SHALL LOOK AT PROTEIN SYNTHESIS.

• CONSIDER PROTEIN STRUCTURE AT THE MOLECULAR LEVEL.

• DISCUSS DIFERENT USES OF PROTEINS.

• BREIFLY LOOK AT ENZYMES.

Protein synthesis

• Protein synthesis is the making of proteins, using the information that is found in DNA (Chromosomes).

chromosomes

CELL

Proteins

• Proteins are very important molecules for a cell.

• Proteins are used to build cell structures and are used as enzymes.

Chromosomes

The cellNucleus

Proteins

• Proteins are long chains of small molecules called amino acids.

• Different proteins are made using different sequences of amino acids.

• The pieces of information in DNA are called genes.• Genes describe how to make proteins by putting the

correct amino acids into a long chain in the correct order.

The cell

Piece ofDNA

SelectedFor

study

chromosomes

Nucleus

Nucleus

Piece ofDNA

Selected for study

Let’s zoom in onThis short segment ofDNA to see how its

information Is used.

DNA inside the nucleus

• Protein synthesis begins with the stored genetic information of a DNA molecule.

• The DNA of this gene will ‘unzip’ like DNA does during replication.

DNA

Only one side of the DNAis used now.

[Both sides are used for DNAReplication, to copy the

Chromosome.]

Unused strand

RNA subunit

A single-strand of RNAForms, one subunit at a time, and Transcribes [copies] the genetic

Information from the DNA.

DNA

DNA

RNA

The new strand is an RNA molecule. Note that there is one difference in the subunits: RNA contains yellow Uricil instead of

purple Thymine.

DNA RNA

DNA

The RNA now has copied the subunit sequence of the gene.

The DNA is no longer needed in the process of protein synthesis.

DNA

DNA

RNA

RNA

mRNA

Code for one Amino acid

At the ribosome

Once the messenger RNA [mRNA]Is at the ribosome, the genetic information will

be translated by ribosome to make a protein

At the ribosome

At the ribosome

• The genetic information is interpreted and used to assemble a protein.

• We should remember, the mRNA is a sequence of subunits (like a chain) that tells how to build a protein

• A protein is a sequence of subunits – a chain of amino acids.

• The mRNA contains information in sets of three subunits.

• Each set of three is the code for a particular amino acid.

mRNA

The information of the messenger RNA (mRNA) describes which amino acids should be in the

protein chain.

A molecule of transfer RNA (tRNA) will carry in the proper amino acid, one at a time.

Amino acid

The tRNA matches up to the mRNA,Just like the two strands of DNA

Molecule match up.The sequence of three subunits of the mRNACan only match up with one particular tRNA.

mRNA

mRNA

Amino acid

Two differentAmino acids

Two different tRNA molecules

A different set of three mRNA subunits means a differenttRNA molecule. That means a different amino acid will be

Carried in.

mRNA

The two amino acids are linked By a peptide bond.

Then a tRNA molecule leavesThe ribosome.

The next tRNA willCarry in the proper

amino acid and the process will

continue.

The chain of amino acids is called a ‘polypeptide’

And when it is very long it is called a protein.

polypeptide

A polypeptide chain

• Even this is a very, very short polypeptide chain. Most have hundreds or thousands of amino acids.

A very short polypeptide chain, or part of a protein

The end of protein synthesis at the ribosome.

• We will look at the main elements found in proteins.

• Recall how proteins are constructed.

• Look at the structure of proteins.

• Overview the major functions of proteins.

PROTEIN STRUCTURE

The building blocks of proteins

• Like carbohydrate and lipid molecules proteins contain the elements : Oxygen(O), Carbon(C),and Hydrogen(H)

• In addition they always contain the element Nitrogen(N).

• Before we can understand how proteins are constructed, the structure of amino acids needs to be considered.

N C C

H

H

R

H

O

OH

AN AMINO ACID

Amine groupCarboxylic acid

group

R represents groups such as CH3 or C2H5

How are proteins constructed

• First the Amino acids bond together.

• They are joined together by what is known as a peptide bond.

Formation of a peptide bond via condensation.

H R O H R O N C C + N C C

H H H OH OH H

Amino acid Amino acid

A peptide bond between two amino acids.

H R O H H O

N C C N C C

H H R OHH20 [WATER]

A condensation reaction

Protein construction

• When two amino acids join together they form a dipeptide.

• When many amino acids are joined together a long-chain polypeptide is formed.

• Organisms join amino acids in different linear sequences to form a variety of polypeptides in to complex molecules, the proteins.

Primary protein structure

Peptide bond

Amino acid

primarystructure

This is the linear sequence of amino acids

Secondary protein structure

Polypeptides become twisted or coiled.

These shapes are known as the secondaryStructure.

There are two common secondary structures

The alpha-helix and the beta-pleated sheet.

Amino acid

Hydrogen bonds hold shapetogether

Secondary protein structureAlpha-helix

Secondary Protein structure [The beta pleated sheet]

Amino acid

Hydrogen bonds

The polypeptides are held in position by hydrogen bonds.

In both alpha-helices and beta pleated sheets the C=O of one amino acid bonds to the

H-N of an adjacent amino acid.As below:C=O----H-N

Secondary structures

• Both secondary structures give additional strength to proteins. The alpha-helix helps make fibres like in your nails, e.g. Keratin.

• The beta pleated-sheet helps make the strength giving protein in silk, fibroin.

• Many proteins are made from both alpha-helix and beta-pleated sheet.

Fibrous proteins

• A fibrous protein only achieves a secondary structure .

• The simple alpha-helix polypeptides do not undergo further folding.

Structure of a fibrous protein

Coiled alpha-helix structure

Tertiary protein structure

• This is when a polypeptide is folded into a precise shape.

• The polypeptide is held in ‘bends’ and ‘tucks’ in a permanent shape by a range of bonds including:

• Disulphide bridges [sulphur-sulphur bonds]• Hydrogen bonds• Ionic bonds.

Tertiary protein structure

Quaternary protein structure

• Some proteins consist of different polypeptides bonded together to form extremely intricate shapes.

• A haemoglobin molecule is formed for separate polypeptide chains.

• It also has a haem group, which contains iron.

• The inorganic group is known as the prosthetic group.

• In haemoglobin it aids oxygen transport.

Quaternary protein structure

How useful are proteins?

• Cell membrane proteins: Transport substances across the membrane for processes such as facilitated diffusion and active transport.

• Enzymes: Catalyse biochemical reactions, e.g. pepsin breaks down protein in to polypeptides.

• Hormones: are passed through the blood and trigger reactions in other parts of the body e.g. insulin regulates blood sugar.

• Immuno-proteins: e.g. antibodies are made by lymphocytes and act against antigenic sites on microbes.

• Structural proteins: give strength to organs, e.g. collagen makes tendons tough.

• Transport proteins: e.g. haemoglobin transports oxygen in the blood.

• Contractile proteins: e.g. actin and myosin help muscles shorten during contraction

• Storage proteins: e.g. aleurone in seeds helps germination, and casein in milk helps supply valuable protein to babies.

• Buffer proteins: e.g. blood proteins, due to their high charge, help maintain the pH of plasma.

Enzymes

• Living cells carry out many biochemical reactions.

• These reactions take place rapidly due to enzymes.

• All enzymes consist of globular proteins.

Enzymes

• The tertiary folding of polypeptides are responsible for the special shape of the ‘active’ site.

• Some enzymes require additional non-protein groups to enable them to work efficiently. e.g the enzyme dehydrogenase needs coenzyme NAD to function.

The lock and key theory

• Substrate Enzyme

+

Enzyme-substrate complex

A catabolic reaction [substrate broken down]

• enzyme-substrate

• complex2 x products

An anabolic reaction[substrates used to build a new

molecule]

substrate

Anabolic reaction continued

• Enzyme substrate complex

Metabolic reactions

• Metabolic reactions = anabolic reaction + catabolic reaction.

• Metabolism is a summary of build up and break down reactions.

Induced fit theory

• The active site is a cavity of a particular shape.• Initially the active site is not the correct shape in

which to fit the substrate.• As the substrate approaches the active site, the

site changes and this results in it being a perfect fit.

• After the reaction has taken place, and the products have gone, the active site returns to its normal shape.

Induced fit theory

• Enzyme Sustrate

+

Induced fit continued

Induced fit

Enzyme-substrate complex

products

enzyme

Lowering of activation energy

• Every reaction requires the input of energy.

• Enzymes reduce the level of activation energy needed as seen in the graph.

substrate

Reaction withoutenzyme

Reaction with

enzyme

products

Progress of reaction

e

nergy

Two minute summary

• Now you have seen the presentation !

• Summarise the most important points of this presentation.

• What was the ‘muddiest’ point in the presentation?

• Hand in your paper to the teacher before you leave the classroom.

END OF PRESENTATION by S S Khalsa [science PGCE]