Protein Synthesis

gene

a sequence of nucleotide bases in a DNA molecule that codes for the production of a specific sequence of amino acids, that in turn make up a specific polypeptide (protein)

where does transcription occur?

nucleus

Transcription (step by step)

• Part of a DNA molecule unwinds

• Hydrogen bonds between the complementary base pairs break

• This exposes the gene to be transcribed

• A complimentary copy of the code from the gene is made from mRNA 

  • This reaction is catalysed by RNA polymerase

• Free activated RNA nucleotides pair up, via hydrogen bonds, with their complementary bases on the exposed strand of the DNA molecule

• The sugar-phosphate groups of these RNA nucleotides are bonded

  • catalysed by enzyme RNA polymerase

• Sugar-phosphate backbone of the mRNA molecule formed

• When the gene has been transcribed and the mRNA molecule is complete, the hydrogen bonds between the mRNA and DNA strands break

• double-stranded DNA molecule reforms

• The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope

antisense/template strand

• the strand that is transcribed

sense/non-template strand

• the strand which is not transcribed

In what direction does the RNA Polymerase move?

3’ to 5’ direction

In what direction does the mRNA molecule grow

5’ to 3’ direction

Translation (step by step)

• mRNA attaches to a ribosome

• free tRNA molecules bind with their specific amino acids

• the anticodon on each tRNA molecule pairs with the complimentary codon on the mRNA

• Two tRNA molecules fit onto the ribosome at any one time

• a peptide bond is formed between adjacent amino acids

• continues until stop codon is reached

Where does translation occur?

Cytoplasm

anticodon

• triplet of unpaired bases at one end

• amino acid can attach

start codon

AUG

Which amino acid does the start codon code for

methionine

The three main components of the genetic code

• non-overlapping

• degenerate

• universal

non-overlapping genetic code

• each base is only read once

• adjacent codons do not overlap

degenerate genetic code

• multiple codons can code for the same amino acids

• limits the effect of mutations

How many different codons are possible?

4³ = 64

universal genetic code

• almost every organism uses the same genetic code

• enables genetic engineering

protein definition

• polymer of amino acids

General structure of amino acids

• amine group - NH₂

• carboxylic acid group -COOH

• hydrogen atom

• R group

Peptide bonds

• OH lost from carboxylic group of one amino acid

• H lost from amine group of one amino acid

• remaining carbon atom on first amino acid bonds to nitrogen of second amino acid

• condensation reaction

• water released

Breaking down of peptide bonds

• hydrolysis reaction

• addition of water breaks peptide bonds

The four levels of protein structure

• Primary

• Secondary

• Tertiary

• Quaternary

Primary structure

• sequence of amino acids bonded by covalent peptide bonds

• determined by DNA

• specific to each protein

Secondary structure types

• alpha helix

• beta pleated sheets

How is the Secondary structure formed?

• the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds

alpha helix

• occurs when the hydrogen bonds form between every fourth peptide bond (between the oxygen of the carboxyl group and the hydrogen of the amine group)

beta pleated sheet

• the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds

What is the Tertiary Structure

• bonds forming between R groups, hold together further folding of protein:

  • Hydrogen (these are between R groups)

  • Disulphide (only occurs between cysteine amino acids)

  • Ionic (occurs between charged R groups)

  • Weak hydrophobic interactions (between non-polar R groups)

What is quaternary structure?

• multiple alpha helix and beta pleated sheets bonded together

How does incorrect folding effect the function of a protein?

• tertiary structure altered

• Active site changed

• No enzyme-substrate complexes formed

• Unable to catalyse reaction

globular protein main 2 features

• compact

• roughly spherical

How do globular proteins form a spherical shape?

• Non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings

• Their polar hydrophilic R groups orientate themselves on the outside of the protein

• folding due to interactions between R groups results in shape

prosthetic group

Non-protein part of a protein molecule

globular protein function

• soluble

• molecules surround polar hydrophilic R groups

• easily transported around organisms

haemoglobin structure

• quaternary structure

• 4 subunits: 2 alpha globins, 2 beta globins

• each subunit has a prosthetic haem group

What bonds hold together the four globin subunits in haemoglobin?

disulphide bonds

How does sickle cell anaemia come about?

• base substitution results in the amino acid valine (non-polar) replacing glutamic acid (polar)

• makes haemoglobin less soluble

How does haemoglobin carry oxygen?

• haem group contains iron II

• reversibly combines with oxygen molecule to form oxyhaemoglobin

• each subunit can carry one oxygen molecules

How does haemoglobin transport oxygen?

• haemoglobin is more soluble than oxygen in water

• carried more efficiently with haemoglobin

• as each oxygen molecule binds, quaternary structure is altered

• haemoglobin has higher affinity for subsequent oxygen molecules

• they bind more easily

• due to haem group and iron II

Benefits of iron II

• allows oxygen to bind reversibly

  • none of the amino acids in haemoglobin are well suited to binding with oxygen

fibrous protein structure

• long strands of polypeptide with cross linkages due to hydrogen bonds

Fibrous protein features

• insoluble in water

• strong

How are fibrous proteins insoluble in water

• large number of hydrophobic R groups

Fibrous protein examples

• keratin

• elastin

• collagen

collagen structure

• three polypeptide chains

• held together by hydrogen bonds

• forming a triple helix

• covalent bonds form between R groups

• in interacting triple helices

collagen fibrils

triple helices of held together by cross links

How are the collagen molecules positioned?

• they are positioned the fibrils so that there are staggered ends

collagen fibre

• many fibrils are arranged together

function of collagen

• forms connective tissues

How does collagen have great tensile strength?

• many hydrogen bonds within the triple helix structure

• staggered ends of collagen molecules within fibrils provide strength