D1.2 Protein synthesis

transcription

• in transcription one of the two strands of DNA is used as a template for synthesising a molecule of RNA → process carried out by RNA polymerase

• only one part of the DNA molecule is transcribed → usually one gene

• RNA polymerase binds to as site on the DNA at the start of the gene and then moves along it, transcribing the gene in a series of stages

Transcription stages

1. RNA polymerase unwinds DNA and separates it into two single strands

2. RNA polymerase pairs up free RNA nucleotides to DNA nucleotides on the template strand by complementary base pairing (linked by hydrogen bonds)

3. RNA polymerase links the RNA nucleotides together with covalent bonds (phosphodiester bond) → continuous strand of RNA nucleotides

4. assembled RNA strand separates from the template DNA strand

5. DNA strands pair up again and wind back into a double helix

hydrogen bonding in transcription

• same as in replication except adenine binds with uracil not thymine

• bases pair up by hydrogen bonding → can easily be broken to separate RNA transcript from DNA strand

• hydrogen bonds then form again between bases in the template strand + other DNA strand (sense strand)

conservation of DNA templates

• components of DNA are all chemically stable

• linked together in a strand of DNA by strong covalent bonds (phosphodiester bonds)

• strong sugar-phosphate backbone

• stability of DNA → ensures that the base sequence of a gene rarely changes during transcription → genes can be prescribed many times

gene expression

• a gene is expressed when the information it holds in its base sequence is used and an observable characteristic is generated

• at any specific time → some genes are being expressed but most are not (cells are specialised for particular functions and only develop the characteristics that they need)

how is gene expression controlled

transcription of a gene can be turned on and off

first stage in expression of a protein-coding gene

• transcription

• an RNA copy of the sense strand’s base sequence is produced and moves to a ribosome

second stage in expression of a protein-coding gene

• translation

• the base sequence of an RNA transcript is translated into the amino acid sequence of a polypeptide by a ribosome

third stage in expression of a protein-coding gene

• polypeptide is formed

• structural polypeptides are the direct cause of observable characteristics

• many polypeptides are enzymes that catalyse a reaction → product of reaction causes an observable characteristic

translation

• the synthesis of a polypeptide with its amino acid sequence determined by the base sequence of an RNA molecule.

• The RNA molecule is transcribed from a protein coding gene (mRNA)

• each base in the polypeptide is coded for by one codon on the mRNA

what is a codon

a sequence of 3 bases

Ribosomes and translation

• ribosomes are the site of translation

• have 2 subunits → large & small

large + small subunits of ribosomes

• small → has a binding site for mRNA

• large → has 3 binding sites for tRNA → tRNA is attached to at least 2/3 sites at all times during translation

tRNA in translation + linking amino acids

• the amino acid carried by the most recently arrived tRNA is linked to the growing chain of amino acids held by the previous amino acid to arrive

• the amino acids are linked by peptide bonds made at a catalytic site on the surface of the large subunit

RNA in translation - stages

1. mRNA binds to a site on the small subunit of the ribosome

2. tRNA molecules are present around the ribosome in large numbers carrying an amino acid that corresponds to their anticodon

3. The bases on the codon and the complementary anticodon link through the formation of a hydrogen bond (through complementary base pairing)

4. amino acids carried by tRNA are bonded together by a peptide linkage → dipeptide is formed

5. tRNA on the left detaches

6. ribosome moves along the mRNA to the next codon

7. another tRNA carrying an amino acid with the complementary anticodon binds

8. a chain of amino acids is formed

tNRA shape

• each type of tRNA has a distinctive three-dimensional shape

• this is recognised by an enzyme that links on the amino acid corresponding to the anticodon

the genetic code

• triplet - e.g. codon (3 bases) codes for one amino acid → 3 bases allow for 64 different codons → more than enough for 20 amino acids

• degeneracy - more than minimum amount of codons needed to code for the 20 amino acids → there are 2+ codons for most amino acids

• universality → the 64 codon have the same meanings in the cells of all organisms (few minor variations exist)

what is a degenerate code

a genetic code in which more than one symbol is used to represent the same thing

what is the universality of genetic code strong evidence for

all life on earth having evolved from the same original cells

what do 3 vs 1 codons represent

• 3 → indicates when the synthesis of the polypeptide is complete and translation should end

• 1 → represents the start signal + a specific amino acid

mutations and protein structure

• protein structure can be changed by a mutation as small as a single base change in the gene coding for the protein

• a single base substitution changes one codon in mRNA transcribed from the gene

• if the substitution is between hydrophilic and hydrophobic amino acids → big chain in protein structure

example of a point mutation that affects protein structure

• sickle cell mutation

• HBB is the gene that codes for the beta polypeptide of haemoglobin (consists of 146 amino acids)

• A base substitution changed adenine to thymine in the codon for the 6th amino acid bringing in valine instead of glutamic acid

• this changed the original allele of the gene into the sickle cell allele