Higher Biology

Unit 1: DNA and the Genome

2. Gene Expression

Notes

Proteins

All proteins are contain the elements:

Carbon (C)

Hydrogen (H)

Oxygen (O)

Nitrogen (N)

And sometimes Sulphur (S)

The subunits of proteins are amino acids. There are 20 different types of amino acids.

Proteins are arranged into four structural levels.

Primary (1o) Structure

  • Sequence of amino acid residues in the polypeptide chain.

.

Secondary (2o) Structure

  • Two main types of secondary structure.
  • helix and sheet arrangements.
  • Generated from interactions between the atoms of the amino acid residues in the polypeptide chain.

  • In the -sheet arrangement, polypeptide chains are linked together in a side-by-side configuration.
  • This is again by hydrogen bonding. These bonds are WEAK bonds.
  • -sheets can either be PARALLEL (where the adjacent polypeptide strands extend in the same direction) or ANTIPARALLEL (the strands extend in opposite directions).

Antiparallel Parallel

Tertiary (3o) Structure

  • More complex than the Secondary structure.
  • Describes the way in which the polypeptide folds to give the final protein structure.
  • Determined by HYDROPHOBIC interactions (hate water).
  • Contain an additional covalent bond called the DISULPHIDE BOND.
  • In the tertiary structure, -helix and -sheet arrangements are found.

Quanternary (4o) Structure

  • Some proteins are composed of two or more polypeptide SUBUNITS.
  • Each subunit has its own specific conformation.
  • The organisation of the subunits in a multi-subunit protein is known as the QUANTERNARY structure of a protein.
  • Haemoglobin is an example of this.
  • It is composed of four chains of the protein globin.
  • It has two - and two -globin subunits, each with its own prosthetic haem group.

Haem Group

  • Folded proteins can have non-protein groups associated with them.
  • Haem is an iron containing group of haemoglobin.
  • Proteins may also have carbohydrate, lipid or nucleic acid groups associated with them.

Proteins can be fibrous or globular:

Some proteins may contain non-protein chemicals


RNA and Protein Synthesis

DNA / RNA
Sugar
Deoxyribonucleic Acid / Sugar
Ribose Acid
Base
ATCG / Bases
AUCG
Strands
Double Stranded / Strands
Single

RNA Nucleotide

Transcription

( The synthesis of mRNA strand from a section of DNA)

The following takes place in the nucleus of the cell:

  1. DNA double helix ______
  2. Weak ______bonds between bases break, separating the two DNA strands
  3. Free ______nucleotides pair with their complementary base pair on the ______strand. Weak hydrogen bonds form between ______.
  4. RNA polymerase can only add nucleotides to the 3’ end of the growing mRNA molecule
  5. Strong chemical bonds form between the ______and ______of neighbouring nucleotides (bond formation catalysed by RNA polymerase).
  6. A strand of messenger RNA has now been made
  7. The molecule elongates until a terminator sequence of nucleotides is reached don the DNA strand.
  8. The mRNA strand is called primary transcript of mRNA.

Modification of primary transcript

In eukaryotes long stretches of DNA exist which do not code for proteins – called introns.

Coding regions are called exons

Splicing

The introns are cut out and removed from the primary transcript of mRNA and the exons are spliced together to form mRNA with continuous sequences of nucleotides coding for proteins.

The mRNA then passes out of the nucleus via a pore in the nuclear membrane into the cytoplasm

Translation

(The synthesis of protein as a polypeptide chain under the direction of mRNA)

Each triplet of bases on mRNA is called a

codon; each codon codes for an amino acid.

There are 64 triplets.

Transfer RNA (tRNA) is found in the cytoplasm and carries a triplet of bases called an anticodon

Each anticodon corresponds to a particular

amino acid, carried by the tRNA at its attachment

site

Start and stop codons

The mRNA codon AUG (complementary

to tRNA anticodon UAC) is unusual in

that it codes for methionine (met) and

acts as a start codon.

mRNA codons UAA, UAG and UGA do

not code for amino acids but instead

act as stop codons.

The anticodon on the tRNA molecule forms weak hydrogen bonds with the corresponding codon on the mRNA

The Ribosome

Translation stages

  1. Ribosome binds to the 5’ end of the mRNA template to that the mRNA’s start codon (AUG) is in position at binding site P.
  2. tRNA molecule picks up its appropriate amino acid (methionine) from the cytoplasm
  3. The tRNA carries the amino acid to the ribosome and becomes attached at site P by hydrogen bonds between its anticodon (UAC) and the start codon (AUG).
  4. The mRNA codon at site A forms hydrogen bonds with the complementary anticodon on the tRNA molecule carrying its amino acid.
  5. When the first two amino acids molecules are next to each other they join with a peptide bond.
  6. As the ribosome moves along one codon he tRNA that was at site P is moved to site E and discharged from the ribosome to be reused.
  7. At the same time the tRNA that was site A is moved to site P.
  8. The next tRNA occupies the now vacant site A, and the amino acid the tRNA caries bonds to the growing polypeptide chain.
  9. The process is repeated many times , thus translating the mRNA into a complete polypeptide chain.
  10. When a stop codon is reached the site A on the ribosome releases the polypeptide. This whole process needs energy from ATP.

One gene can code for many proteins, how?

Particularexonsof a gene may be included, or excluded from, the final, processedmRNA produced from that gene.

Consequently the proteinstranslated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions .

Alternative splicing allows thehuman genometo direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.

It is thought that at least70%of the approximately 25,000 genes in the human genome undergo alternative splicing and that, on average, a given gene gives rise to4alternatively spliced variants - encoding a total of90-100,000proteins which differ in their sequence and therefore, in their activities

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