Topic 4A- DNA, RNA and Protein Synthesis

Nuclear Eukaryotic DNA

• It is linear and associated with proteins

• Eukaryotic cells contain linear DNA molecules that exist as chromosomes which are found in the nucleus

• The DNA molecule is really long so it has to be wound up so it can fit in the nucleus

• The DNA molecule is wound around proteins called histones

• Histone proteins also help to support the DNA

• The DNA and protein is then coiled up very tightly to make a compact chromosome

• The mitochondria and chloroplasts in eukaryotic cells also have their own DNA. This is similar to prokaryotic DNA because it is circular and shorter than DNA molecules in the nucleus, it is not associated with histone proteins.

Prokaryotic DNA

• DNA molecules are shorter and circular in Prokaryotes.

• Prokaryotes also carry DNA as chromosomes- but the DNA molecules are shorter and circular.

• The DNA isn’t wound around histones- it condenses to fit in the cell by supercoiling.

What is a gene?

A gene is a base sequence of DNA that codes for the amino acid sequence of a polypeptide chain or a functional RNA.

DNA contains genes

• The sequence of amino acids in a polypeptide forms the primary structure of a protein.

• Different polypeptides have a different number and order of amino acids. The order of bases in a gene determines the order of amino acids in a polypeptide.

• Each amino acid is coded for by a sequence of three bases in a gene called a triplet or a codon. The genetic code is universal, non-overlapping and degenerate.

• Non-overlapping- Each codon is read in sequence, separate from the codon before and after it. Codons do not share bases.

• Degenerate- There are more possible combinations of codons than there are amino acids. Some amino acids are coded for by more than one codon.

• To make a polypeptide, DNA is first copied into messenger RNA (mRNA). This is the first stage of protein synthesis.

• Genes that don’t code for a polypeptide code for functional RNA instead eg tRNA and rRNA.

• A gene occupies a fixed position, called a locus, on a particular DNA molecule.

What is the genome?

The genome is the entire set of genes or genetic material present in a cell or organism.

What is the proteome?

The proteome is the full range of proteins that can be expressed from those genes/cell is able to produce from the genome.

Codon

• A group of three bases codes for a particular amino acid.

• Each group of 3 bases that codes for a particular amino acid is known as a codon.

The genetic code is non-overlapping, degenerate and universal

• The genetic code is the sequence of base triplets (codons) in mRNA which code for specific amino acids.

• In the genetic code, each base triplet is read in sequence, separate from the triplet before it and after it. Base triplets don’t share their bases- the code is non-overlapping

• Although each codon is specific to an amino acid, the genetic code is described as degenerate or redundant, each amino acid may be coded for by more than one codon.

• The genetic code is also universal- the same specific base triplets code for the same amino acids in all living things.

• Some triplets tell the cell when to start and stop production of the protein- called start and stop codons. They’re found at the beginning and end of the mRNA.

Splicing

• Most DNA in Eukaryotic cells doesn’t code for polypeptides

• Some genes don’t code for polypeptides- they code for functional RNA

• In eukaryotic DNA, genes that do code for polypeptides contain sections that don’t code for amino acids

• These sections of DNA are called introns

• All the bits of DNA that do code for amino acids are called exons

• Introns are removed from the DNA by a process called splicing during protein synthesis- so they do not affect the amino acid order

• Prokaryotic DNA doesn’t have introns

• Eukaryotic DNA also contains regions of multiple repeats outside of genes- these are DNA sequences that repeat over and over. These areas don’t code for amino acids either, so they’re called non-coding repeats

Alleles

• Genes can exist in different forms called Alleles

• A gene can exist in more than one form. These are called alleles- an allele is a different version of a gene.

• The order of bases in each allele is slightly different, so they code for slightly different versions of the same polypeptide.

Chromosomes

• In a eukaryotic cell nucleus, DNA is stored as chromosomes.

• Humans have 23 pairs of chromosomes, 46 in total.

• Pairs of matching chromosomes are called homologous pairs.

• In a homologous pair, both chromosomes are the same size and have the same genes, although they could have different alleles.

• Alleles coding for the same characteristic will be found at the same fixed position (locus) on each chromosome in a homologous pair.

RNA

• There’s more than one type of RNA

• RNA is a single polynucleotide strand and it contains uracil (U) as a base instead of thymine

• Uracil always pairs with adenine during protein synthesis

Ribosomes Structure:

• Ribosomes are made of mostly ribosomal RNA (rRNA) and protein.

• They do not have a membrane

• Ribosomes are found ‘free’ in the cytoplasm or bound to the ER to form rough ER

Messenger RNA (mRNA)

• mRNA is made during transcription

• It carries the genetic code from the DNA to the ribosomes, where it is used to make a protein during translation

• mRNA is a single polynucleotide strand

• In mRNA, groups of three adjacent bases are usually called codons (they’re sometimes called triplets or base triplets).

Transfer RNA (tRNA)

• tRNA is involved in translation

• It carries the amino acids that are used to make proteins to the ribosomes

• tRNA is a short single polynucleotide strand of RNA that’s folded into a clover leaf shape

• Hydrogen bonds between specific base pairs hold the molecule in this shape

• Every tRNA molecule has a specific sequence of three bases at one end called an anticodon binding site- complementary to the codon on the mRNA

• They also have an amino acid binding site at the other end- three exposed bases

Protein Synthesis

• Protein Synthesis is the process which produces proteins from the information in the DNA code. It takes place in two stages:

• Transcription- the DNA code is copied (transcribed) into a single strand of RNA called messenger RNA

• Translation- the mRNA is read by a ribosome and the code is ‘translated’ into a polypeptide chain

• Transcription takes place in the nucleus of cells. The DNA molecule itself is a large molecule that cannot get through the nuclear pores so smaller mRNA is used to copy a section of DNA which codes for a protein and this mRNA then leaves the nucleus and joins with a ribosome where the protein is then synthesised (translation)

First stage of Protein Synthesis- Transcription

• During transcription, an mRNA copy of a gene is made from DNA

• In eukaryotic cells, transcription takes place in the nucleus

• Prokaryotes don’t have a nucleus so transcription takes place in the cytoplasm

  1- Transcription starts when RNA polymerase (an enzyme) binds at the start codon. DNA helicase binds and breaks the hydrogen bonds between the bases of the two DNA strands on a section of DNA containing the gene for the desired protein, separating the strands and the DNA molecule uncoils, exposing some of the bases.

  2- One of the DNA strands is then used as a template strand to make an mRNA copy. RNA nucleotides align by complementary base pairing. In RNA, Uracil base pairs with adenine on DNA. The RNA polymerase moves along the template strand and joins adjacent RNA nucleotides by phosphodiester bonds to form a pre- mRNA strand (remember the base T will be replaced by a U when making mRNA)

  3- The DNA bases re-join behind the RNA polymerase as it moves along. The hydrogen bonds between the uncoiled strands of DNA reform once the RNA polymerase has passed by and the strands coil back into a double helix

  4- The RNA polymerase will stop and detach when it reaches a particular DNA sequence at the end of the gene called a stop codon

  5- Pre-mRNA is then spliced to remove the introns and form mRNA before it leaves the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm, where the next stage of protein synthesis takes place

Splicing

DNA contains regions which code for proteins (called exons) and regions of DNA that do not code for proteins (called introns).

In pre-mRNA both exons and introns are present, but the introns must be removed or ‘spliced out’ to only leave exons. Introns are removed and the exons joined together during splicing, forming mRNA strands. This takes place in the nucleus.

This happens in eukaryotes ONLY prokaryotes don’t have introns therefore there is no splicing because there are no introns in prokaryotic DNA.

Second Stage of Protein Synthesis- Translation

• In both eukaryotes and prokaryotes, translation occurs at the ribosomes in the cytoplasm

• During translation, amino acids are joined together to make a polypeptide chain following the sequence of codons carried by the mRNA.

  1- A ribosome attaches to the start codon on the mRNA. A tRNA molecule (carrying an amino acid) with an anticodon that’s complementary to the codon on the mRNA, attaches itself to the mRNA by specific base pairing. The tRNA molecule has a specific amino acid attached. ATP provides the energy needed for the bond between the amino acid and the tRNA molecule to form.

  2- The ribosome moves along to the next codon. The process is repeated and the enzyme catalyses the condensation reaction between amino acids to join them with a peptide bond, forming a polypeptide.

  3- The ribosome continues to move along the mRNA and tRNAs arrive with amino acids at each codon until a stop codon is reached. The ribosome, mRNA and tRNA separate and the polypeptide is complete.