CIE AS LEVEL BIOLOGY: Nucleic acids and protein synthesis

What is a nucleic acid

Nucleic acids such as DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are macromolecules (giant molecules) Like proteins (polypeptides) and carbohydrates (polysaccharides), these nucleic acids are polymers ('poly' meaning 'many') This means they are made up of many similar, smaller molecules (known as subunits or monomers) joined into a long chain

What are the subunits that make up DNA and RNA

The subunits that make up DNA and RNA are known as nucleotides. Therefore DNA and RNA can also be known as polynucleotides

Components of nucleotides

Nucleotides are made up of three components:
A nitrogen-containing base (also known as a nitrogenous base)
A pentose sugar (containing 5 carbon atoms)
A phosphate group

What is ATP

Adenosine triphosphate (ATP) is the energy-carrying molecule that provides the energy to drive many processes inside living cells. ATP is another type of nucleic acid and hence it is structurally very similar to the nucleotides that make up DNA and RNA. It is a phosphorylated nucleotide Adenosine (a nucleoside) can be combined with one, two or three phosphate groups.
One phosphate group = adenosine monophosphate (AMP)
Two phosphate groups = adenosine diphosphate (ADP)
Three phosphate groups = adenosine triphosphate (ATP)

What are the nitrogenoud base molecules that are found in the nucleotides of DNA and RNA molecules

The nitrogenous base molecules that are found in the nucleotides of DNA (A, T, C, G) and RNA (A, U, C, G)

Name pureins

The bases adenine and guanine are purines - they have a double ring structure

Name Pyrimidines

The bases cytosine, thymine and uracil are pyrimidines - they have a single ring structure

The structure of DNA

DNA molecules are made up of two polynucleotide strands lying side by side, running in opposite directions - the strands are said to be antiparallel. Each DNA polynucleotide strand is made up of alternating deoxyribose sugars and phosphate groups bonded together to form the sugar-phosphate backbone. These bonds are covalent bonds known as phosphodiester bonds. The phosphodiester bonds link the 5-carbon of one deoxyribose sugar molecule to the phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond to the 3-carbon of the deoxyribose sugar molecule of the next nucleotide in the strand. Each DNA polynucleotide strand is said to have a 3' end and a 5' end (these numbers relate to which carbon on the pentose sugar could be bonded with another nucleotide) As the strands run in opposite directions (they are antiparallel), one is known as the 5' to 3' strand and the other is known as the 3' to 5' strand
The nitrogenous bases of each nucleotide project out from the backbone towards the interior of the double-stranded DNA molecule

Hydrogen bonding in DNA molecules

The two antiparallel DNA polynucleotide strands that make up the DNA molecule are held together by hydrogen bonds between the nitrogenous bases These hydrogen bonds always occur between the same pairs of bases

What is adenine bonded to

The purine adenine (A) always pairs with the pyrimidine thymine (T) - two hydrogen bonds are formed between these bases

What is guanine bonded to

The purine guanine (G) always pairs with the pyrimidine cytosine (C) - three hydrogen bonds are formed between these bases. This is known as complementary base pairing
These pairs are known as DNA base pairs

What is the shape of the DNA molecule

DNA is described as a double helix, This refers to the three-dimensional shape that DNA molecules form

When does DNA replication occur

DNA replication occurs in preparation for mitosis, when a parent cell divides to produce two genetically identical daughter cells - as each daughter cell contains the same number of chromosomes as the parent cell, the number of DNA molecules in the parent cell must be doubled before mitosis takes place. DNA replication occurs during the S phase of the cell cycle (which occurs during interphase, when a cell is not dividing)

Semi-conservative replication of DNA

The hydrogen bonds between the base pairs on the two antiparallel polynucleotide DNA strands are broken
This 'unzips' or unwinds the DNA double helix to form two single polynucleotide DNA strands
Each of these single polynucleotide DNA strands acts as a template for the formation of a new strand - the original strand and the new strand then join together to form a new DNA molecule
This method of replicating DNA is known as semi-conservative replication because half of the original DNA molecule is kept (conserved) in each of the two new DNA molecules
Semi-conservative replication was shown to be the method of replication by Meselson and Stahl in 1958. They used coli (a bacteria) and two nitrogen isotopes, a heavy form 15N and the 'normal' form 14N, to demonstrate how the density of DNA changes over generations as the 15N isotope was replaced with the 14N isotope

Role of DNA polymerase

In the nucleus, there are free nucleotides to which two extra phosphates have been added (these free nucleotides with three phosphate groups are known as nucleoside triphosphates or 'activated nucleotides')
The extra phosphates activate the nucleotides, enabling them to take part in DNA replication
The bases of the free nucleoside triphosphates align with their complementary bases on each of the template DNA strands
The enzyme DNA polymerase synthesises new DNA strands from the two template strands
It does this by catalysing condensation reactions between the deoxyribose sugar and phosphate groups of adjacent nucleotides within the new strands, creating the sugar-phosphate backbone of the new DNA strands
DNA polymerase cleaves (breaks off) the two extra phosphates and uses the energy released to create the phosphodiester bonds (between adjacent nucleotides)
Hydrogen bonds then form between the complementary base pairs of the template and new DNA strands

Leading and lagging strands

DNA polymerase can only build the new strand in one direction (5' to 3' direction)
As DNA is 'unzipped' from the 3' towards the 5' end, DNA polymerase will attach to the 3' end of the original strand and move towards the replication fork (the point at which the DNA molecule is splitting into two template strands)
This means the DNA polymerase enzyme can synthesise the leading strand continuously
This template strand that the DNA polymerase attaches to is known as the leading strand
The other template strand created during DNA replication is known as the lagging strand
On this strand, DNA polymerase moves away from the replication fork (from the 5' end to the 3' end)
This means the DNA polymerase enzyme can only synthesise the lagging DNA strand in short segments (called Okazaki fragments)
A second enzyme known as DNA ligase is needed to join these lagging strand segments together to form a continuous complementary DNA strand
DNA ligase does this by catalysing the formation of phosphodiester bonds between the segments to create a continuous sugar-phosphate backbone

What does RNA contain

Unlike DNA, RNA nucleotides never contain the nitrogenous base thymine (T) - in place of this they contain the nitrogenous base uracil (U). Unlike DNA, RNA nucleotides contain the pentose sugar ribose (instead of deoxyribose)
Unlike DNA, RNA molecules are only made up of one polynucleotide strand (they are single-stranded) Each RNA polynucleotide strand is made up of alternating ribose sugars and phosphate groups linked together, with the nitrogenous bases of each nucleotide projecting out sideways from the single-stranded RNA molecule The sugar-phosphate bonds (between different nucleotides in the same strand) are covalent bonds known as phosphodiester bonds These bonds form what is known as the sugar-phosphate backbone of the RNA polynucleotide strand The phosphodiester bonds link the 5-carbon of one ribose sugar molecule to the phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond to the 3-carbon of the ribose sugar molecule of the next nucleotide in the strand

What is a gene

A gene is a sequence of nucleotides that forms part of a DNA molecule (one DNA molecule contains many genes) This sequence of nucleotide bases (the gene) codes for the production of a specific polypeptide (protein

The genes in DNA molecules, therefore, control protein structure (and as a result, protein function) as they determine the exact sequence in which the amino acids join together when proteins are synthesised in a cell

What are protein molecules made up of

Protein molecules are made up of a series of amino acids bonded together. The shape and behaviour of a protein molecule depends on the exact sequence of these amino acids (the initial sequence of amino acids is known as the primary structure of the protein molecule)

What are triplets

The DNA nucleotide base code found within a gene is a three-letter, or triplet, code. Each sequence of three bases (in other words each triplet of bases) codes for one amino acid These triplets of bases are known as codons (each codon codes for a different amino acid - there are 20 different amino acids that cells use to make up different proteins) For example:
CAG codes for the amino acid valine
TTC codes for the amino acid lysine
GAC codes for the amino acid leucine
CCG codes for the amino acid glycine

What are start and stop codons

Some of these triplets of bases code for start (TAC - methionine) and stop signals. These signals tell the cell where individual genes start and stop. This ensures the cell reads the DNA correctly (the code is non-overlapping) and can produce the correct sequences of amino acids (and therefore the correct protein molecules) that it requires to function properly

What is the genetic code

There are four bases so there are 64 different triplets possible (43), yet there are only 20 amino acids that commonly occur in biological proteins. This results in multiple codons coding for the same amino acids thus the code is said to be degenerate (this can limit the effect of mutations). The genetic code is universal, meaning that almost every organism uses the same code (there are a few rare and minor exceptions). This means that the same codons code for the same amino acids in all living things (meaning that genetic information is transferable between species)

Stages of protein synthesis

Transcription - DNA is transcribed and an mRNA molecule is produced
Translation - mRNA (messenger RNA) is translated and an amino acid sequence is produced

Transcription

This stage of protein synthesis occurs in the nucleus of the cell
Part of a DNA molecule unwinds (the hydrogen bonds between the complementary base pairs break)
This exposes the gene to be transcribed (the gene from which a particular polypeptide will be produced)
A complimentary copy of the code from the gene is made by building a single-stranded nucleic acid molecule known as mRNA (messenger RNA)
Free activated RNA nucleotides pair up (via hydrogen bonds) with their complementary (now exposed) bases on one strand (the template strand) of the 'unzipped' DNA molecule
The sugar-phosphate groups of these RNA nucleotides are then bonded together by the enzyme RNA polymerase to form the sugar-phosphate backbone of the mRNA molecule
When the gene has been transcribed (when the mRNA molecule is complete), the hydrogen bonds between the mRNA and DNA strands break and the double-stranded DNA molecule re-forms
The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope

Translation

This stage of protein synthesis occurs in the cytoplasm of the cell
After leaving the nucleus, the mRNA molecule attaches to a ribosome
In the cytoplasm, there are free molecules of tRNA (transfer RNA)
These tRNA molecules have a triplet of unpaired bases at one end (known as the anticodon) and a region where a specific amino acid can attach at the other
There are at least 20 different tRNA molecules, each with a specific anticodon and specific amino acid binding site
The tRNA molecules bind with their specific amino acids (also in the cytoplasm) and bring them to the mRNA molecule on the ribosome
The triplet of bases (anticodon) on each tRNA molecule pairs with a complementary triplet (codon) on the mRNA molecule
Two tRNA molecules fit onto the ribosome at any one time, bringing the amino acid they are each carrying side by side
A peptide bond is then formed between the two amino acids
This process continues until a 'stop' codon on the mRNA molecule is reached - this acts as a signal for translation to stop and at this point the amino acid chain coded for by the mRNA molecule is completeThis amino acid chain then forms the final polypeptide

What is the DNA template strand

Free activated RNA nucleotides then pair up with the exposed bases on the DNA molecule but only with those bases on one strand of the DNA molecule.This strand of the DNA molecule is called the template strand or the transcribed strand This is the strand that is transcribed to form the mRNA molecule (RNA polymerase bonds the RNA nucleotides together to create the sugar-phosphate backbone of the mRNA molecule) This mRNA molecule will then be translated into an amino acid chain

What is the non-template strand of DNA

The strand of the DNA molecule that is not transcribed is called the non-template strand or the non-transcribed strand

What are exons

The coding sequences are called exons and these are the sequences that will eventually be translated into the amino acids that will form the final polypeptide

What are introns

The non-coding sequences are called introns and are not translated (they do not code for any amino acids)

What happens after transcription(splicing)

When transcription of a gene occurs, both the exons and introns are transcribed
This means the RNA molecule formed (known as the primary transcript) also contains exons and introns As the introns are not to be translated, they must be removed from the RNA molecule The exons are then all fused together to form a continuous RNA molecule called mature mRNA that is ready to be translated This process is sometimes called 'splicing' and is part of the process of post-transcriptional modification (referring to the modification of the RNA molecule after transcription but before translation occurs)

What is a gene mutation

A gene mutation is a change in the sequence of base pairs in a DNA molecule that may result in an altered polypeptide Mutations occur continuously As the DNA base sequence determines the sequence of amino acids that make up a protein, mutations in a gene can sometimes lead to a change in the polypeptide that the gene codes for Most mutations do not alter the polypeptide or only alter it slightly so that its structure or function is not changed (as the genetic code is degenerate)

Insertion of nucleotides

A mutation that occurs when a nucleotide (with a new base) is randomly inserted into the DNA sequence is known as an insertion mutation An insertion mutation changes the amino acid that would have been coded for by the original base triplet, as it creates a new, different triplet of bases Remember - every group of three bases in a DNA sequence codes for an amino acid

An insertion mutation also has a knock-on effect by changing the triplets (groups of three bases) further on in the DNA sequence This is sometimes known as a frameshift mutation This may dramatically change the amino acid sequence produced from this gene and therefore the ability of the polypeptide to function

Deletion of nucleotides

A mutation that occurs when a nucleotide (and therefore its base) is randomly deleted from the DNA sequence Like an insertion mutation, a deletion mutation changes the amino acid that would have been coded for Like an insertion mutation, a deletion mutation also has a knock-on effect by changing the groups of three bases further on in the DNA sequence This is sometimes known as a frameshift mutation This may dramatically change the amino acid sequence produced from this gene and therefore the ability of the polypeptide to function

Substitution of nucleotides

A mutation that occurs when a base in the DNA sequence is randomly swapped for a different base Unlike an insertion or deletion mutation, a substitution mutation will only change the amino acid for the triplet (a group of three bases) in which the mutation occurs; it will not have a knock-on effect

Three forms of substitution of nucleotides

Silent mutations - the mutation does not alter the amino acid sequence of the polypeptide (this is because certain codons may code for the same amino acid as the genetic code is degenerate)
Missense mutations - the mutation alters a single amino acid in the polypeptide chain (sickle cell anaemia is an example of a disease caused by a single substitution mutation changing a single amino acid in the sequence)
Nonsense mutations - the mutation creates a premature stop codon (signal for the cell to stop translation of the mRNA molecule into an amino acid sequence), causing the polypeptide chain produced to be incomplete and therefore affecting the final protein structure and function (cystic fibrosis is an example of a disease caused by a nonsense mutation, although this is not always the only cause)

Effect of gene mutations

Most mutations do not alter the polypeptide or only alter it slightly so that its appearance or function is not changed
However, a small number of mutations code for a significantly altered polypeptide with a different shape This may affect the ability of the protein to perform its function.
For example:If the shape of the active site on an enzyme changes, the substrate may no longer be able to bind to the active site. A structural protein (like collagen) may lose its strength if its shape changes