Flashcards in Genetic Control of Protein Structure and Function Deck (53):
What does the sequence of nucleotides in DNA form?
A code that determines the sequence of amino acids in the proteins of an organism.
Where does the synthesis of protein occur?
What is the genetic code?
The sequence of nucleotide bases on mRNA
Refers to the sequence of three bases (triplet) on mRNA that codes for a single amino acid.
What are the main features of the genetic code?
-Each amino acid in a protein is coded for by a sequence of three nucleotide bases on mRNA.
-A few amino acids have only a single codon.
-The code is a degenerate code.
-Three codons do not code for any amino acids. These are called stop codons
-The code is non overlapping, each base in a sequence is only read once.
-Universal code, the same codon codes for the same amino acid in all organisms.
Most amino acids have more than one codon.
Do not code for any amino acids, mark the end of a polypeptide chain.
Describe the structure of a NUCLEOTIDE in DNA.
-Made from a pentose sugar (5C), a phosphate group and a nitrogenous base.
-Sugar is a deoxyribose sugar.
-Each nucleotide has the same sugar and phosphate. The base can vary though.
-4 possible bases - Adenine, thymine, guanine and cytosine.
Describe double helix structure of DNA.
-Nucleotides join up between the phosphate group of one nucleotide and the sugar of another, creating a sugar-phosphate background.
-Two DNA polynucleotide strands join together by hydrogen bonding between the bases.
-Each base can only join with a specific partner- specific base pairing.
-The two strands wind up to form a double helix.
Describe ribonucleic acid (RNA)
RNA is a polymer made up of repeating mononucleotide sub-units. It forms a single strand of which each nucleotide is made up of:
-Pentose sugar ribose
-One of the organic bases adenine (A), guanine (G), cytosine (C) and uracil (U).
-A phosphate group
Why is DNA copied into RNA?
-DNA molecules found in nucleus of the cell, but the organelles for protein synthesis (ribosomes) are found in the cytoplasm.
-DNA is too large to fit through nuclear pores, so a section is copied into RNA (TRANSCRIPTION)
-The RNA leaves the nucleus and joins with a ribosome in the cytoplasm, where it can be used to synthesise a protein. (TRANSLATION)
Single polynucleotide strand. In mRNA, groups of three adjacent bases are usually called codons (otherwise triplets or base triplets). mRNA is made in the nucleus during transcription. Mirror copy of one part of DNA strand.
Describe function of mRNA.
It carries the genetic code from the DNA into the nucleus to the cytoplasm, where it's used to make a protein during translation. Leaves the nucleus via pores in the nuclear envelope and enters the cytoplasm, where it associates with ribosomes. There it acts as a template for whihc proteins are built.
Why is the structure of mRNA suited to its function?
Possesses the correct sequences of the many triplets of organic bases that code for specific polypeptides. Also easily broken down and therefore exists only while it is needed to manufacture a given protein.
Describe the structure of tRNA.
A single polynucleotide strand that's folded into a clover 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. They also have an amino acid binding site at the other end. Made up of around 80 nucleotides.
Describe the function of tRNA.
Found in the cytoplasm where it's involved in translation. It carries the amino acids that are used to make proteins to the ribosomes.
During protein synthesis, the anticodon pairs with the three complementary organic bases that make up the triplet of bases (codon) on mRNA.
How is the tRNA structure related to function?
The tRNA structure, with its end chain for attaching amino acids and its anticodon for pairing with the codon of the mRNA, is structurally suited to its role of lining up amino acids on the mRNA template during protein synthesis.
How does the quantity of DNA/mRNA/tRNA vary in different cells?
DNA- Constant for all cells
mRNA- Quantity varies from cell to cell and with level of metabolic activity.
tRNA- Quantity varies from cell to cell and with level of metabolic activity.
How stable are DNA/mRNA/tRNA?
DNA- Chemically v. stable
mRNA- Chemically unstable- easily broken down.
tRNA- Chemically more stable the mRNA but less than tRNA.
What is transcription?
The process of making pre-mRNA using part of the DNA as a template.
1. Transcription starts when RNA polymerase (an enzyme) attaches to the DNA double-helix at the beginning of a gene.
2. The hydrogen bonds between the two DNA strands in the gene break, separating the strands, and the DNA molecule uncoils at that point.
3. One of the strands is then used as a template to make an mRNA copy.
4. The RNA polymerase lines up free RNA nucleotides alongside the template strand. Specific base pairing means that the mRNA strand ends up being a complementary copy of the DNA template strand (except T being replaced with U.
5. Once the RNA nucleotides have paired up with their specific bases on the DNA strand they're joined together, forming mRNA molecule.
6. The RNA polymerase moves along the DNA, separating the strands and assembling the mRNA strand.
7. The hydrogen bonds between the uncoiled strands of DNA re-form once the RNA polymerase has passed by the strands coil back into a double-helix.
8. When RNA polymerase reaches a particular sequence of DNA called a stop signal, it stops making RNA and detaches from DNA.
9. The mRNA moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm, where the next stage of protein synthesis takes place.
Code for protons
Do not code for protons.
Why do introns need to be removed?
Interfere with the synthesis of a polypeptide.
In pre-mRNA intervening non-functional introns are removed and the functional exons are joined together.
Once the introns have been removed, the remaining exons can be rejoined in a variety of different combinations.
This means that a single section of DNA (gene) can code for up to a dozen different proteins.
What can effect the splicing of pre-mRNA and what does this cause?
Mutations can affect the splicing of pre-mRNA. Certain disorders such as Alzheimer's disease, are the result of splicing failures that lead to a non-functional polypeptides being made.
What is translation?
Occurs at the ribosome in the cytoplasm. During translation, amino acids are joined together to make a polypeptide chain (protein), following the sequence of codons carried by the mRNA.
1. The mRNA attaches itself to a ribosome and transfer RNA (tRNA) molecules carry amino acids to the ribosome.
2. A tRNA molecule, with an anticodon that's complementary to the first codon on the mRNA, attaches itself to the mRNA by specific base pairing.
3. A second tRNA molecule attaches itself to the next codon on the mRNA in the same way.
4. The two amino acids attached to the tRNA molecules are joined by a peptide bond (ATP and an enzyme). The first tRNA molecule moves away, leaving its amino acid behind.
The ribosome moves along the mRNA, bringing together two tRNA molecules at any one time.
5. A third tRNA molecule binds to the next codon on the mRNA. It's amino acid binds to the first two and the second tRNA molecule moves away.
6. This process continues, producing a chain of linked amino acids (a polypeptide chain), until there's a stop signal on the mRNA molecule.
7. The polypeptide chain (protein) moves away from the ribosome and translation is complete.
8. Up to 50 ribosomes can pass immediately behind the first, so that many identical polypeptides can be assembled simultaneously.
How is a functional protein made?
Sometimes a single polypeptide chain is a functional protein. Often a number of polypeptides are linked together to give a functional protein (quarternary function).
What happens to the polypeptide next depends upon the protein being made, usually involves the following:
-The polypeptide is coiled or folded, producing its secondary structure.
-The secondary structure is folded, producing a tertiary structure.
- Different polypeptide chains, along with any non-protein groups, are linked to form a quarternary structure.
Any change to the quantity or the structure of the DNA of an organism.
When are mutations passed onto the next generation?
Mutations arising in body cells are not passed on to the next generation. Mutations occurring during the formation of gametes may be inherited, often producing a sudden and distinct change between individuals.
Variation shown when the characteristics of organisms fall into distinct categories e.g. blood groups
Substitution of bases mutation
The type of gene mutation in which a nucleotide in a DNA molecule is replaced by another nucleotide that has a different base is known as a substitution.
Chemicals called base analogs can substitute for a base during DNA replication, changing the base sequence in the new DNA.
What are the 3 possible consequences of a base being substituted?
-A nonsense mutation
-A mis-sense mutation
-A silent mutation
Describe a nonsense mutation.
Occurs if the base change results in the formation of one of the three stop codons that mark the end of a polypeptide chain. For example GTC, if the first base, guanine is replaced by adenine, then GTC becomes ATC. The triplet ATC is transcribed as UAG in mRNA. UAG is one of the three stop codons. As a result the production of the polypeptide would be stopped prematurely. The final protein would almost certainly be significantly different and the protein could not perform its normal function.
Describe a mis-sense mutation.
Arises when the base change results in a different amino acid being coded for. For example, if the final base, cytosine, is replaced by guanine, then GTC becomes GTG. GTG is one of the DNA triplet codes for the amino acid histidine and this then replaces the original amino acid glutamine. The polypeptide produced will differ by one amino acid. The significance of this depends on the precise role of the original amino acid. If it is important in forming bonds that determine the tertiary structure of the final protein, then the replacement amino acid may not form the same bonds. The protein may then be a different shape and therefore not function properly. For example, if the protein is an enzyme, its active site may no longer fit the substrate and it will no longer catalyse the reaction.
Describe a silent mutation.
Occurs when the substituted base, although different, still codes for the same amino acid as before. This is due to the degenerate nature of the genetic code, in which most amino acids have more than one codon. For instance, if the third base in our example is replaced by thymine, the GTC becomes GTT. However, as both DNA triplets code for glutamine, there is no change in the polypeptide produces and so the mutation will have no effect.
Describe the deletion of bases.
A gene mutation by deletion arises when a nucleotide is lost from the normal DNA sequence. Usually the amino acid sequence of the polypeptide is entirely different. This is because the genetic code is read in units of three bases. One deleted nucleotide creates what is known as a "frame shift" because the reading frame that contains each three letters of the code has been shifted to the left by one letter. The gene is now read in the wrong three base groups and the genetic message is altered. One deleted base near the end of the sequence is likely to have a smaller impact but can still have consequences.
Gene mutation can occur spontaneously during DNA replication, spontaneous mutations are permanent changes in DNA that occur without any outside influence.
What is the mutation rate?
Despite being random occurrences, mutations occur with a set frequency. Varies between organisms but is typically around one or two mutations per 100000 gametes per generation.
Give two examples of mutagens.
-High energy radiation that can disrupt the DNA molecule.
-Chemicals that alter the DNA structure or interfere with transcription.
Any agent that induces a mutation
ADV/DISADV of mutations.
ADV- They can produce the genetic diversity necessary for natural selection and speciation.
DISADV- Often produce an organism that is less well suited to its environment.
Mutations that occur in body cells rather than in gametes can disrupt normal cellular activities, such as cell division.
What is cell division controlled by?
What two genes control cell division?
-PROTO-ONCOGENES that stimulate cell division
-TUMOUR SUPPRESSOR GENES that slow down cell division.
What is the role of proto-oncogenes
Stimulate cell division. In a normal cell growth factors attach to a receptor protein on the cell surface membrane and, via relay protons in the cytoplasm, switch on the genes necessary for DNA replication.
What can a gene mutation do to a proto-oncogene?
Turn into oncogenes.
How do oncogenes affect cell division?
-The receptor protein on the cell-surface membrane can be permanently activated, so that cell division is switched on even in the absence of growth factors.
-The oncogene may code for a growth factor that is then produced in excessive amounts, again stimulating excessive cell division.
The result is that cell divides too rapidly and a tumour or cancer develops.
What is the role of tumour suppressor genes?
Have the opposite role to proto-oncogenes in the cell, that is, they inhibit cell division. A normal tumour suppressor gene will therefore maintain normal rates of cell division and prevent the formation of tumours.
What happens if a tumour suppressor gene mutates?
It is inactivated. It stops inhibiting cell division, which therefore increases. The mutant cells so formed are usually structurally and functionally different from normal cells. Most mutated cells die. However, any that survive are capable of making clones themselves and forming tumours. Not all tumours are harmful (malignant); some are harmful (benign).
Types of mutagenic examples. (Examples)
-Certain chemicals can remove groups from nucleotide bases. Nitrous acid can remove an -NH2 group from cytosine in DNA, changing it into uracil.
-Other groups can add groups to nucleotides. Benxpyrene is a chemical found in tobacco smoke. It adds a large group to guanine that makes it unable to pair with cytosine. When DNA polymerase reaches the affected guanine it inserts any of the other bases.
-Ionising radiation, such as X-rays, can produce highly reactive agents, called free radicals, in cells. These free radicals can alter the shape of bases in DNA so that DNA polymerase can no longer act on them.
- UV radiation from the Sun or tanning lamps affects thymine in DNA, causing it to form bonds with the nucleotides on other side of it. Seriously disrupts DNA replication.
What is a chemical that can substitute a base?
5-bromouracil is a base analog that can substitute for thymine. It can pair with guanine (instead of adenine), causing a substitution mutation in new DNA.