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What is a gene?
A length of DNA that codes for one (or more) polypeptides.
Genes code for proteins/polypeptides, but why is it also involved in synthesis of all non-protein molecules found in cells?
Because genes code for enzymes, they are involved in the control of all metabolic pathways, including sinthesis of all non-protein molecules.
What is the meaning of the term "genetic code"?
- The sequence of nucleotide bases on a gene that provides a code which has instructions for the construction of a polypeptide.
- The three-letter (or triplet) code by which information is contained in a DNA molecule; a group of three bases specifies a particular amino acid to be added to a growing polypeptide chain.
How many different triplet sequences can there be? And how many amino acids are used for protein synthesis?
- As there are 4 bases arranged in groups of 3... 43 = 64 combinations.
- There are only 20 amino acids used for protein synthesis, so this is more than enough.
All amino acids except methionine have more than one code. So how else can we describe the genetic code? Also 2 more things to remember about genetic codes:
- A degenerate code - more than one base triplet code for one amino acid. (helps to reduce effects of point mutations)
- Remember: Some codes don't correspond to an amino acid but indicate 'stop' - end of polypeptide chain.
- Remember 2: genetic codes are widespread but no universal. So some triplet codes code fot he same amino acid in any organism, but some don't.
What is a genome?
- The genome of an organism is the entire DNA sequence of that organism.
- (The human genome consists of about 3 billion nucleotide base pairs).
What are the two processes involved in protein synthesis?
Outline the process of transcription.
- 1. A gene to be transcribed unwinds and an enzyme called DNA helicase "unzips" gene by breaking hydrogen bonds between bases.
- 2. Free RNA nucleotides bind with exposed complementary bases on the template strand. (There is no base T's in RNA so T is replaced by U - uracil)
- 3. Condensation reactions occur between adjacent RNA nucleotides. These reactions are catalysed by RNA polymerase. This enzyme also checks that bases have paired up correctly. 4. When the end is reached, the complete mRNA molecule breaks away. The end is signalled by particular triplet of bases that codes 'stop here' rather than coding for another amino acid.
- 5. mRNA molecule passes through nuclear pore into the cytoplasm and arrives at a ribosome.
Explain the difference between the two different strands of DNA in transcription.
- Template strand: the strand that the free RNA nucleotides bind to.
- Coding strand: is the strand that the mRNA is the exact copy of, and hence the strand that codes for the amino acids in the cytoplasm.
What name is given to triplets of nucleotide bases on the mRNA?
Where is RNA made and what is it made up of?
Also briefly explain how its shape is adapted to its function.
- Assembled in the nucleolus of eukaryotic cells
- From ribosomal RNA (rRNA) and protein.
- Ribosome made up of 2 subunits and there is a groove into which length of mRNA can move along. This allows it to read genetic code and assemble amino acids in correct order to make functioning protein.
Why is the sequence of amino acids in a protein important?
- It forms primary structure of protein, and this determines tertiary structure.
- Tertiary structure is what allows protein to function, so need amino acid sequence to have correct hydrophobic interactions between R groups of amino acids or hydrogen or ionic bonds, for protein to function.
Describe the structure of Transfer RNA (tRNA) that enables it to fulfill its function. (Also, where is it made and where is it found?)
- Lengths of RNA that fold into haripin shapes.
- Has an amino acid binding site at one end (where there are 3 exposed bases where the amino acid can bind).
- At other end, there are 3 unpaired nucleotide bases, known as an anticodon. This binds to its complementary codon in the mRNA.
- Made in nucleus and found in cytoplasm.
Outline the process of translation.
- 1. mRNA held in cleft in the ribosome, so that 2 codons (6 bases) are exposed.
- 2. A tRNA with anticodon that is complementary to the first codon (which usually is always codon AUG. tRNA brings methionine) binds with it (maybe using energy and enzyme - CHECK).
- 3. A second tRNA, bearing different amino acid, binds to second exposed codon with its complementary anticodon.
- 4. Peptide bond forms between the two adjacent amoni acid (catalysed by enzyme present in ribosome).
- 5. Ribosome now moves along mRNA, reading next codon. A third tRNA brings amino acid, and peptide bond form between it and the dipeptide. Meanwhile the first tRNA breaks away, and now available to bring another of its amino acids.
- 6. The whole polypeptide chain gradually built up until a stop codon is reached.
What then activates the complete proteins and how?
Cyclic AMP (cAMP) activates proteins by changing their 3D shape so that their shape is a better fit to their complementary molecules.
Just quickly, what is protein synthesis like in prokaryotes?
In prokaryotes the DNA is not inside nucleus, so translation begins as soon as some mRNA has been made.
What is the binding site that is not the active site in an enzyme called?
What is a mutation?
- A random change in the amount of, or arrangement of, the genetic material in the cell.
- In our case where we only study DNA mutations - mutations cause changes to the sequence of nucleotides in DNA molecules.
What are the two types of mutations?
- DNA (gene) mutations: changes to genes due to changes in nucleotide base sequences. [This is the one we need to know about]
- Chromosome mutations: involve changes to strcuture of chromosomes and/or to their number.
What can cause mutations?
- During DNA replication
- Certain substances (mutagens) - such as tar in tobacco, UV light, X-rays and gamma rays.
Mutations can happen when DNA is replicated before nuclear division, by either mitosis or meiosis. Explain the difference in the two mutations.
- Mutations associated with mitosis are somatic and are not passed on to offspring.(But may contribute to ageing process or lead to cancer).
- Mutations associated with meiosis and gamete formation can be inherited.
There are 2 main classes of DNA mutations. What are they?
- Point mutations: in which one base pair replaces another - also called substitutions.
- Insertion/deletion mutations: in which one or more nucleotide pairs are inserted or deleted from a length of DNA. These cause a frameshift.
Which class of mutation usually has more effect? Why?
- Deletion/insertion mutations cause greater changes to the resulting protein.Deletion involves loss of a base pair from DNA, so it produces a frameshift. As base pairs are read as triplets, if one pair is lost or added, the whole sequence is read differently.
- Point mutations, however, changes a pair of bases, and, as each amino acid is degenerate (each amino acid coded for by more than one triplet), it quite often has no effect (silent mutation). Although obviously can have great effects too.
List 3 diseases and what mutations it is caused by.
- Cystic fibrosis: often caused by deletion of a triplet of base pairs - deleting one whole amino acid.
- Sickle-cell anaemia: point mutation
- Huntington's disease: expanded triple nucleotide repeat. (symtoms include dementia and loss of motor control)
How are tumours/cancer caused by mutations?
Growth-promoting genes - called protooncogenes can be changed to oncogenes by point mutation, altering ability of protoncogene to be switched off - therefore remains permanently switched on - unregulated cell division - tumour.
If a gene is altered by a change to its __ sequence, it becomes another version of the same gene, and is called an __ of the gene.
What is an allele?
An alternative version of a gene. It is still at the same locus on the chromosome and codes for the same polypeptide but the alteration to the DNA base sequence may alter the protein's structure.
Give the ways in which mutation can have neutral effect on the organism.
- Mutation is in a non-coding region of the DNA
- It is a silent mutation (although triplet changed, it still codes for same amino acid) [Both of the above do not change the organism].Even if mutation does cause change in the structure of protein and hence different characteristic, if the changed characteristic gives no particular advantage or disadvantage to organism, then the effect is neutral. (eg. different types of ear lobes)
The same mutation can sometimes be beneficial or harmful depending on the environment. Give an example.
- The pigment melanin in the skin can protect a person from harmful effects of UV light, but lessens the amount of vitamin D synthesised from sunlight.
- In countries such as Africa, it is beneficial to have melenin. However, in climates with less sunlight, a mutation changing the skin colour (more pale - so less pigment), can be advantageous because it increases the greatly needed vitamin D synthesis. (so darker skin might be harmful in these environments with little sunlight, so less vitamin D).
Ron, often consider natural selection as a mechanism for evolution when dealing with questions about genetic mutations being beneficial or harmful, considering climate, competition, adaptations, survival etc.
List the different names for the effects of mutations. (4)
- Missense: mutation causes a change in an amino acid (CHECK THESE)
- Nonsense: mutation changes an amino acid into a stop code, so polypeptide it truncated.
- Silent mutation: change in base triplet does not affect the protein produced because it still codes for same amino acid.
- Frameshift: during deletion/insertion mutations when the whole sequence after the mutation is shifted and altered and read differently.