4. Genetic info, variation & relationships between organisms

• What is a gene? What does it determine and how? What are the genes responsible for in an organism? What is the position of a gene called?

  A gene is a sequence of nucleotides in DNA or RNA that encodes the information for a synthesis of a gene product, either functional RNA or protein. The sequence of the bases is what determines the coded information, therefore the genes determine the proteins (including enzymes).

  Enzymes are vital in controlling reactions of an organisms development so genes are also responsible of this development. The position of a gene on a DNA molecule is called a locus.
• How did the scientists discover there must be at least three bases within a codon/base triplet?

  The genetic code:

  Scientists reasoned there must be at leats three bases in order to code information:

  - Only 20 different amino acids regularly occur in proteins

  - Each amino acid must have its own code of bases on the DNA

  - Only four different bases (A, G, C and T) are present in DNA

  - Three bases is required in order to code for 20 different amino acids. Three bases can produce 64 different codes.
• How many triplets code for amino acids? What type of code is it?

  Some amino acids are coded for by only a single triplet. The remaining amino acids are coded for by two or six triplets each.

  The code for amino acids is the degenerate code because most amino acids are coded for by more than one triplet.
• What are some features of the genetic code?(2)

  The code is non overlapping so each base is only read once. 6 bases would be read as the first three and then second three.

  The code is universal - with a few minor exceptions each triplet codes for the same amino acids in all organisms. (Evidence for evolution)

  The code is degenerate - many triplets code for the same amino acid because there are 64 different triplet combinations but only 20 naturally ocurring amino acids
• How is a strand read? What is the start and end of the coding region?

  Triplets are always read in one particular direction along the DNA strand.

  The start of a coding region is always the same triplet, coding for methionine.

  There are a certain three triplets that do not code for any amino acid, instead they are stop codes marking the end of the polypeptide.
• Which areas of DNA do not code for polypeptides? What form can these regions be in?

  Much of the DNA in eukaryotes does not code for polypeptides and this is non-coding DNA. It can be in the form of multiple repeats between genes (tandem repeats) or even within the genes there are introns which are non-coding sequences in between exons (coding sequences).
• What are tandem repeats? Where are they found? How are they used?

  Tandem repeats are repeats in the non coding regions of DNA.

  - Found in genomes and the number of repeats varies (number of individuals have the same pattern of repeats)

  - Can compare Tandem repeats for DNA profiling in criminology and paternity tests

  - Identical twins will have the same tandem repeats
• What are the features of DNA in prokaryotes?

  In prokaryotic cells, the DNA molecules are shorter, circular and aren't associated with protein molecules. They form one circular chromosome.
• What are the features of DNA in the organelles of eukaryotes?

  In eukaryotic cells such as mitochondria and chloroplasts the cells have their own DNA - similar to prokaryotic DNA because it is circular and shorter than DNA molecules in the nucleus. They are also not associated with histones.
• What are the features of DNA in eukaryotes?

  In eukaryotic cells, DNA is linear and very long so it must be wound around proteins called histones which support the DNA. The DNA-histone complex is the coiled very tightly, folded into loops which pack together to make a compact chromosome. It is found in the nucleus.
• How is the structure of DNA adapted to its function? (6)

  1. The sugar-phosphate backbone on the outside of the molecule makes the molecule more stable. It protects the bases (on the inside) reducing the risk of being damaged and altering the sequence

  2. DNA coils up into a double helix, wraps itself around histones and coils once more so that it's more compact, so lots of information is stored in a small place

  3. The sequence of bases allows it to carry coded information for making proteins

  4. It is very long so it stores lots of information

  5. Complementary base pairing allows the molecule to replicate itself accurately, reducing mutations

  6. The bases are held together by weak hydrogen bonds allowing the molecule to 'unzip' (separate) easily to replicate
• What is a cells genome and proteome?

  Genome - the complete set of genes in the cell

  Proteome - full range of proteins that the cell can be produced (depending on the genome)
• What is a homologous pair? In what type of organism does it occur in?

  In sexually produced organisms, the mother and father each contribute one complete set of chromosomes to the offspring. This means in each pair of chromosomes one is provided from the mother and one is provided by the father.

  These are homologous pairs and the total number of chromosomes is the diploid number (46 in humans).

  A homologous pair always carries the same genes but not necessarily the same alleles in the genes. They are the same size.
• What is an allele? How do alleles differ and what are the similarities?

  A gene can exist in more than one form - alleles. The order of bases in each allele is slightly different, so although they code for a similar polypeptide with a slightly different amino acid sequence. Alleles code for the same gene however the genes may be different versions.

  An allele therefore is one of the forms of a gene (there are at least two for each gene).
• How can mutations arise? What affect does this have?

  Mutations can occur when the base sequence is changed which can change the sequence of amino, acids slightly altering the polypeptide so that a new allele is produced. This in turn effects how the protein produced folds - the tertiary structure - giving it a different shape which has the potential to alter the function.
• What is protein synthesis? What are the two stages

  Protein synthesis is the production of proteins from the information stored within the cell's DNA. There are two stages:

  - Transcription - this is where DNA code is copied in the form of mRNA. It occurs in the nucleus

  - Translation - the mRNA is then joined to a ribosome and the code synthesises a polypeptide chain from amino acids.
• What is RNA? What does each nucleotide have?

  RNA is a single polynucleotide strand containing Uracil instead of Thymine. Like DNA it is a polymer made up of mononucleotide sub units and each unit has:

  - The pentose sugar ribose (DNA has a ribose sugar

  - An organic base including either adenine, guanine, cytosine and uracil

  - A phosphate group
• What is mRNA? What is the structure? How is it adapted to carry information?

  mRNA is a form of RNA made during transcription and carries genetic code from the DNA to the ribosomes so it can be used as a template to make the proteins during translation. mRNA is a single polynucleotide strand.

  It possesses information in groups of three adjacent bases referred to as codons, triplets or base triplets which determine the amino acid sequence of the polypeptide. Each nucleotide is a base a pentose sugar and a phosphate group.

  Its single strand makes it small enough to leave the nucleus via the nuclear pores.
• What is tRNA? What is it's function? How is it adapted?

  tRNA is a form of RNA involved in translation, carrying the amino acids used to make proteins to the ribosomes.

  tRNA is a single polynucleotide strand folded into a clover shape. Hydrogen bonds between specific, complimentary base pairs hold the molecule together. Every tRNA molecule has a specific sequence of three bases at one end (middle 'clover' lead) called the anticodon.

  The other side has an amino acid binding site, so tRNA is specific to one amino acid (depending on the anticodon).

  
• How is the structure of tRNA important during translation:

  The tRNA line up amino acids on the mRNA template during protein synthesis, using the complimentary base pairing between the codon and the anticodon and the end attachment site joined to the amino acid.

  tRNA is specific to one amino acid which ensures that the corresponding amino acid (to the mRNA codon) is joined to the polypeptide chain.
• What is transcription? How are proteins synthesised (what do they use)? Where does it take place in prokaryotes vs eukaryotes?

  Proteins are synthesised using the instructions in DNA so in transcription, an mRNA copy of the DNA is made. In eukaryotic cells this takes place in the nucleus. In prokaryotes transcription takes place in the cytoplasm because they don't have a nucleus.
• How does RNA polymerase attach to DNA? What effect does this have? What other enzyme is involved?

  RNA polymerase attaches to the DNA:

  RNA polymerase attaches to the DNA double-helix at the beginning of the gene. The hydrogen bonds between the two DNA strands in the gene are broken by a DNA helicase attached to RNA polymerase. This separates the strands and the DNA molecule uncoils exposing the gene's bases that code for the protein.

  One of the strands will then be used as a template for the mRNA copy.
• How is mRNA formed? What does RNA polymerase lines up free RNA nucleotides? How are they joined?

  Complementary mRNA is formed:

  The RNA polymerase lines up free RNA nucleotides alongside the exposed bases on the template strand. The free nucleotides are attracted to the exposed bases and specific complementary base pairing means the mRNA strand becomes a complementary copy of the DNA template strand (with T replaced by U).

  When RNA nucleotides have paired up with specific DNA bases they are joined by RNA polymerase forming the mRNA polymer strand.
• What does the RNA polymerase do as it moves down the strand?

  RNA polymerase moves down the DNA strand:

  The RNA polymerase moves down the DNA assembling the mRNA strand. The hydrogen bonds between the uncoiled strands of DNA reform once the RNA polymerase has passed it and the DNA coils back into a double helix
• When does RNA polymerase stop? What happens after?

  RNA polymerase reaches stop signal:

  When RNA polymerase reaches a particular sequence of DNA - the stop signal it stops making mRNA and detaches from the DNA. In eukaryotes, before mRNA can leave the nucleus, the pre-mRNA must be spliced to form mRNA. It then moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm so the next stage of protein synthesis can take place.
• What must occur in eukaryotes before the mRNA can leave the nucleus

  Before translation can occur in eukaryotes, splicing must occur. The introns and exons in mRNA are copied during transcription so at this stage it is pre-mRNA. Splicing occurs in the nucleus.

  Splicing removes the introns from the pre-mRNA. In prokaryotes this stage is unnecessary because there are no introns in their DNA.
• What is translation? What occurs during translation?

  Translation is in the second stage of protein synthesis. In both eukaryotes and prokaryotes translation occurs at the ribosomes in the cytoplasm. During which, amino acids are joined together to form a polypeptide chain that can fold into the protein, based on the sequence of codons in mRNA.
• What occurs when a second and third tRNA molecule attaches to the next codon? How are they joined?

  A second tRNA molecule attaches itself to the next codon on the mRNA. The two amino acids on the tRNA are joined by a peptide bond using an enzyme and ATP - hydrolysed to provide the energy required.

  When a third tRNA molecule attaches to the next codon and forms a peptide bond with the second amino acid the first tRNA is released from the amino acid.
• How does the mRNA attach to the ribosome? What does tRNA do next?

  First mRNA attaches to a ribosome via the start codon at the end of the mRNA. Transfer RNA molecules carry amino acids to it (the amino acids are bonded to the attachment site using ATP). A tRNA molecule attaches itself to the mRNA by complementary base pairing between the tRNA's anticodon and the mRNA codon.
• How does the process end?

  This process continues until it reaches a stop signal on the mRNA molecule. Finally the polypeptide chain is complete and the ribosome, mRNA and last tRNA molecule separate.
• How does the DNA sequence of bases determine the protein created?

  The DNA sequence of bases that make up the gene for the protein determine the sequence of codons on mRNA which determine the order in which the tRNA molecules carrying a specific amino acid line up. This means the DNA sequence of bases is responsible for the protein created as the 3D structure is determined by the order of amino acids.
• What is genetic mutation? What does a change result in? In what way can the mutations occur?

  Gene mutations involve a change in the DNA base sequence of chromosomes. If a mutation occurs in a gene the sequence of amino acids in a polypeptide will be change - changing the overall protein structure.

  Errors can occur by substitution (one base substituted of another) or deletion (one base is deleted).
• What effect does genetic mutation caused by substitution have?

  When the genetic mutation is caused by substitution of a base there are little to no changes. Often this will result in a different amino acid because a change to the base may affect which amino acid the codon codes for. This means that one amino acid in the polypeptide chain will be altered however the rest of the chain remains the same.
• Why is there sometimes no affect on the amino acid sequence when a base is substituted?

  Due to the degenerate nature of the genetic code, multiple base triplets can code for the same amino acid which means that some substitution of bases will still code for the same amino acid. This means the protein will not be affected.
• What increase the rate of mutations? What are some examples?

  Mutations occur spontaneously - for example when DNA is misread during replication. There are, however, some things which can increase the rate of mutations - mutagenic agents.

  Some examples of a mutagenic agent is UV radiation, ionising radiation, certain chemicals and some viruses.
• What effect do base deletions have on amino acid sequence?

  Deletions will always lead to a change in amino acid sequence because it changes the number of bases present. This shifts the base triplets by one now read differently. All of the base triplets following the codon of the deleted base will be altered so almost all of them will then code for different amino acids, completely changing the structure therefore the protein can no longer perform its function
• What affect do mutagenic agents have on risk of mutations? What is unknown?

  There is always a a risk of genetic mutations but this risk is generally low. The probability is increase by exposure to mutagenic agents. The exact time or place of the DNA mutation is unknown but the likelihood of a mutation occurring somewhere is increased.
• What are the two forms of chromosome mutations?

  - Polyploidy (A change in a whole set of chromosomes)

  - Non disjunction (changes in the number of individual chromosomes)
• What type of chromosome mutation is polyploidy?

  Changes in a whole set of chromosomes - this occurs when organisms have three or more chromosomes instead a pair of two. This is polyploidy
• What is nondisjunction? What does it result in? How is it caused? When does it occur?

  Non disjunction (no separation) - changes in the number of individual chromosomes. Sometimes individual homologous pairs of chromosomes do not separate in the early stages of meiosis. This results in one more or one less chromosome. Then after fertilisation with another gamete to form a zygote the offspring will have more or fewer chromosomes in all body cells. This causes hereditary conditions such as down syndrome.

  This can cause polyploidy (having extra chromosomes after fertilisation with another gamete)