DNA and the Genome Flashcards
(32 cards)
Prokaryotes vs Eukaryotes
• Prokaryotes:
- circular chromosomes
- can also contain plasmids
- no nucleus
• Eukaryotes:
- contains membrane bound organelles (eg. mitochondria, chloroplasts)
- has nucleus
- linear chromosomes
- strings of DNA wrapped around proteins (histones) are present in the nucleus
DNA structure
- DNA = deoxyribonucleic acid
- Found in the nucleus
- Double stranded helix shape
- Made up of nucleotides:
- phosphate covalently bonded to a deoxyribose sugar which has a weak hydrogen bond to a base
- base can be either adenine, thymine, guanine or cytosine
- Base pair rule: A always pairs with T, and G always pairs with C
- DNA strands run anti parallel to one another
DNA replication
- takes place prior to cell division
- semi-conservative process: half of the new DNA comes from the old DNA
- Enzyme control process
- Requirements: DNA template, nucleotides, ATP, enzymes (helicase, ligase, DNA polymerase)
- Process:
- Helicase uncoils DNA by breaking hydrogen between bases, causing DNA strands to separate
- Y-shaped replication fork is created
- On the leading strand a primer binds to the complimentary sequence on DNA (annealing) and DNA polymerase adds nucleotides to 3’ end continuously
- On the lagging strand a primer binds to the DNA once it is exposed and DNA polymerase adds nucleotides to the 3’ end which creates Okazaki fragments. As more of the DNA strand is exposed more primers are added and DNA polymerase extends the new strand so it meets the previous fragment and is joined together by ligase.
- This results in two identical strands being formed (ie. the DNA stand is replicated)
DNA vs RNA
• DNA:
- deoxyribonucleic acid
- double stranded molecule
- DNA nucleotide consists of a phosphate, deoxyribose sugar and a base. The bases can be either adenine, thymine, guanine or cytosine.
• RNA:
- ribonucleic acid
- single stranded molecule
- RNA nucleotide consists of a phosphate, ribose sugar and a base. The bases can be either adenine, uracil, guanine or cytosine.
Types of RNA
• mRNA:
- messenger RNA
- the sequence of bases of the DNA is transcribed into mRNA. mRNA then carried the information to the ribosome. A sequence of three bases on a mRNA code for a particular amino acid is known as a codon.
• tRNA
- transfer RNA
- Transfers amino acids from the cytoplasm to the ribosome. The sequence of three bases on the tRNA is called an anticodon, and is complimentary to the mRNA codon.
• rRNA
- ribosomal RNA
- Is bound to structural proteins to form a ribosome
Protein synthesis
• Transcription
- Occurs in the nucleus
- Information from the DNA molecule is copied into an mRNA molecule
- Helicase uncoils DNA molecule and breaks the hydrogen bonds that hold the bases together
- RNA polymerase helps RNA nucleotides to pair up with complimentary DNA nucleotides, forming the mRNA strand (aka. primary transcript)
- RNA splicing occurs -> when introns (non-coding regions) are removed an the exons (coding regions) join together to form the mature mRNA transcript
• Translation
- mRNA attaches to a ribosome
- tRNA picks up specific amino acid from cytoplasm and carried it to the ribosome
- the anticodon on the tRNA molecule lines up with the complimentary codon on the mRNA
- peptide bonds the form between the amino acids creating a polypeptide chain (protein) until a stop codon is reached and released from the ribosome
- the mRNA and tRNA are then free to be reused
PCR
- PCR = polymerase chain reaction
- used to amplify (make more copies of) a specific section of DNA
- Requirements: DNA, DNA polymerase (must be able to withstand high temperatures, eg.taq-polymerase), primers, nucleotides
- Method:
- DNA is heated (around 90 degrees celsius) to separate strands in order to get single stranded DNA
- Temperature is lowered and primers bind (anneal) so DNA polymerase will synthesise new DNA strand
- This process is repeated to mass produce sections of DNA
Types of proteins
• Fibrous protein
- formed by polypeptide helixes aligning parallel to each other and forming cross links between the polypeptides
- rope like structure (regular)
- structural protein
- eg. Collagen (found in tendons, ligaments),, keratin (found in hair)
• Globular protein
- consists of several folded polypeptide chains
- spherical shape (folded)
- eg. Antibodies, enzymes, hormones
• Conjugated
- is a globular protein with a extra non-protein component
- eg. Haemoglobin (carries oxygen in blood, extra component is iron),, chlorophyll (has green pigment, absorbs sunlight for photosynthesis, extra component is magnesium)
Protein shapes
• Primary structure
- amino acid chain held together by strong peptide bonds
• Secondary structure
- weak hydrogen bonds form between certain amino acids in a polypeptide chain causing it to fold into an alpha-helix or a beta-pleated sheet
• Tertiary structure
- strong bonds (such as disulphide S-S bridges) form between certain groups of amino acids causing further folding and determines its function
• Quaternary structure
- when polypeptide chains link together (each chain forms a domain) and sometimes other non-protein elements are added to create a large, complex protein
Genome
- The genome is all the hereditary material encoded in DNA within an organism. (Genome = genes + non-coding sections)
- DNA can be either non-coding or coding
- Non-coding DNA (function: unknown/ regulate transcription/ transcription of non-translated RNA/ involved in expression) can be transcribed to form RNA.
- Coding DNA (function: aka. genes, codes for proteins) —[transcribed]-> primary transcript, —[alternative RNA splicing]-> mature transcript, —[translated]-> proteins, —[post translational modification]-> altered protein.
Gene expression
- Genes are DNA sequences that code for particular proteins. Alleles are different forms of the gene. One gene can code for many proteins, due to different methods of gene expression:
- Alternative RNA splicing: the primary mRNA transcript undergoes alternative splicing where different sequences of exons are assembled for translation (forms different mature transcripts)
- Post-translational modification: when the protein structure of the amino acid chain is altered by the removal of a section of polypeptide, adding on phosphate groups, ect. (doing so can change proteins from inactive to active forms)
Mutations
• Mutation
- change in structure/ amount of organisms genetic material
- random, rare, spontaneous change in genome that can result in no protein/ altered protein being expressed
- only source of new alleles (different forms of the gene)
- leads to variation which is the raw material for evolution
- Mutant: when a mutation produces a change in phenotype
- Mutagenic agents: increases the rate of mutations. Eg. Radiation (x-rays, UV-light), chemicals (mustard gas)
- Types of mutations:
- single gene mutation
- chromosomal mutation
Single gene mutations
• Types of single-gene mutation::
> Substitution:
- when a base is replaces for another from a section of DNA
- point mutation (only affects one code, one amino acid)
> Insertion:
- the addition of one or more nucleotide into a section of DNA
- frameshift mutation
> Deletion:
- the removal of one or more nucleotide(s) from a section of DNA
- frameshift mutation
• Effect of single-gene mutations:::
> of point mutations (substitution)::
- silent: codon that codes for an amino acid is substituted for one that codes for the same amino acid. This has no effect on the function of the protein produced.
- neutral: codon that codes for an amino acid is substituted for one that codes for a very similar amino acid. This has little to no effect on the function of the protein produced.
- missense: codon that codes for an amino acid is substituted for one that codes for a very different amino acid. The effect of this in the function of the protein produced varies depending on its location and chemical properties.
- nonsense: codon that codes for an amino acid is substituted for one that is a stop codon. This can result in an abnormally short protein which is likely non-functional.
> of frameshift mutations (insertion and deletion)::
- frameshift: when one or two nucleotides are inserted/ deleted all bases downstream are moved up/down from their place altering the reading frame. Therefore all the amino acid‘s from the mutation onwards are altered. The position of the stop codon will also be altered, leading to a shorter/longer protein.
- Repeats: some regions of the genome are made up of nucleotide repeats, which must be a certain length to function normally. Insertions of groups of three nucleotides expand these repeats and alter the protein structure.
> of splice site mutations:
- Splice site: When substitution/insertion/deletion occurs at site where introns are removed from the primary mRNA transcript. This could stop/add a splice, creating an altered mature transcript and leading to an altered/ faulty protein.
Chromosomal mutations
• chromosomal mutations occur during meiosis (gamete formation) at the point when pairs of chromosomes line up along the cell equator
•Types of chromosomal mutations::
> Inversion: when a chromosome breaks in two places and the segment of the chromosome between the two breakpoints inverts (reverses) before rejoining occurs.
> Deletion: when a chromosome breaks in two places and a segment of chromosome between the two breakpoints is lost.
> Duplication: When there is a single break point in each of a homologous pair followed by the exchange of segments. One chromosome produced contains a duplication (Repeated sequence of DNA) whereas other chromosome contains a deletion.
> Translocation: when there is a single breakpoint in two (non-homologous) chromosomes followed by the exchange of segments.
> Non disjunction:
- single spindle fibre failure: causes trisomy (an extra copy) of a chromosome, (this can cause Down’s syndrome in humans).
- complete spindle fibre failure: creates a cell with multiple extra sets of chromosomes (polyploid cells). Polyploidy in plants is often artificially induced to develop high crop yield, bigger fruit, ect. However, in animals it is often lethal.
Meiosis
- meiosis results in the formation of gametes (aka. sex cells, has 23 chromosomes (haploid))
- In meiosis chromosomes line up as pairs along the cell equator unlike in mitosis where they line up as single chromosomes
Differentiation
- Differentiation is the process by which unspecialised cells become altered to form a specific function
- Plants:
- Meristems are the specific regions of growth on a plant that contains unspecialised cells. These cells divide by mitosis to differentiate and develop into specialised plant tissues. They have the potential to become any type of plant cell.
- Primary growth of a plant occurs at the apical meristems. These are located at the root/ shoot tips and cause an increase in plant length.
- Secondary growth of a plant occurs at the lateral meristems. These are located in the stems of plants and cause an increase in plant width.
• Animals:
- Stem cells are unspecialised cells that can undergo cell division to produce more stem cells (self-renewal) or can differentiate to become a cell with a specialised function. Stem cells are needed to form heathy tissues for growth and repair. Industrially they can be used for skin graphs, bone marrow transplants, and grow embryos.
- Embryonic: can be obtained from embryo (controversial). Are pluripotent (can become any cell type).
- Adult: obtained from bone marrow, umbilical cord, ect. Are multi-potent (can become any sub-set of cell types, can only become a small variety of cell types).
Evolution
- Evolution is the gradual change in the characteristics of a population of organisms over generations, as a result of variation in the population’s genome (ie. to the change of allele frequency)
- Results in offspring better adapted to the environment than the previous generation (due to survival of the fittest - natural selection)
- Involves gene transfer (inheritance), selection, genetic drift and speciation
Gene transfer (inheritance)
- Genetic material (genes) can be inherited/ transferred by sexual or asexual reproduction.
- In sexual reproduction two genetically different parents combine their genetic material to produce a new organism. This increases variation. This is an example of vertical gene transfer (between generations).
- In asexual reproduction one parent produces a genetically identical offspring. There is no variation present. This is an example of vertical gene transfer (between generations).
- Horizontal gene transfer is the passing of genetic material (eg. as part of a single circular chromosome/ plasmid) between the same generation. This results in rapid evolutionary change.
- Eukaryotes can reproduce sexually or asexually. They can only carry out vertical gene transfer and not horizontal gene transfer.
- Prokaryotes most frequently reproduce asexually but some can reproduce sexually. They can carry out vertical gene transfer and some (such as bacteria) can carry out horizontal gene transfer.
- Prokaryotes (such as bacteria and viruses) can transfer genetic material horizontally into the genomes of Eukaryotes.
Selection
- Selection is a non-random process where the frequency of advantageous alleles to the environment increases as they are selected for, and the frequency of disadvantages alleles to the environment decreases as they are not selected for.
- Types of selection is either natural selection or sexual selection.
- Natural selection (ie. survival of the fittest):
- Organisms produce too many offspring for the environment to support, giving rise to competition (eg. lack of food, overcrowding)
- Organisms with favoured adaptions (eg. resistance to disease) are more likely to survive and reproduce, passing on their advantageous characteristics to the next generation
- This process is repeated over generations and the organisms best suited the environment are naturally selected and eventually pre-dominate in the population
• Sexual Selection::
> increases the frequency of DNA sequences that increase the reproductive success of the species
> Male-to-male competition:
- involves direct aggression over territories and access to females
- dependent on physical size, strength
- use if weapons (ie. antlers) to battle for mates
- some animals engage in ritualised display behaviour to warn off other competitors
- most aggressive, strongest wins and can pass in alleles to the next generation
> Female choice:
- Females have to invest a large proportion of their resources (time, energy) to produce a small amount of gametes so have little to gain from excessive mating.
- Therefore females are selective in mating, choosing males with the most impressive masculine characteristics (ie. bright, well-kept plumage/ display)
- Some of these secondary sexual characteristics have an associated risk (eg. worse camouflage) but as it is selected for it is passed on to the following generations
Effects of selection
- Selection can alter the frequency of a trait/ phenotype in a population by:
- Stabilising Selection:
- selection against extreme variants in a phenotype
- favours the median (intermediate versions) of the trait
- leads to reduction in genetic diversity without changing the mean value
- operates in an unchanging environment
- results in the best adapted genotypes in the population
- eg. human birth mass: too low can be fatal, too high can cause birthing complications
• Directional Selection:
- most common during period of environmental change
- favours version of the characteristic initially less common
- results in the shift of the population’s mean value for the trait
- eg. dark peppered moth became more common than the light peppered moth during the industrial era
• Disruptive Selection:
- extreme versions of the trait are favoured at the expense of the intermediates
- results in population being split into two distinct groups, each with its own mean value
- under natural conditions it occurs when two different habitats/ types of resources become available
- eg. environment becomes cold n snowy, white rabbit is selected for but back rabbit stands out and is selected against
Genetic drift
- Genetic drift is the process of random changes to the allele frequency in a population
- Genetic drift has the most noticeable effect on smaller populations. Some alleles may be overrepresented and others are under-represented. Wild fluctuations in gene frequencies occur simply by chance from one generation to the next. Can cause an allele to disappear completely from a small population, therefore reducing variation, driving population towards uniformity and leading to evolutionary change.
- The founder effect is a type of genetic drift.
- occurs when a small group becomes isolated and forms a new population
- small population size has a reduced genetic variation and random sample of alleles from the original population’s gene pool
Gene migration
• The movement of alleles between population’s by individuals arriving from a different population and breeding. These individuals have a different gene pool and therefore introduce new alleles into the population.
Gene equilibrium
• Gene equilibrium is when the gene pool of a population is not undergoing any changes
Neutral mutations
- The majority of mutations found in the genome are neutral
- Therefore are not subject to natural selection
- Changes in the frequency of these neutral mutations is thought to be the result of random genetic drift
