Module 6 - Genetics evolution and ecosystems

What is a mutation?

A random change in the base sequence of DNA

What are the three point mutations?

Silent, nonsense and missense

What are the three indel mutations?

Insertions, deletions, expanding triplet

What is the third base in a codon known as?

The wobble position, often results in silent mutations

What is a silent mutation?

Has no effect on primary structure of protein, same amino acid is coded for due to degenerate nature of genetic code

What isa nonsense mutation?

Codes for a stop codon, protein is truncated and degrades in the cell producing no protein

What is a missense mutation?

Codes for a different amino acid , changing the structure of the protein

What is an insertion or deletion mutation?

A base is added or removed from the base sequence of DNA, resulting in a frameshift, due to the genetic codes non-overlapping properties

What is an expanding triplet mutation?

does not result in a frame shift, more amino acids are added

How do prokaryotes regulate gene expression at a transcriptional level?

lac Operon, Regulatory gene codes for a repressor protein, RNA polymerase cannot bind to the promotor region and structural genes are not transcribed.

How do eukaryotes regulate gene expression at transcriptional level?

Transcription factors, activating or repressor

How is gene expression controlled at a post-transcriptional level in eukaryotes?

Through (alternative) splicing.

Genes contain coding regions - exons, and non-coding regions - introns. Both are transcribed to primary mRNA, Introns are then removed and exons rejoined. to form mature mRNA .

How is gene expression controlled at a post-translational level in eukaryotes?

It involves the activation of proteins, usually by phosphorylation.

Hormone - G Protein (Associated with adenyl cyclase) - ATP, cAMP - Tyrosine Kinase

What is body plan development?

The arrangement of an organism’s parts, regulated by homeobox genes

What are Homeobox genes?

homeotic / regulatory gene, containing a homeobox sequence made up of 180 bp, that codes for 60 aa homeodomain sequence which binds to DNA as transcription factors for the control of body plan

What are Hox genes?

Sub-group of homeobox genes, only present in animals. Regulate embryo development down the anterior-posterior axis. Involved in apoptosis, mitosis and cell migration

What is collinearity?

The order of genes and how they are switched on during development

What is the process of apoptosis?

Enzymes digest cytoskeleton - cell membrane forms blebs - chromatin condenses, nuclear envelope breaks down - cells break down in vesicles engulfed by phagocytes

Reasons for variation

Mutation, miosis, environment, sexual reproduction, adaptation, mutagenic agents

In chromosome variation what is deletion?

A section of chromosome is deleted and becomes too short

In chromosome variation what is inversion?

A section of chromosome is flipped

In chromosome variation what is translocation?

A section of chromosome is broken off and attached to another chromosome, one is too long one is too short

In chromosome variation what is Duplication?

A section of chromosome is duplicated

In chromosome variation what is non-disjunction?

A pair of chromosomes don’t separate meaning one gamete has an extra chromosome

In chromosome variation what is aneuploidy?

The chromosome number isn’t a multiple of the haploid number due to a chromosome not separating

In chromosome variation what is polyploidy?

If a diploid and haploid gamete fertilise, triplet zygote forms with three sets of chromosomes

Who carried out research into monogenic inheritence?

Gregor Mendel

What is the expected ratio of F2 generation from two homozygous individuals (RRYY / rryy)?

1 : 3 : 3 : 9

What is codominance?

When both alleles are expressed in the phenotype

What is an example of multiple alleles?

Blood type

What is sex linkage?

A gene present on a sex chromosome e.g. haemophillia A

What is autosomal linkage?

When gene loci present on the same chromosome are more likely to be inherited together

What is epistasis?

The interaction of non-linked gene loci where one masks the expression of another

What is evolution?

The change in the frequency of an allele within a population over time

How can evolution occour?

Genetic drift, natural selection, gene flow

What is stabilising selection?

Individuals with intermediate phenotypes are more likely to survive, in an unchanging environment, reduces genetic variation

What is directional selection?

Individuals with an extreme phenotypes in one direction are more likely to survive, in a changing environment

What is disruptive selection?

Individuals with both extreme phenotypes are more likely to survive

What is genetic drift, what are the two ways it can happen?

Chance dictates which alleles are passed on, genetic bottlenecking, founder effect

What is genetic bottleneck?

The reduction in the size of a population size due to an environmental catastrophe , as the population expands again it is less genetically diverse and there is a change in the allele frequency

What is the founder effect?

A population is established in a new place, the gene pool is not as diverse as the original population

What is the Hardy-Weinberg principle?

It predicts the frequencies of alleles in a population that won’t change between generations.

p + q = 1

p² + 2pq + q² = 1

p + q = 1

p² + 2pq + q² = 1

What do they stand for?

p = frequency of dominant allele

q = “ recessive allele

p² = “ homozygous dominant individuals

q² = “ homozygous recessive individuals

2pq = “ heterozygous individuals

What are the assumptions of Hardy - Weinberg?

• No natural selection

• no mutation

• no migration

• large population

• random mating

• no genetic drift

What is speciation, what are the two types?

The splitting of a genetically similar population into two or more groups that undergo genetic differentiation and eventually, reproductive isolation, leading to the formation of two or more species.

Allopatric (geographical)

sympatric (reproductive)

What is allopatric speciation?

When organisms become geographically isolated by a physical barrier, due to different selection pressure and random mutations the species are unable to reproduce to produce fertile offspring. Results in directional selection.

What is sympatric isolation?

Organisms become reproductively isolated, unable to produce fertile offspring. Results in disruptive selection.

4 ways reproductive isolation can happen?

Gamete incompatibility, behavioral, seasonal, mechanical incompatibility

What is artificial selection?

When humans breed organisms for specific traits. If done repeatedly can result in an inbreeding depression.

How can you avoid inbreeding depression?

Outbreed, to increases heterozygosity, promoting hybrid vigor.

What is DNA sequencing?

A technique that allows genes to be isolated and read. Discovers the base sequence of a section of DNA.

What are the two types of DNA sequencing?

Sanger (chain termination)

Pyrosequencing

What is PCR?

Polymerase chain reaction. Amplifies DNA fragments outside of a living organism, artificial DNA replication.

What is required for PCR?

Target DNA, DNA primers, DNA nucleotides, thermostable DNA polymerase (TAQ), Buffer, Mg²⁺

What are the three stages of PCR and temperatures?

Denaturation (95), Annealing (68), Elongation (72)

How do you calculate exponential increase?

OG strands x 2 ^{number of rounds}

What is gel electrophoresis?

It is a process used to separate DNA or protein fragments by length and mass.

What extra steps are involved when separating proteins by gel electropherisis?

Heat to denature and expose any charged R-groups, Add negatively charged detergent (SDS)

What is DNA profiling?

A forensic technique whereby scientists compare similarities between two DNA samples.

What is found in DNA that makes DNA profiling possible?

Short tandem repeats (STRs), different number in each individual makes them distinguishable

Steps for producing a DNA profile / DNA fingerprint

1. Amplification of STRs by PCR, fluorescently tagged primers on either end of the STRs

2. Digestion and gel electrophoresis

3. Analysis of results

How to produce a DNA probe

1. DNA digestion - restriction enzymes

2. Gel electrophoresis

3. Blotting - transfers results to a nylon membrane

4. Probe labelling - tagged fluorescently or radioactively

5. Hybridization and washing

6. Detection - x ray or uv

What are DNA probes / used for?

Short single stranded DNA, complementary to a known base sequence. Identify inherited conditions, locate genes for genetic engineering

What is microarray?

Using multiple DNA probes on a fixed surface to identify sequences.

What is a transgenic organism?

An organism containing DNA from another organism

What is recombinant DNA?

Transferring a fragment of DNA from one organism to another

What are the 3 methods of obtaining a gene fragment for genetic engeneering?

Using mRNA, Using restriction endonuclease enzymes, gene machine

How do recstriction endonuclease enzymes work?

They recognise and cut specific palindromic sequences

How is recombinant DNA made?

1. Add promotor, terminator and sticky ends if necessary.

2. Isolate vector

3. Cut vector using the same restriction endonuclease enzyme

   1. Add DNA ligase to catalyse the formation of phosphodiester bonds

How does recombinant DNA enter the recipient cell?

• Heat shock treatment (0-42)

• Electroporation/electrofusion

• Transfection - DNA inserted into bacteriophage to enter the cell

  • Infection - Agrobacterium tumefaciens is used to infect plant cells

How can transformed cells be identified?

Using marker genes

What is gene therapy, what are the two types?

Inserting functioning alleles for a particular gene into a cell which contains mutated or non-functioning alleles for that gene.

Germ-line (Inserted into gamete or zygote)

Somatic-cell (Inserted into body cell)

What are the two ways a functioning allele can be inserted into a cell for gene therapy?

Virus vector or liposomes

What is an ecosystem?

All the living things in a specific area at a specific time, along with all the biotic and abiotic factors they interact with.

What is a saprotroph?

An organism that feeds on dead or decaying matter by secreting enzymes (amylase, protease, lipase) to digest the material and absorb it.

In the nitrogen cycle how does N₂ gas get to be organic material in plants?

Nitrogen fixation by Rhizobium bacteria found in root nodules of leguminous plants

In the nitrogen cycle how does N₂ gas get to become organic N₂ in the soil?

Nitrogen fixation by free-living Azotobacter

In the nitrogen cycle how does N₂ gas get to be ammonium (NH₄⁺ ) in the soil?

Nitrogen fixation in the Haber process

In the nitrogen cycle how does N₂ gas get to be Nitrates (NO₃^- ) in the soil?

Nitrogen fixation through Haber process or Lightning striking

In the nitrogen cycle how does Organic nitrogen in plants and animals get into the soil as organic N₂ or urea?

Death and excretion

In the nitrogen cycle how does Organic N₂ and urea in the soil get to become Ammonium (NH₄⁺)?

Ammonification

In the nitrogen cycle how do Ammonium ions (NH₄⁺) become Nitrite ions (NO₂^-)?

Nitrification by Nitrosomonas

In the nitrogen cycle how do Nitrite ions (NO₂^-) become Nitrate ions (NO₃^-) ?

Nitrification by Nitrobacter

In the nitrogen cycle how do Nitrate ions (NO₃^-) become organic material in plants?

Assimilation (through the roots)

In the nitrogen cycle how do Nitrate ions (NO₃^-) become N₂ gas?

Denitrification by anaerobic denitrifying bacteria

Carbon cycle, Animal → Detritus, humus & waste?

Excretion and death

Carbon cycle, Animals → Carbon dioxide

Respiration

Carbon cycle, Animals → Fossil fuels

Death

Carbon cycle, Plants → Animals

Feeding

What is succession?

How ecosystems change over time as species colonize, outcompete and replace one another.

What is primary succession?

Occurs on newly formed or exposed land with no soil or organic material e.g. volcanic rock

Secondary succession?

Occurs in areas where an existing community has been removed e.g. after a forest fire

What are the stages of succession?

1. Initial colonization by pioneer species

2. Alteration of conditions - organic matter forms

3. Diversification - soil improves more species join

4. Settlement by intermediate species

5. Development of climax community

What is deflected scuession?

When succession is stopped or interfered with such as grazing or mowing.