Genetics, variation and independence

Prokaryotic DNA

• single-stranded

  • single, circular loop of DNA = nucleoid (not a chromosome)

• 1 or more plasmids

  • small circular DNA molecules

  • can be exchanged between cells

  • usually only contain a few genes

  • plasmids > accessible for proteins required for gene expression and therefore contain genes required often, quickly/ in emergencies

  • contain genes for antibiotic resistance

Eukaryotic DNA

Eukaryotic chromosomes

• human cells have 23 pairs

• haploid (n) = cell/ nucleus containing single copy of each chromosome

• diploid (2n) = cell/ nucleus containing 2 sets of chromosomes/ 2 copies of each chromosome

  • no of chromosomes diff for all organisms

• loci = position of gene on chromosome

Gene

= base sequence of DNA that codes for the amino acid of a polypeptide/ a functional RNA (e.g. tRNA/ rRNA)

• allele = alternative form of a gene

• shape and behaviour of protein molecule depends on exact sequence of these amino acids (i.e. primary structure)

• genes in DNA control protein structure

Non-coding DNA

• genome contains many non coding sections of DNA (doesn’t code for amino acids)

• found between genes, as non-coding multiple repeats

  • means contain same base sequence repeated multiple times

• can be found within genes: introns

  • coding exons separated by 1 or more introns

• during transcription, eukaryotic cells transcribe whole gene (all introns and exons) to produce pre-mRNA molecules

• before pre-mRNA exits nucleus, introns removed and exons (coding sections) joined in process = splicing

Proteome

full range of proteins produced by genome

• usually large amount of post-translational modification of proteins (often in Golgi)

• each gene also capable of producing multiple different proteins via alternative splicing

genome = complete set of genes (e.g. in a cell)

• but not every gene expressed in every cell, depends on cell type

DNA

• double

• long

• double helix

• deoxyribose

• AT CG

• found in nucleus

• constant (no variability of quantity)

• very stable (double stranded)

mRNA

• single

• short

• single strand

• ribose

• AU CG

• found in cytoplasm

• variable with level of protein synthesis

• least stable

tRNA

• single

• short

• clover-leaf as forms H bonds between complementary bases within strand

• ribose

• AU CG

• found in cytoplasm

• variable with level of protein synthesis

• more stable than mRNA

• anticodon = 3 bases complementary to codon on mRNA

• amino acid specific to anticodon

transcription

1. DNA helicase breaks H bonds to unzip DNA

2. 1 template strand used to produce mRNA molecule by complementary base pairing with complementary base pairing with free RNA nucleotides

3. RNA polymerase joins nucleotides with phosphodiester bonds

4. DNA strand rejoins behind

5. mRNA leaves nucleus through nuclear pore

Post-transcriptional modification

Splicing

• only eukaryotes, mRNA produced by transcription is modified inside nucleus, before translation

• immediately translation for prokaryotes

Alternative splicing

• exons can be spliced in many diff ways to produce diff mature mRNA molecules

• so single eukaryotic gene can code for more than 1 polypeptide chain

  • (so proteome bigger than genome)

translation

1. mRNA binds to ribosome

2. ribosome moves to start codon

3. tRNA brings specific amino acid

4. anticodon on tRNA binds to complementary codon on mRNA

5. ribosome moves along to next codon

6. amino acid joined by peptide bonds by condensation reactions using ATP

7. continues until stop codon reached, mRNA molecule complete

destination of proteins syntehsised on

• free ribosomes (in cytoplasm) for polypeptides for internal cell use

• ribosomes bound to RER for use in lysosomes/ secretion

triplet code

sequence of 3 DNA bases that codes for specific amino acid, or is stop/start codon

codon

sequence of 3 mRNA bases that codes for specific amino acid

anticodon

sequence of 3 tRNA bases complementary to codon

no. of diff amino acids

20 amino acids, 64 different triplet bases

stop codons

don’t code for amino acids, causes ribosome and mRNA to detach

start codon

codes for amino acid Met

causes ribosome and mRNA binding

degenerate

more than 1 mRNA codon / triplet codon code for same amino acid

universal

codons code for same amino acids in all species

non-overlapping

each base only read once in codon part of

gene mutations

= change in nucleotide base sequence of DNA

• DNA base sequence determines primary structure, can lead to changes in polypeptide that gene codes for

Deletion (+insertion) of nucleotides

• changes amino acid coded for

  • knock-on effect by changing groups of 3 bases further on in DNA sequence

• frameshift mutation

  • may dramatically change amino acid sequence produced from this gene and ability of polypeptide to function

substitution of nucleotides

• only change amino acid for triplet where mutation occured

silent mutations

• doesn’t alter amino acid sequence of polypeptide and protein function

• degenerate nature

missense mutations

• alters single amino acid

• change in tertiary structure: change in type and position of bonds between R groups

nonsense mutations

• creates premature stop codon

  • signal for cell to stop translation of mRNA molecule into amino acid sequence

  • short and incomplete polypeptide chain affecting final protein structure

causes of mutations

• can arise spontaneously during DNA replication

• rare but occur at predictable frequency

mutagenic agents

• high ionising radiation can disrupt DNA structure

• chemicals e.g. NO2 can directly alter DNA structure/ interfere with transcription

mutation passed onto offspring if

• mutation occurs in cell that will ‘divide into’ a gamete e.g. ovary/ testes

chromosome mutations

• non-disjunction occurs when chromosomes fail to separate during meiosis

• occurs spontaneously

• gamete may end up with extra pair or no copies of particular chromosome

  • = diff no. of chromosomes

• if abnormal gametes take part in fertilisation, chromosome mutation occurs as diploid cell will have incorrect no. of chromosomes

2 types of chromosome mutation

• change in whole set of chromosomes (structure)

• change in no. of individual chromosomes

meiosis

• produces genetically diff daughter cells

• meiosis I

  • homologous chromosomes pair up and separate

• meiosis II

  • chromatids separate and gametes formed, each with half original no. of chromosomes

independent assortment

• how homologous chromosomes pair up on spindle in metaphase I

• random

• alleles of 2/more diff genes get sorted into gametes

• how homologous chromosomes line up in random orientations at middle of cell

independent segregation

• how homologous pairs separate in anaphase I

• 2²³ possible combinations of chromosomes per human gamete

independent crossing over

• metaphase I

• homologous pairs = bivalent

• chromosomes break, exchange DNA between non-sister chromatids and rejoin

• = recombinant chromosomes = new combination of alleles

importance of meiosis

1. produce haploid gametes

   • important to maintain diploid number at fertilisation

2. results in genetically varied gametes, with novel allele combinations

how meiosis results in genetic variation

1. independent segregation of homologous chromosomes

2. crossing over

3. random fusion of gametes during fertilisation

   = unique combination of alleles

mitosis

mitosis

• produces 2 daughter cells per cycle (diploid)

• produces genetically identical daughter cells

  • unless mutation occurs during DNA replication

• 1 nuclear division per cycle

meiosis

• produces 4 haploid cells, genetically varied through

  • crossing over to produce new combinations of alleles

  • independent segregation of homologous chromosomes

• 2 nuclear divisions per cycle

• take place in testes, ovaries, anthers

genetic diversity

no. of different alleles of genes in a population

• genetic variation transferred down generations and results in genetic diversity

• new allele may be dis/advnatageous or have no effect on phenotype

  • new alleles may remain hidden within population for several generations before contribute to phenotypic variation

gene pool

all of genes and their diff alleles present in an interbreeding population

effect of genetic diversity

• genetic diversity → allows NS → adaption

• diff alleles → diff phenotypes within population

• environmental factors act as selection pressure

  • biotic/ abiotic

  • increase chance of individuals with specific, favoured phenotype to survive and reproduce (have higher fitness)

• small gene pool = < likely to be able to adapt to changes in environment and so become vulnerable to extinction

higher fitness

= able to survive and pass allels to offspring

Discontinuous variation

• genetic factors

• characteristics controlled by single gene, not influenced by environmental factors

  • few distinct forms, no intermediate types

• e.g. ABO blood groupings

Continuous variation and environmental influences

• e.g. environmental factors limiting height of buttercup plant

  • biotic (competition, pests, pathogens)

  • abiotic (light intensity, temp, wind speed, humidity)

continuous variation due to polygenes

• many characteristics controlled by multiple genes and environment

• leads to normal distribution curve on graph

principle of natural selection

• random mutation can result in new alleles of gene

• individuals with advantageous allele more likely to survive, reproduce and pass on their allele to next generation

• over many generations, new allele increase in frequency in population

(sexual selection, those with advantegeous allele more likely to reproduce, NOT survival)

selection

= process by which organisms that are better adapted to their environment are > likely to survive and reproduce

selection pressure

= environmental factors that affect chance of survival of organism

stabilising selection

• keeps allele frequency constant over generations

• preserves average phenotype

  • selects for 1 phenotype and selects against extreme phenotypes and so against evolutionary change

• occurs when environment constant

• variation decreases, mean constant

• e.g. birth weight, no. of offspring, cactus spine density

directional selection

• occurs in changing environments

  • when there is clear advantage in population changing in 1 particular direction

• combination of alleles at 1 extreme of phenotype selected against and those at other end selected for

• variation constant, mean shifts in 1 direction

• e.g. development of antibiotic resistance in bacteria, peppered and melanic forms of peppered moth

disruptional selection

• results in polymorphism

• can lead to speciation

• extremes selected for

• mean selected against

• e.g. long fur and active in winter, short fur and active in summer

anatomical adaptations

• structural / physical feature

• e.g. white fur of polar bears provides camouflage in snow so has < chance of being detected by prey

physiological adaptations

• biological processes within organism

• e.g. mosquitos produce chemicals that stops animal’s blood clotting when they bite, so can feed more easily

behavioural adaptations

• way organism behaves

• e.g. cold-blooded reptiles bask in sun to absorb heat

effect of adaptation and selection on population

• evolution = change in adaptive features of population over time as result of natural selection

• over generations, those features better adapted to environment become > common

  • = whole population > suited

• if 2 populations of species isolated from each other and become so diff in phenotype that can no longer interbreed. to produce fertile offspring = 2 new species

  • → accumulated genetic differences

• evolution drives speciation

species

group of organisms with similar characteristics which can interbreed to produce fertile offspring

issues with species definition

• asexual organisms don’t interbreed

• extinct species, only have fossil records

• some species interbreed to produce fertile offspring (often not well adapted)

• ring species: species with geographic barrier and form ring

  • still have gene flow but can only interbreed with groups closest to them

courtship

enables organisms to

• female selection of advantageous alleles (sexual selection) and resources

• recognise members of own species

• identify mate that is capable of breeding

• form pair bond

• synchronise mating

  • for external fertilisation, to release sperm and egg at same time to maximise chance of them meeting

• become able to breed

importance of classification

• common name for species

• group organisms with shared characteristics

• how closely related organisms are

binomial system of classification

1. genus (shared with all closely related species)

2. species (unique type of organism)

phylogenetic classification

• attempts to arrange species into groups based on evolutionary origins and relationships

• uses hierarchy in which smaller groups placed within larger groups, no overlap

Kingdom

Phylum

Class

Order

Family

Genus

Species

keep

ponds

clean

or

frogs

get

sick

archaea

• most live in extreme environments

• no nucleus so prokaryotic

• unicellular (single-celled)

• 70s ribosomes

• proteins synthesis more similar to eukaryotes, more complex form of RNA polymerase than bacteria

• circular ‘chromosomes’

• histones

• cell wall not murein/peptidoglycin

• fatty acid chains attached to glycerol by ether linkages

bacteria

• no membrane-bound organelles

• unicellular

• 70s

• DNA: circular, shorter, no chromosomes

• no histones

• cell wall made of murein

• fatty acid chains atached to glycerol by ester bonds

eukarya

• membrane-bound organelles e.g. nucleus and mitochondria

• multi/uni

• 80s

• DNA: double helix, linear, arranged into chromosomes

• histones

• cell wall: plants - cellulose, fungi - chitin

• fatty acid chains attached to glycerol by ester bonds

artificial classification

divides organisms according to morphological features

• can be analogous: same function but not evolutionarily related e.g. wings

phylogenetic classification

based on evolutionary relationships between organisms and shared features derived from common evolutionary ancestry

• homologous characteristics

• phylogeny = evolutionary relationships between organisms

genome sequencing for evolutionary relationships

• using DNA/ mRNA/ amino acids of a protein

• scientists choose specific proteins/ sections of genome for comparison between organisms

  • looking at multiple proteins/ regions of genome = > accurate

  • NB protein needs to present in wide range of organisms and show sufficient variation between species

• > similar sequence = > closely related

  • = separated species > recently

  • separated for longer = > time to accumulate mutations and changes to their DNA, mRNA and amino acid sequences

immunology

• to compare proteins of organisms

• albumin = protein found in many species

Methodology

1. pure albumin samples extracted from blood samples taken from multiple species

2. each sample injected into diff rabbit

3. each rabbit produces antibodies fro that specific type of albumin

4. diff antibodies extracted from diff rabbits and are mixed with diff albumin samples

5. ppt (antibody-antigen complexes) resulting from each mixed sample is weighed

Results

• > weight of ppt = > degree of complementarity between antibody and albumin

• e.g. antibodies produced against human albumin will produce > amount of ppt when exposed to chimpanzee albumin than rat albumin as > closely related

species richness

no. of diff species in community

• community = group of populations of diff organisms living in same place at same time that interact with each other

• can be misleading as doesn’t take into account abudnance

species evenness

no. of individuals in each species (abundance)

biodiversity important because

• allows adaptation to changing conditions e.g. climate change, new pathogen)

• food webs and symbiotic relations (e.g. pollinators)

• medicines

ecosystem/ habitat diversity

• range of habitats in particular area/ region

• > diff habitats = > biodiversity

  • e.g. coral reef with lots of microhabitats and niches to be exploited

• 1/ 2 diff = < biodiversity

  • e.g. large sandy deserts as same conditions in whole area

species diversity

• richness and evenness

• > = > stable as > resilient to environmental change

  • doesn’t have dominant species

index of diversity

• looks at evenness and richness

• describes relationship between no. of species present and how each species contributes to total no. of organisms present in that community

d = N(n-1)/ ∑n(n-1)

• n = total no. of organisms for single species in community

• N = total no. of organisms in community (all species)

• > num = > biodiversity

impact of farming on biodiversity

• fertilisers: eutrophication

• selective breeding

• pesticides: kill pests

  • kill pollinators and other species

• herbicides kill weeds and other plants

• hedgerow removal

  • pollinators and birds and others live on hedgerows

• deforestation

• filling in ponds, draining marshland (habitat)

• monocultures: 1 type of plant grown on fields

  • supports fewer species

decrease biodiveristy

conservation methods in farming

• maintain ponds

• crop rotation

  • grow nitrogen-fixing crops e.g. legumes to replace nitrates

• limit/ regulate use of

  • pesticides → use biological controls e.g. natural predators)

  • fertilisers → use organic = manure (still causes eutrophication)

  • herbicides

• conserve/ replant

  • hedgerows

  • field margins e.g. wild flowers

  • natural meadows

    • don’t cut grass until after flowering

biodiversity vs profit

• high yield + profit = 2 factors that make farming viable

• difficult to find balance between conservation and farming

  • practices to increase biodiversity = expensive, labour and time intensive

genetic isolation

• 2 groups reproductively isolated → genetically isolted

• changes that occur in allele freq of each group not shared so evolve independently which can lead to 2 diff species

  • can’t successfully interbreed

investigating genetic diversity

• now:

  • displays of measurable characteristics

  • nucleotide base seq of DNA/ proteins

• originally

  • comparison of observable characteristics to suggest evolutionary relationships (could be analogous)

investigating diversity using mtDNA

• zygote only contains mitochondria of egg so only maternal mtDNA present in zygote

  • = no crossing over so base seq can only be changed by mutation

  • so scientists can research origin of species, genetic drift and migration events

investigating diversity using mRNA analysis and comparison

• diversity in mRNA bases will be complementary to base seq of DNA after transcription

• mRNA = easier to isolate as found in cytoplasm and there are usually multiple copies of same mRNA

  • can still give comparison between diff species

• mRNA = only coding regions

investigating diversity using amino acid seq analysis and comparison

• protein easier to isolate than DNA

• amino acid seq of proteins evolve much slower than DNA, especially if protein of high importance

  • likely closely related species will have same amino acid seq even though split from common ancestor millions of yrs ago

  • bc shape and function and specificity of protein determined by amino acid sequence as position of amin o acid determines IMF between R groups

phylogenetic tree

• conflicting evidence for relationships between organisms e.g. primates(order) illustrates need to use variety of evidence from diff sources in drawing valid scientific conclusions