topic 4 - genes, variation on relationships

What is a gene?

A base sequence of DNA that codes for a specific sequence of amino acids that can form a polypeptide chain or a functional RNA molecule

What is functional RNA?

RNA molecules other than mRNA - tRNA & rRNA - which perform special tasks during protein synthesis.

What is a locus?

The location of a gene a chromosome - plural is loci

What is an allele?

Different forms of one gene.

The order of bases in each allele is slightly different to the others so they code for the same polypeptide but for a slightly different version of it - e.g. blood types.

What is a homologous pair?

Pairs of chromosomes with genes for the same features at the loci - homologous pairs carry the same gene but not always the same allele

What is a genome?

The complete set of genes in a cell.

What is a proteome?

The full range of proteins that a specific cell is able to produce - changes depending on the cell.

How is DNA stored in a eukaryotic cells?

• The DNA is very long, linear & in a double helix form

• It’s wound around a single histone protein forming a nucleosome

  • histones allow the very long DNA to coil & so fit in the nucleus and help support the DNA

• Multiple histones with DNA wound around them coil around themselves forming chromatin

• The chromatin fold to form loops which further coil to form chromosomes

How is DNA stored in a prokaryotic cell?

• DNA is shorter and circular - the chromosome is joined at the ends - but still in a double helix

• DNA is not wrapped around histones it instead condenses to fit in the cell by supercoiling

  • the DNA winds around itself without any histones

• DNA in mitochondria and chloroplasts are similar to prokaryotic DNA

• The DNA is not found in a nucleus

What is the genetic code?

The sequence of sets of 3 bases - codons in mRNA which code for specific amino acids.

What are the features of the genetic code?

• Degenerate → multiple triplets code for the same amino acid (limits mutation)

• Non-overlapping → always read in sets of 3 & each base is read once and is part of one triplet (if mutation occurs, it only affects 1 codon therefore 1 amino acid)

• Universal → same triplets code for same amino acids in all organisms (allows genetic engineering)

What are the differences between DNA & RNA?

• DNA is double stranded while RNA is single stranded

• DNA has thymine while RNA has uracil - DNA bases = ATCG vs RNA bases = AUCG

• DNA has deoxyribose sugar while RNA has ribose sugar

• DNA is longer while RNA is shorter

• DNA has introns while RNA doesn’t

• mRNA & tRNA quantities vary depending on the protein needed or the type of cell whereas DNA quantity is the same in all cells - gametes

• DNA is stable, tRNA is less stable, mRNA is unstable & easily broken down

What are introns and exons?

Introns - sections of DNA in a gene that codes for a polypeptide but which doesn’t code for an amino acid

Exons - sections of DNA in a gene that do code for amino acids

*exons will contain multiple triplets

What are non-coding multiple repeats?

Sections of DNA in eukaryotic cells that are made up of DNA sequences that repeat over and over but don’t code for amino acids.

They’re found outside of the genes.

What are the stages of protein synthesis?

• Transcription - DNA is transcribed & an mRNA molecule is produced - transcribed = same “language” of the genetic code

• Translation - mRNA joins a ribosome and an amino acid sequence is produced - different “languages” from genetic code to amino acid sequence

What is splicing?

Where introns are removed from the pre-mRNA during transcription leaving only exons/coding parts of DNA in a gene so they don’t effect the final sequence of amino acids formed.

When does splicing occur?

Splicing occurs in transcription after the pre-mRNA strand has been formed from it’s DNA template.

What is mRNA?

Messenger RNA :

• made during transcription so in the nucleus

• found mainly in the cytoplasm & ribosomes

• carries the genetic code from the DNA to the ribosomes so translation can occur

• single polynucleotide strand

• a set of 3 bases that will eventually code for an amino acid is called a codon

What is tRNA?

Transfer RNA :

• involved in translation

• found in the cytoplasm

• manufactured in the nucleus

• carries the amino acids to the ribosomes so they can be used to make proteins

• single polynucleotide strand but contains some hydrogen bonds so the tRNA folds into a clover shape

• contains an anticodon - specific sequence of 3 bases at one end of its structure that corresponds with an amino acid & a codon on mRNA

• contains an amino acid binding site at the other end that will bind to the anticodon’s corresponding amino acid

What is the purpose of mRNA & tRNA?

mRNA - transfers genetic information from DNA to the ribosomes for protein synthesis.

tRNA - transfers amino acids to the ribosomes to be joined together in the correct order (determined by the codons on the mRNA) into a polypeptide by the formation of peptide bonds

Where do transcription and translation take place?

Transcription - at the nucleus

Translation - at the ribosomes

What is produced at the end of transcription vs translation?

Transcription - a strand of mRNA

Translation - a polypeptide/protein

What is the difference between a triplet, codon and an anticodon?

Triplet - a sequence of 3 bases on a DNA molecule - can be made up of Adenine, Thymine, Cytosine & Guanine

Codon - a sequence of 3 bases on a mRNA molecule that is complementary to a triplet - made up of Adenine, Uracil, Cytosine & Guanine

Anticodon - sequence of 3 bases on a tRNA molecule that is complementary to a codon & therefore the same as the original triplet - made up of Adenine, Uracil, Cytosine & Guanine

What is RNA polymerase?

An enzyme that synthesises pre-mRNA molecules from a DNA template.

Unlike in DNA replication/DNA polymerase - RNA polymerase can both unwind the DNA double helix and line up complementary RNA nucleotides & form phospodiester bonds between them.

What are the general stages of transcription?

• RNA polymerase binds to the DNA at a start of a gene

• Complementary mRNA is formed

• RNA polymerase moves down the DNA template

• RNA polymerase reaches a stop triplet/signal

What happens in transcription - in depth?

• RNA polymerase attaches to the DNA double helix at the start of a gene

• The 2 strands are separated by RNA polymerase breaking the hydrogen bonding

• DNA molecule unwinds,exposing bases & allowing for one of the strands to be used a mRNA template

• RNA polymerase lines up free RNA nucleotides along the exposed bases

• Free bases on the nucleotides are attracted to the DNA ones and they pair up - specific, complementary base pairing

• This means the pre-mRNA will be complementary to the DNA

• The paired up nucleotides are joined together by RNA polymerase

• RNA polymerase moves down the DNA template continuing this

• DNA double helix reforms once the enzyme has passed by via hydrogen bonds reforming

• RNA polymerase reaches a stop signal and it detaches from DNA

• Splicing occurs & mRNA is formed

• mRNA moves out of the nucleus via nuclear pore to a ribosome

Why does splicing not occur in prokaryotic transcription?

Introns aren’t present in prokaryotic DNA - only exons are present.

What are the advantages of using mRNA instead of DNA for translation?

• shorter & contains uracil - breaks down quickly so no excess polypeptide forms & means mRNA can move out of the nuclear pores

• single-stranded & linear - ribosome moves along strand & tRNA binds to exposed bases

• contains no introns - pre-mRNA contains introns but once they are spliced out mRNA has been formed

What is required for translation to take place?

• Transcription must have already taken place

• Ribosomes in the cytoplasm

• mRNA - spliced, assembled & in the cytoplasm

• tRNA molecules - each with an anticodon & it's corresponding amino acid

• Amino acids -free in a pool to replace tRNA molecules that have given up their amino acid to form a polypeptide chain

What happens in translation - in depth?

• mRNA has traveled to the cytoplasm

• mRNA combines with a ribosome

• The ribosome draws a tRNA carrying an amino acid & has an anticodon complementary to the 1st codon on the mRNA

• A second tRNA attaches itself to the next codon in the same way - specific base pairing

• The 2 amino acids lined up are joined by a peptide bond and the 1st tRNA moves away

• This allows for another tRNA to bind onto the next codon - ribosome can only accommodate 2 tRNAs bonded onto mRNA at a time

• This process is repeated until a stop codon is reached and a complete polypeptide chain has formed

• The polypeptide moves away from the ribosomes

• Translation is complete

What is produced at the end of transcription vs translation?

Transcription - a strand of mRNA

Translation - a polypeptide/protein

What is meiosis?

A form of cell division that produces four genetically different haploid cells (cells with half the number of chromosomes found in the parent cell) known as gametes.

What does it mean for normal body cells to be diploid?

Each cell contains two of each chromosome - one paternal one maternal - this means that there are 46 chromosomes in total and 23 homologous pairs/pairs of chromosomes.

The chromosomes that make up each pair are the same size and have the same genes but different alleles.

How is meiosis different to mitosis?

• Mitosis produces two genetically identical daughter cells while meiosis produces four genetically different daughter cells

• Mitosis has diploid daughter cells while meiosis has haploid daughter cells

• Mitosis has 1 division while meiosis has 2

What are the stages of meiosis?

Meiosis 1:

• Interphase

• Prophase 1

• Metaphase 1

• Anaphase 1

• Telophase 1

Meiosis 2:

• Prophase 2

• Metaphase 2

• Anaphase 2

• Telophase 2

What happens in interphase of meiosis/before meiosis?

• DNA replication in S phase

• The paternal & maternal chromosomes are replicated so that a pair of homologous chromosomes is formed

• This includes a pair of maternal sister chromatids and a pair of paternal sister chromatids

• The 4 chromatids together are 1 homologous pair

What happens in Prophase 1?

• DNA condenses and becomes visible as chromosomes (each chromosome consists of two sister chromatids joined together by a centromere)

• Chromosomes arranged side by side in homologous pairs/biavelents/ tetrads

• Chiasmata are formed where the pairs homologous chromosomes twist around each other

• Centrioles migrate to opposite poles and the spindle is formed

• Nuclear envelope breaks down, nucleolus disintegrates

What happens in Metaphase 1?

• Pairs of homologous chromosomes line up on the equator

• They attach to spindle fibers by their centromeres,

• Independent assortment occurs

• Crossing over also occurs

What happens in Anaphase 1?

• Homologous chromosomes are pulled apart to opposite sides of the cell by the spindle fibres shortening

• The pairs chromatids are still intact with their centromeres

• Independent segregation takes place

What happens in Telophase 1?

• Separated chromosomes reach opposite poles

• Nuclear envelope forms around each set of pairs of chromatids

• Cytokenisis starts

• 2 cells are formed but they have pairs of chromatids and aren’t identical anymore due to independent assortment, crossing over & independent segregation

What happens in Prophase 2?

• The chromosomes condense

• The nuclear envelope breaks down

• Centrioles move to opposite poles while spindle formation occurs again.

What happens in the rest of Meiosis 2?

Meiosis 2 is the same as a mitotic split so:

• Metaphase 2 - pairs of chromatids line up on the equator attached by their centromeres, with independent assortment of chromatids occurring.

• Anaphase 2 - centromere splits and chromatids are pulled apart to opposite poles of the cell, leading to independent segregation of chromatids

• Telophase 2 - separated chromosomes reach opposite poles and a nuclear envelope forms around each of the four, non-identical haploid cells

How does genetic variation occur?

• independent assortment

• random assortment

• crossing over

• random fertilisation

What is the main cause of genetic variation during meiosis?

Independent assortment/random assortment - aka the orientation of the paternal & maternal chromatids during metaphase 1 & then which poles they are randomly pulled to in anaphase 1.

What is independent assortment ?

Occurs in metaphase 1 of meiosis and is how when the pairs of homologous chromosomes line up along the equator it is random whether the maternal chromatids are on top or the paternal chromatids.

What is random assortment?

Occurs in anaphase 1 of meiosis and is when the spindle fibres pull the homologous chromosomes apart leading to a random combination of which paternal/maternal chromosomes/pairs of chromatids are pulled to each pole.

What is crossing over?

• regions of non sister chromatids swap over within homologous pairs

• chromatids become twisted which causes tension so they break and exchange alleles and when they recombine, new combinations of alleles are made

• this means a paternal chromatid could have the maternal allele for eye colour

What happens in random fertilisation?

A haploid sperm fuses with a haploid egg, making a normal diploid cell with half of its chromosomes from the egg and half from the sperm.

This results in variation because during sexual reproduction, any sperm can fertilise any egg and so is random. Random fertilisation produces zygotes with different combinations of chromosomes to both parents.

What are the two types of chromosome mutations that can occur?

• Non-disjunction - when individual homologous pairs do not separate during meiosis, leading to one gamete in a pair having one more of one chromosome and the other one having one less

  • e.g. trisomy 21 which causes Down syndrome

• Polyploidy - where individuals have three or more sets of chromosomes, usually occurring in plants, occurring when chromosomes do not form two distinct sets in meiosis, forming diploid gametes, which then fuse - either one haploid and one diploid (forming a triploid) or two diploids (forming a tetraploid)

What is a mutation?

A change in the quantity or structure of DNA.

What are the two general types of mutations?

• Chromosome mutations - changes to the number of chromosomes in a gamete

• Gene mutations - any change to one or more bases or any rearrangement of bases in the DNA

What are the types of gene mutations?

• Subsitution

• Deletion

• Insertion

What is a subsitution mutation?

• When one or more bases is swapped for another base

• This can result in:

  • no change to the amino acid as the base could be replaced with the same base or the codon codes for the same amino acid - genetic code is degenerate

  • a different amino acid being produced

  • stop codon is coded for so the rest of the protein isn’t coded for

• Substitution bases only effect one amino acid (if only one base has been substituted) so tend to have the least effect out of the 3 types of gene mutations

What does it mean for substitution mutation to be a :

• nonsense mutation

• mis-sense mutation

• silent mutation?

• nonsense mutation - the mutation codes for a stop codon

• mis-sense mutation - mutation which codes for an amino acid but one which is not the original/intended one

• silent mutation - mutation which codes for a new codon which still produces the same amino acid

What is an insertion mutation?

• involves the addition of a nucleotide base and changes the amino acid that has been coded for

• creates a frame shift so changes all future amino acids & significantly changes the polypeptide, resulting in a non-functioning protein

What is a deletion mutation?

• removal of an base which changes sequence of future codons - frame shift - significantly changing the polypeptide which could lead to a non-functioning protein

• might not be significant because it could occur at end codon

Why might a mutation not lead to change in the amino acid sequence?

The genetic code is degenerate meaning a different mutated triplet can code for the same amino acid as the original triplet so even if a mutation has occurred there will be no “visible” change.

Mutations can also happen in the introns/ non-coding sections of the DNA sequence & these will be spliced out etc.

What is a mutagenic agent?

Factors that increase the rate of gene mutation.

• X-rays,

• UV light,

• gamma rays,

• certain chemicals e.g. in alcohol and tobacc

What is genetic diversity?

The number of different alleles of genes in a population or species /the genetic differences between individuals that are caused by different types of alleles

What does allele frequencies mean?

How often an allele occurs in a population.

What advantage does variation/genetic diversity provide?

Ability for a species to survive after a widespread disease or extinction event as it means some organisms in a population will survive.

Allows natural selection to occur.

How can genetic diversity be increased?

• Mutations - form new alleles which are usually rarely advantageous but there are some advantageous ones

• Gene flow - different alleles being introduced into a population when individuals from another population migrate into it and reproduce

• Natural selection

• Genetic drift

• Non-random mating

Natural selection is the only one which will make a population better adapted to it’s environment/habitat.

What is evolution?

The gradual change in species over time.

What is a population?

All the organisms of a particular species that live in the same place.

What is a community?

All the different species that live in one area and interact with each other.

What is a genetic bottleneck?

A reduction in population that reduces the types of alleles :

• Relies on chance

• Caused by a massive population crash - e.g. the hunting of seals which originally had a wide variety in fur colour but all the brown seals were hunted so only white seals were able to survive

• Doesn’t create any adaptive change

• Genetic bottlenecks reduce genetic diversity - as the number of different alleles in the gene pool is reduced

What is the Founder Effect?

The Founder Effect occurs when a small group of individuals migrate away or become isolated from a population.

• This means the founding population is small.

Inbreeding may be a problem if the individuals are closely related and the founding population can have a non-representing sample of alleles from the parent population so the probability of having a more rare disease increases if an original founder had its allele etc.

Overall the founding population may evolve quite differently from the original population especially if the environment is different & certain alleles may go missing altogether as a consequence - resulting in a loss of genetic diversity.

What is natural selection?

• leads to evolution, which is the change in allele frequency over many generations in a population

• results in species becoming better adapted for their environment

What is the process of natural selection and how does it result in new characteristics in a species ?

• new alleles for gene are created by random gene mutation

• new alleles increase survival chance in that environment so they are more likely to survive and reproduce

• new genes are passed onto next generation

• over time, frequency of allele increases in the population

What are the two types of natural selection?

• Directional → occurs when environmental conditions change meaning that individuals with phenotypes suited to the new extreme will survive and pass on their genes. Over time the mean of the population will move towards these characteristics & shift towards the extreme.

• Stabilising → occurs when there is no change in the environment & modal trait has selective advantage - reults in less genetic diversity

What is an example of directional selection?

Antibiotic resistance. Bacteria with a mutation allowing them to survive in the presence of antibiotics will reproduce. Therefore frequency of this allele will increase and the population will shift to have greater antibiotic resistance

What happens in evolution?

• Competition - resources are scarce for most organisms & there is competition between individuals to get them

• Selection/Survival of the Fittest - those that are better adapted are more likely to get the resources & survive

• Reproduction - those that survive are more likely to reproduce - this is differential reproductive success & the offspring will have the new genetic variant/the new allele so the allele frequency for the new allele increases

What is an example of stabilising selection?

Birth weight; babies that weigh around 3kg are more likely to survive than those at lower or higher weights

What is a niche?

The role of a species within its environment. Species sharing the same niche will compete with each other.

What are the three types of adaptation?

• Anatomical - changes to body structure e.g. oily fur.

• Physiological - changes to bodily processes e.g. venom production.

• Behavioural - changes to actions e.g. hibernation.

What is a species?

A group of organisms that can interbreed to produce fertile offspring.

What is courtship behavior?

Behavior carried out by organisms to attract a mate of the same species which can take the form of physical attributes, chemical signals & also behaviors like singing etc.

What is the difference between simple and complex courtship behavior?

Simple - not complicated actions e.g. visual displays, making sound & releasing chemicals

Complex - series of events or making something that signals an animal is ready to mate - e.g. building nests, dancing

How can courtship behavior be used to classify a species?

Courtship behavior is ultimately controlled by the genetic makeup of the species so these behaviors can be used to classify as the more similar the behavior the more closely related.

What are the advantages of courtship behaviour?

• Individuals can recognise sexually mature members of their own species of the opposite sex,

• prevents interbreeding

• form a pair bond, and successfully breed to form fertile offspring

What is classification?

The process of arranging organisms into groups/taxa

What is hierarchical classification?

• groups within groups - taxa

• no overlap between groups

What are the eight groups of classification hierarchy for organisims?

• domain

• kingdom

• phylum

• class

• order

• family

• genus

• species

(Domain) King Phillip Came Over For Good Soup

What is the binomial naming system?

System used to give species a unique universal name.

Generic name - the genus the organism belongs to. Two closely related species will share the same genus.

Specific name - the species the organism belongs to.

e.g. Felis catus

What is phylogenetic classification?

The process of arranging organisms into groups based on their evolutionary origins and relationships into a phylogenentic tree etc.

How do you read a phylogenetic tree?

First branch = common ancestor

First branch off that = first group to diverge

More closely related species diverged away from each other most recently.

The longer the branch the older the species.

How can we clarify evolutionary relationships between organisms?

By analysing their molecular differences.Advances in immunology/genome sequencing provide clear pictures of how related two organisms are

We can use : genome sequencing ,amino acid sequences or immunological comparisons

How do we use genome sequencing to clarify evolutionary relationships between organisms?

Genome sequencing means we can determine the entire base sequecne of an organisms DNA.

This can then be compared to the DNA base sequence of another organism to see how closely related they are - the higher the % similarity of their DNA sequence the closely related they are.

How can we use amino acid sequences to clarify evolutionary relationships between organisms?

Because the primary structure of a protein is coded by the base sequence in DNA, related organisms will have similar DNA sequences & so amino acid sequences.

The more similar the amino acid of a certain protein is the more closely related they are to each other.

How can we use immunological comparisons to clarify evolutionary relationships between organisms?

Similar proteins will also bind to the same antibodies, so if a protein from a different species is able to bind onto a human antibody we know that they are similar.

What is biodiversity?

The variety of living organisms. It can be measured in terms of species diversity - number of species in a community, ecosystem diversity - range of different habitats and genetic diversity

What impact does farming have on species diversity?

decreases species richness

• farmland is typically used for only 1 species (monoculture)

• use of pesticides/ herbicides

What impact does agriculture have on genetic diversity?

decreases it

• farmers select for certain characteristics, which reduces number of different alleles in the population

How can biodiversity be increased in areas of agriculture?

• Use hedgerows instead of fences.

• Grow different crops in the same area, or rotate crops around after a season.

• Limit use of pesticides and herbicides.

What are the different ways you can measure genetic diversity?

• Frequency of observable characteristics.

• Base sequence of DNA - different alleles of the same gene will have slightly different DNA base sequences - comparison between organisms allows scientists to find out how many different alleles there are in that population

• Base sequence of mRNA - different alleles will also produce slightly different mRNA sequences

• Amino acid sequence - slightly different amino acids will be produced from these alleles

What is meant by gene technology?

Sampling DNA or mRNA in order to read and compare the base sequence of organisms.

Or using an amino acid sequence which can be studied as this will also provide information on the organism’s mRNA and DNA sequences.

Why do scientists prefer to use gene technology instead of observation?

Simply inferring DNA differences by observing an organism’s characteristics is not reliable as the characteristics could be coded for by more than one gene, or could be influenced by the environment.

What is meant by interspecific and intraspecific variation?

Interspecific - differences between individuals of different species.

Intraspecific - differences between individuals of the same species.

What is sampling?

Selecting a group of individuals to measure that will represent the whole target population.

How can a random sample be achieved?

Create a grid for your sample area, and then randomly generate coordinates where a quadrat or transect can be placed. Repeat until required sample size is reached