Heredity

Introduction to Reproduction

Mechanisms of Reproduction

What is Reproduction

  • reproduction is the production of offspring

  • it is necessary for the continuation of life


what are ways can organism can reproduce

  1. sexual reproduction

    • 2 parents are involved, one male and one female —> each provide half of the genetic information for the new offspring in the form of a sex cell (sperm and egg)

    • similar characteristics to parents but NOT identical

  2. Asexual reproduction

    • 1 parent and no fertilisation

    • genetically identical to parent - they are clones


Reproduction in Different Organisms

Animals

  • Sexual reproduction

    • male sperm and female egg fuse together during fertilisation to form a new organism


what are the different types of fertilisation

  1. external

    • fertilisation outside of the female body

    • both the male and female release their sex cells directly into their surrounding environment

    • fish and amphibians fertilise externally


  • advantages:

    • large number of offspring can be produced because of the huge number of sex cells that can be released

    • can allow fertilisation to occur without the parents meeting


  • disadvantages:

    • environmental conditions mean that the chances of the sex cells surviving are reduced

    • wasted resource as many of the sex cells released do not get the chance to fertilise

    • no guarantee any offspring will survive


  1. internal

    • fertilisation within the female’s reproductive system

    • usually land based - mammals, reptiles and birds fertilise internally


    • advantages:

      • offspring have higher chances of survival because the environment inside of the female body is more contained and protects sex cells

      • organism can save on resources and produce less sex cells

      • allows the animal to choose its mate


    • disadvantage:

      • only a few offspring can be produced at once

      • parents must physically meet


Plants

  • sexual reproduction

    • pollination

      • insects, birds or wind transport pollen (male sex cells) from one flower to another deep inside the plant are ovules (female plant sex cells) after fertilisation the female part of the flower develops into a fruit and the ovules turn into the seeds

  • asexual reproduction

    • runners:

      • side branches with little clumps of leaves and roots called plantlets distributed along them. They grow along the ground and the roots dig down and establish the plantlets as individual plants

    • bulbs:

      • from the bulbs little buds form and grown form new plants

    • cuttings

      • branch from the parent plant is cut off and planted into the ground where it will grow roots and establish itself as a new plant


Fungi

  • Fungi are eukaryotic organisms that can be either unicellular or multi-cellular

  • can reproduce sexually or asexually

  • determination of which reproduction to use it based on the environment

    • good conditions —> reproduce asexually and spread quickly (budding or spores)

    • bad conditions —> reproduce sexually through spores as two spores from two different fungi fuse together to form a single new cell

      • sexually increases genetic variation and he species chances of survival


Bacteria

  • Bacteria is prokaryotic single celled organism

  • asexual reproduction - Binary fission

    1. cell replicates its DNA

    2. cell grows to about twice its original size

    3. cytoplasm divides and a new cell membrane forms


Protist

  • Protist are eukaryotic single celled organism

  • asexual reproduction - binary fission



Evaluating Reproduction

Comparing Sexual and Asexual Reproduction

features

sexual reproduction

asexual reproduction

number of parents

two

one

genetics of offsprings

unique

identical

type of cell division

meiosis

mitosis, binary division, vegetative propagation and budding

advantages

  • increases genetic diversity

  • population is more likely to be able to adapt in response to change

  • more efficient

  • does not need to spend time finding or competing for a mate

  • a population is able to increase in size very quickly

disadvantages

  • cost the parents time, energy and resources

  • slower reproductive rate

  • low genetic diversity

  • equally vulnerable to environmental factors, infections and pests

organisms

animals, plants, fungi

plants, fungi, bacteria, protists

Mammalian Reproduction

what is a mammal

  • warm-blooded

  • vertebrate (has a backbone)

  • lactates (able to produce milk)

  • have hair


mammalian reproduction

  • fertilisation refers to the fusion of the egg and sperm

    • internal fertilisation occurs within the female’s reproductive tract

  • implantation refers to the attachment of the fertilised egg to the uterine lining

  • pregnancy refers o the time the offspring spends within the female’s body


fertilisation

  1. ovulation - ovary releases egg

  2. egg travels through the fallopian tube (oviduct)

  3. male releases semen (containing sperm) during sex

  4. the egg and sperm fuse to create a zygote

  5. zygote forms strong outer membrane to stop more sperm entering


implantation

  1. the zygote travels down to the cervix where it buries deep into the lining of the uterus

  2. as the embryo develops the amniotic sac, placenta and umbilical cord form

    • amniotic sac —> bag containing fluid which helps keep embryo at optical temperature and provides cushioning

    • placenta —> provides nutrients and removes waste

    • umbilical cord —> connects offspring to placenta where it allows substances to move between


role of hormones

  • hormones are the chemical messengers produced by the body, which travel in the blood to other cells where they have a specific effect


  • Oestrogen

    • made by the placenta

    • stimulates ovulation

    • aids blood flow to offspring

    • aids organ development

    • stimulates progesterone


  • progesterone

    • progesterone is made by the ovaries, and them by the placenta

    • stimulates thickening of uterus lining

    • aids placenta function and relaxes uterus

    • helps mother’s immune system tolerate infant


  • other hormones

    • relaxin

      • loosens uterine muscles during pregnancy

    • oxytocin

      • stimulates production of milk

      • triggers uterine contractions



Manipulation in Agriculture

Reproduction in Agriculture

What is Agriculture

  • Agriculture is the growth of crops and animals for human needs

    • provides us with food and clothing


Manipulating Reproduction in Agriculture

selective breeding refers to the creation of organisms with certain desirable characteristics


  • Natural Breeding

    • involves placing a male and female from the same species in a enclosed environment, and waiting for them to mate

    • this is the most simple and easy way to manipulate reproduction


  • Artificial Insemination

    • involves taking sperm form a male (who has desirable traits) and inserting it directly into the female’s reproductive tract


  • Artificial Pollination

    • involves taking pollen from one flower and inserting it directly into another flower using a small brush


  • cloning

    • involves creating a genetically identical copy of an organism using genetic engineering techniques

    • this is the most complex way to manipulate reproduction


Impacts of Manipulating Reproduction on Agriculture


advantages:

  • increased sales

    • increased production

    • improved food quality

  • increases resistance to certain pests and diseases

    • farmers save money

    • less environmental contamination


disadvantages:

  • reduced biodiversity (if used excessively)

    • as ‘undesirable’ traits are bred out, variation in a species decreases which means the population is more likely to suffer from changes in the environment



DNA and RNA

DNA and RNA

What does DNA do

  • a type of nucleic acid that is responsible for storing genetic information in cells

  • acts as an instruction manual: contains information needed for growth, survival and replication

  • eukaryotes

    • relatively large amount of DNA

    • DNA is bounded

    • forms linear chromosomes

    • chromosomes reside in the nucleus

  • prokaryotes

    • relatively small amount of DNA

    • DNA is unbounded

    • have a single, circular chromosome

    • chromosome reside in the cytoplasm


DNA structures

  • consists of two chains of building blocks that twist together form a double helix

  • consists of building blocks called nucleotides

    • Deoxyribose sugar

    • Phosphate group

    • Nitrogenous base

      • Guanine

      • Cytosine

      • Adenine

      • Thymine

  • each base has a complementary base pairing

    • A + T

    • C + G

    • this ensures the ‘rungs’ are all the same length

  • deoxyribonucleotide join together forming a long chain

  • two chains twist around each other to form a double helix structure

    • the deoxyribose sugars and phosphate groups are on the outside whereas the nitrogen bases make up the rungs on the inside


What is RNA

  • a type of nucleic acid that is responsible for interpreting genetic information (from DNA) into proteins

  • DOES NOT STORE GENETIC INFORMATION

  • helps to turn DNA into proteins


RNA Structure

  • consists of nucleotides which contain sugar, phosphate and nitrogen base

  • RNA is single stranded

  • there is a specific type of nucleotide in RNA called ribonucleotide

  • RNA does NOT have thymine they HAVE uracil

    • G + C

    • A + U


DNA Replication

  • as cells are constantly replicating, DNA has to as well


  1. unravelling the DNA

    • the enzyme DNA helicase breaks the hydrogen bonds between the bases, ‘unzipping’ the double helix into two single strands


  1. Building a new strand

    • semi- conservative: when DNA is produced, one of the strands in each new DNA molecule comes from the old DNA molecule

    • reduced the chance of copying a strand incorrectly

    • know how to draw an annotated diagram of a DNA replication or whatever

    • DNA polymerase helps bind free nucleotides in the cell nucleus to the single strand






Draw a labelled diagram demonstrating the difference in the form of DNA between prokaryotic and eukaryotic cells.

DNA is Prokaryotes and Eukaryotes

Prokaryotes

  • a cell is prokaryotic if it does NOT have a nucleus or any other membrane bounded organelles

  • DNA is found in the cytoplasm, and, it is small and circular

  • examples

    • bacteria and archaea

    • usually unicellular

    • earliest life forms


Eukaryotic

  • a cell is eukaryotic if it DOES have a nucleus and membrane bound organelles

  • DNA is found in the nucleus and is linear

  • has lots more DNA compared to prokaryotes

  • examples

    • animals and plants

    • multicellular (cell has organelles and can perform more complex and specialised functions)


DNA in Prokaryotes vs Eukaryotes


DNA features

Prokaryotic cells

Eukaryotic cells

DNA shape

Circular

Linear

DNA location

Cytoplasm

Nucleolus

Relative amount of DNA

Small

Large

DNA and Replication

DNA replication

  1. Unravelling the DNA

    • DNA is made up of two polynucleotide stands held together by hydrogen bonds between complementary bases

    • The enzyme DNA helicase breaks the hydrogen bonds between the bases, ‘unzipping’ the double helix into two single strands

  1. building a new strand

    • helicase is still acting on the strands

    • the exposed strands act as templates for a new strand


  • semi-conservative: when DNA is produced one of the strands in each new DNA molecule comes from the old DNA molecule

    • reduced the chance of copying a strand incorrectly

    • know how to draw an annotated diagram of a DNA replication

    • DNA polymerase helps bind free nucleotides in the cell nucleus to the single strand



  1. Forming the DNA backbone

    • DNA polymerase stitches these newly joined nucleotides together so that the sugar-phosphate backbone is formed

    • initially, only the bases are held together by weak hydrogen bonds, the new strand is then reinforced by the sugar-phosphate backbone

    • in baby words:

      • Bases Pair First: The free nucleotide bases (A, T, C, and G) pair up with their complementary bases on the original DNA strand using weak hydrogen bonds. This forms the "steps" of the ladder.

      • DNA Polymerase Builds the Backbone: DNA polymerase connects the sugar of one nucleotide to the phosphate of the next nucleotide, forming the sugar-phosphate backbone. This backbone runs along the outside of the DNA strand and gives it strength.

  • two identical DNA molecules are produced!


all of the steps overlap !


Mitosis and Meiosis

  • cell replication is the process by which cells replicate their genetic material and divide to form new cells

Mitosis

  • is a type of cell division where 1 parent cell divides once to produce two identical daughter cells

  • DNA is located in the nucleus and is wrapped around in a protein, this is called a chromatin

  • parent cell:

  • usually there are lots of smaller pieces of chromatin’s rather than just one big one

    • half of the chromatins comes from the mother and the other half comes from the father


step 1 involves the replication of DNA / chromatin

  • the two identical chromatin pieces are still joined in the middle and they quickly shorten and thicken

  • when coiled up in the X shape it is called a chromosome

  • the chromosomes come in matching pairs, also known as homologous chromosomes


step 2: chromosomes line up individually

step 4: spindle fibres attach to centromeres

step 5: spindle fibres shorten, centromeres break and chromatids move apart

step 6: cytoplasm separates, cell and nuclear membranes from, chromosomes uncoil

  • identical daughter cells


name

definition

DNA replication

DNA replicates

Prophase

Chromatin shorten and thickens to form chromosomes

Metaphase

Chromosomes line up individually
Spindle fibres attach to centromeres

Anaphase

Spindle fibres shorten, centromeres break and chromatids move apart

Telophase

Cytoplasm separates, cell and nuclear membranes form, chromosomes uncoil

why is mitosis important

  • it creates new body cells that are needed for growth, repair, and maintenance

    • important for the individual

      • allows us to heal injuries, grow and survive

    • important for the species

      • increases and organism’s chances of reproducing


Meiosis

  • is a type of cell division where 1 parent cell divides twice to produce 4 non-identical daughter cells


MEIOSIS I

step 1: DNA replication

step 2: chromatin shortens and thickens to form chromosomes

step 3: chromosomes line up in homologous pairs

step 4: crossing over occurs (homologous chromosomes swap sections)

step 5: spindle fibres attach, shorten, and homologous chromosomes break move apart

MEIOSIS II

step 6: chromosomes line up individually

step 7: spindle fibres attach to centromeres

step 8: spindle fibres shorten, centromeres break and chromatids move apart

step 9: cytoplasm separates, cell and nuclear membrane form, chromosomes uncoil

step 10: four non-identical daughter cells (gametes / sex cells)


why is meiosis important

  • allows for the continuity of a species because it means that organisms can produce offspring with new gene combinations

    • evolution (natural selection): a population that has variation is more likely to survive environmental changes



Cell Replication In Practice

Sources of Genetic Variation in Sexual Reproduction

Genetic Variation

  • is a term used to describe the differences between the genomes of individuals of the same species

    • genome - an organism’s complete set of DNA

    • species - group of organisms which can interbreed to produce live, fertile offspring

  • differences in the DNA of a group of similar organism


where does this variation come from?

Random Segregation and Crossing over (Meiosis)

  • independent assortment - pairs of homologous chromosomes arrange independently to each other,

  • as a result

  • random segregation - when the chromatids segregate the set of chromosomes in the daughter cells is random (different combinations = genetic variation)

  • crossing over also contributes to genetic variation because it changes the genetic composition of the chromosomes


Fertilisation

  • contributes to genetic variation because it allows for different gametes (containing different alleles) to combine

    • there are lots of unique organism in a species, which all have lots of unique gametes (due to meiosis). Any of these gametes can combine during fertilisation to form different zygotes


mutation

  • refers to a change in the base sequence of an organism’s DNA

  • a change in the DNA = different genes = different traits = different phenotype




DNA and Polypeptide Synthesis

Key terms in Genetics

Genome

  • is an organisms complete set of genetic material (DNA)

  • it includes all of the information the organism needs to grow and survive


gene

  • a section of genetic material (DNA), each gene codes for a different characteristic

  • the different sections of the genetic information control a particular feature of the organism

  • each gene acts as a template for a particular mRNA strand which is translated into a particular polypeptide which determines a particular characteristic


alleles

  • alleles are alternative forms of the same gene (that’s why people have different hair and eye colours)

  • alleles are found at the same place on the same chromosome (in different organism from the same species)


genotype

  • refers to an organism’s genetic make-up for a particular characteristic


phenotype

  • refers to an organism’s physical expression of a particular characteristic

  • it is determined why two main things

    • which genes are present (genotype)

    • environmental factors


Genotypes and Phenotypes

Genotype

  • refers to an organism’s genetic makeup for a particular characteristic

  • typically an individual’s genotype for a trait consists of two alleles, one inherited from their mother and one from their father

  • genotype is determined at fertilisation, when a sperm and egg fuse to form a zygote


Phenotype

  • refers to an organism’s physical expression of a particular characteristic

  • it is observable or expressed characteristics of an organism

  • determined by which alleles are present (the genotype) as well as environmental factors


Proteins

Structure

  • consists of building blocks called amino acids which are linked together via peptide bonds

  • amino acids are made of carbon, hydrogen, oxygen and nitrogen

  • proteins are the only biological molecules that contain nitrogen


Function

  • two classifications of protemone

    • structural proteins: maintain cell shape and make out connective tissues

      • collagen which increases the flexibility of skin and bone


    • enzymes: biological catalysts - living proteins which speed up chemical reactions occuring in cells. they act on specific substrates to either break it down or combine it

      • sucrase breaks sucrose down into glucose and fructose

      • DNA polymerase bonds nucleotides together during DNA replication


    • hormones: proteins which are secreted into the blood by endocrine cells (glands) - travel to target tissues, where they cause a change in activity

      • insulin which regulates blood glucose


    • immunity: antibodies are proteins involved in the immune response - antibodies react with antigens (foreign particles) to help remove them from the body


Testing for Proteins (Biuret Test)

  1. add a few drops of sodium hydroxide to the sample (makes the solution alkaline which is required for the test to work)

  2. add a few drops of copper sulfate

  3. if it remains blue, protein is not present but if it turns purple then protein is present


Protein Synthesis

Introduction to Genes

  • gene: a portion of DNA that tells the cell how to make a specific protein

  • codon: each set of three codes for one particular amino acid in the polypeptide chain

    • the order of codons and the bases within them determine which amino acids are produced and in what order

    • special codons that say when to start and stop reading code

  • translating DNA is like code breaking, and the genetic code is the template

  • specific codon —> specific amino acid

    • different codons can code for the same amino acid

  • the genetic code if ‘degenerate’


protein synthesis

  1. transcription

    • an mRNA copy of a gene is made using DNA as a template

    • takes place in the cell nucleus (1)

    • RNA polymerase attaches to the DNA at the desired gene and separates the strands to expose the nucleotides in that region (only the section with the gene is pulled apart, NOT the whole DNA strand) (2)

    • mRNA is made by complementary base pairing, not matching identical bases

    • RNA polymerase adds RNA nucleotides one at a time (3)

      • DNA strands rejoin so the bases are not left exposed


  • in prokaryotes this is where it is completed but in eukaryotes there is one more step

  • in eukaryotes, introns are spliced out of the strand and exons are stuck together to form the final mRNA strand

    • introns: don’t code for proteins

    • exons: expressed, code for proteins

  • mRNA molecules leave the nucleus and enter the cytoplasm through a nuclear pore to the cytoplasm where it attaches to a ribosome for translation


  1. translation

    • nucleic acid is translated into protein. A polypeptide chain is formed according to the sequence of codons

    • mRNA attaches to the ribosome at a particular start codon

    • anticodon: a triplet bases that corresponds to a specific mRNA codon

    • the tRNA molecule with the correct anticodon pairs up with mRNA in the ribosome

      • each tRNA molecule is bound to a specific amino acid

      • a second tRNA molecule attaches to the next codon on the mRNA strand

    • the ribosome catalyses the formation of a peptide bond between the two amino acids

      • the first tRNA molecule moves away from the ribosome leaving its amino acid, these repeats for the other tRNA until the stop codon where the last tRNA is bound to the ribosome

    • when a stop codon is reached the mRNA, tRNA and ribosome separate, leaving a finished polypeptide chain




Genetic Variation

Inheritance

introduction to inheritance

  • inheritance explains how characteristics are passed from one generation to the next, based on the transfer of DNA


multiple alleles

  • alleles are different versions of the same gene, and are found at the same place on homologous chromosomes


dominant and recessive alleles

  • dominant allele is always expressed in the phenotype

  • the recessive allele is only expressed in the phenotype when there is no dominant allele

  • a heterozygous of non-pure-breeding organism has 2 different alleles for a particular gene (brown and blue eye allele)

  • homozygous or pure-breeding organism has 2 identical alleles for a particular gene (brown and brown eye allele) (blue and blue eye allele)


punnett squares

  • predict the possible genotypes and phenotypes of the offspring produced by a particular male and female


  • as every gamete has the dominant tall allele (T), 100% of the pea plants will be tall


autosomal and sex-linked inheritance

types of chromosomes

  • humans and 23 homologous (matching) pairs of chromosomes (46 in total)

  • each pair of homologous chromosomes codes for the same genes

  • classified into two categories based whether they code for sexual characteristics

    • sex chromosomes

      • female: 2 similar chromosomes (XX)

      • male: 2 dissimilar chromosomes (XY)

    • autosome

      • don’t code for any sexual characteristic - normal


autosomal inheritance

  • patterns in the expression of characteristics which are found on autosomes

    • dominant/recessive

    • co-dominant

    • incomplete


sex-linked inheritance

  • patterns in the expression of characteristics which are found on sex chromosomes (X and Y)

  • sex-linked inheritance is different to autosomal inheritance due to 2 facts

    • the y chromosome has fewer genes than the x chromosome

    • males only have one copy of the x chromosome


  • x-linked

    • transmission of genes which are found on the x chromosomes

    • recessive: affect men more than woman as there is a higher chance of a man inheriting one faulty x chromosome

    • dominant: affects gender equally


  • y-linked

    • transmission of genes which are found on the y chromosome

    • only passed from father to son: never seen in females


Codominance and incomplete

Codominance

  • refers to a situation in which both alleles are expressed in the phenotype

    • use different capital letters to represent codominant alleles in punnett squares

example: human blood type

  • blood type consists of A, B, AB, and O

  • a person’s blood type is determined by their combination of alleles

  • there are multiple alleles for blood type: by I^A, I^B and i

  • these alleles code for glycoproteins in the outer membrane of red blood cells


incomplete dominance

  • the dominant allele is only partially expressed - it does not completely control the phenotype of a heterozygous organism

  • red flower and white flower make pink flower = the red allele only partially masks the white allele resulting in the pink phenotype


Pedigrees

features of pedigrees

  • diagram which shows how traits are passed on over many generations




applications of pedigrees

  • identify patterns

  • determine genotypes

  • predict phenotypes


Reading Pedigrees



Examining Data

Allele Frequency

  • allele frequency refers to the relative proportion of a particular allele in a population

    • allele frequency = number of an allele in a population / total number of alleles in the population

  • you can work out allele frequencies by taking a sample of the population, as long as the sample is big enough for us to say that it is likely to be representative

  • allele frequencies can be calculated from information about alleles, or by looking at phenotypes so long as we know the relationship between genotype and phenotype.


The Hardy-Weinberg Model

  • describes and predicts alleles frequencies in a non-evolving population

  • states the alleles frequencies will stay the same across generations as long as no evolutionary processes occur

  • is used to calculate genotype frequencies in a population, based on given alleles frequencies



Predicting Speciation

  • there are several evolutionary processes which can cause populations to move away from the predictions of the hardy-Weinberg model, including

    • natural selection

    • preferential mating

    • migration

    • mutations

    • and random events

  • the influence of evolutionary processes means that the model can not always accurately predict allele and genotype frequencies in a population

  • if allele frequencies in a population are not following the hardy-Weinberg equilibrium we can assume that the speciation is occurring

    • speciation typically occurs when there is a barrier to gene flow

    • if the allele frequencies in two populations are different there is probably a barrier to gene flow

    • if we measure frequency data for enough alleles we many be able to work out of two populations have stopped interbreeding making them different species



Population Genetics

Population Genetics in Conservation

measuring extinction risk

  • location: Galapagos Island, what: heavy rains, impact: cactuses produced smaller seeds

    • the change seeds had knock-on effects for species feeding on the seeds, such as the common cactus finch

  • if the finch population has high genetic diversity

    • variation in observable traits exists (including beak size)

    • finches with smaller beaks can easily eat the smell seeds

    • finches with smaller beaks more likely to survive than finches with larger beaks

  • in finches population has low genetic diversity

    • less variation in genes contributing to beak size

    • lower number of finches with favourable small beaks

    • population could be significantly reduced or eradicated


  • populations with greater genetic diversity withstand environmental changes better

  • conservation scientists measure population genetics to calculate the risk of extinction


monitoring inbreeding

  • inbreeding refers to when closely related individuals breeding together (this occurs when individuals only have access to a small range of potential mates)

  • closely related individuals have similar ancestors, so are more likely to inherit the same unhealthy allele

    • unhealthy alleles are often recessive

    • inheriting two copies of the unhealthy allele led new born choughs to die soon after birth

    • the high death rate among young birds led the Scottish Chough population to fall rapidly.


  • inbreeding may occur if population size suddenly falls or if population is split into smaller groups


  • comparing the genomes of a random population sample can allow us to monitor inbreeding by:

    • allowing us to determine how closely related population members are

    • allowing us to measure the allele frequencies for unhealthy mutations

      • allele frequencies —> the relative proportion of a particular allele in a gene pool

  • conservation scientist look at population genetics to monitory inbreeding


investigating speciation

  • speciation refers to the formation of new species

    • species —> a group of organisms that interbreed to produced fertile offspring

  • cryptic species are groups of species originally through to be the same but are different

  • during speciation, populations stop inbreeding, preventing DNA from being shared between populations, creating a barrier to gene flow

    • alleles may be lost in one population and not the other

    • new alleles ay arise in one population and not the other

  • population genetics allows us to compare the allele frequencies within and between populations

    • if allele frequencies are becoming very different, it suggests speciation is occurring

  • conservation scientist look at population genetics to better understand ecosystems


Population Genetics in Disease Inheritance

disease affected by multiple genes

  • many genetic disorders are affected by more than one gene

  • polygenetic inheritance refers to when the inheritance of an observable trait is determined by many genes

    • genes showing polygenic inheritance often have environmental influences such as cardiovascular disease and some mood disorders


  • identifying the regions of DNA associate with a genetic disorder shows:

    1. who is likely to be affected

    2. what goes wrong in the cell to cause the disease

    3. how we can treat the disease


Genome-Wide Association Studies

  • can be used to identify single nucleotide polymorphisms (SNPs) that affect you chance of inheriting a genetic disease

    • contribute to risk of getting a disease

    • are found near a region of DNA contributing to the risk of getting a disease

    • can be associated with a particular ethnicities of heritages

      • population stratification can be used to ensure we identify SNPs associated with disease rather than ethnicities




Population Genetics in Human Evolution

primate evolutionary relationships

  • humans are classified as Homo sapiens

  • we can base our ideas about the evolutionary relationships of different species on their observable characteristics as well as DNA evidence


DNA and Evolutionary Relationships

  • As humans share 99% of their DNA with chimpanzees (and only 98% with gorillas) they share ore recent common ancestor with and are more closely related to chimpanzees than to gorillas

  • there has been more time for the DNA of humans and gorillas to evolve differences

  • the more we collect and analyse DNA samples the more accurate our understanding of primate evolution is

  • on average, each base pair of primate DNA has a one in a billion chance of mutating per year


studying human migration

  • analysing DNA can inform us of evolutionary relationships

  • if we know the rate of DNA mutation we can work out when the last common ancestor of two species of populations lived


Inheritance Patterns in a Population

PCR and Gel Electrophoresis

PCR

what is PCR

  • Polymerase Chain Reaction (PCR) is a technique used to amplify DNA, in vitro

    • amplify DNA —> PCR involves making lots of copies of a specific region of DNA (usually necessary if we want to test, analyse or use a DNA sample)

    • in vitro —> PCR is performed in a test tube, rather than a living organism

  • scientists way of DNA replication

    • involves copying DNA

    • occurs in a test tube

    • only a specific region is copied


Materials needed for PCR

  • Template —> DNA sample which is going to be copied in PCR

  • free nucleotides —> building blocks of DNA

  • Heat-table DNA polymerase —> enzyme which catalyses DNA synthesis, according to the base sequence of the template

    • since PCR involves large temperature changes, its important that we have a DNA polymerase which can survive them - heat-stable

  • primers —> short single stranded pieces of chemically synthesised DNA which flank the target region

  • buffer —> liquid into which all of the other ingredients are added; prevents sudden pH changes


steps in PCR

  • put the mixture into a thermal cycler (PCR uses variations in temperature to control the replication process)


  1. Denaturation

    • PCR reaction mixture is heated to 95 deg

    • DNA is denatured —> separates to form two single strands

  2. Annealing

    • PCR reaction mixture is cooled to 55 deg

    • allows primers to anneal (bind) to the template DNA

  3. extension

    • PCR reaction mixture is heated to 72 deg

    • DNA polymerase moves down the template, synthesizing new DNA

  4. Denaturation

    • PCR reaction mixture is reheated to 95 deg

    • separates the DNA and stops DNA synthesis, so that the process can be repeated


Gel Electrophoresis

steps in Gel electrophoresis

  1. prepare the set up

    • pour liquid agarose gel into a mould

    • insert a well comb

    • once the mould has set, place it into a gel box

    • immerse gel with buffer (can conduct electricity)

  2. Load DNA samples and DNA ladder

    • each DNA sample is transferred intro its own well

    • a DNA ladder is added into one well

    • NOTE: don’t forget to record what you put in each well

  3. Run the gel

    • turn on the power - a current runs though the gel

    • DN migrates through the gel, towards the positive pole (opposites attract)


  • as the gel has lots of tiny pores the small DNA fragments can fit through the pores while the larger ones can’t thus the smaller DNA fragments go through the gel faster than the larger DNA fragments


  1. visualising the DNA fragments

    • add a dye to stain the DNA fragments

  • band —> contains a large number of DNA fragments of the same size which have ultimately travelled to the same position in the gel


applications of PCR and Gel electrophoresis

  • DNA sequencing —> process of determining the base sequence (ATCG) of a DNA sample

    1. use PCR to amplify DNA

    2. use sanger reaction to produce fragments for sequencing

    3. run fragments on electrophoresis gel to determine sequence


  • DNA profiling —> process of analysing DNA variations, for the purpose of identification

    1. use PCR to amplify short tandem repeats (STRs)

    2. run fragments on electrophoresis gel to determine the size of the STR fragments


  • recombinant DNA —> DNA which contains genes from two or more different sources

    1. PCR can be used to amplify a targets gene

    2. run recombinant DNA on electrophoresis gel to determine whether gene has been successfully inserted



DNA Sequencing

DNA Sequencing

What’s DNA Sequencing

  • process of determining the sequencing of nucleotide (ATCG) in a piece of DNA

  • the scale of DNA sequencing varies

    • single gene

    • whole genome


steps in DNA sequencing (according to the sanger method)

gel electrophoresis

  1. collect a DNA sample

    • obtained from any material which contains cells

    • hair, saliva, blood

  2. extract DNA from sample

    • chemicals are added which break open the cells

    • DNA is separated from the other cell components such as proteins

  3. Amplify DNA

    • involves using PCR to make lots of copies of the DNA

    • optional: only necessary if the sample was too small to provide enough DNA

  4. perform sanger sequencing reaction

    • GOAL: separately identify the position of each nucleotide

    • use 4 ‘special’ PCRs = normal PCRs with a chain-terminating nucleotide

  5. determine DNA sequence

    • run all 4 PCR reactions on an electrophoresis gel, to determine the lengths of the fragments in each reaction

RULES FOR DETERMINING A DNA SEQUENCE

  1. work from smallest to largest fragment (one at a time)

  2. identify which PCR reaction the fragment came from

  3. the next nucleotide is complementary to the chain-terminating nucleotide in that reaction


capillary electrophoresis

  1. collect a DNA sample

    • obtained from any material which contains cells

    • hair, saliva, blood

  2. extract DNA from sample

    • chemicals are added which break open the cells

    • DNA is separated from the other cell components such as proteins

  3. Amplify DNA

    • involves using PCR to make lots of copies of the DNA

    • optional: only necessary if the sample was too small to provide enough DNA

  4. perform sanger sequencing reaction

    • GOAL: separately identify the position of each nucleotide

    • use 4 ‘special’ PCRs = normal PCRs with a florescent chain-terminating nucleotide

  5. Determine DNA sequence

    • run all 4 PCR reactions on a capillary electrophoresis gel

      • smaller fragments move towards the end of the tube faster

      • as each fragment passes the laser, its fluorescent tag lights up

      • fluorescence is measured by a detector and recorded to produce an electropherogram

RULES FOR DETERMINING A DNA SEQUENCE

  1. work from left to right

  2. the next nucleotide is complementary to the fluorescent chain-terminating nucleotide


Applications of DNA sequencing

  • in medicine, DNA sequencing can be used to determine if a patient is at risk of a genetic disease

    • genetic diseases are usually associated with the presence of particular genes

    • an example of a genetic disease that can be identified using DNA sequencing is sickle cell anaemia

  • DNA sequencing is a useful tool in scientific research because it can be used to study genomes and the proteins they encode, at a molecular level

    • in genome mapping, DNA sequencing is used to determine he locations of genes and the distance between them

    • potential drug targets and variations in drug targets can be identified using DNA sequencing. this provides an opportunity for personalised medicine

  • DNA sequencing is used in evolutionary biology to determine inheritance patterns

    • evolutionary biology is the study of how different organisms are related and how they evolved

  • the uniqueness of a persons genetic code means that we can identify them by sequencing their DNA

    • this can be used to determine parentage or the identity of a culprit/victim involved in a crime.