Genetics

DNA

the genetic blueprint which codes for and determines the characteristics of an organism

gene

a DNA sequence that encodes for a specific trait

chromosome

an organised and discrete structure that DNA is packaged into

locus

the position of a gene on a particular chromosome

alleles

alternative forms of a gene that code for the different variations of a specific trait, possess a very similar DNA sequence

genetic mutation

a change in the nucleotide sequence of a section of DNA coding for a particular trait

beneficial mutations

change the gene sequence (*missense mutations*) to create new variations of a trait

detrimental mutations

truncate the gene sequence (*nonsense mutations*) to abrogate the normal function of a trait

neutral mutations

have no effect on the functioning of the specific feature (*silent mutations*)

sickle cell anemia

* caused by a base substitution mutation
* a change to the 6th codon for the beta chain of haemoglobin
* DNA: GAG to GTG on the non-transcribed strand
* mRNA: GAG to GUG at the 6th codon position
* glutamic acid changed to valine
* alters the structure of haemoglobin, causing it to form *insoluble fibrous strands,* which cannot carry oxygen
* red blood cells get a sickle shape, which may form clots in capillaries and are also destroyed more easily, which leads to anemia - low RBC count

genome

the totality of genetic information of a cell or an organism

the human genome consists of:

* 46 chromosomes (barring aneuploidy)
* \~3 billion base pairs
* \~21,000 genes

the human genome project

The Human Genome Project (HGP) was an international cooperative venture established to sequence the human genome

* The HGP showed that humans share the majority of their sequence, with short nucleotide polymorphisms contributing diversity
* completed in 2003

outcomes:

* **Mapping** – The number, location, size and sequence of human genes is now established
* **Screening** – This has allowed for the production of specific gene probes to detect sufferers and carriers of genetic diseases
* **Medicine** – The discovery of new proteins have lead to improved treatments (pharmacogenetics and rational drug design)
* **Ancestry** – Comparisons with other genomes have provided insight into the origins, evolution and migratory patterns of man

point mutations

changes to one base in the DNA code

types of point mutations

* substitution
* deletion
* insertion
* inversion

silent mutation

does not alter the amino acid sequence of the polypeptide

* This is possible because the genetic code is degenerate and certain codons may code for the same amino acid

missense mutation

DNA change alters a single amino acid in the polypeptide chain

* Sickle cell anaemia is an example of a disease caused by a single base substitution mutation

nonsense mutation

DNA change creates a premature STOP codon which truncates the polypeptide

* Cystic fibrosis is an example of a disease which can result from a nonsense mutation (this may not be the only cause though)

frameshift mutation

the addition or removal of a base alters the reading frame of the gene

* This change will affect every codon beyond the point of mutation and thus may dramatically change amino acid sequence

why are people with sickle cell anemia less susceptible to malaria?

Malaria is caused by an endoparasite (*Plasmodium falciparum*) which reproduces inside red blood cells (but not sickle cells)

DNA of prokaryotes

* naked in the cytoplasm
* consists of a single chromosome called genophore
* may possess circular DNA molecules called plasmids

bacterial conjugation

Bacterial cells may exchange plasmids via their sex pili, in a process known as bacterial conjugation

* This exchange of genetic material allows bacteria to evolve new features __within__ a generation (horizontal gene transfer)

genetic material of eukaryotes

* multiple linear molecules of DNA that are associated with histone proteins
* complexed with eight histone proteins (an octamer) to form a complex called a *nucleosome*
* Nucleosomes are linked by an additional histone protein (H1 histone) to form a string of *chromatosomes*
* These then coil to form a *solenoid structure* (\~6 chromatosomes per turn) which is condensed to form a *30 nm fibre*
* These fibres then form loops, which are compressed and folded around a protein scaffold to form *chromatin*
* Chromatin will then supercoil during cell division to form *chromosomes* that are visible (when stained) under microscope

homologous chromosomes

chromosomes that share:

* The same structural features (e.g. same size, same banding patterns, same centromere positions)
* The same genes at the same loci positions (while the genes are the same, alleles may be different)

diploid nuclei

* Nuclei possessing *pairs of homologous chromosomes*
* These nuclei will possess two gene copies (alleles) for each trait
* All somatic (body) cells in the organism will be diploid, with new diploid cells created via mitosis
* Diploid cells are present in most animals and many plants

haploid nuclei

Nuclei possessing *only one set of chromosomes* are haploid (symbolised by **n**)

* These nuclei will possess a single gene copy (allele) for each trait
* All sex cells (gametes) in the organism will be haploid, and are derived from diploid cells via meiosis
* Haploid cells are also present in bacteria (asexual) and fungi (except when reproducing)

heterosomes

sex chromosomes

the Y chromosome

contains the genes for developing __male sex characteristics__ (specifically the SRY gene)

* In its absence of a Y chromosome, female sex organs will develop

karyotype

the number and types of chromosomes in a eukaryotic cell – they are determined via a process that involves:

* Harvesting cells (usually from a foetus or white blood cells of adults)
* Chemically inducing cell division, then arresting mitosis while the chromosomes are condensed
* The stage during which mitosis is halted will determine whether chromosomes appear with sister chromatids or not

karyogram

The chromosomes are stained and photographed to generate a visual profile that is known as a **karyogram**

* The chromosomes of an organism are arranged into homologous pairs according to size (with sex chromosomes shown last)

autoradiography

Cairns’ technique for measuring the length of DNA molecules

autoradiography - procedure

* Cells are grown in a solution containing radioactive thymidine (tritiated thymidine – 3H-T)
* The tritiated thymidine is incorporated into the chromosomal DNA of the cell (3H-T is used as thymidine is not present in RNA)
* The chromosomes are isolated by gently lysing the cells and fixing the chromosomes to a photographic surface
* The surface is then immersed in a radioactively-sensitive emulsion containing silver bromide (AgBr)
* The radiation released from the tritiated thymidine converts the Ag+ ions in silver bromide into insoluble metal grains
* Following a period of exposure, excess silver bromide is washed away, leaving the silver grains to appear as small black dots
* When the photographic film is developed, the chromosomal DNA can be visualised with an electron microscope

chromosome number

Chromosome number is a characteristic feature of members of a particular species

* Organisms with different diploid numbers are unlikely to be able to interbreed (cannot form homologous pairs in zygotes) \n
* In cases where different species do interbreed, offspring are usually infertile (cannot form functional gametes)
* For instance, a horse (diploid = 64) and a donkey (diploid = 62) may produce an infertile mule (non-diploid = 63)

gametes

haploid sex cells formed as a result of meiosis; each gamete carries only one allele of a gene as they possess a single set of genes

genotype

the gene composition for particular traits

phenotype

The observable characteristics of a specific trait

complete dominance

* The dominant allele will mask the recessive allele when in a heterozygous state
* Homozygous dominant and heterozygous forms will be phenotypically indistinguishable
* The recessive allele will only be expressed in the phenotype when in a homozygous state

co-dominance

pairs of alleles are *both expressed equally* in the phenotype of a heterozygous individual, e.g. human blood groups A and B (O is recessive)

hemizygote in males

Human males have only **one** X chromosome (and therefore only one allele) and are *hemizygous* for X-linked traits

why are there more X-linked diseases than Y-linked diseases?

because the X chromosome is larger and contains more genes

autosomal dominant inheritance

* If *both parents are* __*affected*__ *and an offspring is* __*unaffected*__, the trait **must** be dominant (parents are both heterozygous)
* All affected individuals **must** have at least one affected parent
* If both parents are unaffected, all offspring **must** be unaffected (homozygous recessive)

autosomal recessive

* If *both parents are* __*unaffected*__ *and an offspring is* __*affected*__, the trait **must** be recessive (parents are heterozygous carriers)
* If both parents show a trait, all offspring **must** also exhibit the trait (homozygous recessive)

X- linked dominant inheritance

* If a male shows a trait, so too **must** all daughters as well as his mother
* An unaffected mother **cannot** have affected sons (or an affected father)
* X-linked dominant traits *tend* to be more common in __females__ (this is not sufficient evidence though)

X-linked recessive inheritance

* If a female shows a trait, so too **must** all sons as well as her father
* An unaffected mother *can* have affected sons *if* she is a carrier (heterozygous)
* X-linked recessive traits *tend* to be more common in __males__ (this is not sufficient evidence though)

lethal alleles

alleles that cause an organism to die only when present in a homozygous condition

* e.g. achondroplasia

epistasis

a condition whereby one gene controls the expression of another gene

pleiotropy

a single gene affects multiple traits – hence mutations will tend to be severe and affect multiple systems

mosaicism

the presence of two populations of cells with distinct genotypes within a single organism

* It is caused when either mutation or division error creates two distinct cell types which divide into separate cell lines

stages of PCR

1. denaturation - 95 degrees for 1 min to separate the strands
2. annealing - 55 degrees for 1 minute, primers attach to 3’ end
3. elongation - heat-tolerant DNA polymerase (Taq) binds to the primer and copies the strand (\~72ºC for 2 min)

DNA separation by gel electrophoresis

* restriction endonuclease cuts DNA into fragments of different length
* fragments separate due to the negative charge on the phosphate group
* DNA fragments are placed in agarose gel, their size is calculated by comparing against known standards

protein separation by gel electrophoresis

* proteins treated with anionic detergent, which imparts a uniform negative charge
* proteins placed in *polyacrylamide* gel
* electric current separates the fragments

how are fragments separated by the electric current?

* the lightest travel the furthest
* the heaviest travel the closest

satellite DNA

* long stretches of DNA
* made up of short tandem repeats
* within the non-coding regions of an individual’s genome
* each individual has a different number of tandem repeats, hence they can be used for DNA profiling

Bt maize pollen vs monarch butterflies

* study: compared caterpillars fed on pollen-dusted milkweed vs caterpillars fed on non-dusted milkweed
* caterpillars exposed to Bt pollen were found to have eaten less, grew more slowly and exhibited higher mortality rates
* A second study was conducted comparing the survivor rates of monarch butterflies based on proximity to Bt corn fields:
* There was no significant increase in mortality when monarch larva were placed in or near an actual Bt corn field
* From this it was concluded that exposure to Bt pollen poses no *significant* risk to monarch butterfly populations 

clones

groups of genetically identical organisms or a group of cells derived from a single original parent cell

somatic cell nuclear transfer

* Somatic cells are removed from the adult donor and cultured (these cells are diploid and contain the entire genome)
* An unfertilised egg is removed from a female adult and its haploid nucleus is removed to produce an enucleated egg cell
* The enucleated egg cell is fused with the nucleus from the adult donor to make a diploid egg cell (with the donor’s DNA)
* An electric current is then delivered to stimulate the egg to divide and develop into an embryo
* The embryo is then implanted into the uterus of a surrogate and will develop into a genetic clone of the adult donor 

monozygotic twins

fertilised eggs splits into two identical cells and forms an embryo

dizigotic twins

an unfertilised egg splits into two identical cells and each is fertilised by a different sperm cell

human cloning methods

Identical twins will be clones of one another (genetically identical), while non-identical twins will share 50% of the same DNA