Advanced Molecular Biology Flashcards
What is cell cycle?
Cell cycle is the ordered sequence of events that occur in a cell in
preparation for cell division
4 stages of the cell cycle
G1
S
G2
Mitosis
G1 phase
the cell increases in size
S phase
the cell copies its DNA
G2 phase
the cell prepares to divide
Interphase
It is the period between two cell divisions. Made of G1, S and G2 phase
Classification of proteins that play a role in stimulating cell division (4)
growth factors,
growth factor receptors,
signal transducers, and nuclear regulatory proteins (transcription factors)
G0
A deviation from the four cell cycle stages where a cell is not actively preparing to divide (It becomes quiescent)
Two ways cell cycle can be regulated
Regulation by external events such as growth hormone, cell size and neighboring cell death
Regulation by internal checkpoints located at the end of G1 and the S/mitosis transition. Also in metaphase.
What is a cell cycle checkpoint
A checkpoint is one of
several points in the eukaryotic cell cycle at which the progression of a
cell to the next stage in the cycle can be halted until conditions are
favourable.
What is the G1 checkpoint
The G1
checkpoint, also called the restriction
point (in yeast), is a point at which the cell irreversibly commits to the
cell division process. External influences, such as growth factors, play a
large role in carrying the cell past the G1
checkpoint.
Major role of the G2 checkpoint
the most important role of the G2
checkpoint is to
ensure that all of the chromosomes have been replicated and that the
replicated DNA is not damaged.
M checkpoint
The M checkpoint is also known as the spindle checkpoint,
because it determines whether all the sister chromatids are correctly
attached to the spindle microtubules
Two classes of cell cycle regulatory molecules
Positive
Negative
Positive regulatory cell cycle molecules
Cyclins
Cyclin dependent kinases
Cyclins regulate the cell cycle only when they are tightly bound to Cdks.
The 4 cyclin molecules
Cyclin D, E, A, B
How do cyclins and cdks work together
Cyclins flunctuate depending on the cell cycle stage and determine the cyclin-cdk complexed that form.
the cyclin-cdk complex must be phosporylated at certain parts to become active
CDKs
Cyclin-dependent kinases (Cdks) are
protein kinases that, when fully activated, can
phosphorylate and thus activate other proteins
that advance the cell cycle past a checkpoint.
To become fully activated, a Cdk must bind to a
cyclin protein and then be phosphorylated by
another kinase.
Cdk inhibitors
Molecules that prevent the full activation of Cdks
How can cdk inhibitor blocks on cdk be removed
Only when the specific event the inhibitor monitors has been completed
3 main negative regulatory molecules
Retinoblastoma protein, p53 and p21. All act primarily in the G1 checkpoint
Mode of action of the 3 main negative regulatory molecules
If damaged DNA is
detected, p53 halts the cell cycle and recruits enzymes to repair the DNA.
If the DNA cannot be repaired, p53 can trigger apoptosis, or cell suicide,
to prevent the duplication of damaged chromosomes.
As p53 levels rise,
the production of p21 is triggered. p21 enforces the halt in the cycle
dictated by p53 by binding to and inhibiting the activity of the Cdk/cyclin
complexes.
Rb exerts its regulatory influence on other positive regulator proteins.
Chiefly, Rb monitors cell size. In the active, dephosphorylated state, Rb
binds to proteins called transcription factors, most commonly, E2F. Transcription factors “turn on” specific genes, allowing the
production of proteins encoded by that gene. When Rb is bound to E2F,
production of proteins necessary for the G1
/S transition is blocked.
As the cell increases in size, Rb is slowly phosphorylated until it becomes
inactivated. Rb releases E2F, which can now turn on the gene that
produces the transition protein, and this particular block is remove
Proto-oncogenes
The genes that code for the positive cell cycle regulators. Proto-oncogenes are normal genes that, when
mutated in certain ways, become oncogenes, genes that cause a cell to
become cancerous
Oncogene
An oncogene is the altered form of any positive regulatory genes of the cell cycle in a way that it leads to an increase in the rate of cell cycle progression
Tumor suppressor genes
These are genes that code for negative regulatory molecules of the cell cycle. They are like car brakes, a malfunctioning brake would lead to a crash.
What is apoptosis?
Apoptosis (programmed cell death) is a genetically regulated
self-orchestrated naturally occurring cell death process that is active
during the course of development and induced during pathological
conditions for the overall benefit of the organism
What is necrosis
Unprogrammed/random cell death that causes inflammation
8 causes of cell death
ischemia,
hypoxia,
exposure to certain drugs and chemicals,
immune reactions, infectious agents,
high temperature,
radiation, and
various disease states
A hallmark feature of apoptosis
plasma membrane blebbing.
Apoptotic budding
separation of cell fragments into apoptotic bodies
Why does apoptosis not cause inflammation
apoptotic cells
or apoptotic bodies do not release cellular contents, are quickly
phagocytosed
4 biochemical features of apoptosis
Protein cleavage,
protein cross-linking, breakdown of DNA, and phagocytic recognition
What are caspases
Caspases are a family of molecules with proteolytic activity that can cleave
proteins at aspartic acid residues
Mention 10 caspases, grouping them into the 3 caspase groups
initiators (caspases-2, -8, -9, -10),
effectors or executioners
(caspases-3, -6, -7), and inflammatory caspases(caspases-1, -4, -5)
Phosphatidylserine
Normally facing inward in the cell’s plasma membrane. During apoptosis, phosphatidylserine is
oriented to the outside of the cell, where it is a well-known recognition
ligand for phagocytes.
Two other phagocytic markers
Proteins:
annexin I and calreticulin
Two stages of apoptosis
induction and execution
Three main apoptotic pathways
the intrinsic, or mitochondrial
pathway,
the extrinsic, or death receptor pathway
and Granzyme A and B pathways
Hallmark of extrinsic pathway
Activation of
transmembrane receptors, known as death receptors, by death ligands
What family do the death receptor/death domain belong
tumor necrosis factor (TNF) receptor superfamily, characterized by
the presence of extracellular cysteine–rich domains
5 death ligands/receptors
FasL/FasR,
TNF-a/TNFR1,
Apo3L/DR3,
Apo2L/DR4,
Apo2L/DR5
How is death receptor activation controlled
By inducible de novo expression of the
respective death ligands
Explain the extrinsic pathway using TNF-a and TNFR1
TNF-a binds to TNFR1, activating it’s death domain.
This leads to the recruiting cytosolic proteins like TNFR1 death domain protein- TRADD, Fas associated death domain protein- FADD and Receptor interacting protein- RIP.
These proteins interact with procaspase 8 which through autocatalytic activation becomes activated. This whole complex is the death inducing signalling complex- DISC, which then recruits and activates procaspase 3 to bring about the effector stage.
Perforin/Granzyme Pathway
Used by sensitized cytotoxic t-lymphocyte (CTL) cells and natural killer cells to clear harmful cells.
Involves the secretion of perforin which forms pores on the target cells. Then the CTL cells secrete cytoplasmic granules containing the proteases- granzyme A and B. These go in and ultimately lead to apoptosis. Granzyme B cleaves proteins at aspartate residues, activates procaspase 10 and cleaves factors such as inhibitor of
caspase-activated DNAse (ICAD). It can also directly activate the effector caspase- procaspase 3. It can also use the intrinsic pathway to amplify the death signal through the release of cytochrome c from the mitochondria.
Granzyme A plays a role in
CTL-induced apoptosis through the activation of a caspase-independent
pathway. Granzyme A causes DNA nicking by activating a specific tumor suppressor, and causing apoptotic DNA degradation.
Constitutive genes
Always turned on in the cell. Most important and control DNA replication, expression and repair
Regulated genes
Ones needed only occassionaly
Operon
A cluster of co-regulated genes including a promoter, operator which constitutes the regulatory part and the genes themselves which constitutes the coding part
Attenuation
A prokaryote specific regulatory process which involves the use of mRNA structure to stop both transcription and
translation depending on the concentration of an operon’s end-product enzymes.
3 regulatory methods of gene expression prokaryotes use
Repressor/Activator proteins
Attenuation
RNA polymerase structure
Default state of gene expression in eukaryotes
off
Role of histones in gene expression
Histones are proteins that are bound tightly to DNA in eukaryotic cells to form chromatin. They are dna silencers.
When the DNA is wound tightly around the histone, dna polymerase is unable to start transcription. However, histones are modifiable through specific chemical changes. It does this through the histone code. This
code includes modifications of the histones’ positively charged amino
acids to create some domains in which DNA is more open and others in
which it is very tightly bound up.
Methylation causes stricter silencing, acetylation causes histone unbinding.
Chromatin remodeling complexes
Complexes of proteins that use ATP to repackage DNA in more
open configurations
What is epigenetics
the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself:
Transcription factors
a type of protein that regulates the synthesis of RNA from DNA during transcription by binding to specific DNA sequences. Could be activators or repressors
Two parts of a transcription factor
Effector and binding domain
Function of the effector domain of transcription factors
Recruiting RNA polymerase II
Two regions transcription factors bind to
Promoters and enhancers
4 ways eukaryotic gene expression can be regulated
Histone silencing
Transcription factors
Imprinting
X inactivation
Imprinting
involves the silencing of one of the two alleles of a gene for a
cell’s entire life span
Trp Operon regulation
When high levels of trp are present, the
repressor protein trpR binds the operator of the trp operon, preventing
continued expression of trp-synthesizing enzymes. However, trpR
requires the ligand tryptophan, the product of the enzymes encoded by
the operon, in order to bind the operator. It cannot bind the operator in
the absence of trp, thereby allowing continued expression of the trp
operon when the amino acid is needed
Trp attenuation procedure
Leader mRNA is the main player. The DNA region that codes for it is located between the operator and the coding region. This leader mRNA is able to change conformation depending by forming base pairings with itself. 2 possible pairings, one allows transcription and translation of the coding regions, the other stops it. It does this by using two tryptophan codons it has. When translation of the leader occurs, one of the two conformations form, depending on if the translating ribosomes stall at the tryptophan regions (meaning not enough tryptophan) or continues normally (meaning high tryp levels). If the ribosome stalls, the conformation for continued transcription and translation is formed, if not then the attenuator stops transcription.tryptophan is readily added, it signifies excess in the cell. As such the mRNA interacts with itself in a way that it stops further transcription and translation. If the translation stalls at the tryptophan region, it means tryptophan is not readily available and as such, the structure formed allows the continuous transcription and translation.
Induction in gene expression
This brief delay from
basal expression to induced expression
Lac operon regulation process
Lac repressor protein is always bound to the promoter of the lac operon in the absence of lactose to prevent synthesis of enzymes that break down lactose (Note: It’s not perfect so there is still a basal transcription, hence production of these enzymes). When lactose is present, allolactose, a molecule formed from lactose binds to the repressor and causes it to separate from the promoter, allowing transcription. The amount of lac proteins produced is still minimal and depends on positive control for the levels to rise.
For positive control, a particular protein CAP (catabolite activator protein) is necessary to bind to the activator binding site for increased lac gene transcription. But to be activated, it has to be bound to cAMP. As glucose levels drop, cAMP levels rise, causing it to bind to CAP, ultimately leading to the increased production of the lac genes mRNA
2 levels of eukaryotic gene expression regulation
Control from the amount of mRNA produced (Transcriptional)
control via post-transcriptional mechanisms that regulate translation. (Translational)
The most important
structural difference between eukaryotic and prokaryotic DNA is
the
formation of chromatin in eukaryotes
6 Differences Between Prokaryotic and Eukaryotic Gene Expression and Regulation
Structure of genome:
Prokaryotes- Single, generally circular
genome sometimes
accompanied by smaller pieces
of accessory DNA, like
plasmids
Eukaryotes- Genome found in
chromosomes; nucleosome structure limits DNA accessibility
Size of genome:
Pro- Relatively small
Eu- Relatively large
Location of gene transcription and translation:
Pro- Coupled; no nucleoid envelope
barrier because of
prokaryotic cell structure
Eu- Nuclear transcription and
cytoplasmic translation
Gene clustering:
Pro- Operons where genes with
similar function are grouped
together
Eu- Operons generally not found
in eukaryotes; each gene has
its own promoter element
and enhancer element(s)
Default state of transcription:
Pro- On
Eu- Off
DNA structure:
Pro- Highly supercoiled DNA with
some associated proteins
Eu- Highly supercoiled chromatin
associated with histones in nucleosomes
Example of transcription factor families
MADS proteins, SOX proteins, POU factors
Housekeeping genes meaning
Same as constitutive
Role of chromatin
Serves for structural regulation of DNA expression
Structure of intracellular receptors
Has 3 domains:
Amino-terminus- involved in activating or
stimulating transcription by interacting with other components of the
transcriptional machinery
DNA binding domain: Amino acids in this region are responsible for
binding of the receptor to specific sequences of DNA.
Ligand-binding domain: This is the region that
binds hormone.
When steroid hormones binds to intracellular receptors, what are the 3 steps that occur
Receptor activation: conformational changes
in the receptor induced by binding hormone. The major consequence of
activation is that the receptor becomes competent to bind DNA.
Activated receptors bind to “hormone response elements”, which are
short specific sequences of DNA which are located in promoters of
hormone-responsive genes.
Transcription from those genes to which the receptor is bound is affected.
Most commonly, receptor binding stimulates transcription. The
hormone-receptor complex thus functions as a transcription factor
Viruses
Viruses.
Viruses are obligate parasites that depend on hosts not only for survival
but also for genome replication. They contain only the bare minimum of
genetic information as RNA or DNA
Gene
Units of inheritance, usually occurring at specific locations (loci) on a chromosome. They are DNA sequences that specify the order of amino acids in a protein.
Allele
An alternative form of a gene that occurs at the same locus on homologous chromosomes.
Dominant allele
An allele that masks the presence of a recessive allele in the phenotype. Usually expressed if an individual is homozygous dominant or heterozygous.
Recessive allele
An allele that is masked in the phenotype by the presence of a dominant allele.
Recessive alleles are expressed in the phenotype when the genotype is homozygous recessive
3 laws of Mendel
Law of dominance, segregation and independent assortment
Law of dominance
States that in a heterozygouscondition, the allele whose characters are expressed over the other allele is called the dominant allele and the characters of this dominant allele are called dominant characters
Law of segregation
This law states that when two traits come together in one hybrid pair, the two characters do not mix with each other and are independent of each other.
Law of independent assortment
This means that at the time of gameteformation, the two genes segregate independently of each other as well as of other traits. Law of independent assortment emphasizes that there are separate genes for separate traits and characters and they influence and sort themselves independently of the other genes.
Thislawalso says that at the time of gamete and zygote formation, the genes are independently passed on from the parents to the offspring.
Pedigree of dominant inheritance
A pedigree that depicts a dominantly inherited trait has a few key distinctions. Every affected individual must have an affected parent. Dominantly inherited traits do not skip generations. Lastly, males and females are equally likely to receive a dominant allele and express the trait. In this pedigree both heterozygous and homozygous individuals are affected since the trait is dominant.
X-linked inheritance
Genes on the X chromosome
Describe the Ames test
What is a mutagen
A mutagen is a chemical or physical agent capable of inducing changes in DNA called mutations. Examples of mutagens include tobacco products, radioactive substances, x-rays, ultraviolet radiation and a wide variety of chemicals.
Types of mutagens
Physical mutagens: These include ionizing radiation, such as X-rays, gamma rays and alpha particles. Ultraviolet radiations can also behave as potential mutagens.
Chemical mutagens: Elements such as arsenic, nickel and chromium are considered to be mutagens. Some organic compounds like benzene are also considered to be mutagenic in nature.
Biological mutagens: Examples of biological mutagens involve transposons and viruses. Furthermore, certain bacteria such as Helicobacter pylori can increase the risk of developing stomach cancer.
What is the cell cycle
is the series of growth and development steps a cell undergoes between its “birth”—formation by the division of a mother cell—and reproduction—division to make two new daughter cells.
What happens in the G1 phase of the cell cycle
The cell grows larger, copies its organelles and makes molecular building blocks needed in later stages
What happens in the S phase
In S phase, the cell synthesizes a complete copy of the DNA in its nucleus. It also duplicates a microtubule-organizing structure called the centrosome. The centrosomes help separate DNA during M phase.
What happens in G2 phase
More growth and duplication of organelles. Preparation for mitosis
Ames test
A biological assay for assessing the mutagenic potential of a particular chemical substance. It uses bacteria.
Principle of Ames test
It uses multiple strains of bacteria (Ecoli or salmonella) that carry a particular mutation. In Ecoli this mutation is in its tryptophan operon, in salmonella, it is in its histidine operon. These bacteria strains cannot produce these amino acids, hence cannot grow unless those amino acids are present in their environment. Ames test uses this to assess mutagenic potential by introducing the suspected mutagen into a culture containing these his -/trp - bacteria, without their required amino acids. If a large number of bacteria survive and thrive, it signifies a reversal in the initial mutation on the gene that codes for their necessary amino acid. This means that the chemical substance is a mutagen.
Ames test method
Isolate an auxotrophic strain of salmonella
Prepare a test suspension with the strain and add the test chemical. Add a little bit of histidine for initial bacterial growth, when this histidine gets depleted, only those that have their mutation reversed would form colonies.
Prepare a control suspension without the test chemicals.
Incubate both at 37 degrees for 20 mins
Prepare two agar plates and spread the suspension on the agar plates
Incubate again at 37 degrees for 48 hours.
After 48 hours, count the colonies in each plate.
Auxotroph
A mutant organism, especially bacteria or fungi that requires an additional nutrient which the original strain does not
Ames test result interpretation
If there are larger amounts of colonies on the test plate compared to the control plate, it means the test compound is a mutagen
Father of genetics
Gregor Mendel
Standard organism used in mendel’s theories
Garden pea
Why did Mendel choose peas 3 reasons
They reproduce quickly
Are easy to grow
Are capable of self fertilization
Mendel’s experimental design
Mathematical Probability
Experimental predictions
Testing by experiment
Statistical analyses
Homozygous
Having the same allele at the same locus on pair
of homologous chromosomes. Homozygous also refers to a genotype consisting
of two identical alleles of a gene for a particular trait. Individuals who are
homozygous for a trait are referred to as homozygotes
Genotype
refers to an individual’s the “genetic potential”: what kind of genes
s/he carries
Phenotype
Traits that an individual actually shows
Hybrid
offspring that are the result of mating between two genetically
different kinds of parents
Monohybrid cross
is a cross between parents differing in only one trait or in
which only one trait is being considered.
Dihybrid cross
cross is a cross between parents in which two pairs of contrasting
characters are studied simultaneously for the inheritance pattern
Law of purity of gametes
Also law of segregation
The word mutation was coined by who
Hugo de Vries
What is mutation
the process a gene or chromosome changes structurally
2 classifications of mutations depending on the way they occur
Spontaneous
Induced
Induced mutations
produced when an organism is exposed to a mutagenic agent, such occur at much higher frequencies than spontaneous mutations do.
2 sources of mutations
1 Inaccuracy in DNA replication – during replication,some errors escape detection and repair by proof reading machanism.
- Chemical changes to genetic material- organic and inorganic chemical and radiations breaks backbone and chemically alters bases.
Types of DNA damages
Replication Errors
Strand breaks
Phosphodiester bond formation
deoxyribose ring DNA damage
Insertions/Deletions
Formation of Bulges
2 Agents that could lead to mutations
Uv rays
Chemical agents
How does UV radiation cause mutations
It causes two neighbouring pyrimidines to bind to each other. When the DNA is copied, the both of them are deleted
Point mutations
involves a single change in the nucleotide sequence.
Creates a new codon that when translated could give a different amino acid/proteins resulting in new phenotypes/lethality.
They can be substitutions, deletions and additions. Deletions and additions are the worst as they affect the reading frame (Frame- shift mutations) and stop codon misread.
Transitions
Purine/Purine change or
Pyrimidine/Pyrimidine change
Transversions
Purine/Pyrimidine change
Pyrimidine/Purine change
3 examples of chemical mutagens
Deaminating agents (HNO3)
Alkylating agents
Oxidizing agents
chemical mutagenesis (HNO3)
nitrous acid (HNO2) introduces oxidative deamination of primary amine groups in Adenines and Cytosines, leading to transitions in base pairing. Specifically, cytosine transforms to uracil, which pairs with adenine on the complementary strand and then thymine.
Adenine transforms to Hypoxanthine which has affinity for cytosine causing a pair with G in the next strand that is double bond instead of tripple bond.
Alkylating agents of chemical mutagenesis
add a methyl or ethyl group to reactive sites on the bases and to phosphate in DNA backbone.
which alters H-bonding causing G→ (O6-methylguanine) to pair with-T instead of C leading to → A-T pair when damaged DNA is replicated.
Oxidizing agents of chemical mutagenesis
OH, H2O2, O2
create reactive oxygen species or free radicals.
The radicals can bind to guanine, creating oxo8 which is highly mutagenic and pairs with either cytosine or adenine.
When paired with adenine – G:C to T:A transversion occurs (a common mutation in human cancer).
How does UV rays cause DNA damage
Ultraviolet light radiation with a wave length of ~260nm which is strongly absorbed by bases, causes photochemical fusion of two pyrimidines occupying adjacent positions in the same chain eg thymine dimers
These links are not able to pair causing a stop in replication.
X-rays and gamma rays cause breaks in DNA which are difficult to repair.
Can be used in killing cancer cells.
How can UV light damage be corrected
Using photolyase.
Photolyase is a photoreactive enzyme that binds at pyrimidine dimers and uses energy of visible light to break the dimers
How do gram negative bacteria detect errors in DNA replication
Through DNA methylation.
DNA methylase adds methyl to adenine within GATC in Parental strand
* Newly synthesized strand is unmethylated to allow corrections of replication errors.
3 Methods of DNA repair
Mismatch Repair (MMR)
Base Excision Repair (BER)
Nucleotide Excision Repair (NER)
Mismatch repair
Errors detected are removed with endonuclease and exonuclease activity which removes mismatch base.
The gap is filled with polymerase and ligase which adds the correct pair.
Base Excision Repair (BER)
DNA glycosylase removes damaged base by cleavage of glycosidic bond leaving just sugar-phosphate. AP endonuclease removes the sugar-phosphate and the gap is repaired by polymerase I and ligase
Nucleotide Excision Repair (NER)
Specific to larger regions of damaged DNA than BER
Cleaves backbone at two places and each side of the lesion (mutation) for removal.
The gap is filled with polymerase and ligase.
Classification of Mutations based on the type of cells they occur in
Somatic mutations
Germ line mutations
Effects of germ line mutations
No changes in phenotype. This can happen in many situations: perhaps the mutation occurs in a stretch of DNA with no function, or perhaps the mutation occurs in a protein-coding region, but ends up not affecting theamino acidsequence of theprotein.
Small changes in phenotype e.g a single mutation caused cat’s ears to curl backwards slightly
Big change occurs in phenotype e.g DDT resistance in insects
Silent mutations
Mutations that occur in Non-coding DNA region
What is a genetic disease
any disease caused by an abnormality in an individuals genome/genetic make up.
Types of genetic mutation
Single gene inheritance
Multifactorial
Chromosome abnormality
Mitochondrial inheritance.
Single gene inheritance
Caused by mutation in a single gene. Examples are Cystic fibrosis, sickle cell anemia, marfan syndrome, huntington`s disease and hemochromatosis.
Multifactorial genetic inheritance
caused by a combination of environmental factors and mutation in multiple genes.
Examples include; heart disease, HBP, Alzheimer, arthritis, diabetes, cancer and obesity.
Chromosome abnormalities
Particularly in the number of chromosomes. Chromosome abnormality usually occurs due to a problem with cell division. Example Down syndrome, Turner syndrome
Mitochondrial genetic inheritance
caused by mutations in the non-nuclear DNA of mitochondria. Mitochondrial DNA is always inherited from the female parent.
Examples: A type of dementia and a type of epilepsy called MERRF
Sex linked genetic diseases
genetic characteristics determined by genes located on sex chromosomes (X linked or Y linked gene).
X-linked recessive traits
phenotype expressed in males and masked in female e.g Haemophilia, colour blindness
X-linked dominant traits-
one mutated copy is enough to express disease e.g. muscular dystrophy and fragile X syndrome.
Y-linked
mutated gene is located on the Y- chromosome.
Can only be passed to males e.g. male infertility
Aberration in sex chromosomes
E.g Klinefelter’s syndrome
2n+1 =47 (trisomic males) with XXY instead of XY.
Symptoms of klinefelter’s syndrome
Lower IQ
Tall stature
Poor muscle tone
Reduced secondary sexual characteristics
Development of breast tissue
Small testes/infertility
Turners syndrome
2n – 1 = 45 (aneuploid monosomic) female having only one X chromosome (X0) instead of (XX).
Reverse of Klinefelter`s but more serious.
Characteristics: phenotypically females, ovaris fail to develop properly, hardly mensurate, webbed neck, stunted body, shield-like chest and impaired intelligence, suffer abnormality of the aorta.
Occur 1 in 10,000 live female births as most result in spontaneous abortions.
Down’s syndrome
2n + 1 trisomic condition of chromosome 21.
7 chromosomal related diseases
Klinefelter’s syndrome
Turner’s syndrome
Down’s
Patau’s
Philadelphia Chromosome
Edwards syndrome
Cri du chat syndrome
Recombinant DNA
Recombinant DNA are DNA sequence from multiple sources
7 Steps in recombinant DNA tech/Gene cloning
Choice of host organism and cloning vector
Preparation of vector DNA
Preparation of DNA to be cloned
Creation of recombinant DNA with DNA ligase
Introduction of recombinat DNA into host organism – electroporation, transformation, transduction and transfection.
Selection of organism containing vector sequence.
Screening for clones with desired DNA insert and biological properties
Gene cloning
A molecular technique that makes identical copies of a gene
Genomics
Study of the whole genome of an organism. Uses a combination of rDNA, DNA sequencing methods to assemble and analyse the structure and function of the genome.
5 Applications of Genomics
Genomic medicine/clinical genetics
Synthetic biology and bioengineering
Disease gene discovery
Evolutionary analysis
Vaccine development for preventing killer infections e.g. malaria parasite, HIV.
Cancer genomics
5 Branches of genomics
Functional genomics
Computational genomics
Personal genomics
Imunomics
Proteomics
What is population genetics
the study of changes in allele frequency for a particular trait over time. It analyzes the causes leading to those changes
Phenotype is
Basically the physical presentation of a gene/how something actually looks. At any given time, the phenotype is the result of
the genes of the individual interacting with the environment
Genotype is
The description of the complete set of genes
that an individual inherits from its parents
f The genotype of an individual remains
unchanged throughout its life, regardless of the
environment surrounding and affecting it
What is polymorphism?
‘Presence of many forms’
In genetic terms, it refers to the coexistence of
two or more alternative phenotypes in a
population or among populations. In general,
these diverse phenotypes are caused by
alternative alleles of one gene
A population is
Ecologically: Ecologically:
A group of individuals of the same species living within
a restricted geographical area that allows any two
individuals to interbreed
Genetically:
A group of individuals who share a common gene pool
and have the potential to interbreed
Three levels of population structure
- Individual organisms
- Subpopulations
- Total population
Gene flow
Gene flow is the passage and establishment of genes typical of one population in
the genepool of another by natural or artificial means
Allele frequency
Allele frequency is the concept used to quantify
genetic variation
It is defined as a measure of the commonness
of a given allele in a population, that is, the
proportion of all alleles of that gene in the
population that are specifically this type
Formula for allele frequency
P(A) = [2(AA) + (Aa)]/2n
Twice the number of homozygous genotypes
with that allele (because homozygotes carry two
copies each of the same allele),
f plus the number of heterozygous genotypes
with that allele (because heterozygotes carry
only one copy of a particular allele),
f divided by two times the total number of
individuals in the sample (because each
individual carries two alleles per locus
Genotype frequency
This is the frequency of a given genotype in a population
Hardy-Weinberg principle
When all the causes of genetic variation aren’t involved, the frequency of a genotype is eaual to the product of allele frequencies
P2 + 2Pq + Q2 = 1
Chi-square test
This hypothesis test is useful for determining
whether the allelic frequencies are in H-W
equilibrium
Factors that affect gene variation
Natural and sexual selection
Recombination
Mutation
Gene flow/ migration
Genetic drift
