Genetic and Phenotypic Variation

Question 1

What is genetic variation?

Answer 1

Heritable contribution to the variation that exists for a particular biological property

Question 2

Mendels mutations – classical ‘discrete’ phenotypes

Answer 2

Discrete traits
Single-gene inheritance
Two variants at each locus (i.e Y or y)

Question 3

Purine: Definition

Answer 3

A purine is composed of a six-member nitrogen-containing ring and a five-member nitrogen-containing ring joined together, like a hexagon and a pentagon pushed together. Purine bases in DNA and RNA include adenine and guanine and are therefore the best known bases of the category

Question 4

Pyrimidine: Definition

Answer 4

Pyrimidines have a six-member nitrogen-containing ring, like purines, but no corresponding five-nitrogen ring.
Pyrimidine bases in DNA include cytosine and thymine; pyrimidines in RNA include cytosine and uracil.

Question 5

How much genetic variation is there

Answer 5

• Numerous alleles are possible at a locus (>2)
• result in a range of effects on gene function
• interact to produce a range of phenotypes
• Many genes can interact to produce a trait or have additive effects (complex phenotypes)
* Also overlooks the vast amount of genetic variation that is not readily observable (molecular variation)

Question 6

The genetics of melanin biosynthesis

Answer 6

Multiple gene influences:
Type of melanin produced
Amount of melanin produced
Body site distribution of melanocytes
Density of melanocytes
How the melanin is transported throughout the skin and hair
Activation (regulation) of melanin production

Question 7

Albinism

Answer 7

• most common form cause by a defect of the tyre gene which encode the tyrosinase enzyme
• it is an autosomal recessive condition, non functional copy of the gene lead to no or very little tyrosinase enzyme
• the gene have many alleles. the gene is very large with 5 exon 65kbs.

Question 8

Genotype to Phenotype- pigmentation

Answer 8

• Mutation of MCR1 gene are reccessive, leading to red hair, reduce pigmentation of the skin and UV sensitivity.
• But some alleles of the gene are dominant

Question 9

what should we consider when talking about genetic variation

Answer 9

• How does genetic variation arise?
• How does a genetic variant effect a gene product?
• How can we detect and classify the genetic variation that exists?
• Why do some mutations affect the function of a gene product whereas others have no effect?
• How do the different alleles of a gene interact, in diploids etc (Dominance)?
• When a trait is influenced by more than one gene, how do the different gene
  products interact to produce a given phenotype?

Question 10

Key point of mutation

Answer 10

Mutations are the source of all genetic variation.
A couple of key points about mutations first is that they’re avoided as much as possible.
And cells have many processes that are involved, often redundantly, to prevent any DNA areas or damage that can lead to mutilation.
-if the damage cannot be repair, the cell self terminate
-large error can lead to cell survival and accumulation of mutation
-Less extensive DNA areas that are not repaired, resulting mutations and can ultimately result in a polymorphism in the rare instances where they increase in frequency and a population.

Question 11

How common is mutation/ where can mutation occur

Answer 11

Second, very important point about mutations is that they occur completely at random.
They can occur anywhere in a genome, although in some cases they are more likely to be a certain associated with certain regions that contain repetitive sequence elements

Question 12

All genetic variation results from mutations

Answer 12

Mutations can be small or large-scale:
- single base pair substitution (transition between P or translocation)
- deletion or insertion of several base pairs (indels)
- major alteration in chromosome number or structure
All genetic variation results from mutations

Question 13

Cause of ,utation

Answer 13

-Error in duplication
-Change in location of a gene
• Damage to bases in DNA
- depurination, deamination, oxidation
• DNA replication errors
- Tautomeric shifts
- Slippage
Mutations can also be induced by mutagens

Question 14

How can the location mutations affect phenotype

Answer 14

Based on Nature of the mutation and where it occurs
Mutations can occur in coding and non-coding regions of the genome
- Non-coding mutations can affect the expression of the gene
- Coding mutations can affect the gene product

Question 15

Mutation in an intergenic region

Answer 15

May alter the effect of the gene or have no effect and is then preserve

Question 16

Promoter/regulatory region mutations

Answer 16

• may affect (increase or decrease) the synthesis of a gene product but not its
  sequence/structure

Question 17

Mutation in an intron

Answer 17

-Can effect the splcing process GUAG rule

Question 18

Consequences of mutations in coding regions of a gene

Answer 18

• Silent (synonymous) – no change in amino acid
• Missense (non-synonymous) – change in amino acid. Either:
• conservative substitution where the amino acids are chemically similar
• non-conservative substitution where the amino acids differ chemically
• Nonsense – premature STOP codon
• reduced function or no function, dependent on the extent to which the polypeptide is truncated
• Frameshift – all amino acids encoded after the mutation are changed
• Reduced, altered or no function depending on the proportion of polypeptide
sequence affected

Question 19

Silent mutations resulting from base substitution

Answer 19

An alteration in DNA that changes a codon to a different codon for the same amino acid – usually 3rd position
Silent mutations are due to redundancy in the genetic code

Question 20

Missense mutations resulting from base substitution

Answer 20

An alteration in DNA that converts a codon for one amino acid into a codon for a different amino acid

Question 21

Nonsense mutations resulting from base substitutio

Answer 21

An alteration in the DNA sequence that converts a codon for an amino acid
into a termination codon

Question 22

Frameshift mutations resulting from Indels

Answer 22

A loss or gain of nucleotides in a gene that change the reading frame

Question 23

New definition of alleles

Answer 23

-Change in the genetic code regardless of its effect on the final product, function or observable characteristic

Question 24

New definition of phenotype

Answer 24

any biological property that we can detect and measure

Question 25

Classification of genetic variation

Answer 25

- DNA - Protein - Function - Phenotype

Question 26

Molecular Variation effect on polypeptide

Answer 26

changed in the DNA sequence can also lead to polymorphisms detected at the level of the polypeptide This is because certain properties of the polyp peptide can differ including size and charge

Question 27

How can we detect changes at a molecular level

Answer 27

-Northern blotting:s a technique where we can separate mRNA on the basis of size and then use a probe to detect the mRNA of a specific gene. -Western bloting used to separate proteins on the basis of size. And then a specific protein product can be identified using an antibody.

Question 28

DNA sequence variation

Answer 28

where we have a polymorphism that is due to a substitution mutation at a single nucleotide. Then this is appropriately called a single nucleotide polymorphisms -insertion or deletion are called indel There's a subtle change that required techniques with high resolution, such as DNA sequencing in order to be detected.

Question 29

Simple sequence length polymorphism

Answer 29

a type of polymorphism based on the presence of different numbers of repeats of a simple sequence. These are typically, but not always found in non coding regions of the genome.

Question 30

Minisatellite marker

Answer 30

* Repeated sequence is 15-100 nucleotides in length | * Repeated in tandem of 5-50 times

Question 31

Microsatellite markers

Answer 31

• Repeated sequence is 2-10 nucleotides in length • Repeated in tandem 5-50 time

Question 32

Structural difference between polypeptide that have the same fuction

Answer 32

One form off protein markers are allozyme. allozyme are variant forms of an enzyme that produced from different alleles of the same gene. To be classified as an AL The differences between the variant forms are limited to their structural properties, and there is no difference in how the proteins actually function. The gene products can have different charges resulting in faster or slower moving protein.

Question 33

using antibodies to detect differences in the types of proteins

Answer 33

-If a person receive blood with different antigen this lead to a raection Detection of blood groups is done using in aggluteminassate where the blood sample is exposed to different antibodies. If there is a reaction, it's the same as his blood type

Question 34

Northern blotting in depth

Answer 34

DNA is cut with the restriction enzyme, Either side of this mini satellite is a recognition sequence for a restriction enzyme that is able to cut the DNA striction digestion of the DNA of this locus will result in different sized fragments, which we look better to be different alleles at this lockers -Step1 : extract and purify the DNA -Step 2:is to digest the genomic DNA with the suitable restriction enzyme that will allow you to detect a polymorphism at a particular lockers. -step 3we need to use gel electrophoresis in order to separate the different sized fragments of DNA that have produced after digestion. negatively charged DNA due to the phosphate back brain moves towards the positively charged end at the bottom of the gel.

Question 35

Southern Privatisation

Answer 35

Step 1 transfer the DNA into a solid bearing membrane Step 2 know as hybirdisation which we make aprobe that that is specific to the DNA sequence that we want to be able to detect. The probe is able to bind or hybridise to the specific dna in a band complementary base pairing enerally, the probe is radioactively labelled so that we can detect it using an X ray and be able to pinpoint the exact location of our DNA sequence of interests

Question 36

STR analysis of microsatelite

Answer 36

- The region where the repeat sequence is located is amplified using PCR with primaries that correspond to the DNA sequence flanking the repeated sequence. - Different sized bands are then produced depending on the number of repeats that a present given the subtle size difference between these pre PCR products. - The detection of different bands requires a high resolution gel electrophoresis.

Question 37

Mircro satalite in exon

Answer 37

-some micro statlite can be found in exon which it can act as genetic marker for investigation

Question 38

Genome wide study using SNP

Answer 38

Used to find out the corelation between condition and a particular snp looking at the association of particular variance with its trait on these variants may be anywhere in the genome SNP can be a marker of a trait because they occur within or close to the gene that causes the trait

Question 39

mechanism behind Alleles that do not change gene function

Answer 39

- sometimes not all of the gene product is required to contribute to the function of a gene. domains of a protein or specific amino acids, maybe important or contribute to gene function, while the rest are redundant - If a change occurs in a gene product in a region that is not required for gene function, then it's not likely to affect the ability of the gene product - change in the area that are crucial for gene function but it is silent or the new amino acid are chemically similar

Question 40

Loss or reduced fuction alleles

Answer 40

- Amorphic mutant: loss of function - Hypomorphic : reduced function - Most common class of mutation - A large portion of the gene product is defective or a key essential residue or amino acid - Usually produce a phenotype that is recessive in the presence of a wild-type allele

Question 41

Gain or altered function alleles

Answer 41

``` Hypermrophic- increase fuction -Because it is expressed a higher level, it is more efficient or effective at doing its job -The mutation may affect a key essential residue, or amino acid in the polypeptide that may be involved in turning the activity of the protein down or off under certain conditions. Neo morphic gain function - rarer class of mutation ```

Question 42

Conditional mutation

Answer 42

-the function of the Gene product is dependent on the conditions which is know as a permissive condition where the gene is or partially fuctional -Very rare mutations Extremely valuable for genetic studies - allow you to switch protein function on and off. - allow you to isolate mutations in genes that are essential (i.e. loss-of-function is lethal).

Question 43

How do we know if a mutation can effect the gene based on its location

Answer 43

-The mutation occur in the binding site of mrna, in the intro splice site and the coding region of the gene

Question 44

Levels of protein structure and how they are determined

Answer 44

Primary Structure is a polypeptide chain:- strong covalent bonds (peptide bonds)Determined by the coding sequence of a gene Secondary Structure Folding within regions of a protein Tertiary Structure Interactions between different regions Quaternary Structure Association between polypeptides to form a functional complex 2-4 occur due to hydrogen bond Determined by the properties of the amino acids. Specifically the R- group

Question 45

How do proteins adopt the appropriate conformation

Answer 45

* Spontaneous folding | * Guided by molecular chaperones

Question 46

Quaternary structure of proteins

Answer 46

Association between polypeptides to form a functional complex Any number of subunits same protein is homodimer different is heterodimer

Question 47

Not all amino acid are equal

Answer 47

there are some positions where even no or very little change is tolerated in these places. These amino acids are either completely conserved, with only a single minute single amino acid tolerated, whereas others can have early conservative change Other position allow for some toleration before function is affected

Question 48

method to predict or determine the effect of a mutation using genetics?

Answer 48

Forward genetics • Frequency with which a class of mutant arises (common vs rare) • dominance properties of the phenotype observed (recessive/dominant/semidominant) e.g. common and recessive suggests loss-of-function rare and dominant suggests gain-of-function. Reverse genetics • Study the mutation by creating and observe the effects of the specific mutation (using model organisms) Comparative sequence analysis • Conservation of sequences between the same gene in different organism Functional genomics • Systematic large-scale (genome wide) approach to evaluate the effects of possible mutations

Question 49

Forward genetics approach

Answer 49

Start with the phenotype Naturally occurring or selected phenotype • Disease or other trait • Lab based mutagenesis screen Identify gene affected & causative mutation - Mapping (in relation to known markers) - Cloning by complementation - Sequencing

Question 50

Reverse genetics approach

Answer 50

Particular gene/gene region/ residue predicted to have an important role Create mutation Observe the effect -> Phenotype Same as wild-type? or Mutant phenotype?

Question 51

How important is a residue(gene variation) in a protein sequence in regard to natural selection

Answer 51

Synonymous/Silent and Residue not important for m protein structure/function OR conservative change are selection neutral Loss of function is not likely to be selected by Gain of function/altered function may be selected

Question 52

Comparative Sequence Analysis

Answer 52

Mutations occur at random, those that are detrimental to function will be eliminated -> conservation of amino acid sequence suggests that those residues are important for the function of the protein

Question 53

What determines if an allele produces a dominant phenotype?

Answer 53

Phenotypic outcomes resulting from the interaction between any two alleles can vary depending on: •Function of the gene product & level of gene activity/abundance •Also influenced by the genetic background (penetrance and expressivity) Dominance can be classified as: •Complete dominance (recessive) •Incomplete dominance •Co-dominance •Determined by the phenotype produced when both alleles are present -heterozygote

Question 54

The relationship between genotype and phenotype in haploid

Answer 54

Haploid. Genotype = phenotype

Question 55

The relationship between genotype and phenotype in diploid

Answer 55

Genotype does not equal phenotype Loss of function resulting in a recessive phenotype Loss of function resulting in incomplete dominance Loss of function resulting in a dominant phenotype Loss of function resulting in a recessive lethal phenotype Gain or altered function resulting in a dominant phenotype Antimorphic variants and dominant negative phenotypes

Question 56

Nomenclature - naming of genes relates to trait and dominance

Answer 56

•Gene locus/name usually named after mutant phenotype •Whether the allele symbol is capitalized or lower case is dependent on dominance of the phenotype produced by the mutant allele Drosophila- allele symbol is consistently upper or lower case. Wild-type allele is given a super-script + and mutant allele is not (can be given a super-script - ). Traits carried on sex-chromosome also have additional convention.

Question 57

Dominant-negative mutation/allele

Answer 57

- Another rare class of mutation - Loss- of function or altered function, but interferes with the wild-type protein -occur when a protein is made up of multiple amino acid chain wild-type and mutant subunits can also form inactive dimers

Question 58

Consequences of mutation in a subunit of a multimeric protein

Answer 58

- WT and mutant subunits produced - they are arranged randomly - out of 4 possible configuration, 3 are useless

Question 59

Molecular phenotypes and dominance

Answer 59

All alleles of a gene are co-dominant at the DNA sequence level Dominance dependent on the level at which we measure phenotype

Question 60

Example in dominations of sickle cell anemia

Answer 60

Phenotype that can be scored Dominance of phenotype Anemia Recessive Malaria resistance Dominant Presence of sickled or normal red blood cells Co-dominant Presence of fast or slow migrating hemoglobin Co-dominant DNA sequence variant Co-d

Question 61

Pleiotropy

Answer 61

one gene many effects

Question 62

Pleiotropy example

Answer 62

* Agouti * Yellow pigmentation * Increased growth and obesity – hyperphagia, hyperinsulinemia and hyperglycemia * Increased tumorigenesis * Recessive lethal * Gene product is an antagonist of MC1R * WT expression restricted to hair follicles, mutation causes ubiquitous over-expression

Question 63

Loss of function resulting in a recessive phenotype explaination and example

Answer 63

-homozygous wt, full gene product - hetero: half gene product produced - homo mutant: no product *only one wild type alleles is needed for sufficient activity, know as haploid sufficient EXP; albinism where on wt is enough

Question 64

Loss of function resulting in incomplete dominance exp

Answer 64

-hetero create an intermediate between wt and mutant -neither phenotype mask another exp flower colors

Question 65

Loss of function resulting in a dominant phenotype

Answer 65

- the lack of gene product lead to inabiliy to produce wt phenotype aka haploid insufficient - exp: hypertrophic Prada myopathy, which results from defective sarcomere, which are an important structural unit in the heart. MYCBE3+

Question 66

Loss of function resulting in a recessive lethal phenotype

Answer 66

- the homo mutant is lethal while heterozygous is phenotype insufficient

Question 67

Gain or altered function resulting in a dominant phenotype

Answer 67

-Variants are typically hyperactive, that is, that they are either expressed highly expressed in the wrong cell or tissue types. We'll have constitutive activity where the activity is not turned down under certain conditions EXP: RAS gene turn into RAS oncogene in fruit fly. Normal ras cycle between an inactive GDP form and active GTP form. a missense mutation from Val to Gly lead to inability to revert back to inactive form

Question 68

Mutation of a polygene can alter the phenotype

Answer 68

Multiple genes can work together to contribute to a phenotype Mutation of any of these genes can contribute to a mutant phenotype - In some cases mutation of different genes can produce the exact same phenotype

Question 69

How can we determine which genes in a polygene are contributing to a similar phenotype

Answer 69

Cross pure-breeding variants and observe phenotypes in the F1 hybrid the F1 will then cross with each other. those that does not have gene activity have the same gene mutation Mutant phenotype èmutations in the SAME gene Wild-type phenotype èmutations in DIFFERENT genes.

Question 70

Complementation summary

Answer 70

Complementation tests allow us to determine whether mutants are due to mutations in the same, or different, genes. wild type phenotype mutant phenotype Complementation No complementation 2 different genes 1 gene = alle

Question 71

Bacteriophage Lytic Cycle

Answer 71

``` Adsorption of phage to host cell Entry of phage DNA into host Phage commandeers host cell machinery Phage proteins produced and nucleic acid replicated. Host DNA degraded. Assembly of phage particles Phage commandeers host cell machinery Lysis of host cell and release of progeny ```

Question 72

Mutants in bacteriophage- cannot complete lifecycle

Answer 72

Mutants are missing a component required for bacteriophage production and cell lysis Different mutants can be affected in different genes Able to be maintained using ‘helper phages’

Question 73

Coinfection

Answer 73

Coinfection can allow mutant bacteriophage to complete their lifecycle Coinfection of host cell using a high multiplicity of infection Coinfection creates a 'diploid state' for the phage If the phage carry mutations in different genes, then within this cell all of the components necessary to make new phage will be present If the phage carry mutations in the same gene, then there will still be a missing component required to make new phage

Question 74

Independent contributions

Answer 74

polygene that are indepedant from each other

Question 75

Dependent contributions

Answer 75

polygene that one gene product controll another gene expression

Question 76

possible double mutant effect on phenotype

Answer 76

Double mutant phenotype is novel= not the same as either of the single mutants Double mutant phenotype is equivalent to the single mutants combined Additive effect Double mutant phenotype is the same as one or both of the single mutants

Question 77

How can we observe if there is or is not a genetic interaction

Answer 77

•Need to compare single and double mutant phenotypes punnet square: Pure-breeding mutant A x Pure-breeding mutant B 9 WT : 3 mutant A phenotype : 3 mutant B phenotype : 1 double mutant phenotype

Question 78

What do we expect to see when there is no genetic interaction in poly punnet

Answer 78

Aphenotype dominant to aphenotype Bphenotype dominant to bphenotype aa bb double mutant to be combination (additive) of aa B- and A- bb phenotypes

Question 79

Synthetic phenotypes explained

Answer 79

- affect the same phenotype but have different biochemical pathway ( parallel) - mutation in one of the gene lead to only one part of the pigment to be produced

Question 80

Gene interaction in a biochemical pathway

Answer 80

-genes affect the same phenotype and operate in the same biochemical pathway 0Mutations in any of the genes alter the pigment produced

Question 81

Gene interaction between a regulatory protein and its target

Answer 81

- mutation in gene that encode the regulatory protein which affect the expression of the gene - mutation of the gene that encode for the gene product leading to lack of gene product - mutation in both

Question 82

Epistasis

Answer 82

the genetic variant at one locus masks the effect of a genetic variant at another locus

Question 83

Hyphostasis

Answer 83

the genetic variant of one locus that is masked by another genetic variation

Question 84

Gene interaction can involve modifiers

Answer 84

A suppressor is a mutant allele of a gene that reverses the effect of a mutation of a different gene - results in a wild-type or near wild-type phenotype An enhancer is a mutant allele that enhances the effect of a mutation of a different gene

Question 85

A molecular mechanism for suppression

Answer 85

-WT: don't have those mutations, but we can see that we get an inductive protein complex -First MT: mutation in this first unit, these genes can no longer interact. -Second MT mask 1 mt: a secondary mutation in our suppressor site which has enabled our proteins to once again interact, even though we still have that original mutant present suppressor MT: depend on the normal expression of the gene, may have no effect

Question 86

Penetrance

Answer 86

Percentage of individuals with a given genotype that exhibit the corresponding phenotype.