1. Intro + Genetic Mutations

Genetics:

Genetics:

Branch of biology concerned with the study of heredity and variation

Sub disciplines of genetics

Transmission Genetics: The study of heredity and the mechanisms by which genes are transferred from parent to child.

Molecular Genetics: The study of the structure and function of genes at the molecular level eg DNA, RNA, and proteins

Population Genetics: The study of genetic variation within and between populations. This involves the examination and modellingof changes in gene/allele frequencies in populations over time and space.

Quantitative Genetics: The study of the effects that heredity and environment have on traits that can be quantitatively meausured such as size ( color variations for different things)

Developmental Genetics: The study of the way in which genes control the growth and development of an organism throughout its lifecycle

Central dogma of modern biology

DNA —(transcription)—> RNA—(translation)—→ polypeptide/protein—→ phenotype

Phenotype: The observed physical and/or biochemical attributes of an organism as determined by both genetic makeup and environment

genetics

Gene: A sequence of nucleic acid [typically DNA] coding for a polypeptide or a functional RNA

Relationship between ds DNA and ss RNA

Gene= transcription unit plus regulatory sequences that regulate transcription [e.g. promoter (P)and terminator (t)]

look at the diagram of it

+1= Start point of transcription

sense or partner strand 5’ to 3’ Antisense or template strand 3’ to 5’

—> Primary transcript 5’ to 3’

—> downstram direction (downstream or 3’ flanking region)

←- upstream upstream or 5’ flanking region

Revised view of transcription unit

Transcription unit

Primary Transcript 5’ —E1—I—E2—-I—-E3—3’ Intron splicing

Final mRNA 5’ C—E1—E2—-E3-AAAA

E= Exon or “expressed sequence” I=intron or '“intervening sequence”

Alleles

Alternate forms of the same gene

Diploid individual may have up to 2 different alleles

Population may have more than 2 alleles for a gene

Alleles are generated by the process of mutation

Mutation

A permanent change in the DNA of a cell or organism

Different ways of categorizing

By cell type

Somatic cell mutation- mutation in a differentiated somatic [i.e. body] cell.

- affects individual, not passed on to future generations

Germ line mutation

- mutation in any one of cells [going back to zygote] that are progenitors of or are gamete-producing cells

-mutation may or may not affect individual but will be inherited by offspring and potentially all future generations

more serious than somatic cell mutations from an evolutionary perspective

Point Mutations

A mutation that affects one or a few nucleotides/base pairs at a single locus [location]. -by definition, affects a single gene.

-effects depend upon site of point mutation in the gene and the exact nature of the point mutation.

Point Mutations in a Promoter 1

Recall the function of a promoter?

Three general types of outcomes of promoter mutations regardless of the exact nature of the promoter. promoter strength- how many successful initiation per unit time

3 types neutral, better, poorer

[1] Neutral - essentially no effect. -mutated sequence no better and no worse “match” for “ideal promoter structure” -promoter strength not changed

-ability of RNAP to recognize and bind promoter, and to initiate transcription is not changed.

- no noticeabale effect on transcription and translation of gene

[2] Better promoter

-mutated sequence is a better match for “ideal promoter structure”

-increased promoter strength

-increased promoter recognition and binding, and/or initiation of transcription “All other things being equal” expect increase in

[1] rate of transcription

[2] Concentration (amount) of specific transcript

[3] Concentration of specific mRNA

[4] Rate of translation of specific mRNA

[5] Polypeptide concentration of specific polypeptide

NO change in amino acid sequence of polypeptide- WHY? Because the coding sequence hasn’t changed! Same polypeptide just more of it

Poorer Promoter

-mutated sequence is a poorer match for “ideal promoter structure”

-decreased promoter strength

-decreased promoter recognition and binding, and/or initiation of transcription

“All other things being equal” expect decrease in:

[1] rate of transcription

[2] concentration of specific transcript

[3] concentration of specific mRNA

[4] Rate of translation of specific mRNA

[5] Polypeptide concentration of specific polypeptide

NO change in amino acid sequence of polypeptide

Intron Mutations

Two major cases [with some variations]

[1] General Case -mutation affects an internal sequence not involved in intron splicing

-Typically intron still spliced out properly

-Expecrt no change to resulting mRNA, polypeptide sequence or amount

[2] Mutation in sequences critical to intron splicing [5’ slice site, 3’ splice site and/or branchpoint]

-possible effect- intron not spliced out

encodes for "unintended" sequence of amino acids

alters structure and function of polypeptide

-introns tend to be A/U rich

likely that a stop codon will be encountered

trigger premature termination of translation

result: truncated polypeptide with modified C-terminal aa sequence

likely non functional polypeptide

-other scenarios possible

Point Mutations in Coding Sequence

Base substitutions versus Indels

Base substitutions: base pair converted from original state to new state

Indels: Insertion or deletion of one or more bp. (changing number of bp)

Both types have similar effects in promoters and introns

Different effects when mutation in coding sequence!!

Effects of Base Substitutions in Coding Sequence

Base substitutions will have different effects ranging from having no real effect to some rather drastic effects.

-total of five scenarios/subscenarios will be covered

base substitustion types:

Transitions A->G or T->C purine or pyrimidine replaced by a base of the same class (MORE COMMON)

Transversion purine or pyrimidine replaced by a base from the other class A->C or T->G

Silent Mutation

Base substitution that results in change in the DNA coding sequence, a corresponding change in the mRNA sequence BUT NO CHANGE in the amino acid sequence of the polypeptide.

Can occur because of the degeneracy of the genetic code

The change results in the formation of the same polypeptide even though there is a mutation in DNA resulting in change in RNA, but the new codon encodes for the same amino acid

Missense Mutation

Base substitution that results in change in the DNA coding sequence, a corresponding change in the mRNA sequence WITH THE CHANGE OF ONE AMINO ACID in the polypeptide.

Why called “missense”? Because youve changed the meaning of a codon

Missense mutations can have a variety of effects. Let’s consider the two extremes!

1.Neutral Missense: Missense mutation that has little effect on polypeptide/protein structure [folding] and function

usually the amino acid that is being substituted is replaced with one of similar physio-chemical properties, e.g. one hydrophobic amino acid replaced with another hydrophobic amino acid.

Drastic Missense Mutation: Missense mutation that has a serious effect on polypeptide/protein structure [folding] and function

Usually the amino acid that is being substituted is replaced with one of different physio-chemical properties e.g.one hydrophilic amino acid replaced with a hydrophobic amino acid.

keep in mind for silent and neutral missence and drastic missence, everything on either side of the mutation is the same

Sickle Cell Anemia

-caused by point mutation [base substitution]

codon 6 in β-globin gene

GAA[Glu] changed to GTA[Val]

-Hemoglobin, heterotetramer [α-globin2 , β-globin2 ]

-person with 2 copies [homozygous] of allele with GTA can suffer from sickle cell anemia.

-under oxygen stress, hemoglobin in rbcs aggregate

form rigid rod like structures

rbcs change cell shape

from dumbbell shape in XS to rigid sickle shape

effects of sickle cell anemia

Sickled rbcs clog capillaries

-restricts blood flow downstream of blockage

- But condition called “sickle cell anemia”- WHY?

-sickled cells “turned over” [destroyed] more rapidly

body cannot generate new rbcs fast enough to replenish/replace lost rbcs

result is low rbc count or anemia

Person with one “sickle cell allele”

-generally rbcs have “normal” shape

-under extreme oxygen deprivation, cells may sickle

-person is more resistant to malaria

parasite has difficulty infecting rbc

-allele more prevalent/common in human populations where malaria is prevalent. WHY

where malaria is present [selecitve advantage]

Nonsense Mutation

Base substitution where aa-encoding codon becomes a stop codon [WHY called “nonsense”?] doesn’t code for a.a. therefore it doesn’t have a sense

No amino acid encoded AND…..none of the downstream codons are translated

Result: truncated (shortened) polypeptide [missing C-terminal a.a. sequence]. Polypeptide is usually non-functional

Gain of sense mutation

Base substitution converts stop codon into an aa-encoding codon.

This situation would require the tmRNA to finish translation (the one from that assignment)

Ribosome no longer stops at original location

translates trailer region until finds another stop codon or runs out of sequence

Result: Elongated polypeptide with C-terminal a.a. extension. Often non-functional

Indels in Coding Sequence

Insertion/deletion of one or a few bp.

Two basic scenarios

[1] Frame Shift Mutation: Insertion or deletion of bps from coding sequence in that are NOT multiples of 3.

-changes the "reading frame", the groupings ribosomes read as codons

-reading frame is initially established by the identification of the start codon [AUG]

frame shift mutation is what leads to the O blood type

Frame Shift Mutations

Frameshift Mutation:A type of genetic mutation where the insertion or deletion of nucleotides alters the reading frame of the DNA sequence, leading to a shift in the codon reading during translation. FROM AI

Indels in Multiples of 3

because the three base pairs that are involved here span between two codons you will remove an amino acid but you may also change one amino acid that is encoded (a.a substitution)

before and after the mutation stays the same

for every multiple of 3 that is added you will add an amino acid

for every multiple of 3 that is removed you will remove an amino acid

Wild-type allele

Allele that occurs most frequently in a population most frequent in a POPULATION not a species

Arbitrarily, designated as the “normal” allele [Corresponding “wild-type” phenotype is also considered the norm.]

Usually, the wild phenotype is dominant but this is NOT always the case

Naming alleles

Review convention already used.

P/p usually use capital letter for the first word of the descriptive term of the dominant allele Capital=dom lowercase=recessive sometimes first letter of mutant?

Genes/genetic loci usually identified through the identification of “mutant” phenotypes [phenotypes that are not wild-type]

and through the identification for the corresponding “mutant” allele

**When solving a problem you must always define your alleles first

Drosophila melanogaster

Wild type body colour- gray

Mutant phenotype- ebony body colour

Ebony allele is recessive

e : ebony body colour allele

e +: wild type, gray body colour allele [wild-type allele can also be +]

Wrinkled wing dominant to normal wing

Wr : wrinkled wing allele

Wr+ : wild-type wing allele

note because the e is lowercase and you have the plus sign it means it is dominant