MONDAY JANUARY 18TH, 2021

SECTION A – 1H00PM

SECTION B – 400PM
BIO2133 Genetics

Exploring the gene, its expression, and transmission Hypotheses

Classical genetics merges the knowledge of DNA, genes, mutations and

inheritance with the scientific method to deduce information about Conclusions Predictions
genes, alleles, and gene function from analyses of genetic crosses,
pedigrees, and patterns of inheritance.

It also helps us understand how the results of molecular studies help us Observations
understand aspects of human genetics and genetic disease.
 Today’s session…

1. Announcements
2. Recap….
3. FOXP2 gene Case Study….

Phenotype expression:
1. Transcription and Translation…
2. Mutations, genotypes, and phenotype….
3. Gene interactions?
 FOXP2 DNA, RNA, and Protein

DNA Promoter
(Adapted from Fisher and Marcus, 2006)

mRNA

Protein
Identification of the “speech gene” – FOXP2
The story: In 1990, scientists became interested in the KE family in London, half of
whose family members have speech disorders.
 Learning objectives
Compare different types of mutations and describe how each can
affect genes and the corresponding mRNAs and proteins.

• Explain gene expression and phenotype expression in terms of DNA transcription

and translation.
• Defend how each strand of DNA of a chromosome can serve as template to
express RNA (and thus proteins).
• Discuss how various factors might influence the relationship between genotype
and phenotype.
• Draw a simple line diagram showing a segment of DNA from a gene and its RNA
transcript, indicating which DNA strand is the template, the direction of
transcription and the polarities of all DNA and RNA strands.
• Describe the process of transcription, and translation. How are mistakes in these
processes identified and corrected?
 Promoter coding strand
template strand: will Neighbor gene
be transcribed
Transcription start site
5’CG…TATA TATG…ATTA3’ 5’GG…CAT3’
unaffected
3’GC…ATAT ATAC…TAAT5’ 3’CC…GTA5’

5’CG…TATA TATG…ATTA3’ 5’GG…AAT3’

John
3’GC…ATAT ATAC…TAAT5’ 3’CC…TTA5’

5’TATG…ATTA3’ 5’GG…CAT3’
Athena
3’ATAC…TAAT5’ 3’CC…GTA5’
5’CG…TATA TATT…CCTA3’ 5’GG…CAT3’
Phil
3’GC…ATAT ATAA…GGAT5’ 3’CC…GTA5’
5’CG…TTTA TATG…ATTA3’ 5’GG…CAT3’
Cathy
3’GC…AAAT ATAC…TAAT5’ 3’CC…GTA5’
Post-transcriptional
modification

• Removal of introns, splicing

• mRNA degradation rates?

 TRANSLATION

DNA T G AA C C A G T G C A
Transcription
Nucleus

mRNA ACUUGGUCACGU
Translation
Cytoplasm

Protein – Thr – Trp – Ser – Arg-

Different initiation points create
overlapping genes
 Post-translational
modification
• Removal or modification of the N-terminus;

• Individual a.a. are sometimes modified;

• Carbohydrate side chains are added;

• Polypeptides chains may be trimmed; (see

examples – next slides

• Signal sequences are removed;

• Polypeptides complexed with metals

Post-translational modification
Insulin example
Post-translational modification
 Today’s session…

1. Announcements
2. Recap….
3. FOXP2 gene Case Study….

Phenotype expression:
1. Transcription and Translation…
2. Mutations, genotypes, and phenotype….
3. Gene interactions?
 Session Learning Objective

How is genetic information expressed so it affects an

organism’s structure and function?

How do different types of mutations affect genes and the

corresponding mRNAs and proteins?
 Learning objectives
Compare different types of mutations and describe how each can
affect genes and the corresponding mRNAs and proteins.

• Discuss how various factors might influence the relationship between genotype
and phenotype.
• Explain how the expression of a phenotype is the relative expression of both alleles of a
given gene in a diploid organism.
• Discuss how various factors might influence the relationship between genotype and
phenotype (e.g. incomplete penetrance, variable expressivity, and sex-limited phenotype).
• Describe how mutations arise and how environmental factors can increase mutation rate.
• Distinguish between missense, nonsense, synonymous and non-synonymous mutation and
describe how they affect gene function.
• Explain why different mutations in a gene lead to different alleles of the same gene.
• Distinguish between loss of function and gain of function mutations and their potential
phenotypic consequences.
• Predict the most likely effects on protein structure and function of null, reduction of
function, overexpression, dominant-negative and gain of function mutations.
If I were a mutagen…

Randomly pick a base in the coding sequence and change

it to any other base:

Tyrosinase gene sequence

Classification of mutations:

Based on cell type or chromosome locations

• Somatic mutations:

• Germ-line mutations:

• Autosomal mutations:

• X-linked mutations:
Mutations (and consequences)

Based on result at the molecular level

Point
mutations
 DNA sequence dictates protein structure

Genes encode the

order of amino acids
(1˚ structure)

. . . which sets up amino acid interactions . . .

Cys

Cys

. . . that
dictate Lys

protein His
His

conformation
(3˚ structure)
 Changes in the primary structure of proteins can
change folding and alter function of a protein
wild type mutant
shape
change this change
amino acid

active site active site

can’t form enzyme is
defective
Wild type alleles…
- usually code for functional proteins
- usually dominant

Mutant alleles…
- usually code for defective proteins
- often recessive

DOMINANT alleles…indicated by CAPITAL letters

recessive alleles…indicated by lower case letters
Loss of function mutations

LOF: Loss Of Function mutations result in a protein that has little or no

enzymatic activity.

Most mutations associated with a

phenotype are LOF.

Why?

Many changes that affect the normal 3˚ structure would

disrupt the active site (even if the mutation affects an
amino acid that is far away from the active site).
Loss of function mutations

Most LOF mutations are recessive.

Why?

Half the amount of wild type gene product is

usually sufficient to give a wild type
phenotype.
Phenotypes in diploid organisms

Phenotype = physical or observable characteristic

e.g., eye color
hair type
ability/inability to digest lactose
ability to synthesize melanin (pigment)

Alleles of a gene are variant forms of the gene

tyrosinase gene

C gene encodes tyrosinase tyrosinase mRNA

C
tyrosine
* c tyrosinase

melanin
 C tyrosinase

C
tyrosinase

C tyrosinase

* c
tyrosinase

Why does Cc look as pigmented as CC?

 General rule for LOF mutations…
Half the amount of wild type gene product is sufficient to give a wild type phenotype

Example : Tyrosinase wild type allele = C

mutant = c

[enzyme
threshold wild type phenotype
activity]
albino phenotype

Genotype: CC Cc cc

▪ 1 wild type copy → enzyme activity above threshold needed for normal pigmentation, so
carriers unaffected (mutant allele → recessive)
Temperature-sensitive proteins
Proteins unfold upon heating.

Increasing temperature

Missense mutations can destabilize 2˚ and 3˚ structures so the protein unfolds at lower
than normal temperatures.

Tyrosinase protein (for melanin) can be encoded by alleles so that it folds properly only in
the coolest parts of the skin.
Burmese

Siamese
Mutations in regulatory regions and introns

- in promoter could affect transcription

- in intron could affect splicing

pre-mRNA
- in 5’ or 3’ UTR
could affect
mature mRNA translation or mRNA
stability
ORF

Any of these changes could change when, where, or how

much protein is made
“Half the amount of wt gene product is
sufficient for wt phenotype”

Exceptions?
 Rare exception #1—haploinsufficiency

Half the number of t protein

molecules is not sufficient to
tt TT maintain normal tail length

wild type short tail mutant

threshold

amount of normal tail

functional “t”
protein

short tail

genotype: tt Tt TT
Rare exception #2—no threshold
e.g., snapdragon flower color
CR: enzyme that makes red pigment
CI: no enzyme activity

Red x Ivory No
CRCR CICI threshold!

Amount of red
pigment
Pink
CRCI Genotype: CRCR CRCI C IC I

Heterozygote has intermediate phenotype… incomplete dominance

Rare exception #3—“poisonous” subunits

…also called “dominant-negative” mutations

Amount threshold “wt” phenotype

of active
protein
“mutant”
aa Aa AA phenotype
Why does Aa have so little activity?
Example: “Poisonous” subunits

protein assembled
alleles: subunits: enzyme: phenotype:

wild type

mutant

heterozygote is
mutant!
How mutations affect phenotype

GOF: Gain Of Function mutations result in a functional protein that…

…is made at the wrong place

…is made at the wrong time
…has a new activity

GOF mutations need not be beneficial

Very few mutations are GOF.

Why?

Only very specific mutations (e.g., specific amino acid changes) will have this
effect
How mutations affect phenotype

Will GOF mutations be dominant or recessive? Can you predict?

depends on threshold!

Most GOF mutations are dominant

For example, only a small amount of the altered protein is sufficient to produce
the mutant phenotype

But there could be cases in which the altered protein in combination with the
wt protein gives a wt phenotype
GOF example #1–normal protein in the wrong place

Antennapedia in Drosophila
Wild type Antennapedia gene is only expressed in the
thorax; legs are made.

A mutation causes the Antennapedia gene to be

expressed in the thorax and also in the head, where
legs result instead of antennae!

What kind of mutation is this?

What phenotype would you predict for the

heterozygote?
GOF example #2–normal protein at the wrong time
Lactose tolerance in humans

Homozygous wt Homozygous mutant

Gene promoter:
ON OFF ON ON
can digest
lactose
lactase
activity

cannot
3 15 3 15
age age
So which allele is dominant? What would be the phenotype of the heterozygote?

Mutant has gain of function… expect lactose tolerance to be dominant

 Today’s session…

1. Announcements
2. Recap….
3. FOXP2 gene Case Study….

Phenotype expression:
1. Transcription and Translation…
2. Mutations, genotypes, and phenotype….
3. Gene interactions?
 Session Learning Objective

How is genetic information expressed so it affects an

organism’s structure and function?

How do different types of mutations affect genes and the

corresponding mRNAs and proteins?
 Learning objectives
Compare different types of mutations and describe how each can
affect genes and the corresponding mRNAs and proteins.

• Explain how the expression of a phenotype is the relative expression of both alleles of a
given gene in a diploid organism.
• Discuss how various factors might influence the relationship between genotype and
phenotype (e.g. incomplete penetrance, variable expressivity, and sex-limited phenotype).
• Given a diagram or information about a transcription factor, explain how the expression of a
gene can be positively or negatively regulated by the product of another gene (i.e. gene
interaction).
 ROLES FOR GENES
• Enzymes (catalyze reactions)
• Signalling (e.g. Hormones, messengers)
• Receptors (e.g. Adrenergic receptors)
• Constituent (e.g. Actin, myosin; keratin)
GENE EXPRESSION AND INTERACTIONS

Regulation
G1 (promoters) Multiple genes

P1 Proteins

Development of the jaw

and speech centers
GENE EXPRESSION AND INTERACTIONS

Example: 1 gene, 1 product

G1

P1 (e.g. enzyme)

S1 S2
GENE EXPRESSION AND INTERACTIONS

Example: Control of an enzyme

G2
G1
P2 (e.i. modulator)

P1 (e.g. enzyme)

S1 S2
GENE EXPRESSION AND INTERACTIONS

Example: Control of an enzyme

G2
G1 P2 (e.i. modulator)

P1 (e.g. enzyme)

S1 S2
GENE EXPRESSION AND INTERACTIONS

Example: 2 genes, 1 final product (S3)

G1 G2

P1 (e.g. enzyme) P2 (e.g. enzyme)

S1 S2 S3
In Drosophila, red and yellow eye pigments are synthesized through the
pterin pathway. A part of the pterin pathway (simplified) is shown below.
GENE EXPRESSION AND INTERACTIONS

Example: 2 genes, 1 final product (S3)

G1 G2

P1 (e.g. enzyme) P2 (e.g. enzyme)

S1 S2 S3
GENE EXPRESSION AND INTERACTIONS

Gene products
controlling the
expression of
other genes
GENE EXPRESSION AND INTERACTIONS

• Pleiotropy
• Epistasis
• Gene suppressors
• Complementary genes
• Duplicate genes