D2.2: Gene Expression

Question 1

What is gene expression?

Answer 1

The mechanism by which information in genes has an effect on the phenotype
How genetic information is used to produce RNA and proteins

(Geno -> phenotype)

Question 2

What is the genome?

Answer 2

The whole genetic information of an organism
Unique to each individual
Not all genes are expressed

Question 3

What are the stages of gene expression?

Answer 3

Transcription:
Genetic code -> mRNA
Gene expression switched on/off

Translation:
Genetic code translated -> protein at ribo
Function of protein affect phenotype

Question 4

What are the type of non-coding sequences?

Answer 4

Promoter: noncoding sequences near a gene, where RNA polymerase binds (5’ end) to begin transcription

Enhancer/scilencers: noncoding region far from a gene, when and to what extent a gene is expressed
- regulates transcription

Both are NOT TRANSCRIBED

Question 5

What are transcription factors?

Answer 5

Type of protein molecule that binds to the promoter, scilencer or enhancer sequences
Most common method of gene expression/transcription regulation

Question 6

What happens when a transcription factor binds to a promoter sequence?

Answer 6

Either:
Helps RNA polymerase attach to promoter (increase rate)
Repress gene expression by blocking RNA polymerase/other factors (decrease rate)
-> ex: repressor protein

Influence gene expression -> regulate transcription so only required genes are expressed in correct cell/time/level

Question 7

What happens when a transcription factor binds to a enhancer sequence?

Answer 7

Transcription factors called activator protein bind to enhancer
-> form complex that interacts with the promote region and aids RNA poly binding

1 enhancer can interact with multiple promoters -> influence transcription of multiple genes

Question 8

What is an Operon?

Answer 8

Some genes: multiple promoters, used in different developmental stages, tissue types
-> allow fine tuning of expression in different contexts

Others share promoter: operon
-> genes usually transcribed together and have similar/related functions

Question 9

How can intracellular receptors affect gene expression?

Answer 9

When activated by specific molecular:
Activated receptor undergo structural change -> can bind to specific DNA sequences to promote transcription of specific gene

Question 10

What is mRNA persistence?

Answer 10

mRNA synthesized -> translation in ribosome (can be done many times)

Longer mRNA strand persist -> higher likelihood it will be translated many times -> slower degradation by nuclease (method of translation regulation)

Question 11

What does the lifespan of mRNA depend on?

Answer 11

Chemical modifications to mRNA:
Addition of guanine cap at 5’ end
Poly A tail at 3’ end (shortened over time -> decrease chance mRNA will be translated)
-> increase stability

Stabilizing protein:
-> interfere with activity of nuclease (block active site)
OR
-> promotes binding of protected protein to mRNA (alter structure -> increase stability)

Activity and amount of nuclease:
-> + nuclease = + degradation

Cellular stress:
Exposure to toxins, heat -> influence factor activity that determine persistance of mRNA

Question 12

What is epigenesis/epigenetics?

Answer 12

Epigenesis: The development of differentiation patterns in the cells of multicellular organism as it develops from a zygote
-> determined bu genome + pattern of gene expression
-> phenotype altered

Epigenetics: genetic control by factors other than DNA sequences
-> heritable changes in gene function without changes in DNA, just phenotype
-> study of how behaviors + environment affect gene transcription
-> affects the way code is read (phenotype), not the code itself (genotype)

Question 13

What are epigenetics tags?

Answer 13

All cells same genome
Nuclear DNA wrapped around protein = chromatin
-> can be chemically modified to alter gene expression
-> e.g. methylation of DNA, histone modification

Chemical modification = epigenetics tags
-> cells have distinct transcriptomes + proteomes

Question 14

What is the
Epigenome
Transcriptome
Proteome?

Answer 14

Epigenome:
All epigenetics tags in an organism
Is heritable

Transcriptome:
All RNA molecules transcribed from the genome at any given time (dynamic)

Proteome:
Entire set of proteins that is synthesized by a cell/tissue/organism (more dynamic)

Genome stays the same while Transcriptome and proteome CHANGE between cell/tissue types

Question 15

Explain methylation of DNA

Answer 15

Addition of methyl group to a cytosine base of the promoter region
-> replaces H atom
-> locks genes into the ‘off’ position

Suppresses transcription by inhibiting binding of transcription factors
-> can decrease gene expression or silencing

Changes chromatin organization
Can be impacted by environmental, lifestyle or age

Question 16

Explain how the structure of chromatins can affect the amount of transcription

Answer 16

DNA + histone = nucleosome -> regulate chromatin structure + accessibility for transcription

Histone:
Core: central part of nucleosome
Tail: N terminals (protrude out)
Net positive charge (tail -> high density of + AA)
-> neg DNA + pos histone -> nucleosome formation

DNA supercoiled: heterochromatin -> less transcription
DNA loosely packed: euchromatin -> more transcription
Tail of histone can also be chemically modified

Question 17

Explain acetylation of histone

Answer 17

Addition of acetyl (CH3COO-) group of AA to histone tail

Decrease overall charge -> reduced electrostatic attraction between histone + DNA -> DNA less tightly wrapped -> easier for RNA polymerase/transcription factors to access

Removal of acetyl group -> decrease gene expression

Question 18

Explain methylation of histones

Answer 18

Methyl groups added to AA in histone proteins

Depending on which/location of AA -> transcription repressed or activated

Generally deactivate genes by inhibiting binding of transcription factors -> making it less accessible

Question 19

What is epigenetics inheritance?

Answer 19

Inheritance of non genetic information that can influence gene expression and phenotypic traits

Mitosis: daughter cells contain the same epigenetic modifications as parent cells

Meiosis: gametes contain epigenetic tags which will be passed onto offspring

Question 20

What is reprogramming?

Answer 20

If epigenetic tags removed during mitosis/meiosis -> no epigenetic inheritance -> reprogramming

Specialized cell machinery goes though genome and erases epigenetic tags -> genetic ‘blank slate’

In sexual reproduction:
Occurs during formation of gametes

Question 21

What are the conditions for epigenetic inheritance?

Answer 21

Rule out the possibility of genetic changes:
Mutation in larger organisms -> discrete compared to smaller organisms

Show that the epigenetic effect can be passed through enough generations:
Discard the possibility of direct exposure
Direct exposure in pregnant women only impact first threes gens.
Epigenetic would affect the 4th gen. -> rule out direct exposure

Question 22

What are the implications does epigenetic inheritance create for evolution?

Answer 22

Add more complexity

Genome changes slowly through mutations -> takes time for a trait to become common in a species

BUT epigenomic changes are quick and can happen to many people at once
-> flexible to the environment -> allows species to constantly adapt

Question 23

Examples of environmental effects on gene expression:
Air pollution

Answer 23

Chemicals in polluted air

Particulate matter, NOx, O3, polyaromatic hydrocarbons -> decrease DNA methylation -> increased transcription

Increase production of protein regulating immune system -> inflammation -> increased risk of cardiovascular disease or pulmonary conditions, increased scarring and thickening of lung tissue -> decrease rate of diffusion

Question 24

Examples of environmental effects on gene expression:
Diet

Answer 24

Mice:
Nutrients (folic acid, vitamin B12/6, etc) -> one metabolic
pathway -> make methyl groups -> silence genes (specifically agouti gene)

+ methyl donating folate during pregnancy -> offspring have brown coat and low disease risk

— methyl donating folate during pregnancy -> offspring have yellow coat, obsess and higher risk of cancer and diabetes

Question 25

Examples of environmental effects on gene expression: Temperature

Answer 25

In plants: Activate or repress certain a genes involved in different developmental stages like: Flowering Hibernation Production of pigments Reptiles: Sex of reptiles is determined by temperature at which eggs are incubated -> warm = female -> cold = male Increase in global temperatures impact -> lead to skewed sex ratios -> impact reproductive success and survival

Question 26

Why are epigenetic tags removed during egg and sperm development?

Answer 26

Allows for new epigenetic modifications -> cells can differentiate into different types HOWEVER: some tags retained -> IMPRINTING -> organism inherit two functional copies of an gene -> only one copy of an imprinted gene is expressed/inherited, while other is suppressed/methylated/imprinted -> inherited from one parent -> meaning: maternal alleles imprinted and paternal allele carries mutation -> child will have disease bc maternal alleles ‘off’ -> normal recessive mutation can cause disease

Question 27

Epigenetic tagging: tigons and ligers

Answer 27

Tigon: male tiger + female lion Liger: male lion + female tiger Some phenotypic similarities, but also differences -> resulted of imprinted genes Ligers: Larger in size than tigers or lions -> genes for size is imprinted and inherited from male lion Tigons: Same size or smaller than tigers or lions -> don’t inherit imprinted gene for larger size Result of: Female lions mate with many males -> males want large cubs for competitive advantage, females want small cubs for easier birth -> size imprinted Female tigers only mate with one male -> no need for size to be imprinted

Question 28

What are monozygotic twins? How are they useful in the study of epigenetic tagging/environmental impact on gene expression?

Answer 28

Twins originating from a single fertilized egg -> genetically identical individuals Useful for studying the effects of environment on gene expression initially they grow up in same environment -> similar overall patterns of epigenetic tags but still some variation As they age/environment starts to differ -> increase phenotypic differences -> increased similarities over time indicative of a genetic cause -> lower similarities over time indicative of epigenetic cause

Question 29

What is the lac operon?

Answer 29

Cluster of three genes in bacterial DNA that codes for protein in the digestion of lactose (disaccharide) -> bacteria prefer glucose as food source, but can use lactose Includes gene coding for lactase (hydrolyzes lactose) and a lactose membrane transporter

Question 30

What is the structure of the lac operon?

Answer 30

Components of lac operon: Promoter (for structural genes) Operator Structural gene lacZ (codes for lactase) Structural gene lacY (codes for permeate (lactose membrane transporter) Structural gene lacA (codes for transacetylase) To the left (upstream) to lac operon: Promoter (regulatory gene) Regulatory gene lacl (codes for lac repressor protein)

Question 31

What happens to bacteria when lactose is absent?

Answer 31

Regulatory gene is transcribed and translated to produce lac repressor protein Lac repressor protein binds to operator region in lac operon RNA polymerase cannot bind to promoter region due to presence of repressor protein Transcription of structural gene cannot take place No lactase enzyme synthesized

Question 32

What happens to bacteria when lactose is present?

Answer 32

Lactose binds to the second binding site of the repressor protein -> distort shape and therefore cannot bind to operator site RNA polymerase able to bind to promoter region -> transcription occurs -> mRNA for all three structural genes translated Enzyme lactase is produced -> lactose broken down -> used for energy Gene only expressed/lactase only produced when LACTOSE IS PRESENT

Question 33

What is the structure of the lac repressor protein?

Answer 33

lac repressor protein: Two binding sites: bind to operator in lac operon (prevent transcription of structural genes bc RNA polymerase no bind) Bind to lactose (when it binds the protein distorts -> cannot bind to operator)

Question 34

What is the effect of tryptophan on the expression of the tryptophan operon?

Answer 34

Tryptophan operon -> cluster of five genes in bacterial DNA -> necessary for tryptophan (AA) synthesis No tryptophan: RNA polymerase able to bind to tryptophan operon and transcribe gene necessary for tryptophan synthesis Yes tryptophan: Bind to repressor protein -> repressor protein undergo conformational change -> can bind to operator -> inhibits transcription Ensures gene only transcribed when needed

Question 35

What is the effect of oestradiol on oestradiol receptors?

Answer 35

Oestradiol = steroid hormone -> diffuse freely across cell membrane Inside cell -> oestradiol binds to oestradiol receptors -> conformational change and activation Activated -> hormone-receptors complex can move into nucleus -> bind to specific DNA sections near target gene Once bound other protein (co-regulatory, co-activator) recruited to gene -> influence transcription of target gene Specific target gene can vary (incudes genes related to development + function of female reproductive system) -> e.g. gene for: follicle stimulating hormone, luteinising hormone, development of uterine and breast tissue, etc.