D2.2 - Gene Expression

Question 1

Genotype and phenotype

Answer 1

• Genotype: the genetic makeup of an organism in terms of it’s DNA
• Phenotype: the physical traits and characteristics of an organism resulting from
  it’s genotype and environmental influences

Question 2

Genome

Answer 2

• A genome is the entire set of genetic
  instructions for an organism
• This includes all chromosomes, as well as
  mitochondrial and chloroplast DNA found in a
  cell
• It is important to note that all cells in an
  organism have the same genome, however
  no cell will express all of the genes in its
  genome
• The pattern of gene expression (turning on
  and off certain genes) causes cells to
  differentiate (B2.3)

Question 3

Transcriptome

Answer 3

• A transcriptome represents the genetic
  instructions that have been transcribed into
  RNA molecules
• It includes all rRNA, tRNA and mRNA
  sequences (including all variants produced via
  alternative splicing)

Question 4

Proteome

Answer 4

• A proteome is the complete set of proteins
  present in a cell or organism at a given time
• The proteome is significantly larger than the
  transcriptome as proteins may be modified
  (D1.2)
• Note: the proteome of different cell types in
  the same organism will be different as gene
  expression varies between cells

Question 5

Epigenesis

Answer 5

• Epigenesis is the process by which a multicellular organism develops from a zygote through patterns of differentiation in cells
• Epigenetics is the study of how chemical and environmental triggers influence gene expression
  patterns
• Unlike genetic changes (mutations), epigenetic modifications do not alter the DNA sequence and
  are potentially reversible

Question 6

Regulating Gene Expression

3 different ways

Answer 6

1. By regulating gene accessibility and subsequent activity (via the incorporation of epigenetic tags)
2. By controlling the production and activity of RNA (via the regulated action of transcription factors)
3. By moderating the functional levels of RNA within the cell (via targeted degradation)

Question 7

DNA Methylation

Answer 7

• Epigenetic tags are chemical markers that
  attach to DNA or histone proteins and
  influence the transcription of genes
• DNA methylation involves the incorporation of a methyl group to cysteine nucleotides in the
  promoter region of a gene
• Methyl groups (-CH3) can act as epigenetic
  tags by attaching to the promoter region in
  DNA and histones
• This represses the activity of the promoter by preventing RNA polymerase from binding, stopping the gene from being transcribed

Question 8

Histone Methylation

Answer 8

• Methyl groups can also attach to amino acids of histone proteins found in nucleosomes
• Recall: nucleosomes are made of 8 histone
  proteins that DNA wraps to help with
  supercoiling (unique to eukaryotes)
• Supercoiling helps regulate transcription as only certain areas of the DNA are accessible to RNA polymerase
• Methylation of histone proteins causes the DNA to bind tighter to the nucleosome, preventing RNA polymerase from binding and stopping transcription

Question 9

Examples of environmental effects on gene expression in cells and organisms

Answer 9

• An epigenome consists of all of the epigenetic tags on the DNA and histone proteins
• Interaction between the environment and DNA can impact the epigenome of cells and
  organisms
• Examples of environmental influences that can affect the epigenome include:
• Diet: a person’s diet or the diet of their mother while she was pregnant with them can alter
  the epigenome (read linked article)
• Cigarette smoke: epigenetic changes from exposure to cigarette smoke may lead to lung
  cancer (read linked article)
• Air pollution: this can add or remove methyl epigenetic tags from a person’s epigenome,
  changing which genes are expressed (read linked article)

Question 10

Monozygotic Twins

Answer 10

• Monozygotic twins are identical twins resulting from the fertilization of one egg
• Monozygotic twins are clones and have the same genome

Question 11

Case Study

A study compared the methylation patterns of 3-year-old identical twins with 50-year-old identical twins.

Methylation patterns were dyed red on one chromosome for one twin and dyed green for the other twin on the same chromosome.

Chromosome pairs in each set of twins were digitally superimposed.

Answer 11

The result would be a yellow colour if the patterns were the same. Differences in patterns on the two chromosomes results in mixed patterns of green and red patches.

This was done for four of the twenty-three chromosome pairs in the genome.

Question 12

Epigenetic Inheritance

Answer 12

• Epigenetic inheritance refers to the inheritance of non-genetic information that can influence gene expression and phenotypic traits
• Inheritance of epigenetic tags can occur if the tags remain in place during meiosis, meaning
  that egg and sperm cells will carry them
• These tags can then be passed on to offspring during fertilisation

Question 13

Genomic Imprinting

Answer 13

• Genomic imprinting is the process by which
  only one of the two inherited genes for a trait
  is expressed
• One copy of the gene is silenced by
  epigenetic tags during egg and sperm
  formation

Question 14

Ligers and Tigons

Answer 14

• The retention of certain epigenetic tags within
  the ovum or sperm is thought to be responsible for the size differences seen in ligers and tigons (lion-tiger hybrids)
• Ligers (offspring of a male lion and a female
  tiger) are larger than both lions and tigers
• Tigons (offspring of a male tiger and a female
  lion) are the same size as an average lion

Question 15

Liger and epigenetic tags

Answer 15

• The male lion’s sperm is imprinted to
  promote growth
• The female tiger’s egg has no imprinting
• When the egg and sperm combine, larger
  offspring develop

Question 16

Tigers and epigenetic tags

Answer 16

• The male tiger sperm’s sperm has no
  imprinting
• The female lion’s egg is imprinted to restrict
  excessive growth
• When the egg and sperm combing, the
  resulting offspring are regular sized

Question 17

Enhancers and Silencers

Answer 17

• Enhancer and silencer regions are
  sequences of DNA that regulate the
  expression of a nearby gene
• They act as binding sites for transcription
  factor proteins, allowing genes to be turned
  on or off
• Transcription factors can bind to DNA sequences outside of the promoter to mediate RNA polymerase activity
• Turning ON genes:
  when transcription factors bind to enhancer
  sequences, RNA polymerase can bind to the
  promoter, increasing the rate of transcription
• Turning OFF genes:
  when transcription factors bind to silencer
  sequences, RNA polymerase cannot bind to the
  promoter, inhibiting the rate of transcription

Question 18

Gene Expression and External Factors

Answer 18

• Gene expression can be impacted by factors outside of the cell, such as:
• Hormones form hormone-receptor complexes within the cytoplasm of the cell which move into the nucleus and bind to genes, regulating transcription of DNA
• The presence of biochemical molecules which a cell metabolizes (ex: gene expression in E. coli bacteria is impacted by the presence or absence of the sugar lactose)

Question 19

Hormones

Answer 19

• Steroid hormones can freely cross the plasma membrane to induce changes in gene expression
• They bind to receptors in either the cytoplasm or nucleus of the target cell, to form an active
  receptor-hormone complex
• This activated complex will move into the nucleus and bind directly to DNA, acting as a
  transcription factor for gene expression

Question 20

Controlling Translation

Answer 20

• The regulation of transcription controls the quantity of mRNA that is produced, which regulates the rate of translation in a cell
• Translation can be further regulated by the degradation of mRNA by nuclease enzymes
• Nucleases break down mRNA to RNA nucleotides which can be recycled by the cell to produce new mRNA molecules
• In human cells, mRNA may be present from minutes up to days before it is broken down by
  nucleases
• The longer a transcript lasts before degradation, the more protein will be produced by translation