Gene Expression

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Gene Expression: The Basics

Gene expression is the mechanism by which the genetic code in DNA affects the phenotype of an organism.
The main stages are transcription (DNA to mRNA), translation (mRNA to protein at ribosomes), and the function of the protein product (e.g., as an enzyme) which affects the phenotype.
Transcription is a key stage where gene expression can be switched on or off.
Only some DNA sequences code for polypeptides; these are called coding sequences.
Non-coding sequences produce functional RNA molecules (e.g., tRNA) or regulate gene expression (e.g., enhancers, promoters).

From cell to gene

Regulation of Transcription

The promoter is a non-coding sequence near a gene; enhancers are non-coding regions usually found further away.
Promoters and enhancers are not transcribed themselves.
Transcription factors are proteins that bind to promoter or enhancer sequences to help initiate transcription.
They help RNA polymerase attach to the promoter, increasing the rate of transcription.
This ensures that only the required genes are expressed in the correct cells, at the correct time, and to the appropriate level.
This is the most common way cells control gene expression.

Protein synthesis

Regulation of Translation

After transcription, mRNA is modified and transported to ribosomes in the cytoplasm for translation.
Once translation is complete, mRNA remains in the cytoplasm until broken down by enzymes called nucleases.
In human cells, mRNA may take from a few minutes to a couple of days to be broken down.
Degradation of mRNA regulates translation, ensuring proteins are only synthesised when necessary and removing mRNA that has already been translated.

Epigenesis and Epigenetics

Epigenesis is the development of differentiation patterns in cells as a multicellular organism develops from a zygote.
Epigenetics is genetic control by factors other than the DNA sequence; it involves heritable changes in gene function without changes to the DNA sequence.
In eukaryotes, nuclear DNA is wrapped around histones to form chromatin; chromatin can be chemically modified to alter gene expression.
Such modifications are called epigenetic tags; collectively they form the epigenome, which is heritable.
Modifications to the epigenome can be passed on to the next generation at the cellular or whole organism level.
Since the DNA sequence is not changed, the genotype remains the same while the phenotype changes.

Genome, Transcriptome, and Proteome

The proteome includes all proteins synthesised in an organism's cells and is determined by the genome.
Each organism has a unique proteome due to its unique genetic material.
Different proteins are needed in different cell types, so only the genes for the correct proteins are 'switched on' at any time.
This avoids energy wastage from expressing all genes in every cell.
The genome of each cell in an organism is the same, but the proteome varies.
The transcriptome is the range of mRNA transcripts produced in a cell or tissue type, determined by the pattern of gene expression.

Epigenetic Tags: Methylation

Methylation involves the addition of a methyl (-CH₃) group; it can occur on DNA or on histones.
DNA methylation commonly adds a methyl group to cytosine bases of the promoter region.
Methylation of DNA suppresses transcription by inhibiting the binding of transcription factors, locking genes in the 'off' position.
DNA methylation can be affected by environmental, lifestyle, or age-related factors.
Histone methylation adds methyl groups to amino acids of histone tails, making genes more or less accessible to transcription factors, thus activating or deactivating genes.

Epigenetic Inheritance

When epigenetic tags remain during mitosis or meiosis, they are passed on to daughter cells or gametes.
Mitosis results in daughter cells with the same epigenetic modifications as the parent cell.
Meiosis forms gametes containing epigenetic tags that can be passed to offspring after fertilisation.
This is epigenetic inheritance: phenotypic changes can be inherited without changes in the nucleotide sequence.
If epigenetic tags are removed during mitosis or meiosis, epigenetic inheritance cannot take place.

Environment & Gene Expression: Examples

Gene expression can be affected by external conditions such as diet, temperature, chemicals, and air pollution.
Air pollution chemicals can damage lung tissue, leading to asthma or chronic obstructive pulmonary disease, and negatively impact cardiovascular health.
Exposure to air pollution may change methyl tags on DNA or histones, altering gene expression and increasing inflammation and disease risk.
Inflammation in the respiratory system may cause scarring and tissue thickening, decreasing oxygen diffusion into the blood.
Suggested treatments to reduce air pollution impact include exercise and a diet high in B vitamins.

Removal of Epigenetic Tags and Imprinting

During egg and sperm development in mammals, most epigenetic tags are removed to prevent environmental changes from being passed on.
Some tags may be retained and passed on by imprinting.
During imprinting, epigenetic tags may be added to DNA in sperm and egg cells, so only one copy of a gene is expressed while the other is suppressed.
Organisms typically inherit two functional copies of a gene, but for imprinted genes only one functional copy is inherited.
In sperm development, maternal genes are silenced; in egg development, paternal genes are silenced.

Epigenetic Origins of Phenotypic Differences: Tigons and Ligers

Tigons (male tiger × female lion) are about the same size or smaller than their parents.
Ligers (male lion × female tiger) are typically larger than both lions and tigers.
These phenotypic differences are due to genetic imprinting.
Male lions pass on genes that encourage growth, while female lions have imprinted genes that discourage growth.
Tigers do not pass down genes that discourage growth.
A male lion crossed with a female tiger produces a liger that can grow much larger because the female tiger lacks imprinted growth-discouraging genes.

Monozygotic Twin Studies

Monozygotic (identical) twins originate from the same zygote and are genetically identical.
Dizygotic (non-identical) twins result from two different eggs fertilised at the same time and are genetically different.
Monozygotic twin studies help determine the contribution of genetics and environment to phenotypic variation.
If separated twins show similar traits, genes are likely responsible; significant differences suggest environmental influence.
Comparing monozygotic and dizygotic twins can indicate the extent of genetic versus environmental effects.
Even monozygotic twins show variation due to epigenetic changes such as DNA methylation or histone acetylation.

External Factors Impacting Gene Expression: The lac Operon

Regulatory genes control structural genes; in prokaryotes, structural genes can form an operon controlled by one promoter.
The lac operon controls production of lactase (β-galactosidase) and two other structural proteins.
Lactase breaks down lactose for energy; it is an inducible enzyme only synthesised when lactose is present, preventing energy waste.
Components in order: promoter for structural genes, operator, lacZ (lactase), lacY (permease), lacA (transacetylase).
Upstream: promoter for regulatory gene and lacI gene coding for the lac repressor protein.
The repressor has two binding sites: one for the operator and one for lactose.
When lactose is absent, the repressor binds the operator, preventing RNA polymerase binding and transcription; no lactase is made.
When lactose is present, it binds the repressor, changing its shape so it cannot bind the operator; RNA polymerase transcribes the structural genes, and lactase is produced.

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1.Which of the following best describes the term 'gene expression'?
Easy
- AThe mechanism by which the genetic code contained within DNA has an effect on the phenotype of an organism
- BThe process by which DNA is replicated before cell division
- CThe random loss of genes from a chromosome during meiosis
- DThe exchange of genetic material between homologous chromosomes
2.Which of the following best describes the importance of regulating gene expression?
Easy
- ATo ensure that essential genes are expressed all the time in the relevant cells
- BTo ensure that only the relevant genes in the relevant cells are expressed at certain times
- CTo ensure that only the relevant genes are expressed in the relevant cells at all times
- DTo ensure that the same group of essential genes is expressed in all cells of the organism at certain times
3.Which of these features that affect gene expression are not passed directly from parent to offspring?
Medium
- APromoters
- BMethyl groups
- CEnhancers
- DTranscription factors
4.Which of the following statements about DNA methylation are correct? (select all that apply)
Medium
- ADNA methylation varies throughout a lifetime.
- BDNA methylation can be affected by environmental factors.
- CAnalysis of DNA methylation patterns can be used in the early detection of disease.
- DDNA methylation patterns are always lost during meiosis.
5.Which of the following are examples of groups that could be added to the tails of histones to chemically modify them? I. Acetyl II. Hydroxyl III. Phosphate IV. Amino
Medium
- AI. and III. only
- BII. and IV. only
- CI., II. and III.
- DII., III. and IV.
6.In humans, during periods of hypoxia the transcription factor HIF binds to the Hypoxia Response Element (HRE) sequence and increases transcription of the EPO gene. Which kind of regulatory elements are HIF and HRE?
Medium
- AActivator protein and enhancer sequence
- BRepressor protein and silencer sequence
- CEnhancer sequence and activator protein
- DGeneral transcription factor and enhancer sequence
7.Which of the following best describes the outcome of direct methylation of DNA?
Medium
- AIt stimulates the expression of the gene.
- BIt prevents guanine from forming hydrogen bonds.
- CIt inhibits the binding of transcription factors.
- DIt causes breaks in the phosphate deoxyribose backbone.
8.Which of the following applies to both mutations and epigenetics? I. It may affect the visible characteristics of an organism II. The DNA base sequence can change and impact the expression of genes III. Environmental factors may play an important role in the development of changes IV. Modifications may be passed on to the next generation at a cellular level V. The amino acid tails of histones are modified by methylation, acetylation and phosphorylation
Hard
- AI, IV and V.
- BI, III and IV.
- CII, III and IV.
- DI, III, IV and V.

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9.Female embryos contain two copies of the X chromosome. To avoid producing double the amount of polypeptides, the paternal X chromosome is inactivated by methylation of lysine on histones. Which of the following provides the most accurate explanation of how this would inactivate the paternal X chromosome?
Hard
- AAdding a methyl group to lysine will maintain the negative charge to allow chromatin to become more condensed and inhibit transcription of the genes.
- BAdding a methyl group to lysine will maintain the positive charge to allow chromatin to become less condensed and inhibit transcription of the genes.
- CAdding a methyl group to lysine will maintain the positive charge to allow chromatin to become more condensed and promote transcription of the genes.
- DAdding a methyl group to lysine will maintain the positive charge to allow chromatin to become more condensed and inhibit the transcription of the genes.
10.The promoter is a non-coding sequence located near a gene, whereas enhancers are non-coding regions usually found further away.
Easy
True or false?
11.Epigenetic changes alter the DNA nucleotide sequence.
Medium
True or false?
12.Match each term with its correct description.
Medium
- Promoter
- Enhancer
- Transcription factor
- Operator
- Non-coding sequence near a gene where RNA polymerase binds
- Non-coding sequence that can be located far from a gene and increases transcription
- Protein that binds to DNA sequences to regulate transcription
- DNA region in an operon where a repressor protein binds
13.Place the following stages of transcription in the correct chronological order.
Medium
- RNA polymerase binds to the promoter
- DNA strands separate
- RNA polymerase moves along the antisense strand
- Free RNA nucleotides are added to the growing mRNA strand
- mRNA strand is released
14.Match each term related to gene expression with its correct description.
Medium
- Coding sequence
- Promoter
- Enhancer
- Transcription factor
- A DNA sequence that codes for the production of a polypeptide
- A non-coding sequence located near a gene where RNA polymerase binds
- A non-coding region of DNA usually found further away from a gene that regulates transcription
- A protein that binds to promoter or enhancer sequences to help initiate transcription
15.Place the following stages of gene expression in the correct chronological order.
Easy
- Transcription
- Translation
- Protein function
16.Which of the following are ways that cells regulate gene expression after transcription has occurred? (select all that apply)
Medium
- ABreakdown of mRNA by nucleases
- BBinding of transcription factors to enhancers
- CMethylation of DNA at promoters
- DTransport of mRNA to ribosomes for translation
- EModification of mRNA before translation
17.Which of the following best describes the role of transcription factors in gene expression?
Medium
- AThey bind to promoter or enhancer sequences to help initiate transcription.
- BThey catalyse the addition of methyl groups to DNA.
- CThey break down mRNA in the cytoplasm.
- DThey translate mRNA into polypeptides at ribosomes.
18.A scientist treats cells with a chemical that inhibits the addition of methyl groups to DNA. What is the most likely effect on gene expression?
Medium
- AIncreased transcription of genes that are normally silenced by methylation.
- BDecreased transcription of all genes.
- CIncreased translation of mRNA.
- DNo effect on gene expression.
19.Which of the following statements about epigenetic inheritance are correct? (select all that apply)
Hard
- AEpigenetic tags can be passed to daughter cells during mitosis.
- BEpigenetic tags are always removed during meiosis.
- CImprinting can result in only one copy of a gene being expressed.
- DEpigenetic changes involve changes to the DNA nucleotide sequence.
- EEnvironmental factors can influence epigenetic tags that are inherited.
20.Match each component of the lac operon with its correct function.
Medium
- Promoter
- Operator
- lacZ
- lacI
- Site where RNA polymerase binds
- Site where repressor protein binds
- Gene coding for lactase
- Gene coding for repressor protein
21.A researcher measures the amount of mRNA transcribed from gene X in liver cells and in muscle cells from the same organism. The gene X mRNA is present at high levels in liver cells but is almost undetectable in muscle cells. Which of the following best explains this observation?
Medium
- AMuscle cells have lost the gene X coding sequence during differentiation.
- BTranscription factors that bind to the promoter or enhancer of gene X are present in liver cells but not in muscle cells.
- CThe mRNA in muscle cells is translated faster, so less mRNA accumulates.
- DMuscle cells contain a different genome from liver cells.
22.A scientist treats cells with a chemical that prevents the addition of methyl groups to cytosine bases in promoter regions. What is the most likely effect on the expression of a gene whose promoter is normally methylated?
Medium
- ATranscription of the gene will be increased because transcription factors can bind more easily.
- BTranscription of the gene will be decreased because RNA polymerase cannot bind.
- CThe DNA base sequence of the gene will change.
- DThe gene will be translated directly into protein without transcription.
23.In a study of monozygotic twins separated at birth, one twin develops asthma while the other does not. Both twins have identical DNA sequences. Which of the following best explains this difference?
Hard
- AThe twins have different genomes because they are monozygotic.
- BThe difference is due to epigenetic changes such as DNA methylation caused by different environments.
- CThe difference is due to a mutation that occurred after birth in one twin.
- DAsthma is caused by a change in the DNA base sequence of a gene.
24.A bacterium is grown in a medium containing lactose. After a few hours, the lactose is completely used up. What will happen to the production of lactase in the bacterial cells?
Medium
- ALactase production will increase because lactose is absent.
- BLactase production will decrease because the lac repressor protein will bind to the operator and prevent transcription.
- CLactase production will remain constant because the lac operon is always active.
- DLactase production will stop because the bacteria will mutate the lacZ gene.
25.During egg and sperm development in mammals, most epigenetic tags are removed. However, some tags are retained and passed on to the next generation by a process called imprinting. Which of the following is a consequence of imprinting?
Medium
- ABoth copies of a gene are expressed equally.
- BOnly one copy of a gene is expressed while the other copy is suppressed.
- CThe DNA sequence of the gene is changed.
- DThe gene is duplicated so that four copies are present.
26.Which of the following best describes the relationship between the genome, transcriptome and proteome of a cell?
Medium
- AThe genome is the same in all cells, while the transcriptome and proteome vary between cell types.
- BThe genome, transcriptome and proteome are all identical in every cell of an organism.
- CThe transcriptome is the same in all cells, while the genome and proteome vary.
- DThe proteome determines the genome, which determines the transcriptome.
27.A study found that individuals exposed to high levels of air pollution had increased methylation of genes involved in inflammation. Which of the following best explains how this could lead to an increased risk of cardiovascular disease?
Hard
- AMethylation changes the DNA base sequence, causing mutations in heart cells.
- BMethylation alters gene expression, which can increase inflammation and contribute to cardiovascular disease.
- CMethylation increases the rate of transcription of all genes, leading to overproduction of proteins.
- DMethylation prevents the removal of epigenetic tags during meiosis.
28.In a study, monozygotic twins and dizygotic twins were compared for a particular trait. The results showed that monozygotic twins were more similar to each other than dizygotic twins were to each other. What is the best conclusion from this result?
Hard
- AThe trait is entirely determined by environmental factors.
- BGenetic factors are likely to play a significant role in determining the trait.
- CThe trait is caused by epigenetic changes only.
- DDizygotic twins share the same genome as each other.
29.A scientist wants to investigate whether a particular gene is expressed in different tissues of a mouse. Which of the following techniques would be most appropriate to measure the amount of mRNA for that gene in each tissue?
Medium
- AMeasuring the amount of protein produced by the gene in each tissue.
- BUsing a technique that detects specific mRNA molecules, such as quantitative PCR after reverse transcription.
- CSequencing the DNA of the gene in each tissue.
- DMeasuring the rate of transcription by adding radioactive nucleotides to the tissues.
30.A scientist wants to determine whether a specific gene's transcription is being inhibited by methylation of its promoter. Which technique would be most appropriate to directly detect methyl groups on cytosine bases in the promoter region?
Medium
- ADNA sequencing to identify the base sequence of the promoter
- BBisulfite sequencing to detect methylated cytosines
- CRNA interference to knock down the gene's expression
- DChromatin immunoprecipitation to locate histone proteins
31.In an experiment, researchers treated cultured cells with a drug that inhibits histone deacetylase (HDAC). What is the most likely effect on gene expression?
Medium
- AIncreased acetylation of histone tails, leading to more relaxed chromatin and increased transcription
- BIncreased methylation of DNA, leading to tighter chromatin and decreased transcription
- CDecreased acetylation of histone tails, leading to more condensed chromatin and decreased transcription
- DNo effect, because histone modification does not influence gene expression
32.A researcher uses a technique to measure the amount of mRNA for a particular gene in two different tissues. The results show that the gene is highly expressed in tissue A but not in tissue B. Which of the following best explains this observation?
Medium
- ATissue A has a different genome from tissue B, so different genes are present.
- BTissue A has specific transcription factors that bind to the gene's promoter, while tissue B lacks them.
- CTissue B has a mutation in the gene that prevents transcription.
- DTissue B has more nucleases that degrade the mRNA before it can be translated.
33.A scientist studies a gene that is imprinted. In a particular individual, only the maternal copy of the gene is expressed. Which of the following best explains this?
Hard
- AThe paternal copy has a mutation that prevents transcription.
- BThe paternal copy is silenced by epigenetic tags such as methylation.
- CThe maternal copy has enhancers that the paternal copy lacks.
- DThe paternal copy is lost during meiosis.
34.In a study of monozygotic twins, one twin develops a disease while the other does not. Both have identical DNA sequences. Which of the following best explains this difference?
Hard
- AThe twins have different genomes due to mutations after birth.
- BThe twins have different epigenetic tags affecting gene expression.
- CThe twins have different numbers of chromosomes.
- DThe twins have different promoters for the gene in question.
35.Which of the following statements about the lac operon are correct? (select all that apply)
Medium
- AThe lac repressor protein binds to the operator region in the absence of lactose.
- BLactose binds to the repressor protein and causes it to change shape.
- CThe lac operon is an example of a repressible operon.
- DThe structural genes lacZ, lacY, and lacA are transcribed as a single mRNA.
- ERNA polymerase binds to the operator region to initiate transcription.
36.Which of the following are appropriate methods to study epigenetic modifications? (select all that apply)
Hard
- ABisulfite sequencing to detect DNA methylation
- BChromatin immunoprecipitation (ChIP) to identify histone modifications
- CPolymerase chain reaction (PCR) to amplify DNA for sequencing
- DWestern blotting to detect specific proteins
- ERNA sequencing to measure transcript levels
37.The epigenome is not heritable.
Easy
True or false?
38.Place the following steps of the lac operon regulation in the correct chronological order when lactose is present.
Medium
- Lactose binds to the repressor protein
- The repressor protein changes shape and detaches from the operator
- RNA polymerase binds to the promoter
- Transcription of structural genes occurs
- Lactase breaks down lactose
39.Which stage of gene expression involves the genetic code being transcribed into mRNA?
Easy
- ATranscription
- BTranslation
- CProtein function
- DDNA replication
40.Which of the following best describes a coding sequence?
Easy
- AA DNA sequence that codes for the production of a polypeptide
- BA non-coding region where transcription factors bind
- CA sequence that produces functional RNA molecules such as tRNA
- DA region of DNA that is not transcribed
41.Complete the sentence about gene expression.
Easy
The three main stages of gene expression are transcription, translation, and the ____ of the protein product.
42.Name the enzyme that breaks down mRNA in the cytoplasm.
Easy
43.What is the name for all the epigenetic tags in an organism?
Easy
44.In a study, the number of epigenetic tags in a cell was found to be 150. After an environmental change, the number increased by 20%. Calculate the new number of epigenetic tags.
Medium
45.Complete the sentence about epigenetic modifications.
Easy
The addition of a methyl group to DNA is called ____, while the addition of an acetyl group to histone tails is called ____.
46.Complete the sentence about the stages of gene expression.
Easy
The most common stages of gene expression are ____, during which the genetic code is transcribed into mRNA, and ____, when the genetic code is translated into proteins at ribosomes.
47.Complete the sentence about the regulation of transcription.
Easy
A ____ is a non-coding sequence located near a gene, whereas ____ are non-coding regions of DNA usually found further away from a gene; transcription factors bind to these regions to help initiate transcription.
48.Name the type of enzyme that breaks down mRNA molecules in the cytoplasm.
Easy
49.Give the name for the complete set of epigenetic tags in an organism.
Medium
50.Complete the sentence about epigenetic modification.
Medium
DNA methylation involves the addition of a ____ group, and it suppresses transcription by inhibiting the binding of ____ to the DNA.
51.In a study, the number of epigenetic tags in a cell was found to be 150. After an environmental change, the number increased by 30%. Calculate the new number of epigenetic tags.
Medium
52.A scientist counted 240 epigenetic tags on a section of chromatin. Treatment with a drug removed 25% of these tags. Calculate the number of epigenetic tags remaining on the section of chromatin.
Medium
53.Define the term 'coding sequence'.
Hard
54.Explain how methylation suppresses the transcription of a gene.
Hard
55.Explain how methylation of histone tails can affect gene expression.
Hard
56.Explain how methylation of DNA suppresses the transcription of a gene.
Hard
57.Distinguish between epigenetics and mutations.
Hard
58.In a study, the number of epigenetic tags in a cell was found to be 150. After an environmental change, the number increased by 20%. Calculate the new number of epigenetic tags.
Medium
- A216 tags
- B180 tags
- C162 tags
- D198 tags
59.In a study, the number of epigenetic tags in a cell was found to be 150. After an environmental change, the number increased by 30%. Calculate the new number of epigenetic tags.
Medium
- A235 epigenetic tags
- B195 epigenetic tags
- C215 epigenetic tags
- D175 epigenetic tags
60.A scientist counted 240 epigenetic tags on a section of chromatin. Treatment with a drug removed 25% of these tags. Calculate the number of epigenetic tags remaining on the section of chromatin.
Medium
- A216 epigenetic tags
- B180 epigenetic tags
- C198 epigenetic tags
- D162 epigenetic tags

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