Epigenetics

Question 1

Define epigenetics

Answer 1

Is the study of changes to gene expression without changes made to the DNA sequence.
It is involved in regulating gene expression, involves reversible changes & can be influenced via inherited or environmental factors e.g., diet & stress
It involves DNA methylation, histone modification & Non-coding RNAs.
It plays a role in development, disease susceptibility & response to environmental changes

Question 2

Describe DNA methylation

Answer 2

A process in which a CH3 group is added to a DNA via enzyme DNA methyltransferase. This is needed to regulate gene expression

Question 3

Describe the function of DNA methylation

Answer 3

1. Gene silencing: High levels of DM in a promoter region of a gene can prevent the binding of transcription factors, so gene is silenced
2. Development & differentiation: DM patterns are important for cell differentiation, ensuring the right genes are activated/silenced
3. Gene stability: Helps maintain stability by suppressing transposons to prevent instability
   4.. Cancer/disease: abnormal patterns in DM indicate cancer/disease, where tumor suppressor genes may become hypermethylated (silenced)

Question 4

Describe the factors that affect DNA methylation

Answer 4

1. Genetic: certain genes can impact DM patterns, DM patterns can be inherited
2. Environmental factors: Diet, stress & toxins, Deficiencies in nutrients can lead to altered methylation & possibly cause disease. Exposure to toxins e.g., cigarette smoke can influence DM pattern which could change gene expression and contribute to disease. Stress can affect genes in relation to mental health, this could lead to an increased risk of anxiety of depression.
3. Age: as we age DM patterns change, genes involved in DM may be hypermethylated affecting the aging process and increasing chance of disease
4. Development in utero: DNA methylation patterns change dynamically during development, including during early embryogenesis, differentiation, and tissue-specific gene expression.

Question 5

Describe histone modification

Answer 5

This affects the structure of chromatin & regulates gene expression without altering DNA sequence, DNA is wrapped around histone proteins

Question 6

Describe histone modifications, environmental influence & the influence of disease

Answer 6

Modifications:
1. Acetylation: adding a acetyl group to activate genes
2. Phosphorylation: add a phosphate group in response to DNA damage
3. Methylation: adding a CH3, silences or activates genes
Influence: Diet, stress & toxins can alter histone modifications impacting gene expression
Disease: Abnormal histone modifications indicate disease e.g., cancer & Alzheimers

Question 7

Describe the effect of the dutch hunger famine on epigenetics

Answer 7

Before: DM & gene expression influenced by environmental factors & genes. Epigenetic development was stable. Processes were driven by normal access to nutrients providing healthy maternal conditions
During: conditions were not optimal for pregnancy, influenced epigenetic development of embryo, higher risk of diabetes, obesity etc
After: Those pregnant during famine were impacted the most, famine affecting the nutritional environment of pregnant women, which influenced the epigenetic modifications of their foetuses. These changes were especially pronounced in the DNA methylation of genes that regulate metabolism, growth, and stress responses.

Question 8

Describe the prevalence of disease during & after the famine

Answer 8

Lack of nutrition during famine impacted gene expression, and contributed to higher risk of obesity, diabetes etc later in life. Histone modification occurs influecing gene expression. Likely to be caused via stress & immune function, increasing risk to chronic disease

MH: Famine utero people, have increased vulnerability to MH disorders, such as depression & schizophrenia. These effects may be linked to epigenetic alterations in genes related to stress responses. Cognitive development in those exposed to famine was impacted due to lack of nutrition

Question 9

What do we use epigenetics?

Answer 9

1. It allows us to better understand pathologies
2. It allows us to find patterns in diseases
3. It allows new therapies to be made that interact with genes e.g., methylation sequencing

Question 10

Define genetics & genomics

Answer 10

Genetics is the study of inheritance where traits are passed from 1 to the next, genes do not mix, and genetics help us understand disease susceptibility & evolution

Genomics is the functional mapping & structuring of the genome. The genome is the entire set of DNA, introns & exons. Genomics help us understand the function, structure, evolution & interaction of genes. It studies humans, viruses etc using functional studies & tracking viral/gene transfer

Question 11

Define a gene & a chromosome

Answer 11

Gene: a section of DNA that consists of a sequence of amino acids that codes for a protein. It is a functional unit of heredity. Predicted to have about 21,000 genes

Chromosome: Made of chromatin that coils and condenses. It is how DNA is stored & made of DNA & histones. We have 23 pairs of chromosomes. Consists of Telomere, centrosome (joins chromatids)

Question 12

Define DNA, codons & histones

Answer 12

DNA: refers to deoxyribonucleic acid, it consists of 4 bases: adenine, thymine, cytosine & guanine. A pairs with T using 2 hydrogen bonds & C pairs with G using 3 hydrogen bonds. DNA is made of 2 polynucleotide strands that run antiparallel to each other, deoxyribose sugar form phosphodiester bonds with phosphate groups to form the sugar phosphate backbone

Codons: A sequence of 3 nucleotides, these three-letter sequences are part of the DNA (or RNA) and directly determine the sequence of amino acids in a protein. Start codons (AUG) signal the beginning of protein synthesis and stop codons (UAG) signal the end of the process.

Histones: Are proteins that help package DNA & regulate the DNA strand

Question 13

Define purines and pyrimidines

Answer 13

Purines: Adenosine & guanine are purines which have a double ring shape, consisting of a 6-sided ring and a 5-sided ring fused together. They form part of the nucleotide structure, contributing to the encoding of genetic information and its transmission from one generation to the next. Purines also play a role in cellular energy metabolism, as molecules like ATP (adenosine triphosphate) and GTP (guanosine triphosphate) are purine-based nucleotides used for energy transfer in cells.

Pyrimidines: Thymine, uracil & cytosine are pyrimidines, they are a 6-sided ring shape made of carbon & nitrogen atoms. are involved in storing and transmitting genetic information. They are key components of the genetic code in both DNA and RNA, contributing to the coding and structural integrity of genetic material.

Question 14

Define the genetic code and the 3 main features

Answer 14

The genetic code is a set of rules in which DNA & RNA follows to translate into proteins. It specifies how the sequence of nucleotides corresponds to the amino acids. This code is universal for almost all organisms. It suggests one codon codes for one amino acid. The genetic code has redundancy, meaning that multiple codons can code for the same amino acid.

Question 15

Describe the genetic codes influence on protein structure

Answer 15

The GC provides the instructions for assembling A.A’s into proteins, which then fold into specific three-dimensional structures that determine their function in the cell. The GC consists of sequences of codons in DNA or RNA that specify particular A.A’s. There are 20 standard A.A’s and each one is encoded by one or more codons in the genetic code.
e.g., The codon AUG codes for the A.A’s methionine, which is typically the start of protein synthesis. UAG is a stop codon & GGG codes for glycine
PS occurs DNA is transcribed into mRNA which binds to a ribosome on RER during translation, Each codon in the mRNA is read by a corresponding tRNA molecule, which brings the correct amino acid to form the growing protein chain.

Question 16

Describe the stages of amino acid folding to form a quaternary structure

Answer 16

Primary structure: known as the sequence of A.A’s, this is determined via the mRNA sequence, this determines how the protein will fold into its 3D shape
Secondary structure: The A.A’s chain folds into structures e.g., beta pleated sheet or alpha helix, held via H bonds
Tertiary: Further folding of secondary structure into a 3D shape, uses hydrogen bonds, ionic interactions, disulfide bonds, hydrophobic interactions
Quaternary: Some proteins consist of 1 or more polypeptide chains, interaction between chains results in a functional protein which has a quaternary structure

Question 17

Describe the process of DNA replication

Answer 17

This occurs during the S phase of the cell cycle, it involves DNA giving daughter cells the exact copy of genetic information
1. DNA unwinds by enzyme helicase breaking H bonds between bases, strands separate, one strand acts as a template strand, forms replication forks
2. RNA primer is made which compliments DNA template strands, this primer allows DNA polymerase to start adding nucleotides. As RNA primer add a -OH group.
3. DNA polymerase adds nucelotides in a 5’3 direction, the DNA polymerase works continuously in the direction of the replication fork, synthesizing a continuous strand of DNA.
4. After the RNA primers are removed, DNA ligase seals the gaps between the Okazaki fragments, joining them into a continuous strand.

Question 18

Describe the process of transcription

Answer 18

This is the process of copying a segment of DNA into mRNA, this serves as a template for protein synthesis.
1. DNA helicase breaks H bonds, DNA unwinds, RNA polymerase uses one of the strands as a template as is complimentary. Synthesis in 5’3 direction
2. RNA P moves along the strand adding more RNA nucleotides. RNA P reaches a terminator sequence, this signals the end of a gene, when the occurs the mRNA strand has been completed, DNA rejoins together
3. mRNA undergoes modifications to protect from degradation, introns are removed & a poly-A-tail is added

Question 19

Describe the process of translation

Answer 19

Occurs in the RER, involves ribosome, mRNA & tRNA
1. mRNA binds to ribosomes, which pass along mRNA to find start codon e.g., AUG,
2. Each codon specifies a A.A, the tRNA’s carry the complimentary A.A to the ribosome, known as the anticodon
3. as mRNA move along, tRNA transfer the anticodons which bond via peptide bonds, this process continues adding more A.A to form a polypeptide chain, until the ribosomes reach a stop codon e.g. UAG
4. This signals the ribosomes to release the complete polypeptide chain, this forms the primary structure which can then further fold into secondary, tertiary or
quaternay structures

Question 20

What are the 2 types of proteins and give examples

Answer 20

Functional:
Enzymes
RBC
antibodies
hormones

Structural:
collagen
elastin
keratin

Question 21

Describe alternate gene splicing

Answer 21

A process where a single gene can produce multiple mRNA by including or excluding exons during splicing, this increases protein diversity, developmental regulation & tissue-specific gene expression
1. Gene is transcribed in mRNA
2. mRNA is spliced to join exons and remove introns
3. Alternative splicing allows different patterns of exons, e.g., an exon is skipped & excluded from final mRNA
Dysregulation of AS may lead to disease e.g. Cystic fibrosis

Question 22

Describe post-translational modification

Answer 22

Crucial for protein regulation, this process allows proteins to form a wide range of functions. Involved in signal transduction & protein degradation.
Types of PTM include: methylation, phosphorylation, acetylation etc
e.g., Methylation involves adding of CH3 group to a lysine A.A. This regulates protein function & gene expression, occurs during histone modifications.

Question 23

Define a pseudogene

Answer 23

A non-functional gene due to damage or deletion of DNA sequences therefore cannot code for a protein, they lack mature start & stop codons.
2 types of pseudogene:
1. Processed pseudogenes: formed via reverse transcription of mRNA to cDNA, which is then inserted into the genome, has no introns
2. non-processed pseudogenes: arise from gene duplication, including introns, but are susceptible to mutations which prevent functional gene expression

Question 24

Describe the human genome

Answer 24

The human genome contains approximately 20-25000 protein-coding genes. It also contains non-coding regions known as introns, which help regulate gene expression and genomic structure.
Estimated to have about 14,000 non-functional pseudogenes, suggested to have evolutionary/ regulatory purposes
Suggested to have 37 mitochondrial genes which encode genes vital for mitochondrial function

Question 25

Define genetic variation

Answer 25

This refers to the differences in the DNA sequence which influence gene expression without altering the genetic code. This can be influenced via inherited and environmental factors. It can include variations such as deletion, insertion etc

Question 26

Define mutant & variant

Answer 26

Mutant: refers to a cell that carries a mutation in the DNA sequence, leading to epigenetic changes, this may influence gene expression, this can be harmful or advantageous Variant: Is a difference in the DNA sequence that exists in a population, a variant may not cause any functional changes, but may influence gene expression e.g., DNA methylation may be more or less likely to occur, variants widen the gene pool & are not necessarily disease causing or harmful

Question 27

Define genotype & phenotype

Answer 27

Genotype: This is a person's set of genetic material that influences a person's traits, this is inherited from the parents. It includes dominant & recessive alleles, which influence of you are more or less likely to have a trait. The genotype provides the blueprint for the phenotype Phenotype: It is the outward expression of the traits, influenced via genotype & environmental factors. E.g., blond hair, could be genetically inherited or influenced by lots of sunlight.

Question 28

Describe the causes of genetic variation

Answer 28

1. mutation: Randoms changes in DNA sequence are caused by errors in DNA replication, damage, mutagens or environmental factors, some mutations may be silent, beneficial or harmful 2. genetic drift: refers to random changes in allele frequencies in a population due to an event, it can lead to a loss of alleles, can have an impact on gene pool 3. recombination: Occurs during SR where chromosomes exchange genetic material, leading to new allele combinations, leading to genetic diversity 4. sexual reproduction: he fusion of gametes stimulates meiosis which shuffles alleles from both parents through independent assortment & crossing over, this ensures offspring inherit a completely unique combination of genes from both parents

Question 29

Define insertion, deletion, substitution, inversion, translocation, duplication

Answer 29

Insertion: addition of 1 or more nucleotides into DNA sequence Deletion: removal of 1 or more nucleotides in the DNA sequence Substitution: where one nucleotide is subbed, by another nucleotide, may cause a silent mutation, missense or nonsense mutation. It may impact protein structure & function, occur due to error in DNA replication. Inversion: A DNA segment is flipped, altering the DNA sequence translocation: A segment of DNA is transferred from one chromosome to another Duplication: a segment of DNA is copied and inserted into the genome again

Question 30

Describe a silent mutation

Answer 30

Occurs where a substitution mechanism does not change the amino acid sequence of a protein, as genetic code is redundant, more than one codon can code for a A.A. Results in same protein being synthesised.

Question 31

What is the effect of a mutation of the DNA sequence?

Answer 31

Variations in the DNA sequence can occur through sense and non-sense single nucleotide variants (SNVs), frame-shift variants, indels, structural variants, and copy number variants (CNVs).

Question 32

Describe a single nucleotide strand variation (nonsense & sense)

Answer 32

Single nucleotide strands (SNVs): This is a variation where a single nucleotide is altered in the DNA sequence. Point mutations are single base pair changes in the DNA sequence that can be caused by errors during DNA replication, exposure to mutagens, or other environmental factors. SNVs can be sense or non-sense: Missense: These mutations do alter the protein sequence as they still result in a codon that codes for a different amino acid, these variants may result in a different protein being made, an may increase likelihood of disease e.g., sickle cell anemia Non-sense: These mutations introduce a stop codon in the middle of a gene which shortens the protein product, this often leads to a loss of function of the protein or a genetic disease if the protein truncated is vital for cellular function. UAG is most frequently occuring stop function, selection pressures may influence non-sense mutations.

Question 33

Describe frameshift and indels on genetic variation

Answer 33

Frame shift variants: This occurs when the insertion or deletion causes a shift in the reading frame of the genetic code. These nucleotides are added/ removed from the code causing the reading frame to alter the downstream of amino acids. These normally lead to incomplete protein sequences resulting in a non-functional protein, these variants often cause severe disease due to impact of protein function & structure. Indels: Refers to an insertion or deletion of 1 or more nucleotides in the genome, they can occur in coding and non-coding regions. Small indels can lead to a frameshift mutation which affects entire protein sequences. Larger indels may affect gene structure, gene regulation & gene expression

Question 34

Describe structural variants and copy variants on genetic variation

Answer 34

Structural variants: Involve large scale alterations to the structure of chromosomes in coding & non-coding regions. It includes mutations such as duplication, deletions, inversion and translocation. Structural variants can disrupt genes or regulatory regions, leading to diseases like cancer (due to chromosomal rearrangements) or genetic disorders (due to deletions or duplications). Copy variation: Is a variation in the large copies of a particular gene or genomic region, it involves duplications & deletions. Duplications can lead to gene imbalances leading to overexpression of a gene which could lead to disorders or cancers. Deletions cause a loss of function of critical genes, impairing key biological processes and leading to congenital disorders. CVs can have significant effects on gene expression, leading to a range of phenotypic outcomes, including susceptibility to diseases like autism, schizophrenia, and other developmental disorders.

Question 35

Describe germline DNA coding sequences

Answer 35

Germline: refers to the DNA found in the reproductive cells (sperm and egg cells in animals, pollen and ovules in plants). Inheritance: Changes in the germline DNA are passed down to offspring. This is how hereditary traits are inherited from one generation to the next. Function: The coding sequences in germline DNA are responsible for the genetic instructions passed to offspring. These sequences include genes that will be expressed in the offspring's cells, guiding their growth, development, and function. Mutation Impact: Mutations in germline cells can lead to inherited diseases or traits, which can be passed on to future generations.

Question 36

Describe somatic DNA coding sequences

Answer 36

Location: Somatic DNA refers to the DNA in all other cells of the body that are not involved in reproduction (e.g., skin, muscle, nerve cells). Inheritance: Mutations in somatic DNA are not inherited by offspring. These mutations affect only the individual in whom they occur. Function: Somatic DNA coding sequences direct the functions of the specific tissues or organs to which the somatic cells belong. These genes are responsible for normal cellular processes, such as metabolism, repair, and cellular differentiation. Mutation Impact: Mutations in somatic cells can lead to conditions like cancer or other diseases affecting the individual but are not passed to offspring.

Question 37

Summarise the epigenetic regulation on gene expression

Answer 37

DNA Methylation: Methylation of promoter regions typically silences gene expression, while demethylation can activate genes. Histone Modifications: Acetylation generally activates gene expression by loosening chromatin, while methylation can either activate or silence genes depending on the context. Chromatin Remodeling: Changes in chromatin structure, such as opening or closing the chromatin, affect the accessibility of genes for transcription. Non-coding RNAs: MicroRNAs and long non-coding RNAs regulate gene expression at various levels, from transcription to translation. Genomic Imprinting: Parent-of-origin-specific gene expression leads to the silencing of one allele, depending on whether it is inherited from the mother or father. Environmental Factors: External factors can induce epigenetic changes that modify gene expression, influencing traits and health.

Question 38

What are the types of genetic tests

Answer 38

Single gene Whole exome Clinical exome Single cell Whole genome Panel Epigenetic Karyotyping RNA expression

Question 39

Describe how a PCR test is set up

Answer 39

The steps to detect specific mutations or genetic variants in the DNA associated with a monogenic disorder. 1. Sample Collection: Blood is drawn from the patient. 2. DNA Extraction: DNA is isolated from white blood cells. 3. PCR Setup: Specific primers are designed to target the gene of interest associated with the disorder. 4. Amplification: The DNA is amplified through repeated cycles of denaturation, annealing, and extension to create many copies of the target region. 5. Mutation Detection: The amplified DNA is analyzed (e.g., through sequencing or gel electrophoresis) to identify mutations. 6.. Interpretation: The results are compared to reference sequences to confirm the presence or absence of the mutation, diagnosing the disorder.

Question 40

Describe bioinformatics, it's importance and it's pathway

Answer 40

It uses computer algorithms to analyze, interpret & understand genomic data, it uses data sets from sequencing projects, it helps us to understand gene function & disease pathway 1. take a sample e.g., blood 2. select the best test 3. blood is sequenced 4. Data must be controlled 5. Data undergoes deep analysis 6. Result give & report generated 7. Bioinformation will give context to report 8. clinical interpretation 9. Further discussion occurs to see if more testing needed 10 Results and treatment plan is delivered via clinician

Question 41

Describe the applications to healthcare of bioinformatics

Answer 41

Personalized medicine: tailoring treatments based on genetics Disease research: identifying genetic causes for disease Pharmacogenomics: analyzing drug response Agriculture: crop & livestock improvement

Question 42

Describe the use of genomics in healthcare treatment

Answer 42

Healthcare genomics is a rapidly growing field that leverages genetic information to improve healthcare outcomes, personalize treatments, and understand disease mechanisms. It enables pharmacogenomics, targeted therapies, personalized medicine etc e.g., Disease diagnosis & risk assessment Using genetic testing to diagnose disease, assess the risk of development and monitoring disease progression

Question 43

Give at least 3 examples of genomic usage

Answer 43

1. pre-screening/screening 2. monitor high risk groups 3. reduce adverse drug reactions

Question 44

Define Pharmacogenomics, Patient Stratification, and Personalised Medicine

Answer 44

Pharmacogenomics is the study of how genetics influence drug responses Patient stratification: where patients are grouped based on genes, disease, risk factors to personalize treatment and predict outcomes Personalised medicine: tailoring the treatment based on someones lifestyle, genes etc, to optimize treatment and prevent disease

Question 45

Describe the principles of Pharmacogenomics, Patient Stratification, and Personalised Medicine:

Answer 45

Pharmacogenomics helps optimize drug dosing based on genetic factors, reducing adverse effects and improving treatment outcomes via targeted drug dosing creating a tailored dose by using genetic variation, Targeted Therapies also plays a critical role in identifying new drug targets based on genetic variations found in specific diseases. Patient stratification: enables patients to be grouped based on genetic markers that predict disease risk or treatment response, It also reduces unnecessary interventions by identifying patients who are less likely to benefit from certain treatments, stratification helps avoid treatments that could cause harm or unnecessary side effects. Personalized medicine: can predict disease risk early, allowing for preventive measures or early interventions that can significantly improve patient outcomes. Treatment plans are tailored based on the individual’s genetic profile, response to drugs, and disease characteristics. This is particularly important in complex diseases where standard treatments may not work for everyone.

Question 46

Describe how epigenetics can affect the expression of coding genes within the genome.

Answer 46

Epigenetics can significantly impact the expression of coding genes (genes that encode proteins) within the genome through various mechanisms that regulate whether a gene is turned on or off, or how actively it is expressed. These mechanisms influence the structure of the chromatin and the accessibility of DNA to the transcriptional machinery, ultimately affecting gene expression