GAG WK6 Flashcards
What are the two main forms of chromatin in the human genome?
- euchromatin
- heterochromatin
What are features of euchromatin
Less compact, accessible to transcription factors.
What are features of heterochromatin
More compact, less accessible to transcription factors.
What are the two types of heterochromatin?
- facultative heterochromatin
- constitutive heterochromatin
What is facultative heterochromatin
heterochromatin can change its structure to be less condensed
What is constitutive heterochromatin
heterochromatin that remains consistently condensed
What post-translational histone modifications define heterochromatin?
- H3K9me3
- H3K27me3
- histone methylation
What is the effect of heterochromatin on chromatin structure and gene expression?
Heterochromatin tightly condenses chromatin, resulting in less gene expression
How many genes are in the human mitochondrial genome, and what do they code for?
- 37 genes
- 24 genes code for rRNA and tRNA
- 13 genes code for energy production
What are satellite DNAs
tandem repeats
how are centromeric and telomeric repeats conserved?
- centromeric = highly conserved
- telomeric = poorly conserved
What are transposons
segments of DNA that can move around within the genome
What is the function of transposons?
- they can insert themselves in genes and either
- introduce new genetic variation
- disrupt genetic variation
How do retrotransposons transpose, and what enzyme do they require?
- use an RNA intermediate
- need a reverse transcriptase
What are pseudogenes
non-functional copies of gene
How are pseudogenes formed?
A gene can be duplicated, and one copy may accumulate mutations preventing it from functioning properly and forming a pseudogene
What is the evolutionary significance of gene duplications that lead to pseudogenes?
they can mutate allowing for genetic diversity without affecting overall function (and the original gene is functional)
What are the two types of pseudogenes?
- Unprocessed pseudogenes
- Processed pseudogenes (retropseudogenes)
What are unprocessed pseudogenes
- the result of recent gene duplication
- they retain introns and other regulatory sequences of original gene
Where are unprocessed pseudogenes located
located near the original gene copy
How are unprocessed pseudogenes formed
Arise from unequal recombination events that lead to gene duplication
What are processed pseudogenes (retropseudogenes)
- they are pseudogenes that have been inserted into the genome via reverse transcriptase
- they don’t have introns
How are processed pseudogenes formed
formed from RNA through reverse transcription
What role do processed pseudogenes play in genetic diversity?
- Can mediate exon shuffling by incorporating exons into new genes
- Provide genetic backup for the original gene
How do processed pseudogenes facilitate evolution?
- If retrotranscription extends past a weak polyadenylation signal, an exon can be incorporated into a new gene.
- The second gene can mutate without affecting the original gene’s function
What does Metacentric mean
Centromere is in the middle
What does Submetacentric
Centromere is off-center.
What does Acrocentric
Centromere is near the end
What does Telocentric
Centromere is at the end.
What do the chromosome arms “p” and “q” represent?
- p: Short arm of the chromosome.
- q: Long arm of the chromosome
What is a banding system
each chromosome is further divided into bands and sub-bands for detailed identification
What does “proximal” refer to in chromosome nomenclature?
Proximal means closer to the centromere.
What does “distal” refer to in chromosome nomenclature?
Distal means further away from the centromere.
What is a deletion in chromosomal changes?
A segment of a chromosome is lost.
What is a duplication in chromosomal changes?
A segment of a chromosome is copied and inserted.
What is an inversion in chromosomal changes?
A segment of a chromosome is reversed end to end.
What is a translocation in chromosomal changes?
A segment of one chromosome is transferred to another chromosome.
What are the effects of chromosomal changes?
- looping in meiosis
- haploinsufficiency
What is looping in meiosis
- chromosomes can loop
- leads to unequal segregation of genetic material
What is the cause of looping in meiosis
deletions and duplication chromosomal changes
What is haploinsufficiency?
A condition where only one functional copy of a gene is present (due to deletion), and this single copy is not sufficient to maintain normal function
How can deletions occur due to incorrect double-strand break (DSB) repair?
Errors in repairing double-strand breaks in DNA can cause deletions
Name 2 ways tandem repeats lead to chromosomal changes?
- unequal crossover
- repeat expansion
Explain how unequal crossover can lead to chromosomal changes
Tandem repeats can cause unequal crossover, resulting in reciprocal deletions or duplications.
Explain how repeat expansion can lead to chromosomal changes
Replication fork slippage can expand these repeats, potentially leading to genetic diseases.
What is Non-Allelic Homologous Recombination (NAHR)?
when homologous regions that are not alleles recombine, leading to the loss or duplication of genetic material between repeats.
What are Low Copy Number Repeats (LCRs)
homologous regions in the genome.
how do Low Copy Number Repeats relate to NAHR?
NAHR between LCRs can cause variations in gene copy numbers and contribute to deletions.
What is a tandem duplication?
duplicated DNA segment located next to the original segment
What is a displaced duplication?
A duplicated DNA segment on the same chromosome but not adjacent to the original segment.
What is a reverse duplication?
A duplicated DNA segment that is inverted (flipped) compared to the original segment
What is a displaced reverse duplication?
An inverted duplicated DNA segment located at a distance from the original segment.
What are the effects of duplications on chromosomes?
- unstable pairing
- intra-chromosomal recombination recombination
- copy number variations
Explain unstable pairing as an effect of duplication
Duplicated segments can align in various ways during meiosis, causing different pairing outcomes
Explain intra-chromosomal recombination as an effect of duplication
May lead to excision (removal) of the duplicated segment.
Explain the copy number variations as an effect of duplication
Can cause differences in gene copy numbers, potentially leading to gene imbalances.
What is an inversion in chromosomal changes?
An inversion is when a segment of DNA is reversed in orientation.
What are the two types of inversions?
- Paracentric inversion: Does not include the centromere.
- Pericentric inversion: Includes the centromere.
What are the effects of inversions on DNA?
- No DNA loss
- Gene disruption
- altered gene expression
Explain the no loss of DNA as an effect of inversion
Inversions do not involve DNA loss but can have phenotypic effects
Explain the gene disruption as an effect of inversion
Inversion points may disrupt or fuse genes.
Explain altered gene expression as an effect of inversion
Genes within the inversion may be affected due to changes in position relative to regulatory elements
Provide an example of a phenotypic effect caused by an inversion.
In haemophilia A, about 50% of cases are caused by a large inversion disrupting the F8 gene, essential for blood clotting.
What is the effect of inversions during meiosis?
Inversions can suppress recombinants, hindering proper recombination and affecting genetic diversity.
What is a translocation in chromosomal changes?
A translocation is the rearrangement of chromosome segments.
What are the three types of translocations?
- reciprocal translocation
- non-reciprocal translocation
- robertsonian translocation
What is reciprocal translocation
Segments from two different chromosomes exchange places.
What is non-reciprocal translocation
A segment from one chromosome is transferred to another without reciprocal exchange.
What is Robertsonian translocation:
Fusion of two acrocentric chromosomes at their centromeres, forming a single chromosome
What is the basic nature of DNA replication?
DNA replication is semi-conservative, producing two DNA molecules, each with one parental and one newly synthesised strand.
How many origins of replication do eukaryotic genomes have
30,000 to 50,000 origins of replication
What is the function of origins of replication
where DNA replication begins.
How does DNA replication proceed from each origin?
DNA replication is a bi-directional process
What is the difference between the leading and lagging strands during DNA replication?
- Leading strand: Synthesised continuously.
- Lagging strand: Synthesised discontinuously in short segments called Okazaki fragments.
What is required to initiate DNA synthesis?
DNA polymerase requires a primer, which is synthesised by primase and extended by DNA polymerase alpha.
What causes the end replication problem?
- DNA synthesis is in the 5’ to 3’ direction.
- RNA primer at the end of the lagging strand leaves a terminal gap because no upstream template is available for extension
What are telomeres
repetitive DNA sequences at the ends of eukaryotic chromosomes
What are the effects of the single-stranded overhang at telomeres?
- Lagging telomere loss
- Leading telomere shortening
Explain lagging telomere loss
Slight sequence loss with each replication due to primer remova
Explain leading telomere shortening
Significant loss (100-200 nucleotides) due to the lack of a template.
What is the solution to the end replication problem?
Telomerase, a reverse transcriptase, extends telomeres by adding back lost sequences
How does telomerase function?
- Telomerase uses its RNA template to synthesise telomeric DNA repeats
- This helps maintain chromosome length during cell division
Why is genetic variation important?
Genetic variation is the foundation of evolution, providing raw material for natural selection
What is a mutation?
a structural change in a gene’s DNA sequence.
What are the two main types of point mutations?
- transitions
- transversions
What are Transitions point mutations
Change between two purines (A↔︎G) or two pyrimidines (C↔︎T).
What are transversion point mutations
Change between a purine and pyrimidine (A↔︎C or G↔︎C).
What is an insertion mutation?
The addition of one or more nucleotides in a DNA sequence.
What is a deletion mutation?
The removal of one or more nucleotides in a DNA sequence
What are two primary sources of mutations?
- Errors during DNA replication.
- External factors like mutagens
How do organisms limit harmful genetic variation?
Through DNA repair mechanisms that repair and prevent harmful changes.
Name the types of DNA repair
- direct repair
- base excision repair
- nucleotide excision repair
- mismatch repair
- double-strand break repair
What is direct repair
Reversal of specific DNA damage (e.g., photoreactivation).
What is base excision repair
Repairs lesions caused by oxidative damage.
What is nucleotide excision repair
Repairs lesions caused by UV radiation.
What is mismatch repair
Corrects replication errors.
What is double-strand break repair
Fixes breaks using homologous recombination or non-homologous end joining.
What is replication fork slippage, and what does it cause?
Replication fork slippage occurs in DNA repeat regions when DNA polymerase slips, causing misalignments that lead to insertions or deletions of repeats
What can replication fork slippage lead to?
It can cause frameshift mutations
What are nucleotide repeat expansion diseases?
Diseases caused by DNA repeat expansion in a gene, often due to replication fork slippage.
Provide an example of a nucleotide repeat expansion disease.
Huntington’s disease
What is endogenous DNA damage?
Damage caused by internal agents within cells
What are the primary endogenous agents that damage DNA?
- water
- methylation
- reactive oxygen species
How does water damage DNA
Causes hydrolytic damage, leading to DNA breaks.
What types of damage are caused by oxidative stress?
- Strand breakage: Causes single or double-strand breaks in DNA.
- Base attacks: Damages purine bases.
What happens when guanine is oxidised?
Oxidised guanine can pair incorrectly with adenine via Hoogsteen base pairing, leading to mismatches and potential mutations.
What is the primary role of DNA polymerase during replication?
DNA polymerase synthesises the new strand of DNA, selects the correct nucleotide, and improves fidelity through proofreading using exonuclease activity
How does DNA polymerase proofread DNA?
It uses exonuclease activity to remove incorrectly placed nucleotides and replace them with the correct ones.
What happens if DNA polymerase fails to correct a mismatch?
Post-replication mismatch repair (MMR) pathways correct misincorporated nucleotides.
What are base tautomers?
alternative structural forms of DNA bases
Compare the normal and rare forms of tautomers
- Normal forms: Stable and pair normally.
- Rare forms: Less stable and can cause spontaneous mutations by incorrect pairing.
What is an example of tautomerisation at GC base pairs?
Guanine can shift to its enol form, leading it to mispair with thymine instead of cytosine
What is an example of tautomerisation at AT base pairs?
Adenine can shift to its imino form, leading it to mispair with cytosine instead of thymine
Why can’t DNA polymerase synthesise DNA in the 3’ to 5’ direction?
- no high-energy bond to drive the reaction
- Proofreading would be impossible, as removing an incorrect nucleotide would leave no way to continue synthesis
Why is 5’ to 3’ synthesis energetically favourable?
High-energy phosphate bonds in dNTPs provide the energy needed for forming bonds during synthesis.
What is depurination?
Loss of a purine base (adenine or guanine) from DNA due to glycosidic bond cleavage.
What is depyrimidination?
Loss of a pyrimidine base (cytosine or thymine) from DNA due to glycosidic bond cleavage.
What is deamination, and what does cytosine deamination produce?
Deamination converts cytosine to uracil, which is found in RNA but not DNA.
How does the base excision repair pathway handle cytosine deamination?
It removes uracil to prevent mutations
What happens during methylated cytosine deamination?
Methylated cytosine is converted to thymine, resulting in a C to T mutation, corrected by the mismatch repair pathway.
What is the role of methyltransferases in methylation?
Methyltransferases add methyl groups to cytosines using S-adenosylmethionine as the methyl donor.
What is an example of non-enzymatic methylation?
Formation of 3-methyladenine, which distorts DNA and impairs replication and transcription.
What are mutagens?
Agents that cause induced mutations by altering DNA.
What are the 2 types of mutagens
- chemical mutagens
- physical mutagens (ex: UV light)
What are base analogues?
Base analogues resemble normal DNA bases but are prone to tautomeric shifts, causing incorrect base pairing.
Give an example of a base analogue
5-bromouracil (5-Br-dU) substitutes for thymine but can pair incorrectly.
What do deaminating agents do to DNA?
Remove amino groups from bases, altering their pairing properties.
What is an example of a deaminating agent, and what does it produce?
- nitrous acid
- Deamination of adenine produces hypoxanthine, which pairs with cytosine, causing T to C transitions.
What do alkylating agents do
- Add alkyl groups to DNA bases, altering base pairing and causing point mutations
Give an example of alkylating agents
Ethyl methane sulfonate (EMS).
What are intercalating agents
Molecules that insert between DNA bases, disrupting spacing and leading to insertion mutations.
Give an example of intercalating agents
Ethidium bromide.
How does UV radiation damage DNA?
- Causes pyrimidine dimers
- Leads to replication machinery skipping or deleting bases.
What effect does heat have on DNA?
- accelerates hydrolysis of glycosidic bonds, causing loss of bases and forming AP sites.
- AP sites can lead to replication errors
What is the effect of ionising radiation on DNA?
Causes severe DNA damage, including double-strand breaks, depending on type and intensity
Why is DNA repair important?
- To correct spontaneous damage (e.g., base loss, deamination, alkylation)
- protect against environmental and metabolic damage, maintaining genome stability.
What does S-Adenosylmethionine (SAM) do to DNA?
Acts as a weak alkylating agent, causing methylation
What are common sources of DNA damage?
- Endogenous damage: oxidative stress, hydrolysis, methylation.
- Environmental sources: UV light, chemicals.
- Replication errors during DNA synthesis.
What are the disease features of DNA repair defects?
- Cancer susceptibility: Increased mutation rates.
- Progeria: Accelerated ageing due to telomere defects.
- Neurological features: Neurodegeneration and neuronal death.
- Immunodeficiency: Impaired immunoglobulin and T-cell receptor production.
Why do eukaryotic genomes require robust DNA repair mechanisms?
To address both internal DNA damage (oxidative stress, hydrolysis, methylation) and external exposures (UV light, chemicals)
What type of damage does Base Excision Repair (BER) address?
Corrects modified bases and AP sites caused by depurination and depyrimidination.
What are the steps in BER?
- Recognition
- Cleavage
- Backbone Cut:
- Gap Filling:
- Sealing:
What happens during the recognition step of BER
DNA glycosylase identifies the damaged base.
What happens during the cleavage step of BER
Glycosylase cleaves the N-glycosidic bond, creating an AP site.
What happens during the backbone cut step of BER
Endonucleases/phosphodiesterases cut at the AP site
What happens during the gap filling step of BER
DNA polymerase inserts the correct nucleotide.
What happens during the sealing step in BER
DNA ligase seals the DNA strand.
What type of damage does Nucleotide Excision Repair (NER) address?
Repairs bulky lesions that distort the DNA helix
What are the steps in NER?
- Detection
- unwinding
- excision
- synthesis
- sealing
What happens during the detection during NER
Proteins identify DNA helix distortion.
What happens during the uwinding step of NER
Helicases unwind DNA around the lesion.
What happens during the excision step of NER
Nucleases remove a 24-32 nucleotide segment.
What happens during the synthesis step of NER
DNA polymerase fills in the missing nucleotides
What happens during the sealing step of NER
DNA ligase restores the DNA strand.
What type of errors does Mismatch Repair (MMR) correct?
Corrects mismatches, small insertions, and deletions during DNA replication
What are the steps in MMR?
- Recognition
- Incision
- Excision
- Synthesis
- Sealing:
What happens during recognition step of MMR
Proteins identify the mismatch or small insertion/deletion
What happens during the incision step of MMR
PMS2 nuclease cuts near the mismatch site.
What happens during the excision step of MMR
Exo1 exonuclease removes the incorrect bases.
What happens during the synthesis step of MMR
DNA polymerase inserts the correct bases.
What happens during the sealing step of MMR
DNA ligase seals the gap
What causes single-stranded DNA breaks
Caused by replication errors or oxidative damage.
How are single-stranded DNA breaks repaired
- Simple damage: DNA ligase seals the break.
- Complex damage: PARP detects the break and recruits repair machinery.
What is Non-Homologous End Joining (NHEJ)
Directly ligates two free DNA ends without a template.
what are its pros and cons of NHEJ
- Pro: Functions even without a homologous DNA template.
- Con: Error-prone, may introduce small insertions or deletions.
How does Homologous Recombination (HR) repair double-stranded breaks?
- Broken ends are prepared for recombination.
- Single-stranded DNA invades homologous DNA to find a complementary sequence.
- DNA polymerase extends the strand using homologous DNA as a template.
- Recombination structures are resolved, and DNA ligase seals gaps.
what is a locus
position of a gene
what is an allele
version of a gene
what does amorph mean
mutation leads to a loss of gene function
what does hypomorph mean
mutation that leads to reduced gene function
What does hypermorph mean
increased gene function
What does neomorph mean
new gene function
What does antimorph
dominant allele inhibits the function of wild-type gene
What is anticipation in telomerase-related disorders?
Disease worsens or appears earlier in successive generations due to progressive telomere shortening.
What are null mutations,
Null mutations result in a complete loss of gene function
How do null mutations occur
- nonsense mutations
- splicing mutations
- partial deletions
- missense mutations
What is a gain-of-function mutation?
A mutation that causes a gene to be abnormally activated, leading to altered function or expression.
What is the effect of gain of function mutation
May result in proteins that are:
- Continuously active.
- Expressed in inappropriate cell types or at incorrect times.
- Responsive to inappropriate signals.
Provide an example of a gain-of-function mutation in disease
- Chronic Myeloid Leukemia (CML)
- The fusion protein is constitutively active, promoting uncontrolled cell growth and leading to leukemia.
What is pathogenic load
Most mutations are not harmful.
Why are nonsense and frameshift mutations easier to identify as harmful?
They drastically alter protein structure, making their effects more predictable compared to other mutation types
How are missense mutations evaluated for pathogenicity?
- Assessed based on evolutionary conservation of the affected amino acid.
- Highly conserved residues are more likely to have harmful mutations
Why are noncoding RNA mutations challenging to assess for pathogenicity?
Noncoding RNAs are poorly conserved.
What is the redundancy of the genetic code
The genetic code’s redundancy allows for mutations that do not change the resulting amino acid.
What are conservative mutations
Replace an amino acid with one of similar properties.
How do conservative mutations effect vary
- Protein Position: Mutations in active sites are more disruptive.
- Amino Acid Properties: For example, proline disrupts alpha helices, affecting protein structure.
What is nonsense-mediated decay (NMD)
NMD detects and degrades mRNA with premature stop codons to prevent harmful truncated protein production
what is the purpose of NMD?
Prevents dominant negative effects by eliminating defective transcripts
What are splice site mutations
Mutations in critical splicing sequences disrupt normal splicing.
what are the consequences of splice site mutations
- Exon Skipping: Exons are omitted, altering protein structure.
- Intron Retention: Introns are retained, usually creating nonfunctional proteins.
What are cryptic splice sites
Mutations that create new, non-standard splice sites
how do cryptic splice sites affect splicing?
- Produce truncated or extended exons.
- May result in frameshifts or altered protein function.
