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Fundamental Topics In Biology > Fundamental Molecular Biology > Flashcards

Fundamental Molecular Biology Flashcards

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1
Q

What is a genome?

A

An organism’s complete set of DNA, all of its genes. Humans have more than 3 billion DNA base pairs.

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2
Q

What is a mutation?

A

Mutations are changes in the genetic material of a cell (or virus).

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3
Q

What is a gene?

A

A genomic sequence (DNA or RNA) directly encoding functional product molecules, either RNA or protein.

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4
Q

What is a spontaneous mutation?

A

Spontaneous mutations are the result of errors in natural biological processes.

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5
Q

What does natural selection require?

A

Natural selection requires genetic differences, generated by sex (recombination) and by spontaneous mutations.

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6
Q

What is the rate of spontaneous mutation per generation in human germ-line?

A

There is a low rate of spontaneous mutations in human germ-line cells. There are 3 new mutations per 10^8 base pairs per generation. Therefore, 200 new mutations in each human child.

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7
Q

Where do spontaneous mutations originate from?

A

Spontaneous mutations originate from:

  • Replication/repair errors
  • Metabolism itself (reactive oxygen species to blame)
  • Mutagens in food
  • Ionising radiation
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8
Q

Diagram of how DNA copying error/damage becomes a mutation.

A
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9
Q

Net mutation equation

A

DNA damage - repair = Net mutation

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10
Q

How can we increase the net mutation rate?

A

We can increase the net mutation rate by:

  • Increasing rate of DNA damage:
    • Sun bathing
  • Reducing repair efficiency
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11
Q

Howis a T-T dimer produced and why is it so bad?

A

Thymidine Dimers are produced when adjacent thymidine residues are covalently linked by exposure to ultraviolet radiation. Covalent linkage may result in the dimer being replicated as a single base, which results in a frameshift mutation.

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12
Q

What are 2 differences (not including number of chromosomes) between somatic and germ-line cells?

A

The differences between somatic and germ-line cells are:

  • Germ-line : one cell passed onto nect generation vs. somatic which is a genetic dead end, disposable to natural selection (after offspring).
  • The mutation rate in germ line cells are far lower than that of somatic cells.
    • With the somatic mutation rate being 10-1000x that of the germ-line mutation rate.
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13
Q

What regions do most random mutations affect most?

A

Most random mutations affect unimportant regions.

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14
Q

When would a mutation affect the phenotype?

A

A mutation would affect the organism’s genotype if:

  • It landed in key functional residues like protein, RNA coding regions, exons etc.
  • Regulatory regions (gene expression/translation signals)
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15
Q

What is an exon?

A

An exon is a part of a gene that encodes for final mature RNA.

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16
Q

What percentage of the genome do exons make up in humans?

A

Exons make up 1-2% of the human genome. Hence why most DNA is considered unimportant.

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17
Q

What are 3 possible point mutations within the protein coding region of DNA?

A
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18
Q

What is a conservative missense mutation?

A

A conservative missense mutation is where the amino acid formed is similar in function and shape to the reference amino acid. Non-conservative is obvioulsy the opposite.

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19
Q

What is a frameshift mutation?

A

A frameshift mutation occurs when there is an insertion/deletion of x base pairs.

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20
Q

Why do most mutations have no effect? (besides the fact they land in unimportant regions)

A

Most mutations are recessive and can therefore only effect phenotype when homozygous,

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21
Q

What are the operational uses of recessive and dominant alleles?

A
  1. Key to inheritance patterns, probability aka Mendel.
  2. Affects how natural selection acts on mutations and how they spread through populations.
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22
Q

What are the profound uses of recessive and dominant alleles?

A
  • Tells you about how the mutation affects the gene
  • What the gene does
  • Suggests therapy/intervention strategies
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23
Q

What are four biochemically related recessive conditions along the Albanism pathway mutations?

A

Four biochemically related recessive conditions along the Albanism pathway mutations:

  • Albanism
  • Alkaptonuria
  • Phenylketonuria
  • Cretinism
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24
Q

What is the Albanism Pathway?

A
25
Q

What are the four genes which if mutated would affect the conversion of Tyrosine to Melanin in humans?

A

The four genes in humans are:

  • OCA1: Tyrosinase enzyme mutants have severe albanism
  • OCA2: P protein (tyrosinase ‘helper’) mutations of this gene have mild albanism.
  • OCA3: Tyrosinase - related gene (very rare) mutants have weak albanism
  • OCA4: SLC45A2 protein (tyrosinase helper) mutants have mild albanism.
26
Q

What is a ‘Loss of function’?

A

A loss of function mutation is where too little produced.

27
Q

What causes Phenylketonuria?

A

Phenylketonuria is caused by high phenylpyruvic acid. This causes progressive brain dysfunction. This occurs because of a reccessive mutation in the gene that codes for Phe hydroxylase.

28
Q

What causes the high levels of phenylpyruvic acid in the Phenylketonuria?

A

In the condition, no Tyrosinase gets formed because of mutant Phe hydroxylase. Causes build up of Phenylalanine. When a certain amount of Phenylalanine goes into another pathway to form phenylpyruvic acid.

29
Q

What are the effects of: Albanism, Alkapotnuria, Cretinism and PKU?

A
  • Albanism affects pigmentation due to little melanin.
  • Alkapotnuria affects the colour of urine turning it black due to the high levels of phenylpyruvic acid.
  • Cretinism affects cognitive ability (causing mental retardation) due to too little thyroxin.
  • PKU affects brain function (causing progressive brain dysfunction) this is due to too much phylalanine.
30
Q

What’s the commonality in the mutations which cause Albanism, Alkapotnuria, Cretinism and PKU?

A

In all cases, there’s less/no activity of the gene product (enzyme). Each mutation affects the phenotype accumalating too much substrate or too little product.

31
Q

What are most recessive mutations?

A

Most recessive mutations are loss of function mutations and most loss of functon mutations are recessive.

  • Enzyme/ protein/ RNA not working etc.
32
Q

What is a Null allele?

A

A Null allele is one which produces no RNA or protein.

33
Q
A
34
Q

What are most dominant mutations?

A

Most dominant mutations are gain-of-function (can be complete or incomplete dominance) and corollary.

35
Q

What is incomplete dominance?

A

Incomplete dominance is when a dominant allele, or form of a gene, does not completely mask the effects of a recessive allele, and the organism’s resulting physical appearance shows a blending of both alleles.

36
Q

What are the two things a gain-of-function mutation may do?

A

Gain-of-function mutations either:

  1. more of a “normal” function (whatever that is) e.g.,
    i) More active enzyme (e.g., RAS oncogene: stuck in “on” state)
    ii) Produce more protein (hence more overall activity in the pool of gene product)
  2. new function (unrelated to what the normal gene does)

Presence or not of WT allele makes no difference

37
Q

What’s an example of a gain of normal function mutation?

A

Achondroplasia

Most common form of dwarfism: Autosomal dominant (but see next slide)

99% of cases: ONE of TWO missense point mutations in FGFR3

38
Q

What does FGFR3 code for?

A

FGFR3 codes for fibroblasts, growth factor and receptor 3.

39
Q

What is the main role of FGFR3? And how does the gain of function mutation cause Anchondroplasia?

A

FGFR3 acts to slow limb growth, turned on by fibroblast growth factor binding.

Anchondroplasia is caused by a mutant FGFR3 receptor locked in an active state regardless of whether FGF is bound or not.

40
Q

What are some strange facts about Anchondroplasia?

A

•Only 20% have a parent with achondroplasia

* 80% of the mutations are generated in a parent’s germ line

(so called “de novo” [from new] mutations: one of those 200……)

41
Q

What’s an example of a gain of abnormal function mutation?

A

Huntington’s Disease is a dominant gain in abnormal function mutation.

42
Q

Give some facts about Huntington’s disease.

A

Huntington’s Disease

  • Progressive neurodegeneration
  • Autosomal dominant mutation
  • Rare: 1/10,000 people
  • Gene: HTT
  • Protein: Huntingtin – unknown function (cytoskeleton?)
  • Symptoms: Onset 30s-50s
  • First symptom: Loss of limb control
  • Mortality: 10-15 years after first symptoms
43
Q

How many CAG repeats does a person with Huntington’s disease have?

A

In people with Huntington disease, the CAG segment is repeated 36 to more than 120 times. People with 36 to 39 CAG repeats may or may not develop the signs and symptoms of Huntington disease, while people with 40 or more repeats almost always develop the disorder

44
Q

What does CAG base triplet code for?

A

The CAG base triplet codes for glutamine.

45
Q

Why are most mutations (>95%) recessive?

A

Most mutations are recessive because usually a random change to DNA is more likely to cause damage and make it work less efficiently (loss-of-function) as opposed to making it work better or differently from normal (gain-of-function which is largely domniant).

46
Q
A
47
Q

What is a genome?

A

A genome is the haploid set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism.

48
Q

What is a DNA transposon?

A

DNA transposons are DNA sequences, sometimes referred to “jumping genes”, that can move and integrate to different locations within the genome.

49
Q

What’s an example of a DNA transposon?

A

An example of a DNA transposon are viruses.

50
Q

What is an Ortholog?

A

Orthologs are genes in different species that evolved from a common ancestral gene by speciation, and, in general, orthologs retain the same function during the course of evolution. Identification of orthologs is a critical process for reliable prediction of gene function in newly sequenced genomes.

51
Q

What’s a Paralog?

A

Paralogs are homologous genes that have evolved by duplication and code for protein with similar, but not identical functions.

52
Q

What’s an Indel mutation?

A

A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION.

53
Q

What are the affects of an Indel mutation?

A

The affects of an indel mutation are:

  • altered protein product due to a frameshift mutation.
  • alterations to non-coding RNA which may affect regulatory regions.

However most are silent. (Happen outside of genes).

54
Q

What is a Copy Number Variant?

A

A copy number variation (CNV) is when the number of copies of a particular gene varies from one individual to the next. Following the completion of the Human Genome Project, it became apparent that the genome experiences gains and losses of genetic material.

55
Q

What is a SNP?

A

Single nucleotide polymorphisms, frequently called SNPs (pronounced “snips”), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA.

56
Q

How often do SNPs occur throughout a person’s DNA?

A

SNPs occur approximately once in every 1000 base pairs.

57
Q

What is the Hardy-Weinberg Equation?

A
58
Q

What does the Hardy Weinberg equilibrium predict?

A

For a 2-allele system (bi-allelic e.g., SNPs)

Hardy-Weinberg equilibrium predicts that allele and genotype frequencies in a population will remain constant from one generation to the next

i.e., NO EVOLUTION

59
Q
A

Fundamental Topics In Biology (4 decks)

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