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Applied Health Science > Genomics > Flashcards

Genomics Flashcards

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1
Q

Define - Genomics

A

Structural and functional mapping of genomes and their evolution

Study of genes in DNA including their function, development and growth.

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2
Q

Define - Gene

A

Basic physical and functional unit of heredity.

A sequence of nucleotides that encodes the sequence of amino acids that makes up proteins.

Genes are encoded in the DNA strand

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3
Q

What is chromatin?

A

DNA and protein (Histones) within the nucleus.

They have the potential to form chromosomes.

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4
Q

What is a Nucleosome?

A

Set of 8 histones.

These wrap around DNA. Give scaffold for formation of chromatin structure.

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5
Q

What is a benign variant?

A

Not associated with disease.

Yet - not never - there is currently no identifying link.

No deleterious or negative effect on the gene that it is linked with and so has no effect on the body.

Could be too insignificant that it has no known effect but this could change due to scientific discovery.

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6
Q

What is pathogenic variants?

A

Variant that is linked/ associated with disease.

Discovery has show a link between genetic mutation and disease.

This can be loss or gain of function.

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7
Q

What are variants of uncertain significant?

A

Unknown effect of variant on health.

The gene has been mapped however there is no information to link or not link to diseases.

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8
Q

State the three main categories of variants

A
  1. Benign
  2. Pathogenic
  3. Variants of uncertain significance
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9
Q

What do histones do?

A

Help package and regulate the DNA strand.

Give chromosomes their shape and control the activity of genes.

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10
Q

Explain the structure of Deoxyribonucleic acid (DNA)

A

Nucleotide of phosphate group, Deoxyribose sugar and nitrogenous base.

Phosphate + ribose form deoxyribose- phosphate backbone

Complementary base pairs:
Adenine + thymine (2 hydrogen bonds)
Guanine + cytosine (3 h bonds)

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11
Q

State the stages of making proteins

A
  1. Transcription
  2. Splicing
  3. Translation
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12
Q

Explain Transcription

A
  1. RNA polymerase attach to gene
  2. A codon (3bases) provide code for one amino acid.
  3. DNA unwinds exposing bases. DNA polymerase move along attacking complementary base pairs forms single strand of messenger RNA complementary to original(U instead T).

Include exons used in synthesis and introns not used. Splicing then occurs

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13
Q

What is splicing?

A

The removal of introns (non coding) and leaving only coding Exons.

Mature strand of messenger RNA (mRNA) just exons.

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14
Q

What is translation?

A

In cytoplasm
1. MRNA Out nucleus and binds to ribosome
2. Start codon (AUG) Then tRNA bRings corresponding amino acids to strand binding together as each codon read forming polypeptide chain
3. End of translation when stop codon (UAA, UGA, UAG) reached (doesn’t code for an amino acid)

Polypeptide chain is twisted and folded to give final structure.

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15
Q

How many naturally occurring amino acids are there?

A

20

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16
Q

What are the 4 different characteristics of amino acids?

How do they differ?

A
  1. Non-polar (uncharged) side chains
  2. Acidic side chains
  3. Basic (alkali) side chains
  4. Polar (Charged) side chains

Different characteristics due to finals protein structure to complete their different jobs in the final protein.

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17
Q

How many genes does a human have?

A

About 21,000

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18
Q

What are the different effects of mutations?

A
  1. Gain of function mutation – new or enchanted activity for gene product
  2. Loss of function mutations – gene product loses some or all of function
  3. Lethal mutations
  4. Ineffective mutations
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19
Q

State two processes that explain why there are so many proteins to only 20 amino acids

A
  1. Alternative gene splicing
  2. Post-translational modifications
20
Q

What is alternative gene splicing?

A

Some genes produce more than one gene product.

Different splicing of genes so technically different. Different exons are selected by body to produce different proteins from the same gene.

Exons of same gene joined in different combinations - different but related mRNA transcripts

21
Q

What is post-translational modifications?

A

Changes the structure and function of the final protein. IN the Golgi apparatus
1. Add carbohydrates
2. Add lipid parts
3. Modify Amino Acid site chains
4. Add chemical regulators

22
Q

List possible modifications to proteins that occur in post-translational modification

A
  1. Add carbohydrates
  2. Add lipid parts
  3. Modify Amino Acid site chains
  4. Add chemical regulators
23
Q

What is a pseudogene?

A

Non-functional gene produced from a damaged gene sequence.

24
Q

Give examples of elements that can be missing to make a pseudo gene

A
  1. Can be a missing promoter
  2. Missing start codon
  3. premature stop codon
  4. missing introns
  5. partial deletion of gene sequence
  6. no stop codon.
25
Q

How can pseudogenes be easily identified?

A

either no producing protein

Or making a non-functional protein as they lack key regulatory regions.

26
Q

Give some statistics for the structure of the human genome

A
  1. 3.2 billion bases ‘coding letters’
  2. 21,000 genes
  3. 22,000 RNA codes
  4. 14,000 pseudogenes
  5. Only 1.5% genome sequence encodes functional proteins
  6. About 14% unclassified (unknown function, interactions, alternative functions)
27
Q

What’s the genotype?

A

Complete set of generic material including the various variant genes carried.

28
Q

State two causes of genetic variation

A
  1. Sexual reproduction
  2. Random events of mutagens
29
Q

Explain how sexual reproduction causes genetic variation

A
  • Meiosis (cell division)
  • Heritable – variations from parents
  • Genetic recombination events
  • Random crossovers
  • Independent assortment of alleles and gene variants
  • Random fertilisation (picking partners)
30
Q

Explain how random events or mutagens cause genetic variation

Include different types

A
  • During cell life (not transferable to offspring)
  • During cell division – mitosis – not transferable
  • Accidental damage to genetic material – transferable
  • Inappropriate DNA repair mechanisms following damage.
31
Q

What are mutagens (give examples)?

A
  1. Pollutants – environmental triggers (chemical, smoke, mercury and cadmium)
  2. Endogenous mutagens eg. ROS – hydrogen peroxide and superoxides
  3. Viral insertions
  4. Ultraviolet light
  5. Ionising radiation, background radiation x-rays, cosmic background radiation
32
Q

Define mutation (variant)

A

Any heritable change to DNA sequence

33
Q

What are the two terms used to describe types of mutations?

A

Somatic and Germline

34
Q

What is a somatic mutation?

A

Passes to dividing cells in tissues

35
Q

What is a germline mutation?

A

Passed from parent to offspring

36
Q

State the two main types of physical variants?

A
  1. Single nucleotide variants - either missense or nonsense mutation
  2. Insertion or deletion
37
Q

Explain missense mutation as a single nucleotide variant

A
  • Single nucleotide Substituted for different one
  • Code changed, could specify a different amino acid and change protein sequence so function of protein
38
Q

Describe nonsense mutation as a single nucleotide variant

A
  • Single nucleotide substitutes for different one
  • Code changed to stop codon so AA sequence truncated
39
Q

What is insertion or deletion as a physical types of variant?

A
  • Nucleotides added or removed
  • Collectively called indels
  • Can change reading frame, amino acid sequence and function of resulting protein.
  • Deletion causes cystic fibrosis – chromosome 7
40
Q

What are the different types of structural variants?

A
  • Translocations – chromosomal abnormalities (part of chromosomes inserted into another part of a different chromosome.)
  • Inversions – reversal of generic coding region
  • Large deletions – Over 1000bp removed
  • Copy number variants – deletion or duplication of coding region – eg. Charcot-Marie-Tooth – deficits in motor control – over production of mitochondria
41
Q

State the different categories of genetic variation

A
  1. Single nucleotide variants
  2. Missense
  3. Nonsense
  4. Insertions
  5. Deletions
  6. Frameshift variants
  7. Structural variants
  8. Copy number variants
  9. Repeats
42
Q

What are human genome generalities?

A
  1. 2000 known structural variants and 0.5% different between two generous
  2. Several hundred deleterious mutations not necessarily identified
43
Q

What is genetic testing? Briefly describe the process

A
  • Blood testing for mono genetic disorders
    1. Take sample of DNA
    2. Use PCR to copy gene (Polymerase chain reaction)
    3. Electrophoresis to separate different lengths of genes
    4. If gene deletion the smaller copy with show up

These take along time to develop as one gene can be tested at one time.

44
Q

Briefly describe next generation sequencing

A

Rapid automatic system.

  • Sent blood to lab when DNA is extracted and assessed.
  • Placed in next-generation seances which reads DNA letter by letter. Compare to database of bases sequences.
  • Process takes less than a day – also costs a lot less per sequencing.
45
Q

What is bioinformatics?

A

Analysis, storage, annotation and retrieval of genomic data. Using technology.

Also back the management and development of these processes.

Can compare genomes across populations, identify variants, correlate variants with incidence of health issues. Use this insight to tract different health conditions.

46
Q

State the three main types of variant

A

Benign

Pathogenic

Uncertain significance

Applied Health Science (11 decks)

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