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Genetics > Human Genome > Flashcards

Human Genome Flashcards

1
Q

What is a genome?

A

The sum total of all genetic info of an individual is the genome.

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2
Q

How does DNA package in Human chromosomes?

A
  1. DNA double helix is wrapped around histone proteins forming nucleosomes
  2. The chain of nucleosomes then folds into a thicker chromatin fibre
  3. The thick chromatin fibre then folds again, on a non histone protein scaffold to form looped fibres
  4. the folded chromatin then folds further to produce a condensed chromosome
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3
Q

What is a nucleotide?

A

A nucleotide consists of a phosphate group, a deoxyribose sugar and a nitrogenous base

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4
Q

How does it form a strand?

A

Nucleotides are linked by their deoxyribose sugars and phosphates to form a strand with a sugar phosphate back bone
Hydrogen bonds - between bases
Phosphodiester bonds - sugar and phosphate

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5
Q

What direction do the strands run in?

A

The two DNA strands connect running in opposite directions.
The strands are said to be anti parallel
One strand runs 3’ - 5’ the other 3’ - 5’

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6
Q

Features to remember of a DNA molecule for the exam?

A
  • double helix shape
  • Sugar phosphate backbone
  • Anti parallel strands
  • Hydrogen bonds linking strands
  • complementary base pairing rules applied to nucleotide
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7
Q

What is the size of the human genome (in bases)?

A

3.2 billion bases (3 x 109 bp of DNA in the human genome -– 3 billion base pairs.)

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8
Q

What are genomes organized into?

A

Chromosomes

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9
Q

What is the different between genomics and genetics?

A

GENOMICS is the study of the entire DNA sequence that contains the complete set of genes for an organism.
GENETICS is the study of how traits are passed down the generations, and the role of genes in that process.
They are not the same, but they are similar.

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10
Q

What is the proteome?

A

The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time.
It is a source of an additional level of variance.

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11
Q

Define transcriptomics.

A

Transcriptomics is the study of all RNA transcripts produced by a cell, tissue or organism.

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12
Q

What is the difference between the transcriptome and the proteome?

A

DNA is transcribed to RNA and the total RNA content produced is the transcriptome.
RNA is translated into protein, and the total protein content produced is the proteome.

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13
Q

What did Frederick Griffith contribute to DNA discovery?

A

While working with bacteria, discovered that genetic material can be transferred from one cell to another, which is bacterial transformation.

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14
Q

What did Oswald Avery contribute to DNA discovery?

A

Concluded that DNA is responsible for transformation in bacteria.

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15
Q

What did Erwin Chargaff contribute to DNA discovery?

A

Proved that in a molecule of DNA, the amount of adenine always equals the amount of thymine. Discovered base pairing rules.

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16
Q

Alfred Hershey and Marhta Chase contribute to DNA discovery?

A

Used a blender and discovered that the genetic material in bacteriophages is DNA and not protein.

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17
Q

James Watson and Francis Crick contribute to DNA discovery

A

Won the Nobel prize in 1962 for their model of the DNA double helix.

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18
Q

Maurice Wilkins and Rosalind Franklin contribute to DNA discovery

A

Analyzed DNA using X-ray diffraction. They produced the photographs and crystals of DNA.

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19
Q

How many chromosomes are there in DNA

A

46 DNA molecules, or chromosomes, consisting of pairs of chromosomes 1 to 22 (autosomes), numbered sequentially according to their size, and of two sex chromosomes that determine whether an individual is male or female - 2m in length - must fit inside nucleus micrometer in length.

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20
Q

How does the human genome be packaged in chromatin to fit int he nucleus?

A

a DNA molecule wraps around histone proteins to form tight loops called nucleosomes. These nucleosomes coil and stack together to form fibers called chromatin

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21
Q

How many genes code for proteins that perform most life functions

A

30,000

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22
Q

What is the fundamental building block of coiling in DNA Helix (that allows it to fit in the nucleus)

A

nucleosomes - blocks of essentially little spheres of histone proteins around which the DNA is wrapped, like beads on a string, except the beads have the DNA wrapped around them

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23
Q

How are nucleosomes formed?

A

eight separate histone protein subunits attach to the DNA molecule. The combined tight loop of DNA and protein is the nucleosome. Six nucleosomes are coiled together and these then stack on top of each other.

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24
Q

How do we get a double helix -> chromosome

A

DNA in double helix winds around nucleosomes. The nucleosome is further folded to produce a chromatin fiber. Chromatin fibers are coiled and condensed to form chromosomes

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25
Q

Why is chromatin structure important and what would a mutation cause?

A

Chromatin structure is important for regulating gene expression and for the proper condensation and segregation of chromosomes during cell division. Several human genetic diseases have been found to be due to mutations in genes producing proteins known or suspected to be involved in maintaining or modifying chromatin structure.

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26
Q

What are the most abundant proteins in chromatin?

A

Histones

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27
Q

In chromatin, DNA is bound to what?

A

histone and non-histone proteins.

28
Q

What are non-histone proteins and give examples

A

In chromatin, those proteins which remain after the histones have been removed, are classified as non-histone proteins. Scaffold proteins, DNA polymerase, Heterochromatin Protein 1 and Polycomb are common non-histone proteins

29
Q

What is the role of histones?

A

Histones bind DNA mainly as nucleosomes composed of two copies each of H2A, H2B, H3, and H4. ubiquitinylation

30
Q

What are H2A, H2B, H3 and H4

A

Histones H2A, H2B, H3 and H4 are known as the core histones, and they come together to form one nucleosome.

31
Q

How does wrapping of DNA around nucleosomes contribute to the dna being able to fit in the nucleus

A

Wrapping of DNA around nucleosomes represents just the first level in packaging, which effectively shortens the length of chromosomes by 7-fold.

32
Q

What is a histone modification?

A

Histones, particularly their amino- and carboxy-terminal tails, are subject to posttranslational modifications (PTMs) on multiple residues, including methylation, acetylation, phosphorylation, sumoylation, ADP-ribosylation, or ubiquitinylation

33
Q

What does histone modification do?

A

The PTMs made to histones can impact gene expression by altering chromatin structure or recruiting histone modifiers - PTMs regulate the activity of underlying genomic regions by altering how nucleosomes interact with each other and the DNA, thereby controlling access to given DNA sequences, and/or by recruiting effector proteins that bind PTMs directly and interpret whether a region should be active or not.

34
Q

Name a basic regulatory unit of genomes

A

Chromatin - as further packaging within the confines of the three-dimensional (3D) nuclear space can have a direct impact on its activity. (PTM’s)

35
Q

What is Euchromatin?

A

less densely packed form of chromatin that is found in active regions of the genome (approx. 93% of human genome)

36
Q

What is Heterochromatin?

A

very densely packed regions which are genetically inactive (approx. 7% of human genome)

37
Q

What can innapropriate modification in histones lead to?

A

diseases, must control. aberrant profiles of histone modifications contribute to the dysregulation of immune response, resulting in the development of a variety of autoimmune diseases

38
Q

What is structural variation?

A

Structural and quantitative chromosomal rearrangements
Type of variation in the human genome - Structural variation (SV) is a region of DNA approximately 1 kb and larger in size and can include inversions and balanced translocations or genomic imbalances (insertions and deletions), commonly referred to as copy number variants (CNVs).

39
Q

What variation contributes a large extent to the genetic diversity of the human genome?

A

structural variation, and thus are of high relevance for cancer genetics, rare diseases and evolutionary genetics.

40
Q

What do SV’s (structural variations) affect?

A

Recent studies have shown that SVs can not only affect gene dosage but also modulate basic mechanisms of gene regulation.

41
Q

How do SV’s affect gene dosage and basic mechanisms of gene regulation?

A

SVs can alter the copy number of regulatory elements or modify the 3D genome by disrupting higher- order chromatin organization such as topologically associating domains. Therefore, SVs can influence the expression of genes distant from the SV breakpoints, thereby causing disease.

42
Q

How is the human nuclear genome chromosomes arranged?

A

23 pairs of chromosomes, or 46 DNA molecules, decreasing in size (1-22) Total DNA (mb)

43
Q

What is the wrong with chromosome 21 when arranged with the others?

A

above 22 even thought it is a smaller size

44
Q

How much of the DNA is protein coding genes?

A

20,000 protein coding genes (.2% DNA), more non-coding than coding!

45
Q

What are non-coding genes?

A

does not provide instructions for making proteins.

46
Q

What is the purpose of non-coding genes and give an example

A

Noncoding DNA Scientists once thought noncoding DNA was “junk,” with no known purpose. However, it is becoming clear that at least some of it is integral to the function of cells, particularly the control of gene activity. For example, noncoding DNA contains sequences that act as regulatory elements, determining when and where genes are turned on and off. Such elements provide sites for specialized proteins (called transcription factors) to attach (bind) and either activate or repress the process by which the information from genes is turned into proteins (transcription)

47
Q

List non-coding genes

A 
introns
structural dna
Single sequence repeated
pseudogenes
transposable elements
noncoding rna
48
Q

List protein encoding DNA

A

single-copy genes
multigene families
tandem clusters

49
Q

List DNA that is both coding and non coding

A

segmental duplications (Segmental Duplications (SDs) are long DNA sequences (that have nearly identical sequences (90-100%) and exist in multiple locations as a result of duplication)

50
Q

Name a class of non-coding RNAs involved in regulation of gene expression

A

One class of non-coding RNAs involved in this regulation of gene expression is microRNAs (miRNAs).

51
Q

As complexity increases in organisms, what kind of gene also increases in number?

A

Number of non-coding genes

52
Q

List long known classes of RNA’s

A

Transfer RNAs and ribosomal RNAs involved in translation
Small nuclear RNAs involved in splicing events
Small nucleolar RNAs mainly involved in the modification of other small RNAs, such as ribosomal RNAs and transfer RNAs

53
Q

List short regulatory non-coding RNA

A

piwi-associated RNAs
Endogenous short-interfering RNAs
MicroRNAs
(Act as key regulators of gene expression

54
Q

What is the purpose of Long non-protein coding RNAs (lncRNA):

A

play crucial roles in epigenetic control of chromatin, promoter-specific gene regulation, mRNA stability, X-chromosome inactivation and imprinting.

55
Q

How do LncRNA have regulatory functions in the nucleus

A

Long non‐coding RNA transcripts that positively or negatively regulate the expression of neighboring (cis) or distant (trans) genes by modifying chromatin states of targeted gene loci.
Long non‐coding transcripts that organize nuclear architecture by forming, maintaining, or regulating nuclear structures and domains

56
Q

How does LncRNA act in the cytoplasm

A

Long non‐coding transcripts that bind to and regulate proteins or other RNA molecules in the cytoplasm.

57
Q

How often does RNA splicing occur?

A

Using RNA-seq technologies - rna splicing, initiation, and alternative transcription termination occurred far more frequently than anyone had known before, possibly affecting as many as 95% of human genes - if know where all the genes are, we still have considerable work to discover all the isoforms of those genes, and yet more work to determine whether these isoforms have any function or if they just represent splicing errors, as some have argued

58
Q

What are cis and trans genes?

A

Cis genes are close, trans genes are far

59
Q

pre mRNA vs mRNA

A 
pre-mRNA contains Introns
after splicing (removal of introns): mRNA
60
Q

What is alternative splicing

A

a regulated process during gene expression that results in a single gene coding for multiple proteins.

61
Q

What are intergenic LncRNA

A

Located between genes

62
Q

What is alternative splicing

A

alternative patterns of pre-mRNA splicing that produced different mature mRNAs containing various combinations of exons from a single precursor mRNA. a regulated process during gene expression that results in a single gene coding for multiple proteins.

63
Q

Describe alternative RNA splicing

A

cis-acting regulatory elements in the mRNA sequence determine which exons are retained and which exons are spliced out. cis-acting regulatory elements alter splicing by binding different trans-acting protein factors, such as SR (Serine-Arginine rich) proteins that function as splicing facilitators, and heterogeneous nuclear ribonucleoproteins (hnRNPs) that suppress splicing.
The final decision to include or splice an alternative exon is thus determined by combinatorial effects, cellular abundance, and competitive binding between SR activators and hnRNP inhibitors.

64
Q

Give one known process alternative splicing aids

A

Alternative splicing is known to be involved in the regulation of normal physiological functions as well as pathologies. For example, a number of alternatively spliced genes in immunity are known. Studies indicate that alternative splicing of CD44, a protein involved in T cell homing with 10 variable cassette exons and six distinct protein isoforms, is crucial for T cell function.

65
Q

What does the outcome of alternative splicing depend on?

A

the stoichiometry and interactions of splicing activators and inhibitors as well as the steric conformation and accessibility of the splicing sites

66
Q

List three loci for the lncRNA

A

Intergenic IncRNA’s, IncRNA’s expressed from enhancers and promoters, IncRNA’s overlapping other genes

Genetics (2 decks)

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