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[OS 201] 3rd Exam > Trans - Human Genome > Flashcards

Trans - Human Genome Flashcards

2
Q

Percentage of genes in genome

A

2-3%

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3
Q

Correlation between genome size and organism complexity

A

None

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4
Q

Definition of telomere

A

Ends of chromosome

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5
Q

Original definition of genome

A

Collection of genes contained within a haploid chromosome set

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6
Q

Modern definition of genome

A

Locatable region of genomic sequence corresponding to a unit of inheritance associated with regulatory regions, transcribed regions, and/or other functional sequence regions

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7
Q

Definition of centromere

A

Central region of chromosome

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8
Q

Arms of chromosome?

A

Chromatid

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9
Q

Shorter arm of chromosome

A

P arm

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10
Q

Longer arm of chromosome

A

Q arm

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11
Q

Number of rings in purine

A

Two

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12
Q

Number of rings in pyrimidine

A

One

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13
Q

Which bases are purines?

A

Adenine, Guanine

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14
Q

Which bases are pyrimidines?

A

Cytosine, Thymine

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15
Q

Correlation between GC content and melting point

A

Higher GC content, higher melting point

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16
Q

Which is more preferred for expression? AT or CG?

A

AT

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17
Q

Correlation between GC content and level of expression

A

Higher GC content, more silenced genes

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18
Q

Definition of intron and exon

A

[1] Intron –> region of DNA not expressed;

[2] Exon –> expressed region of DNA

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19
Q

Parts of the UTR/Leading sequence

A

[1] Enhancer
[2[ Promoter
[3] Operator
[4] Consensus sequence

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20
Q

Consensus sequence in a) prokaryotes, b) eukaryotes

A

[A] Pribnow box (TATAAT);

[B] Hogness box (TATA)

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21
Q

Parts of coding sequence

A

[1] Start codon (AUG);
[2] Introns and exons;
[3]. Stop codon (UAA, UAG, UGA)

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22
Q

Number of bonds in CG linkage

A

3

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23
Q

Name and define the regions associated with the alternating introns and exons

A

[1] Pre Region –> signal region, determines where the protein will go;
[2]. Pro Region –> determines posttranslational modification
[3] Mature Region –> encodes the protein

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24
Q

Parts of the UTR/trailing sequence

A

[1] 2nd termination signal

[2] Cleavage signal (AAUAA) containing poly-A tail

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25
Q

Central dogma of molecular biology

A

[1] Replication –> DNA duplication;
[2] Transcription –> RNA synthesis
[3] Translation –> protein synthesis

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26
Q

Definition of open reading frame

A

Region of DNA corresponding to coding sequence

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27
Q

Composition of human genome

A

[1] euchromatic portion;

[2] constituitive heterochromatin

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28
Q

Where can constituitive heterochromatin be found?

A

[1] Centromeres;
[2] Long arm of Y chromosome
[3] Short arm of acentric chromosomes (13, 14, 15, 21, 22)
[4] Secondary constriction of long arm of 1, 19, 16

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29
Q

Percentage composition of bases in genome

A

GC –> 41%; AT –> 59%

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30
Q

What are Giemsa bands?

A

[1] Dark bands –> low GC, 37%
[2] Light bands –> high GC, 45%

both bands seen in karyotype

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31
Q

Number of base pairs in human genome

A

3200 M

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32
Q

Number of genes in human genome

A

30,000 - 35,000

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33
Q

Percentage of genes coding untranslated RNA

A

5-10%

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34
Q

Mechanism of gene distribution

A

Hybridization of CpG islands to metaphase chromosomes

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35
Q

Composition of nuclear genome

A

[1] 95.5% noncoding DNA

[2] 4.5% conserved DNA –> 3% untranslated & regulatory, 1.5% coding DNA

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36
Q

General trend in abundance of euchromatin and heterochromatin in genes

A

Chromosome 1 has highest amount of euchromatin and heterochromain, amount decreases as chromosome number increases

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37
Q

Definition of pseudogenes

A

Multiple copies of genes serving as rescue genes in case original genes get damaged

38
Q

Number of BP in mitochondrial genome

A

16,569

39
Q

Number and characteristics of genes in mitochondria

A

37 genes –> 22 tRNA, 2rRNA, 13 protein coding

40
Q

[T/F] mitochondrial genes have introns

A

F

41
Q

Structure and significance of D-loop in mitochondrial genome

A

Triple stranded region, origin for replication of mitochondrial genome

42
Q

Endosymbiont theory

A

Mitochondria may have originated from symbiotic prokaryotic bacteria

43
Q

Subunits of nuclear rRNA

A

[1] large subunit (28S, 5.8S, 5S)

[2] small subunit (18S)

44
Q

RNA polymerase I

A

ribosomal synthesis

45
Q

Significance of mitochondria in apoptosis

A

Contains cytochrome C –> critical component in apoptosis

46
Q

Subunits of mitochondrial rRNA

A

16S & 23S

47
Q

Function of tRNA

A

Carries amino acids during translation

48
Q

Significance of snRNA

A

Involved in RNA maturation, spliceosomal RNA

49
Q

H/ACA snoRNA subfamily

A

guides site-specific pseudourylation of uridine to produce pseudouridine in rRNA

50
Q

Significance of snoRNA

A

Guides site-specific base modification in rRNA & snRNA

51
Q

Significance of miRNA

A

Antisense regulator of genes –> bind to complementary sequence in 3’-UTR to inhibit translation

52
Q

Significance of noncoding 7SK RNA

A

Negative transcriptional inhibition of RNA polymerase II elongation

53
Q

Significance of SRA1 RNA

A

Coactivator of steroid receptors

54
Q

Characteristics of classical gene families

A

[1] High degree of sequence homology

[2] Products have short conserved amino acid motifs

55
Q

Example of conserved amino acid motifs in classical gene families

A

[1] DEAD (Asp-Glu-Ala-Asp)

[2] WD (tryptophan-aspartate)

56
Q

Characteristics of gene superfamilies

A

[1] No significant conserved amino acid motifs;

[2]. Share general common structural features

57
Q

Examples of gene superfamilies

A

[1] Immunoglobulin superfamily –> immunoglobulin genes, T cell receptor genes, HLA genes;
[2] Globin superfamily –> alpha and beta globin, neuroglobin, myoglobin;
[3] G protein-coupled receptor superfamily –> mediate ligand induced signaling between extracellular and intracellular environments

58
Q

Characteristics of pseudogenes

A

[1] Copied at the level of genomic DNA by tandem gene duplication
[2] Contain all elements of a gene but have inappropriate termination codons in exons

59
Q

pericentromeric genes

A

contain sequences that have been copied recently during evolution and are located on several chromsomes

60
Q

Examples of identical proteins coded by different genes

A

Histone, ubiquitin

61
Q

Number of bonds in AT linkage

A

2

62
Q

BLAST

A

[1] Basic local alignment search tool

[2] Searches for sets of optimal local alignments based on a query

63
Q

Ways that a species’ genome may change (4)

A

[1] Expansion –> gene duplication
[2] Genesis –> creation of new genome
[3] Exchange
[4] Deletion

64
Q

Definition of retrogenes

A

Nonprocessed pseudogenes that are integrated in a chromosome next to a promoter and expressed

65
Q

Mechanisms which govern changes at the protein level are most likely due to: _____

A

Nucleotide substitution, insertion, deletion

66
Q

Definition of comparative genomics

A

New field of biological research dealing with the comparison of genomes of different species

67
Q

Changes may give rise to new genes which become fixed if ____________

A

they give the organism an advantage in natural selection

68
Q

Definition of neutral theory

A

[a] Molecular evolution caused by random genetic drift through mutations that are selectively neutral or nearly neutral;
[b] Describes cases in which natural selection is not strong enough to outweigh random events

69
Q

Definition of

a) synonymous substitution,
b) non synonymous substitution

A

[a] substitution in DNA that does not alter the amino acid sequence of the coded protein
[b] substitution in DNA that alters the amino acid sequence of the coded protein

70
Q

Definition of positive selection

A

[1] Darwinian selection fixing advantageous mutations;
[2] Equal to molecular adaptation and adaptive molecular evolution
[3] ex. people who have sickle cell anemia are less affected by malaria

71
Q

Definition of purifying selection / negative selection

A

Natural selection against deleterious mutations

72
Q

Types of nucleotide substitution (6)

A

Given 2 nucleotide sequences, we can ask how their similarities and differences arose from a common ancestor.

[1] single substitution –> 1 change 1 difference;
[2] multiple substitution –> 2 changes 1 difference;
[3] coincidental substitution –> 2 changes 1 difference;
[4] parallel substitution –> 2 changes, no difference;
[5] convergent substitution –> 3 changes, no difference;
[6] back substitution –> 2 changes, no difference

73
Q

Transition vs Transversion

A

Types of substitution:

[1] Transition –> purine for purine, pyrimidine for pyrimidine
[2] Transversion –> purine for pyrimidine

74
Q

Significance of purifying selective force

A

Prevent accumulation of mutation at important functional sites, resulting in sequence conservation

75
Q

Enumerate the types of mutation, and their characteristics

A

[1] Based on effect –> lethal vs nonlethal;
[2] Based on size/position –> Point mutation (missense, nonsense, frameshift);
[3] Based on substitution –> transition vs subversion

76
Q

Differentiate missense, nonsense, and frameshift mutations

A

[1] missense –> single nucleotide change causes a different amino acid to be coded;
[2] nonsense –> single nucleotide change causes premature stop codon;
[3] frameshift –> insertions or deletions that change the reading frame (not divisible by 3)

77
Q

The nucleotide sequences of a pair of homologous genes have a (higher or lower?) information content than the amino acid sequences of their coded proteins

A

Higher, due to the fact that synonymous mutations change the DNA without changing the protein

78
Q

Which occurs more frequently? Transitions or transversions? Why?

A

Transitions occur 2x more frequently than transversions –> easier to replace for the same type

79
Q

[T/F] all mitochondrial genes code for stop codons

A

F, some are added posttranscriptionally

80
Q

[T/F] some coding sequences of mitochondrial genes are overlapping

A

T

81
Q

Euchromatin in nuclear genome - number of BP, characteristics

A

3000 Mb; transcriptionally active

82
Q

RNA polymerase II

A

mRNA, sRNA, miRNA synthesis

83
Q

RNA polymerase III

A

synthesis of tRNA, rRNA 5S, misc small RNAs

84
Q

subtelomeric genes

A

unstable and prone to duplication

85
Q

C/D box snoRNA subfamily

A

guides site-specific methylations in rRNA

86
Q

missense mutation

A

single nucleotide change causes different amino acid to be coded

87
Q

nonsense mutation

A

single nucleotide change causes stop codon to be coded

88
Q

frameshift mutation

A

addition or deletion of nucleotide changes the reading frame

89
Q

stop codons

A

UAA, UAG, UGA

90
Q

start codon

A

AUG

[OS 201] 3rd Exam (10 decks)

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