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ISOM > Week 1 > Flashcards

Week 1 Flashcards

1
Q

Nucleic acids are found in the following 3 locations in a human cell:

Explain fundamentals of nucleic acids

A

nucleus, chloroplasts, mitochondria

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2
Q

What is the purpose of nucleic acids?

Explain fundamentals of nucleic acids

A

to store and express genetic info

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3
Q

What is the central dogma?

Explain the central dogma of molecular bio

A

flow of information from DNA to RNA to protein

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4
Q

What is transcription?

Explain the central dogma of molecular bio

A

DNA to RNA

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5
Q

What is translation?

Explain the central dogma of molecular bio

A

RNA to protein

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6
Q

What is replication?

Explain the central dogma of molecular bio

A

When DNA replicates itself

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7
Q

What is reverse transcription, and when is it used?

Explain the central dogma of molecular bio

A

RNA to DNA. It is used in the PCR technique and by viruses

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8
Q

What is the difference between nucleotides and nucleosides?

Describe the structure, properties, and forms of DNA

A

Nucleotides are the building blocks of DNA (composed of nitrogenous base, sugar, and phosphate group). NucleoSIDEs (just nitrogenous base plus sugar)

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9
Q

State the order of structure of building DNA

Describe the structure, properties, and forms of DNA

A

Nucleoside –> Nucleotide –> Nucleic Acids –> DNA

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10
Q

What is the significance of a phosphodiester bond in regards to DNA/RNA?

Describe the structure, properties, and forms of DNA

A

It is responsible for stablizing the backbone of the structure

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11
Q

What is Chargaff rule?

Describe the structure, properties, and forms of DNA

A

states the amount of purines is equal to pyridimines

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12
Q

What type of bond links the sugar and nitrogenous base?

Describe the structure, properties, and forms of DNA

A

N-Glycosidic linkage

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13
Q

How many hydrogen bonds link adenine and thymine?

Describe the structure, properties, and forms of DNA

A

2

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14
Q

How many hydrogen bonds link cysteine and guanine?

Describe the structure, properties, and forms of DNA

A

3

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15
Q

What charge is a histone and why is this significant?

Assess the histones

A

it is positive and since DNA is negatively charged, they can interact to form chromatin

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16
Q

What is a nucleosome?

A

a section of DNA wrapped around a group of proteins (like a histone)

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17
Q

What are the five classes of histones?

Assess the histones

A

H1, H2A, H2B, H3, H4

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18
Q

Explain the organization of DNA into chromosomes.

Explain the organization of DNA into the chromosomes

A

DNA –> “bead on a string” nucleosomes –> 30nm chromatin –> chromosome extended form –> chromosome condensed –> paird metaphase chromosome

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19
Q

What is Tm (melting temperature)?

A

It is the temperature at which 1/2 of the DNA is unwinded

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20
Q

What are the forms of DNA?

Describe the structure, properties, and forms of DNA

A

B form (most popular), A form, Z form

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21
Q

What is B form DNA?

Describe the structure, properties, and forms of DNA

A

most common form of DNA. Double-stranded, right-handed, 10 bps per turn

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22
Q

What is A form DNA?

Describe the structure, properties, and forms of DNA

A

dehydrated B form DNA, right-handed, 11 bps per turn, 20 degree twist

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23
Q

What is Z form DNA?

Describe the structure, properties, and forms of DNA

A

left-handed, 12 bps per turn

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24
Q

Transitions between which two forms of DNA is crucial for gene expression?

Describe the structure, properties, and forms of DNA

A

B and Z

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25
Q

What must be modified for gene expression?

A

Histone modification (like methylation)

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26
Q

This process weakens the DNA-histone interactions and makes DNA accessible to factors needed for transcription.

A

Lysine acetylation

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27
Q

This process is catalyzed by histone acetyltransferases (HATs) and is important for transcription activation

A

Histone acetylation

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28
Q

This type of chromatin is densely packed and is genetically inactive.

A

Heterochromatin

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29
Q

mRNA accounts for what percent of total RNA?

A

5%

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30
Q

Describe what monocistronic is and how it relates to RNA.

A

Eukaryotic RNA is monocistronic meaning it only codes for one gene. This is opposite of prokaryotic RNA which is polycistronic.

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31
Q

How many subunits does the prokaryotic RNA poly have and name them.

A

5 subunits. 2 alpha, 1 beta, 1 beta prime, 1 omega

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32
Q

Which subunits of pro RNA pol are responsible for enzyme assembly?

A

alpha and omega

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33
Q

Which subunit of pro RNA pol are responsible for template binding?

A

beta prime

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34
Q

Which subunits of pro RNA pol are responsible for 5’ to 3’ polymerase activity?

A

beta

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35
Q

What is the holoenzyme?

A

it is the core enzyme plus the sigma subunit. together this makes the pro RNA pol

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36
Q

What is the name of the subunit responsible for the RNA polymerase recognizing the promoter?

A

the sigma factor

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37
Q

In prokaryotes, what are the names of the promoter regions of the DNA strand?

A

Pribnow box, -35 sequence

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38
Q

What is the name of the enzyme which is responsible for uncoiling the supercoiled DNA during transcription?

A

DNA topoisomerase

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39
Q

Which direction does transcription occur?

A

5’ to 3’

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40
Q

In regards to prokaryotes, describe the differences between Rho dependent/independent termination.

A

Rho dependent is when a Rho factor binds to the rut site on the RNA. Rho independent utilizes a hairpin loop with a string of uracil residues (week A/U bonds)

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41
Q

Name the 3 distinct type of eukaryotic RNA polymerases and their function.

A
  • RNA Polymerase I (rRNA)
  • RNA Polymerase II (mRNA)
  • RNA Polymerase III (tRNA)
42
Q

In eukaryotes, what is the name of the promoter region for RNA Polymerase II?

A

TATA box

43
Q

This is required for initiation of transcription, recruitment of RNA pol II, and for recognition of the promoter.

A

General Transcription Factors (GTFs), specifically transcription factor IID (TFIID)

44
Q

Can eukaryotic RNA polymerases recognize promoter regions on their own?

A

No; they need GTFs

45
Q

What is Transcription Factor IID?

A

a GTF which binds to DNA and allows the RNA poly II to come and start transcription

46
Q

What type of factor is responsible for binding proximal and distal regulatory elements?

A

Special Transcription Factors (STFs)

47
Q

What are enhancers?

A

They help increase the rate at which transcription occurs. They can be located thousands of base pairs away from the promoter region.

48
Q

Name one modification during RNA processing.

A

*7-Methylguanosine-triphosphate cap added to 5’ end of mRNA
*3’ Poly-A tail

49
Q

T/F Blood is classified as part of the extracellular fluid (ECF)

A

False; (Whole) blood is composed of red and white cells and plasma; therefore blood has both ECF and ICF. Plasma by itself would be considered to be part of the ECF

50
Q

A mutation in the promoter region of DNA will likely cause which process to be defective?

A

initiation of transcription. Mutations in the promoter typically prevent formation of the RNA Polymerase II transcription initiation complex

51
Q

What is the Pribnow box?

A

a sequence on the DNA strand used in prokaryotic transcription initiation

52
Q

What is Rho protein factor?

A

a protein involved in prokaryotic transcription termination

53
Q

What is the sigma protein factor?

A

the subunit of prokaryotic RNA polymerase that recognizes and binds the prokaryotic promoter

54
Q

What is pKa?

A

it is the extent of dissociation of a weak acid in water. it is a constant.

55
Q

The lower the pKa the __ the acid.

A

stronger

56
Q

What type of bond links amino acid residues?

A

peptide bond (a type of amide bond)

57
Q

The peptide bond links which carbon and which nitrogen on the amino acid residues?

A

amino N and carboxylic acid C

58
Q

Name the two secondary protein structures. How are both of the structures stabilized?

A

Beta sheets and alpha helices; hydrogen bonds

59
Q

Cysteine can form ____ bonds which is important for ____ protein structure.

A

disulfide bonds; tertiary

60
Q

Glycine’s R group is ___.

A

H

61
Q

What is a structural motif?

A

smaller combos of 2nd structures

62
Q

Kd is ____ related to binding affinity?

A

inversely

63
Q

The formation of covalent bonds linking amino acids on a growing polypeptide chain is catalyzed by the ____ which is a component of the ___ ribosomal subunit.

A

28S rRNA riboenzyme; 60S

64
Q

Name the stop codons.

A

UGA, UAA, UAG

65
Q

Eukaryotic Translation Initiation: ribosomal subunit binds with the ___ and ____ at the mRNA 5’ cap to form _____.

A

eIF, Met-tRNA, preinitiation complex

66
Q

Eukaryotic Translation Elongation: initial tRNA moves to the ___ site of the ribosome. _____ catalyzes the formation of peptide bond. ____ assists in elongation.

A

A, peptidyl transferase, Eef-2

67
Q

Name the prokaryotic ribosomal subunits.

A

30S, 50S, 70S

68
Q

Name the eukaryotic ribosomal subunits.

A

40S, 60S, 80S

69
Q

The _____ sequence is upstream of the start codon and is needed to start prokaryotic translation.

A

Shine-Dalgarno

70
Q

Macrolide abx such as azithromycin are affect bc they inhibit ____.

A

peptidyl transferase (used in translation)

71
Q

Proteins from the rough ER travel to the _____ to get processed further.

A

golgi

72
Q

After proteins leave the rough ER and golgi complex they then travel to either ____, ____, or ____.

A

lysosomes, cellular membrane, or outside of the cell

73
Q

If ubiquitin is added to a cell what is its fate?

A

It will travel to a proteasome where it will be degraded

74
Q

If pKa > pH, then which form of the weak acid will be favored? deprotonated or protonated?

A

protonated form.

75
Q

What is the name for a combination of 2 alleles on the same chromosome?

A

Haplotype

76
Q

____ is the presence of two or more variant forms likely due to a single nucleotide polymorphism.

A

Polymorphism. DOESN’T IMPLY AFFECT ON PHENOTYPE

77
Q

____ is the rearrangement (anywhere from (2 to >100,000 bp) in the order sections of DNA.

A

Structural variant. Think of this as the broader term which includes variants such as CNV, microsatellites, etc.

78
Q

___ is a large (1kb-1Mbp) homologous DNA sequence present in different amounts.

A

Copy Number Variant (CNV)

79
Q

____ are tandemly (next to each other) repeated sequences of 2-4 nucleotides

A

Microsatellites

80
Q

Allele frequency is defined as

A

of “A” alleles in population/TOTAL # of alleles in population

81
Q

Odds ratio is defined as

A

odds of disease in presence of allele/ odds of disease in absence of allele

82
Q

What is NMD?

A

Nonsense mediated mRNA decay. It is a surveillance system which regulates gene expression by identifying and degrading mRNA which contains PTCs or premature termination codons.

83
Q

____ is a form of alternative splicing that involves the exclusion of specific exons from mature mRNA.

A

Exon skipping

84
Q

____ occurs when a single functional copy of a gene is not sufficient to produce the normal phenotype or function.

A

haploinsufficiency

85
Q

___ is a mechanism where a mutated allele interferes with the function of a normal allele resulting in a dominant phenotype even if only one allele is affected.

A

dominant negative

86
Q

Consanguinity results in a/n ___ in # of affected homozygotes and a/n ____ in # of heterozygotes for _____.

A

increase, decrease, autosomal recessive

87
Q

What is incomplete penetrance?

A

when an individual can have genes, but not show any symptoms

88
Q

What is variable expressivity?

A

range of expression for a phenotype, all individuals have the same genotype

89
Q

What is genetic anticipation?

A

a phenomenon in which the severity and onset of a disease becomes earlier and earlier with generations. Typically due to trinucleotide repeat expansion

90
Q

What is pleiotropy?

A

mutations in a single gene cause diverse phenotypic symptoms in different organ systems

91
Q

___ is a quantitative measurement used to calculate disease risk. It is expressed as a percentage.

A

Penetrance

92
Q

____ is a qualitative measurement used to show the degree to which a particular genotype is expressed as a phenotype.

A

Expressivity

93
Q

____ is mutations in different genes produce the same disorder.

A

Locus Heterogeneity

94
Q

___ is mutations in the same gene produce the same disorder.

A

Mutational (allelic) heterogeneity

95
Q

What chromosomal aberration is indicated by “ins”?

A

insertion

96
Q

What chromosomal aberration is indicated by “inv”?

A

invertion

97
Q

What chromosomal aberration is indicated by “t”?

A

translocation

98
Q

What chromosomal aberration is indicated by “ter”?

A

terminal

99
Q

What chromosomal aberration is indicated by “r”?

A

ring chromosome

100
Q

What chromosomal aberration is indicated by “i”?

A

isochromosome

ISOM (5 decks)

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