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b11 final Flashcards

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1
Q

what is polycistronic mRNA?

A

mRNA with one promoter for many genes

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2
Q

what is monocistronic mRNA?

A

mRNA with one promoter for one gene

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3
Q

what increases the RNA pol’s affinity for promoter sequences?

A

sigma factor

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4
Q

what does the RNA polymerase holoenzyme consist of?

A

RNA polymerase (5 subunits) + sigma factor

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5
Q

What are the two types of transcription termination sequences in prokaryotes?

A
  1. stem-loop hairpins (RNA) : intrinsic causes RNA polymerase to pause
  2. rho factor (protein): protein mediated, there is a binding sequence for the protein (ex. the protein is the rho factor)
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6
Q

what allows 1 gene to be used for production of multiple different sequences of proteins (splice isoforms) ?

A

Alternative splicing

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7
Q

what is a primary transcript/pre-RNA/precursor-mRNA?

A

initial RNA molecule synthesized from the template DNA

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8
Q

what are splicing isoforms?

A

different versions of mRNA that result from alternative splicing (so we have one mRNA transcript and we can cut it into different parts and this produces many parts from one single gene)

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9
Q

which RNA polymerase makes all eukaryotic pre- mRNA?

A

RNA pol II

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10
Q

what is the equivalent of the prokaryotic sigma factor in eukaryotes?

A

general transcription factors (GTFs)

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11
Q

what is assembled at the TATA box?

A

preinitiaiton complex (PIC) that contains general transcription factors (GTFs) and RNA polymerase

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12
Q

which general transcription factor uses ATP hydrolysis to open the DNA double helix at the transcription start point, to expose single-stranded template?

A

TFIIH (kinase and helicase)

*remember H form helicase

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13
Q

what are the roles of the general transcription factor TFIIH? (there are 2)

A
  1. uses ATP hydrolysis to open the DNA double helix aka exposes single-stranded template
  2. phosphorylates RNA polymerase II tail (C-terminal domain, CTD) aka signals that RNA Pol II can being elongation
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14
Q

what is the name for RNA sequences that do not encode protein but play important regulatory roles?

A

Untranslated regions:
1. 5’ UTR: methylated guanosine cap
2. 3’ UTR: Poly(A) tail

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15
Q

what are the three types of processing that need to occur in eukaryotic pre-mRNA?

A
  1. 5’ cap
  2. splicing/alternative splicing
  3. 3’ poly(A) tail
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16
Q

what is the function of the 5’ cap?

A
  1. prevents digestion by exonucleases
  2. plays a role in transport of nucleus
  3. plays a role in initiation of mRNA translation to protein
  4. indicator that mRNA is completed
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17
Q

What is polyadenylation?

A

addition of a string of A (adenine) nucleotides at the 3’ end of the mRNA

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18
Q

how many origins of replication (ori) do bacterial chromosomes have?

A

1

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19
Q
A
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20
Q

points where a pair of replicating segments come together are called what?

A

replication forks

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21
Q

A transcription factor that is activated in response to DNA damage and can prevent cell cycle progression and/or promote apoptosis

A

p53

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22
Q

Transmembrane protein that is activated by dimerization upon growth factor binding

A

EGFR

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23
Q

A transcription factor that can activate genes involved in progression from G1 phase to S phase in the cell cycle

A

E2F

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24
Q

A non-receptor tyrosine kinase that was originally discovered as a viral oncogene

A

Src

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25
Q

Many signaling pathways converge to regulate phosphorylation of this protein, which controls the R point

A

Rb

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26
Q

Form complexes with Cdks to promote/regulate events of the cell cycle

A

cyclins

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27
Q

polypeptides are linear sequences of what?

A

amino acids

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28
Q

amino acids are linked together by what kind of bond?

A

peptide bonds

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29
Q

amino acids are joined by the ______ end of one amino acid and the ______ end of another

A

carboxyl, amino

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30
Q

the amino terminus of an animo acid is also called

A

N-terminus

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31
Q

the carboxyl terminus of an amino acid is also called

A

C-terminus

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32
Q

what promotes protein folding?

A

non-covalent interaction (no sharing of electrons but rather opposite charges are attracted to each other)

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33
Q

what are the structural units of proteins called?

A

protein DOMAINS

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34
Q

can 1 polypeptide contain more than one domain?

A

yes

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35
Q

the ribosome moves what direction along the mRNA?

A

5’ to 3’

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36
Q

what are Shine-Dalgarno sequences?

A
  • a sequence of nucleotides in bacterial (prokaryotic) mRNA that is located upstream from the AUG codon, helps align the ribosome so translation can begin
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37
Q

In prokaryotes, which subunit are initiation factors attached to?

A

small subunit of ribosome

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38
Q

in prokaryotic translation what do initiation factors do? (3)

A
  1. Attachment to mRNA
  2. Attachment of first AA-tRNA
  3. Preventing premature attachment of large subunit
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39
Q

what is a kozak sequence

A

A Kozak sequence is a specific nucleotide sequence found in eukaryotic mRNA that is important for the initiation of translation. It helps the ribosome recognize the start codon where translation begins.

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40
Q

what is a polyribosome or polysome?

A

multiple ribosomes associated with an mRNA

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41
Q

What happens to the CTD of RNA polymerase to cause proteins involved in capping, splicing, and cleavage/polyadenylation to bind to it?

A

it is phosphorylated

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42
Q

Helps loosen DNA/histone interactions to transcribe through nucleosomes

A

transcription elongation factors (Spt4, Spt5, and Elf1)

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43
Q

which is usually longer: introns or exons?

A

introns

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44
Q

what Initiates transcription elongation by phosphorylating RNA polymerase II

A

TFIIH

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45
Q

what Binds to the TATA Box

A

TFIID (with TBP)

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46
Q

Unwinds DNA at the site where transcription will begin

A

TFIIH

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47
Q

Coordinates recruitment of different processing enzymes in close proximity to the growing strand of new RNA

A

CTD

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48
Q

Creates a 5’-5’ triphosphate bridge to a GMP at the 5’ end of the RNA

A

capping enzyme, Guanyl transferase

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49
Q

Adds a string of adenine nucleotides to create the poly(A) tail

A

poly(A) polymerase

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50
Q

Methylates the 5’ cap

A

RNA methyltransferase

51
Q

Binds the RNA consensus sequences for polyadenylation

A

CPSF

52
Q

After transcription begins, this component stays bound to the promoter to assemble the next pre-initiation complex

A

TFIID (with TBP)

53
Q

what synthesizes pre-mRNA in the 5’ to 3’ direction

A

RNA pol II

54
Q

stem cells that produce a related group of cells (ex. Hematopoietic stem cells that create red and white blood cells)

A

multipotent stem cells

55
Q

These stem cells can produce only one cell type but have the property of self- renewal that distinguishes them from non-stem cells.

A

unipotent stem cells

56
Q

what is one feature that distinguishes stem cells from non stem cells?

A

self renewal

57
Q

what is the phenomenon that states that cells can change phenotypically without also changing genotypically

A

genomic equivalence: each somatic cell contains the same DNA

58
Q

detects mRNA through base-pairing with a labeled nucleic acid probe complementary to a specific sequence in the RNA of interest

A

in situ hybridization

59
Q

what is the ultimate proof of genomic equivalence?

A

An entire mammal can be cloned from the DNA in an adult somatic cell

60
Q

what differential gene expression technique is used to separate proteins by charge and mass?

A

two-dimensional gel electrophoresis

61
Q

complete set of RNA transcripts produced by the genome at any given time

A

Transcriptome

62
Q

refers to the continuous and consistent expression of a gene

A

Constitutive expression

63
Q

protein binds to DNA with what kind of bond

A

non covalent bonds

64
Q

can be supplied (expressed) from any chromosome meaning they are usually RNA or proteins.

A

trans regulatory elements

65
Q

are usually sequences (ex. Binding sites) encoded on the same chromosome they affect

A

cis regulatory elements

66
Q

is a large, multi-protein complex that plays a crucial role in the regulation of gene transcription in eukaryotic cells.

A

mediator complex

67
Q

sequences of DNA where RNA polymerase can be recruited to initiate transcription

A

promoters

68
Q

sequences of DNA that impact how much gene product is made from a promoter

A

enhancers

69
Q

what is an example of reporter gene expression

A

GFP: green fluorescent protein

70
Q

DNA regulatory element that can prevent promoter use and inhibit transcription.
Required to restrict gene expression to the proper cells/times

A

silencers

71
Q

bind enhancer DNA elements

A

activators

72
Q

bind silencer DNA elements

A

repressors

73
Q
A
74
Q

use introduction/alteration of DNA sequences to create a therapeutic benefit

A

gene therapies

75
Q

what are hematopoietic stem cells?

A

one that make red and white blood cells

76
Q

How many FDA approved uses for stem cell therapy? and what are they?

A

leukaemia and sickle cell disease

77
Q

what does Cord blood have the do with stem cells?

A

cord blood is an FDA approved source of hematopoietic stem cells to treat diseases of the blood/immune system (ex. leukaemia and sickle cell anemia)

78
Q

are abundant sites for protein degradation and are found in the cytoplasm and nucleus

A

Proteasomes

79
Q

what are two signals for degradation of proteins in the proteasome.

A
  1. polyubiquitin chains
  2. misfolded regions
80
Q

are enzymes that adds ubiquitin to proteins or things

A

ubiquitin ligases

81
Q

_________are transmembrane proteins that help cell adhere to the extracellular matrix (ECM)

A

Integrins

82
Q

Anoikis: a term for apoptosis that occurs in response to loss adhesion (death due to lack of integrin signaling)

A

Anoikis

83
Q

define cancer

A

a group of diseases of abnormal, uncontrolled cell division

84
Q

define transformation

A

process in which a normal cell becomes a cancerous cell

85
Q

abnormal growth with invasion

A

maligant

86
Q

abnormal growth without invasion.

A

benign

87
Q

small intracellular molecules that are formed or released in response to an extracellular signal

A

second messengers (the first messengers being the extracellular signal)

88
Q

who assess a tumor and provides information about tissue of origin, diagnosis, prognosis and treatment options

A

a pathologist

89
Q

a branch of anatomy that studies the microscopic structure of tissues

A

histology

90
Q

how large is the tumor and has it spread to other tissues?

A

stage

91
Q

how abnormal do the cells look and how fast are they growing?

A

grade

92
Q

abnormal number of chromosomes

A

aneuploidy

93
Q

in frame fusion of the coding regions of these genes caused by a reciprocal translation between Chromosome 9 and 22

A

Bcr-Abl

94
Q

most impactful discovery of molecular mechanisms of cancer

A

Philadelphia chromosomes

95
Q

what is a drug that can get rid of CML (in the early stages) by targeting Bcr-Abl

A

Gleevec

96
Q

what is easier to have: loss of function or gain of function?

A

loss of function

97
Q

the majority of tumors are ________ growths arising from a single normal cell of origin

A

monoclonal

98
Q
A
99
Q

cause expansion of unique subpopulation of cells

A

driver mutations

100
Q

hyper or hypophosphorylation of Rb prevents transcription of cyclin that initiated S phase

A

hypophosphorylation

101
Q

hyper or hypophosphorylation of Rb at the R point allows initiation of S phase (DNA replicaiton)

A

hyperphosphorylation

102
Q

what is the most commonly mutated gene in cancer

A

p53 tumor suppressor

103
Q

what are two examples of tumor suppressors

A

p53 and Rb

104
Q

tumor suppressors that are tetramers

A

p53

105
Q

cancers caused by the accumulations of mutations that were not inherited from an individuals parents

A

sporadic cancers

106
Q

an agent that causes cancer

A

carcinogen

107
Q

what is the greatest risk factor for cancer?

A

age

108
Q

What are the limitations to scaffold-mediated signaling?

A

no amplification

109
Q

Explain the roles of Pl3K and PTEN in regulating Akt

A

PI3K activates Akt: promotes cell growth, survival, and proliferation

PTEN counteracts PI3K, dephosphorylates it PI#K –> PI2K
- reduces activation of Akt
- acts as a tumor suppressor because its activity helps regulate cell growth and prevent uncontrolled cell proliferation

110
Q

Rb recruits HDAD and this does what?

A

HAD removes acetyl groups and this promotes a more closed conformation of chromatin

111
Q

what is contact inhibition? and do cancer cells exhibit it?

A

contact inhibition is something present in normal cells. cells grow until they come into contact then they stop growing.

cancer cells do not exhibit contact inhibition because they keep growing on top of each other

112
Q

NHEJ, HR or both?

This pathway involves Ku protein binding the ends of DNA created by double-strand breaks

A

NHEJ

113
Q

NHEJ, HR or both?

This pathway is more active in M phase than in G1

A

HR (G1 NJEH is more active)

114
Q

NHEJ, HR or both?

This pathway can result in translocations

A

both

115
Q

NHEJ, HR or both?

This pathway acts quickly to repair any double-strand breaks without the need for homology in DNA sequences

A

NHEJ

116
Q

NHEJ, HR or both?

This pathway can cause loss-of-heterozygosity

A

HR

117
Q

NHEJ, HR or both?

in combination with CRISPR/Cas9, this pathway is used by researchers to insert specific changes into the genome

A

HR because of specific changes

118
Q

NHEJ, HR or both?
In combination with CRISPR/Cas9, this pathway is used by researchers to disrupt gene function by repair that includes random insertions and deletions

A

NHEJ: random

119
Q

NHEJ, HR or both?
This pathway is involved in crossing over during meiosis

A

HR

120
Q

a gene that encodes a protein which is easily detectable and measurable, used to study gene expression, cellular processes, or protein localization.

A

reporter gene

121
Q

what are two examples of reporter genes

A

GFP (green fluorescent proteins)

and

lac Z gene (beta galactosidase)

122
Q

delete various segments of the DNA and measure transcription (i.e using reporter gene) to determine which specific sequences are required for transcription.

A

deletion mapping

123
Q

what marks completed spice

A

Exon junction complexes (EJC)

124
Q

Maternal contributions proteins and RNA that are stored in the egg until they are needed to orchestrate early development (and determine the fate of particular cells)

A

Psychology (25 decks)

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