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Biology 101 flashcards
1
Q

what is a mutation

A

an alteration in nucleotide sequence in genome, any base-pair change in sequence, single base pair substitution, deletion or insertion, major alteration in chromosomal structure

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2
Q

where do mutations occur

A

everywhere,Coding/noncoding regions, regulatory sequences,

Promoters, enhancers, splicing signals.

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3
Q

what is a point or base substitution

A

change from one base pair to another

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4
Q

types of point mutations

A

missense, nonsense, silent, neutral

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5
Q

missense mutation

A

 changes to a new amino acid (missed the signal)

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6
Q

nonsense mutation

A

 don’t hear it or make a stop codon prematurely stopped codon

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7
Q

silent mutation

A

 mutation but it doesn’t change anything down the road

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8
Q

neutral mutation

A

mutations in noncoding regions

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9
Q

types of base substitutions

A

transitions and transversions

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10
Q

what is a transitions

A

pyrimidine replaces pyrimidine and pruine replaces pruine

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11
Q

what are transversions

A

purine to pyrimidine

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12
Q

frameshift mutation

A

Result from insertions or deletions of nucleotide.
Loss or addition of nucleotide causes shift in reading frame. Change the way in which its read
Frame of triplet reading during translation is altered.
Altered triplets may code for stop codon

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13
Q

how many ways can we read double stranded DNA

A

6

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14
Q

classifications of mutations

A 
loss of funtion 
dominant 
dominant negative
gain of function
supressor
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15
Q

loss of functions

A

reduces/eliminates function of gene product. Loss function of the gene

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16
Q

null mutations

A

results in complete loss of function.

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17
Q

dominant mutations

A

: results in mutant phenotype in diploid organism. Bad alleles can be dominant if it shows its phenotype regardless of the alleles

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18
Q

dominant negative mutation

A

one allele may encode inactive gene product—interferes with function.

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19
Q

what can a dominant negative mutation lead to

A

haploinsufficiency

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20
Q

what is haploinsuffiency

A

one copy of the allele is not enough to sustain life

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21
Q

famous loss of function mutation

A

sickle cell anemia

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22
Q

gain of function

A

Result in a gene product with enhanced, negative or new functions, usually dominant

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23
Q

suppressor mutation

A

Second mutation that reverts or relieves effects of a previous mutation, intragenic and intergenic

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24
Q

intragenic

A

occurs within the same gene

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25
Q

intergenic

A

occurs in genome

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26
Q

mutation rates

A

Likelihood that gene will undergo mutation in single generation or single gamete.
Rate is low for all organisms.
Rate varies for gene to gene

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27
Q

how to study mutations rates

A

compare SNPs, see that a newborn has 60 new mutations compared to parents

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28
Q

what does the number of mutations depend on in babies

A

the fathers age at conception

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29
Q

how do mutations arise

A

from replication, DNA polymerase occasionally inserts incorrect nucleotides, bases can take several forms which increases the chance of mispairing during DNA replication

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30
Q

replication slippage

A

DNA polymerase slips or stutters during replication.
Loop occurs in template strand during replication.
More common in repeat sequences (hot spots).
Hot spots for DNA mutation
Contributes to hereditary diseases
Fragile-X, Huntington disease

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31
Q

where are mutational hotspots

A

in genes associated with cancers, hot spots in repeat domains to see if they relate to the cancer, hot spots in areas with lots of repeats

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32
Q

tautomer

A

purines and pyrimidines exist in tauomeric forms- alternates chemical forms

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33
Q

tautomeric shifts

A

can change the bonding strucutre, may lead to permant base pair changes and mutations

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34
Q

H bonds in G-C

A

3

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35
Q

H bonds in A-T

A

2

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36
Q

what form in thymine usually in

A

keto

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37
Q

what does thymine go to if a tautomeric shift occurs

A

enol

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38
Q

what happens when thymine is in an enol form

A

it will now bind to a guaine with 3 bonds

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39
Q

what form in cytosine usually in

A

amino

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40
Q

what form in cytosine in when a tautomeric shift occurs

A

imino

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41
Q

what happens when cytosine is in an imino form

A

bind to adenine with 2 bonds

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42
Q

what type of mutations is a tautomeric shift

A

spontaneous

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43
Q

what are transposable elements

A

D N A sequences that move within and between chromosomes.
Insert themselves into various locations within genome.
Found in all organisms
Their origins are unclear

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44
Q

how much of the human genome is TE

A

45%

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45
Q

what do TE contribute to

A

spontaneous mutation
genetic rearrangements
horizontal transfer of genetic material

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46
Q

types of TEs

A

DNA vsRNA
viral vs non-viral
replicative mechanism vs exision mechanims

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47
Q

2 classes of transposition

A

Class 1: copy and paste

Class 2: cut and paste

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48
Q

Class one

A

use host RNA pol make RNA intermediate then use reverse transcriptase

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49
Q

class 2

A

no RNA intermediate at all, cut themselves out of genome and put them somewhere else

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50
Q

DNA transposons

A 
Move their location without going through RNA intermediate stage.
Inverted terminal repeats (ITRs) are located at ends of transposable elements, part of class 2
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51
Q

what are ITRS for

A

to be recognized by transposase

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52
Q

direct repeats

A

not part of the trasnposon, foortpring os transpositions

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53
Q

cut and paste transposition

A

cut and paste, binds to both ends of the transposon which consist of inverted repeats, a sequecne of DNA that makes up the target site

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54
Q

transposase

A

encoded by the TE (autonomous) or from another TE (non-autonomous)

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55
Q

what is the DNA at the target site

A

cut in an offset manner, sticky ends

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56
Q

what happens after the transposon is ligated to the host

A

the gaps are filled in

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57
Q

what is a retrotransposon

A

RNA transposable element, main difference is the RNA intermediate, uses reverse transcriptase, makes a copy of itself in RNA, goes to DNA and then inserts itself into a new place

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58
Q

how many types of retrotransponsons are there and what are they

A

2

LTR and nonLTR

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59
Q

LTR transposon

A

Long terminal repeat, on both sides of the transposon is the LTR in the same orientation, is the control center

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60
Q

what makes up the LTRs

A

U3
R
U5

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61
Q

what composes U3

A

enhancer and promoter sequences

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62
Q

what composes R

A

5’ capping sequence and poly A tail

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63
Q

what composes U5

A

dont know, maybe something for adenylation

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64
Q

genes in the LTR transposon

A

gag

pol

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65
Q

what does gag do?

A

group specific antigen, makes up inner shell of viral coat,

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66
Q

what does pol do?

A

one giant gene that encodes reverse transcriptase, inegrase and protease

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67
Q

what does integrase do?

A

what actually puts the RNA into the genome

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68
Q

what does protease do?

A

cleaves the products of these genes, makes the cut so you have 2 separate enzymes instead of 1

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69
Q

where does transcription start for LTR transposons

A

starts in 5’ LTR at the 5’ R sequence

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70
Q

what enzyme carries out transcription of the LTR trasnpsons

A

the hosts enzyme

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71
Q

where is transcription terminated in the LTR transponson

A

3’ LTR

72
Q

where do the enzymes bind when transcription of the LTR transposons begin

A

enzymes bind to U3 but transciption starts at R

73
Q

steps for LTR transposition

A
  1. host tRNA base pairs to the primer binding site near the 5’ end
  2. Reverse transcitpase copies R and U5 sequences into DNA
  3. the new DNA sequence can base pair to the R of the 3’ LTR
  4. the first strand of DNA is then reverse transcribed
  5. the RNA template is degraded by RNAse leaving a fragment to prime the second strand DNA synthesis
  6. the small 3’ fragment is used to make a DNA primer
  7. synthesis proceeds in both directions to give double stranded DNA with an LTR (U3,R,U5)
74
Q

what is the tRNA used as

A

the primer for DNA synthesis by reverse transciptase

75
Q

Steps for non-LTR Transpositions

A
  1. The ORFs are translated by the host’s enzymes. These are read by the host’s ribosomes to make an RNP.
  2. The RNPs bind to the additional RNA copies of the transposable element, and place them into stress granules.
  3. These stress granules empty the RNP/RNA complexes into the nucleus, where the RNAs are reverse-transcribed and integrated into new regions of the genome.
76
Q

What are LINEs

A

Long Interspaced Nuclear Elements

77
Q

What are SINEs

A

Short Interspaced Nuclear Elements

78
Q

What do SINES rely on?

A

LINEs

79
Q

Basic cancer definition

A

Genetic disease at the somatic level is characterized by gene products derived from mutated or abnormally expressed genes

80
Q

Genomic Alterations found in cancer cells

A

Single-nucleotide substitutions
Large-scale chromosome rearrangements
Amplifications and deletions

81
Q

what percentage of cancers are caused by germline mutations

A

5%

82
Q

2 fundamental properties of cancer cells

A

proliferation and metastasis

83
Q

proliferation

A

abnormal cell growth and division

84
Q

metastasis

A

defects in normal restraints that keep cells from spreading and colonizing other parts of the body

85
Q

benign tumor

A

The cell loses genetic control over cell growth
Result in multicellular mass
Removed by surgery, causing no serious harm

86
Q

malignant tumor

A

Cells break loose, enter the bloodstream invade other tissue—form secondary tumors (metastases)—life-threatening

87
Q

clonal origin

A

All cancer cells in primary and secondary tumors are clonal.

Clonal: originated from the common ancestral cell that accumulated numerous specific mutations

88
Q

driver mutation

A

give a growth advantage to tumor cells, Tens of thousands of somatic mutations are present in cancer cells.
Fewer than a dozen mutated genes may be sufficient to create a cancer cell

89
Q

passenger mutation

A

Have no direct contribution to the cancer phenotype.

90
Q

what is the cancer stem cell hypothesis

A

Tumor cells that do proliferate give rise to cancer stem cells that have the capacity for self-renewal.
Stem cells are undifferentiated cells with the capacity for self-renewal

91
Q

what does carcinogen mean?

A

carcino–> cancer gen–> to generate, something that generates cancer, Delay between exposure to carcinogen and appearance of cancer is an indication of a multistep process.

92
Q

tumorigenesis

A

development of malignant tumor

93
Q

what are the genetic alterations from tumorigenesis

A

Release cancer stem cells from normal controls
Each step confers a selective advantage to the growth and survival of a cell
Propagated through successive clonal expansion

94
Q

Cancer cells show higher than normal rates of

A

Mutation.
Chromosomal abnormalities.
Genomic integrity

95
Q

mutator phenotype

A

High level of genomic instability in cancer cells
Highly improbable that these can revert
Mutate more than the normal mutation rate

96
Q

translocation

A

swap pieces of DNA causes a disease, in cancer cells its easy to swap the chromosome pieces

97
Q

Genomic instability in cancer cells is characterized by

A

Somatic point mutations

chromosomal effects

98
Q

Chromosomal effects

A 
Translocations
Aneuploidy
Chromosome loss
DNA amplification
Deletions
99
Q

reciprocal translocation

A

highly prevalent in cancers, both chromosomes swap

100
Q

epigenetics

A

Study of chromosome-associated changes that affect gene expression but do not alter nucleotide sequence of DNA
Epigenetic effects may be present in somatic or germ-line cells.

101
Q

epigenetic modification examples

A

DNA methylation, histone acetylation, and phosphorylation

102
Q

what type of DNA do cancer cells have?

A

altered DNA methylation patterns

103
Q

what are the altered DNA methylation patterns

A

Less methylation in cancer cells than in normal cells

Promoters in genes are hypermethylated in cancer cells

104
Q

what is the result of the DNA methylation patterns in cancer cells

A

repression of transcription

105
Q

what modifications are disrupted in cancer cells

A

histone modifications

106
Q

what is going on in the histone modifications in cancer cells

A

Genes that encode histone-modifying enzymes are often mutated or aberrantly expressed in cancer cells.

107
Q

what control do cancer cells lose

A

cell proliferation control

108
Q

development

A

the slow process of progressive change in an organism has to do with regeneration
the interface of the genotype and the phenotype

109
Q

embryology

A

The study of development between fertilization and birth

110
Q

is all developmental biology embryology?

A

NO

111
Q

what do all organisms arise from

A

a single cell

112
Q

what are the 3 interrelated processes in embryonic development

A

Cell division
Cell differentiation
Morphogenesis

113
Q

what is morphogenesis

A

how to make organs

114
Q

genomic equivalence

A

All cells in the zygote have the same genome

indicates that cells need to regulate their genome during development

115
Q

what does differentiation result from

A

differential gene expression

116
Q

what is cleavage

A

type of mitosis
mitosis without growth (subdivides the fertilized zygote)\
subdivide one cell into many smaller things

117
Q

what is the goal of cleavage

A

“Kick-starts” cell differentiation
Polarized Oocytes differentially localize mRNAs and proteins
Maternal Determinants

118
Q

How Can We Make Cells Different During Development

A

Differential Gene Expression

119
Q

cis regulatory element

A

Regions of non-coding DNA
Found in the vicinity of the genes that they regulate, on the same strand of DNA
Typically regulate gene expression by binding to transcription factors

120
Q

what are the types of transcription factors

A

Promoters
Enhancers
Silencers
Insulators

121
Q

what is an insulator

A

sequences that regulate the level of expression

122
Q

what is a trans regulatory element

A

Genes that modify the function of distant genes
DNA sequences that encode trans-acting factors
These are usually transcription factors
These are also HIGHLY pleiotropic

123
Q

pleiotropy

A

one gene = many functions

124
Q

Methods of Differential Gene Expression

A

enhancer modularity

125
Q

what is enhancer modularity

A

Enhancers or repressors for a gene “code” for expression in different tissues

126
Q

methylation

A

Methyl groups can be added to DNA sequences to modify expression

127
Q

what bases can be methylated

A

cytosine and adenine

128
Q

CpG islands

A

Methylated regions of the vertebrate genome (CG repeats)

Often occur in promoters

129
Q

Cis-regulatory elements DO NOT include

A

TF

130
Q

Trans-regulatory elements include

A

TF

131
Q

Alternative RNA splicing

A

a single gene can encode multiple products

depending on what exons are kept in mRNA you can make different proteins

132
Q

splicing enhancers

A

promote the assembly of the spliceosome at specific intron/exon boundaries
Introns have lots of information specifically enhancers, DNA sequences but they recruit splicesosome to the middle of the area to splice out the intron

133
Q

ribosomal selectivity

A

ribosomes show favoritism
Not all ribosomes translate every single mRNA
is how we make cells different from each other

134
Q

gene regulatory networks are a set of

A

Genes
Proteins
mRNAs

135
Q

what do the parts of gene regulatory networks do

A

Interact to control a specific function

Controls transcription and cell signaling

136
Q

what is the gene regulatory network

A

is the many ways genes interact with each other in a specific cell

137
Q

what are the nodes in the gene regulatory network

A

gene, protein, or mRNA

138
Q

what are the edges in the gene regulatory network

A

interactions between the nodes

139
Q

what to GRNs control

A

animal development

regulate expression of thousands of genes

140
Q

Can GRNs be homologous

A

yes

141
Q

what does it mean to be homologous

A

from the same gene or same common ancestor

142
Q

maternal effect

A

Offspring’s phenotype of particular trait under control of mother’s nuclear gene products present in egg
Nuclear genes of female gamete are transcribed—genetic products accumulate in egg ooplasm

143
Q

what are stem cells important for?

A

Important for maintaining tissue homeostasis throughout adult life
significant for the formation of organs

144
Q

how can stem cells be linked to cancer

A

Mis-regulation of stem cells is linked to multiple cancers

145
Q

what is a stem cell

A

Gives rise to differentiated cells through cell division, while maintaining its “steminess” (Self-Renewal)

146
Q

what is one way stem cells can exist

A

in a quiescence state

147
Q

what does it mean to be in a quiescence state

A

dormant non-proliferative

148
Q

potency

A

the degree of different cell types a stem cell can generate

149
Q

totipotent

A

Cell can make anything

Only the first 4-8 cells are totipotent in humans

150
Q

pluripotent

A

Can make a few different cell types

151
Q

multipotent

A

when the stem cells only produce the cell types in the tissues in which they reside
Most adult stem cells in humans

152
Q

how is self renewal achieved

A

symmetric and asymmetric cell division

153
Q

what is symmetric cell division

A

Results in either the production of two identical stem cells, or two cells that are committed to differentiate

154
Q

what is asymmetric cell division

A

Results in a stem cell, and one that is ready to differentiate
Stabilizes the stem cell pool
This is called “Single Stem Cell Asymmetry”
2 daughter cells are not the same

155
Q

what is population asymmetry

A

Some stem cells are more prone to make cells to differentiate,
While others are prone to make more stem cells.

156
Q

embryonic pluripotent stem cells

A

modified cell cycle,

157
Q

modifications for embryonic pluripotent stem cell

A

Shortened G1
G0 Absent
the G1 and G2 phases lengthen
No oscillatory expression of cyclins or CDKs
ESCs are also characterized by a non-functioning G1 checkpoint

158
Q

what cyclin is always on for embryonic pluripotent stem cells and why

A

cyclin E - Allows for the direct transition from M to Late G1, which is shortened

159
Q

Why would we spend more time in S than G1 and G2 as a stem cell

A

because stem cells don’t need as much growth since its not specified

160
Q

what do stem cells usually need

A

a niche

161
Q

whats a niche

A

is an area of a tissue that provides a specific microenvironment, in which stem cells are present in an undifferentiated and self-renewable state

162
Q

what can cells of the stem cell niche do

A

interact with the stem cells to maintain them or promote their differentiation

163
Q

Common Mechanisms to Maintain Stem Cells in a Niche

A

Physcial Mechanisms
Chemical Regulation
intracellular mechanism

164
Q

physcial mechanims

A

structural and adhesion factors

165
Q

chemical regulation

A

proteins and hormones secreted from other cells

166
Q

intracellular mechanisms

A

Cytoplasmic determinants
Transcriptional Regulation
Epigenetic regulation

167
Q

cytoplasmic determinants

A

movement of these as the cell divides

168
Q

transcriptional regulation

A

the internal network of transcription factors that silence or maintain specific gene expression

169
Q

epigenetic regulation

A

chromatin accessibility

170
Q

how is the pluripotency of stem cells maintained after they are harvested

A

maintained via niche transcription factors

171
Q

what are the trasncription factors important for the niche and mainting the cell pluripotency

A

Oct4, Sox2 and Nanog

172
Q

are all embryonic stem cells equal in potency

A

no

there are 2 pluripotent states of stem cells

173
Q

what are the 2 pluripotent states of stem cells

A

naive and primed

174
Q

naive

A

has the greatest potential for pluripotency

175
Q

primed

A

an ICM cell with some maturation towards the epiblast lineage

Genetics (4 decks)

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