Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Genomic Biology > Post Exam 2 > Flashcards

Post Exam 2 Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

What is GWAS?

A

genome wide association studies

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What genetic/genome change causes cancer?

A

initiation and perpetuation of cell generation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are 3 examples of ways mutations are inherited?

A
  1. autosomal
  2. x/y linked
  3. mitochondrial
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is a monogenic disease?

A

one gene involved (mendelian)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what is a polygenic disease?

A

multiple genes involved

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How do we determine the gene causing a disease?

A

sequencing the genome or sequencing the exomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what are 3 locations mutations can be in the genome?

A

coding
noncoding
regulatory regions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what are 2 reasons we want to know what gene causes a disease?

A

screening purposes
potentially drugable targets

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the goal if GWAS analysis?

A

identify genotypes (mutations in genome) assocaited with specific phenotypes (disease)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are 3 genotypes for a diease?

A

copy number variance
sequence variants
single nucleotide polymorphisms (SNP)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is an example of sequence variants?

A

chromosome rearrangements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the output of GWAS analysis?

A

block of SNPs (haplotype: set of SNPs from one parents inherited together)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what 2 ways can findings from GWAS be used?

A
  1. design drugs/treatment
  2. asses risk using polygenic risk score
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is a polygenic risk score?

A

aggregate the association of many SNPs to find a percentage of risk for a certain disease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How do you interpret a manhattan plot?

A

each dot is a SNP and shows the association each SNP has to a specific trait/disease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

GWAS studies determine ____________ of specific SNPs and how they ___________ with that trait of interest

A

frequency
association

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are the 3 biases of GWAs studies

A
  1. pt self reporting
  2. data collection @biobanks
  3. sample types
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How is data being collected at biobanks biased?

A

in hospitals have sick people
blood drives skeew demographics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How is sample type a bias?

A

tumors have different DNA than regular tissue
blood bias against people who dont like needles
saliva has lots of contaminant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is collecting new SNPs mainly for?

A

studying phenotypes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is trio sampling?

A

samples from mom, dad, and offspring

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is the advantages of trio sampling?

A

gives more context b/c you will know if SNPs in offspring you are study is from mom or dad

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is genotyping?

A

exploring an individuals DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Why are microarrays good?

A

cheaply generate data

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What are microarrays good at detecting?

A

common variance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

what do microarrays measure?

A

hetero/homozygosity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is an issue with microarrays?

A

must know what SNP you are looking at

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What are the steps of microarrays?

A
  1. DNA collection
  2. break DNA into fragments
  3. run fragments over chip
  4. hybridize DNA fragments
  5. DNA fragments stop one nucleotide short of the SNP of interest
  6. add base at end of fragment
  7. look down at chip once fluorescent dye is added
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What does the red/green dye mean in microarrays?

A

homozygous

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

what does the yellow dye mean in microarrays?

A

heterozygous

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What is whole genome sequencing better at?

A

detecting novel variance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

How does exome sequencing work?

A

hybridize DNA and RNA together then degrade RNA so you are only left with DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Cystic fibrous tissue is found where besides the lungs?

A

pancreas and sweat glands

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

salty ___________ is a leading diagnosis for CF

A

salty babies

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

what does the panceras do?

A

secretes bile to break down food

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

people with CF have an ____________________ insufficiency

A

exocrine pancreatic insufficiency

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Is CF a multiorgan disease?

A

yes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

CF is related to an _________ imbalance

A

ion (salty babies)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

From the 1930-80s what was the treatments for CF?

A

focused on treating symptoms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

In the 80s what was discovered about CF?

A

positional cloning to identify chromosomal regions containing CF gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

CF gene is an __________ recessive gene, making it easily readable on a pedigree map

A

autosomal

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

_________ genomics was used to narrow down the regions on the chromosome that were important for CF

A

comparative genomics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

T/F cultured cells from CF patients still had an ion imbalance?

A

true

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What was identified in 1989 in CF research?

A

CTT deletion (Phe at 508 in protein CFTR)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

Around __/__ of CF patients had the CFTR mutation

A

2/3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What is the CFTR responsible for?

A

it is an ABC transporter that transports C1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

What region of the genome is the CFTR mutation located?

A

nucleotide binding region

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What is a current treatment for CF?

A

trikalta: cocktail of 3 small molecules that bind to CFTR and mediate C1 transport

49
Q

Why are males with CF infertile?

A

thier vas deferns gets clogged with mucus and deteriorates

50
Q

Now all new borns are tested for CF, how?

A

genetic testing and sweat conductance test

51
Q

trikalta is only approved for who?

A

patients with f508

52
Q

what is the treatment for patients not approved for trikalta?

A

using thier stem cells to generate organoids

53
Q

heterozygous or homozygous mutations are lethal?

A

heterozygous

54
Q

what is MIOM (mendelian inheritance of man)

A

record of all genes that were auto-dominant, auto-recessive, x-linked, y-linked, mitochdrial
also has a standard nomenclature of diseases

55
Q

what is a aneuploidy ?

A

the abnormal number of chromosomes

56
Q

what is cytogenetics

A

field of studying chromosomes

57
Q

what are 3 aneuploidy diseases?

A
  1. patau syndrome (13)
  2. edwards syndrome (18)
  3. down syndrome (21)
58
Q

most chromosomal trisomies are a result of ______________

A

non disjunction

59
Q

when are chromosomal abnormalities usually detected?

A

in utero

60
Q

what is amniocentesis?

A

taking embroy’s cells

61
Q

What is ataxia telangiectasia?

A

disease where you have a hypersensitivity to radiation and genotoxic drugs

62
Q

what is p53?

A

tumor supressor gene

63
Q

What does ATM detect?

A

double stranded breaks

64
Q

infectious diease has been decreasing but cancer has been __________

A

increasing

65
Q

What did Theodor Boreri suggest?

A

cancer was chromosomal

66
Q

a ________ set of mutations can induce cancer

A

small

67
Q

cancer is a disease of the _______

A

genome

68
Q

what are the two types of cells?

A

somatic and germ line

69
Q

what type of cell has a variety of life spans?

A

somatic cells

70
Q

cell death and birth is very ____________

A

regulated

71
Q

What are neoplasm/tumors?

A

cells that give rise to progeny with uncontrolled growth

72
Q

are carcinomas or sarcomas more common?

A

carcinomas

73
Q

what tissue is carcinomas from?

A

epithelial skin, lung, gut

74
Q

what tissue is sarcomas from?

A

bone, fat mesodermal

75
Q

what cancer is leukemas?

A

blood

76
Q

what are lymphomas?

A

diff. lymphocytes

77
Q

what are mylomas?

A

plasma cells B cells

78
Q

what is ataxia telangiectasia caused by?

A

mutation in DNA replication and repair

79
Q

what is helicobacter pylori?

A

bacteria that causes stomach cancer

80
Q

mutations that lead to transformation are assocated with what 3 types of genes?

A
  1. oncogenes
  2. tumor suppressor genes
  3. apoptosis related genes
81
Q

What do oncogenes do?

A

promote cell growth

82
Q

what do tumor suppreesor genes do?

A

suppress cell growth

83
Q

what do apoptosis related genes do?

A

control cell death

84
Q

What are 6 hallmarks of cancer?

A
  1. self sufficency in growth signal
  2. insensitivity to antigrowth signals
  3. evading apoptosis
  4. limitless replication
  5. angiogensis
  6. mutastasis
85
Q

what are driver mutations?

A

DNA sequence of genes that cause cells to become cancer cells and grow and spread in the body

86
Q

what are passenger mutations?

A

those which do not alter fitness but occurred in a cell that coincidentally or subsequently acquired a driver mutation, and are therefore found in every cell with that driver mutation. (no functional consequences)

87
Q

how does radiation treat cancer?

A

induce DNA damage to initate apoptosis

88
Q

how does chem treat cancer?

A

induce DNA damage to initiate apoptosis

89
Q

what are alkylating agents?

A

crosslink DNA damage to initiate apoptosis

90
Q

what are antimetabolites?

A

chemically resemble nucleotides

91
Q

what are antimicrotubules?

A

block cell cycle

92
Q

what 2 things inhibit cancer treatment?

A

topoisomerase
angiogenesis

93
Q

what 3 things are involved in triple negative breast cancer?

A

estrogen receptor
progesterone receptor
HER2

94
Q

How is cancerous estrogen receptors targeted?

A

with tamoxifen (competes with ER and blocks cell growth)

95
Q

How is cancerous HER2 targeted?

A

with monoclonal antibodies that adds a toxin to HER2

96
Q

why is neoadjuvant chemotherapy/surgery (personalized med) bad?

A

very toxic, only works half the time

97
Q

how does single cell sequencing work?

A

1.remove single cells form a tumor
2. one cell per plate
3. add a barcode (8-10nt long) to each plate
4. mix together
5. NGS
6. use barcode to deconvolve

98
Q

What is the process of single cell sequencing?

A
  1. remove single cells from tumor
  2. add one cell per plate
  3. add a barcode (nt fragment) to each cell
  4. mix
  5. NGS
  6. use barcode to deconvole
99
Q

what is intratumor heterogencity?

A

individual cells can accumulate thier own mutations

100
Q

what are 2 options for chemoresistant cells?

A
  1. chemoresistant cells were present all along (not all died off or they were able to adapt)
  2. chemotherapy caused these cells
101
Q

What are the challenges of gene therapy?

A
  1. so many cells
  2. how do we get the new DNA in
  3. need to understand the exact problem
  4. safety
  5. expensive
102
Q

what 3 genes/diseases work best for gene therapy?

A
  1. heritable genes
  2. monogenetic diseases
  3. tissue specific disease
103
Q

what are 3 advantages to using lentivirus for gene therapy?

A
  1. infect dividing and non dividing cells
  2. can permanently integrate into host genome
  3. carry long pieces of DNA
104
Q

what is a disadvantage of using lentiviruses?

A

inserts randomly into genome and leaves some viral genome behind

105
Q

What is Zynteglo?

A

treatment for B-thalassemia using lentivirus carrying a functional hemoglobin

106
Q

what are 3 advantages to using adeno-assocaited viruses?

A
  1. non pathogenic
  2. infect dividing and non dividing cells
  3. stably integrate into one place
107
Q

what is a disadvantage to using adeno-assocaiated virus?

A

carries small pieces of DNA

108
Q

What is Zolgensma?

A

treats spinal muscular atrophy using adeno-associated virus carrying a functional SMN1

109
Q

Who was Jesse Gelsinger?

A

1st person to die in a clinical trial of gene therapy; has orthinin transcarbamylase deficency (OTC) which results in a build up ammonia

110
Q

why is it easy to place treated blood back in body for therapy?

A

all RBC come from stem cells so they are being regenerated all the time

111
Q

What are CAR T cells?

A

detect cancer cells by binding to cancer/diease protein

112
Q

What are CAR T cells built in with?

A

suicide switches that can be injected into pt

113
Q

what are 3 goals of forensics?

A

establish paternity
identify remains
implicating suspects

114
Q

what is DNA fingerprinting?

A

(aka STR profiling) identifying series of short tandum repeats

115
Q

How does DNA fingerprinting work?

A

look for key STR in a suspect for a list of 13 STR and how many repeats occur

116
Q

Why do you not use gel electrophoresis for DNA finger printing?

A

use capillary because its more precise

117
Q

what genetic geneology?

A

using publicly available genetic data base to find relatives of sample (caught the golden state killer)

118
Q

What will tell you what tissue your sample is?

A

look at transcriptomes (microarray)

119
Q

How is measuring microbiomes helpful in forensics?

A

each person has thier own
time of death

Genomic Biology (6 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions