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exam 1 Flashcards

1
Q

genome

A

entire set of DNA instructions found in a cell

in a virus, cell, or organelle

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2
Q

What carries a human genome?

a. 23 chromosomes
b. 23 chromosomes + mtDNA
c. 46 chromosomes
d. 46 chromosomes + mtDNA

A

**a. 23 chromosomes ** or b. 23 chromosomes + mtDNA

context is important

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3
Q

how many genomes are there in a virus

A

1 genome

can be RNA or DNA

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4
Q

how many genomes are there in a bacteria cell

A

1 genome

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5
Q

how many genomes are in an animal cell

A

2 genomes:
1. nucleus (nDNA)
2. mitochondria (mtDNA)

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6
Q

how many genomes are there in a plant cell

A

3 genomes:
1. nucleus (nDNA)
2. mitochondria (mtDNA)
3. chloroplast (cpCNA)

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7
Q

what is the size of eukaryotic genomes

A

10Mb → 100,000Mb

contained in organelles

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8
Q

characteristics of chromosomes in eukaryotic nuclei

A
  • multiple linear chromosomes
  • multiple copies of each chromosome
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9
Q

characteristics of mitochondrial genomes

A

12kb–2400kb
- circular DNA

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10
Q

characteristics of chloroplast genomes

A

120kb–170kb
- circular DNA

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11
Q

viruses

A

infectious particles comprised of a genome surounded by a protein coat

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12
Q

viral genomes

A
  • 2000 to 1 million bp of RNA or DNA
  • linear or circular
  • single stranded, double stranded, or segmented
  • 1 genome (RNA or DNA)

viral genomes frequently invade the genomes of other organisms

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13
Q

prokaryotic genomes

A

1 chromosome (DNA)
* 0.6-12Mb
* circular
* found in the nucleoid
* haploid

may have plasmids
* small circles of DNA
* 1-200kbp
* autonomously replicating
* not present in all bacteria

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14
Q

methods for visualizing chromosomes

A
  1. Geimsa dye staining
  2. microscopy
  3. sorting
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15
Q

karyotype

A

refers to an individual’s complete set of chromosomes (46XX, 46XY)
* also refers to the image of a person’s organized chromosomes
* created by cytogeneticists

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16
Q

cytogeneticists

A

detect and interpret chromosomal abnormalities
1. cells are collected
2. cells are grown for a little while to initiate DNA replication
3. chromosomes are analyzed

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17
Q

types of reproductive genetic testing

A

1. prenatal testing
* amniocentesis (16 weeks)
* chorionic villi sampling (11 weeks)
* maternal blood testing (9 weeks)
2. preimplantation genetic diagnosis (PGD)
note: PGD can only be used with in-vitro fertilization

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18
Q

4 ways of classifying chromosomes based on size and position of centromere

A
  1. metacentric
  2. submetacentric
  3. acrocentric
  4. telocentric
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19
Q

metacentric chromosome

A

centromere in the middle
* forms two equal arms

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20
Q

submetacentric chromosome

A

centromere placed near to one end
* results in one shorter and one long arm

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21
Q

acrocentric chromosome

A

centromere placed closed to one end
* forms one extreme short and one extreme long arm

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22
Q

telocentric chromosome

A

terminally placed centromere

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23
Q

cohesins

A

holds sister chromatids together during mitosis

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24
Q

chromosome number (N)

A

this is the number of unique chromosomes in a “set”

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25
Q

ploidy

A

number of complete sets of chromosomes

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26
Q

what is the best way to count the number of total chromosomes

A

count the number of centromeres

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27
Q

haploid chromosome number (N) and ploidy are…

A

specific to a species
* e.g. Homo sapiens N=23, 2N=46

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28
Q

c-value

A

amount of nuclear DNA in a gamete (haploid)
- this is irrespective of ploidy

note: organismal complexity is not correlated with N, ploidy, or # genes

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29
Q

genome packaging in prokaryotes is ____ organized than in eukaryotes

A

less

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30
Q

C-value paradox

A

organismal complexity is not correlated with N, ploidy, or # of genes

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31
Q

nucleoid

A

region that contains condensed DNA/protein complexes
- attaches to inner membrane

note: this is characteristic of prokaryotes

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32
Q

NAPs

A

nucleoid-associated proteins
- these bind to repetitive sequences to form loops of supercoiled DNA
- ~10,000 bp/loop

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33
Q

microdomains/loop domains

A

help to condense bacterial chromosomes

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34
Q

how does a bacterial genome fit inside the cell?

A

supercoiling helps pack DNA into smaller spaces

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35
Q

what is supercoiling facilitated by

A

enzymes
(i.e. topoisomerases)

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36
Q

topoisomerases

A

enzymes that overwind and underwind dsDNA

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37
Q

positive supercoiling

A

overwinds DNA

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38
Q

negative supercoiling

A

underwinds DNA

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39
Q

drugs that inhibit topoisomerases are one type of…

A

chemotherapeutic agent

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40
Q

eukaryotic genome packaging is

A

organized

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41
Q

nucleosome

A

refers to a single histone/DNA complex
- the fundamental subunit of chromatin

eukaryotic histones in a nucleosome:
- composed of: (1) a core histone octomer & (2) a linker histone

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42
Q

p-arm

A

petit
- this is the short arm

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43
Q

q-arm

A

queue
- this is the long arm

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44
Q

p telomere called…

A

ptel
- this is on the short arm

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45
Q

q telomere called…

A

qtel
- this is on the long arm

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46
Q

do 2 different individuals from the same species have the same banding patterns on their chromosomes?

A

yes

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47
Q

FiSH

A

fluorescent in situ hybridization
- used to visualize specific regions of a genome (typically when abnormalities are suspected)
- a DNA or RNA probe complementary to a specific region of the genome is hybridized to chromosomes
- can also use lots of probes that are labeled with different colors to “paint” chromosomes

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48
Q

FISH can identify differences in…

A

base-pair order

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49
Q

how do chromosomes occupy the nucleus

A

within specific territories
- likely allows for specific interactions between different chromosomes

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50
Q

T/F: regions of genomes will condense and decondense at different times

A

TRUE: genomes are dynamic
- sometimes our cells need to “see” the DNA in an uncondensed form (for DNA replication, gene expression, etc.)

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51
Q

isolated chromosomes contain:

A
  1. DNA
  2. proteins
  3. RNAs
  4. lipids
  5. polysaccharides
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52
Q

when interpreting chromosomal data, what to look for:

A
  1. # of each chromosme
  2. total # of chromosomes
  3. centromere position
  4. chromosome length
  5. chromosome shape (linear)
  6. banding patterns
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53
Q

What % of the human genome is composed of protein coding genes?

the human genome is 3 billion base pairs long

A

2%

the amount of non-coding DNA varies between species

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54
Q

non-coding DNA contains

A
  1. introns
  2. transposable elements
  3. repetitive sequences
  4. stuff we still don’t understand (unique sequences)
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55
Q

introns

A

parts of genes that are transcribed into mRNAs, and then removed before translation

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56
Q

what can create different proteins

A

alternative splicing
- this might explain why humans only have 20% more genes than a single celled plasmodium

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57
Q

introns position

A

members of the same species: tend to have the same introns in the same positions

members of different species: can gain or lose introns, but will maintain ancestral positons of introns more frequently than expected
- suggests functionality

58
Q

transposable elements (TEs)

A

self-replicating, mobile DNA sequences
- “jumping genes”
- classified as “selfish” genetic elements or “genomic parasites”

59
Q

purpose of transposable elements

A

not “junk”, might provide genetic variation that is favored during evolution
- can also contribute to regulatory changes (TE upstream of ISL1 alters gene expression)
- novel proteins through changes in intron splicing ?????

60
Q

repetitive sequences

A

can be:
1. short and sequential
- can consist of (1) simple repeats (SSRs), (2) simple tandem repeats (STRs), and (3) microsatellites
2. long and segmented
i.e. intrachromosomal vs. interchromosomal

61
Q

test cross

A

cross an unknown to an individual with a known, recessive genotype
- offspring will have predictive phenotypic ratios for the possible unknown genotypes

62
Q

what occurs to TEs that copy and insert themselves into important genes

A

they should be selected against over evolutionary time

63
Q

who established “true breeding” pea lines

A

Gregor Mendel
- created peas that were homozygous
- showed that F1 and F2 offspring had predictable ratios of phenotypes

64
Q

what occurs if a TE is copied and inserted into a non-coding sequence

A

it will be maintained
- the larger the non-coding sequence space, the more likely a TE will land in an unimportant region
- this would make the non-coding sequences longer and allow for the expansion of more TEs

65
Q

Mendel’s discoveries

there are 6 of them

A
  1. there are “hereditary determinants of particulate nature” (genes)
  2. genes come in pairs
  3. alternate phenotypes of a single character are determined by different forms of these genes (dominant/recessive alleles) (Law of Dominance)
  4. gametes contain one member of each gene pair (ploidy)
  5. innheritance of alleles was random/random fertilization (Law of Segregation)
  6. genes controlling different traits are inherited independently (Law of Independent Assortment)
66
Q

what are Mendel’s Laws of Heredity

there are 3 of them

A
  1. Law of Dominance
  2. Law of Segregation
  3. Law of Independent Assortment
67
Q

Law of Dominance

A

some alleles are dominant, others are recessive, a heterozygous individual will display the dominant form
- this is one of Mendel’s laws of heredity

68
Q
A
69
Q

Law of Segregation

A

only 1 allele is carried in a gamete
- this is one of Mendel’s laws of heredity

70
Q

Law of Independent Assortment

A

genes of different traits segregate independently to the gametes
- this is one of Mendel’s laws of heredity

71
Q

what are the steps of meiosis

A
  1. interphase
  2. meiosis I
    - prophase I
    - metaphase I
    - anaphase I
    - telophase I
  3. meiosis II
    - prophase II
    - metaphase II
    - anaphase II
    - telophase II
72
Q

what steps can prophase I (meiosis) be further broken down to

A
  • leptotene
  • zygotene
  • pachytene
  • diplotene
  • diakinesis
73
Q

interphase

A

DNA replicates

74
Q

prophase I

A

homologous chromosomes find each other and recombine

75
Q

metaphase I

A

chromosomes align on metaphase plate

76
Q

anaphase I

A

chromosomes move to opposite poles

77
Q

telophase I

A

cell division

78
Q

prophase II

A

chromosome structures condense, no crossing over

79
Q

metaphase II

A

chromosomes align to a central plane

80
Q

anaphase II

A

chromosomes move to opposite poles

81
Q

telophase II

A

cell division

82
Q

monohybrid cross

A

when both parents are heterozygous at 1 locus
- e.g. Aa x Aa

83
Q

dihybrid cross

A

when both parents are heterozygous at 2 loci
- e.g. LlAa x LlAa

84
Q

one meiotic event describes…

A

the entire process of going from one diploid germline cell to 4 haploid gametes

85
Q

consider LlAa where both loci are on separate chromosomes
- if there is no recombination, how many meiotic events woul it take to generate all possible genotypes of gametes?

A

check notes and fill in

86
Q

frequency of recombination depends on…

A

how close the loci is to the centromere
- recombination doesn’t happen at the centromere

87
Q

predicted genotype ratios for mono and dihybrid crosses will…

A

always be the same

88
Q

predicted phenotype ratios will depend on…

A

the relationship of the alleles

89
Q

number of unique gametes (ignoring recombination) =

A

2N

90
Q

heterochromatin

A

these regions are typically full of repetitive sequences
- this may aid in compacting genome

91
Q

segmental duplications

A

1kb-400kb repeated sequences

92
Q

what explains the highest % (~44%) of our genome?

A

transposable elements (TEs)

93
Q

how much of a human genome is variable between individuals?

A

0.1%
- variation is randomly distributed across the genome
- not all variation is in coding sequences

94
Q

T/F: genetic variation is primarily in coding regions

A

FALSE
- variation is randomly distributed across the genome
- not all variation is found in the coding sequences

95
Q

types of genetic variation between individuals

A
  1. single nucleotide polymorphisms (SNPs)
  2. copy number variants (CNVs)
    - trinucleotide repeats TNRs
96
Q

single nucleotide polymorphisms (SNPs)

A

this is a variation at a single position in a DNA sequence among individuals
- between any 2 humans: ~ 1 SNP every 1000 bp
- 3-5 million SNPs/genome

97
Q

copy number variants (CNVs)

A

when the number of copies of a particular gene varies from one individual to the next
- between any 2 humans: ~1500CNVs
- avg. size of CNV=~20k bp

examples:
trinucleotide repeats (TNRs): TAGTAGTAGTAGTAG

98
Q

T/F: the majority of SNPs/CNVs lead to phenotypic differences

A

FALSE

99
Q

what region of the genome do SNPs and CNVs occur in

A

coding and non-coding regions
- they both can cause changes in phenotype but most of the time they have no phenotypic effect

100
Q

trinucleotide repeats

A

3 nucleotides consecutively repeated within a region of DNA
- this is a type of copy number variant (CNV)

101
Q

when can TNRs lead to disease

A
  1. when they occur within important genes
    (e.g. Huntington’s Disease)
  2. when they occur at structurally important regions of a chromosome
    (e.g. Fragile X syndrome)

note: TNRs in non-coding regions that haave o phenotypic effecs are ofen used for identity analysis

102
Q

between which of the following do you expect to differ between individuals of the same species?
1. number of chromosomes
2. chromosome sizes
3. types and positions of introns
4. numbers of genes
5. types of genes
6. alleles
7. CNVs
8. SNPs

A

FILL IN W NOTES

103
Q

which of the following do you expect to differ between individuals of different species?
1. number of chromosomes
2. chromosome sizes
3. types and positions of introns
4. numbers of genes
5. types of genes
6. alleles
7. CNVs
8. SNPs

A

FILL IN W NOTES

104
Q

dominance/recessive relationships

A

when one copy of an allele overrules phenotypes conferred by a different allele
- heterozygotes and homozygotes for completely dominant alleles show the same phenotype

105
Q

codominant relationships

A

heterozygotes for codominant alleles show both phenotypes
- e.g. orange and black alleles in cats- both also happen to be X-linked

106
Q

incomplete dominance

A

heterozygotes for incomplete dominant traits show a phenotype that is somewhere in between both homozygotes
- e.g. piebald spotting in cats

107
Q

which steps of meiosis generates genetic diversity?

A
  1. interphase
  2. prophase I
  3. metaphase I
  4. metaphase II
108
Q

genetic dominance/allelic relationships only compare the relationship between one allele in relationship to other alleles where

A

at the same locus

109
Q

modifier genes/alleles

A

alter the phenotypic effects of other genes
- e.g. modifier genes affect the hair length

110
Q

main/major effect vs. minor effect loci

A

major effect loci has more of an effect on allele than minor effect loci

111
Q

does environment play a role in phenotypic expression

A

yes

112
Q

if event “A” and “B” are independent events…

A

AND = multiply
- mutiply independent probabities
- e.g. AaBb X AaBb, P(A_B_)= P(A_)*P(B)

113
Q

if event “A” and “B” are dependent events

A

OR = add
- add dependent probabilities
- e.g. P(A_) or P(B_) = P(A_) + P(B_)

113
Q

pleiotropy

A

the production by a single gene of two or more apparently unrelated effects

pleiotriopic alleles lead to many different phenotypes (hair color, deaf, eye color)
- 1 gene, many phenotypes

114
Q

epistatic alleles

A

masks the effects of alleles at other genes
- if one allele prevents you from being able to predict the genotype at annother locus, the you have epistasis

115
Q

binomial expansion for phenotypic probability

A

must define your variables
- e.g. a = probability of having a child with normal RBC, b = probability of having sickled RBC
- use Pascal’s triangle

116
Q

binomial equation for 3 children

A

(a+b)^3 = a^3+3a^2b+3ab^2+b^3

117
Q

binomial equation for 5 childre

A

(a+b)^5 = a^5+5a^4b+10a^3b^2+10a^2b^3+5ab^4+b^5

118
Q

are males or females more likely to show phenotypes of sex-linked traits

A

males

119
Q

sex

A

refers to the aatomy of an individual’s reproductive system and secodnary sex characteristics

120
Q

gender

A

refers to social roles or internal awareness based on the sex of a person

121
Q

how do sex chromosomes pair up during meiosis

A

using pseudoautosomal regions
1. primary pseudoautosomal region found on the short arm
2. secondary pasudosomal region found on the long arm

found on both X and Y chromosome

122
Q

what should you do to test for sex linkage

A

perform a reciprocal cross
- a pair of crosses between the male of one strain and the female of another, and vice versa
- if sex linked, phenotypic ratios will be different in a reciprocal cross

123
Q

how to perform a chi squared (x^2) goodness of fit test

A
  1. presnent the assumed genotypes of cross you are testig
  2. present the observed and expected data in a table
  3. state an explicit null hypothesis pertaining to defined cross
  4. calculate the X^2 statistic
  5. state the degrees of freedom (and show its calculation)
  6. determine the X^2crit for the appropriate alpha value (P value) to test for significance
  7. compare the X^2crit to your X^2 value, and state whether or not the H0 is rejected
  8. state the overall conclusion
124
Q

William Warrick Cardozo showed that

A
  1. sickle cell anemia
  2. is more common among people with African ancestry
  3. not all people with sickled red blood cells have anemia
  4. not all sickle cell anemia cases are fatal
125
Q

if a trait is rare, it is safe to assume that…

(pedigrees)

A

non-blood relatives are not carriers
- however if you know mode of inheritance, can deduce that someone entering a pedigree must be a carrier

dominant traits
- the first person in a pedigree to show the trait is most likely heterozygous

126
Q

autosomal dominant traits tend to

A
  1. appear equally in males and females
  2. doesn’t skip generations
  3. affected children have an affected parent
  4. unaffected people do not transmit the trait
127
Q

autosomal recessive traits tend to

A
  1. appear equally in males and females
  2. skip generations
  3. more to appear among progeny of related parents
128
Q

X-linked dominant traits tend to

A
  1. does not skip generations
  2. affected males pass trait to all daughters and no sons
  3. affected heterozygous females pass trait to half of sons and half of daughters
129
Q

X-linked recessive traits tend to

A
  1. affected males produce carrier daughters
  2. no sons of affected males are affected
  3. males more likely to be affected than females
  4. half of the sons from an unaffected carrier will be affected
130
Q

Y-linked traits tend to

A
  1. traits appear only in males
  2. all sons of affected males will be affected
131
Q

mitochondrial (mtDNA) traits tend to

A
  1. affected females pass the trait to all children
  2. affected males never pass down the trait
  3. mtDNA traits often show incomplete penetrance
132
Q

*

incomplete penetrance

A

when not every individual that must be a particular genotype shows the expected phenotype

133
Q

heteroplasmy

A

the coexistence of multiple mtDNA variants in a single cell or among cells within an individual
- mtDNA heteroplasmy is common in humans
- cells have many copies of mtDNA

134
Q

does organelle inheritance follow Mendelian ratios?

A

NO
- random segregation of mtDNA during meiosis annd mitosis leads to unequal inheritance of mtDNAs

135
Q

what happens with an mtDNA variant that contains a disease-causing allele

A

if it reaches a certain threshold, disease symptoms arise

136
Q

what are the 6 modes of inheritance

A
  1. autosomal dominannt
  2. autosomal recessive
  3. X-linked dominant
  4. X-linked recessive
  5. Y-linked
  6. mitochondrial
137
Q

rare vs. common traits

A

autosomal recessive traits can look like autosomal dominant when alleles are common in the population
- if an allele is common, we can’t assume that people entering the pedigrees are NOT carriers

138
Q

what are questions you may need to know to label a pedigree

A
  1. what is the mode of inheritance of the trait?
  2. what are the genotypes (or possible genotypes) of the parents?
  3. what are the possible crosses that could produce an affected child?
  4. what are the individual probabilities of each cross?
  5. what are the total probabilities?
139
Q

conditional probability

A

p(A|B) is the probability of event A occurring, given that event B occurs

140
Q

law of total probability

A

look at notes

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