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Final Exam Study!! Flashcards

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Biology 101 flashcards
1
Q

Genomics

A

Study of genomes, or ALL the DNA of an organism

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2
Q

Structural Genomics

A

Architecture, genetic mapping, sequencing & assembly

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3
Q

Comparative Genomics

A

Multiple genomes allow for comparisons

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4
Q

Functional Genomics

A

What do all the genes do?

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5
Q

Human Genome Project

A

Initiated in 1990 and was completed 13 years later, but now genomes can be sequenced much faster!

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6
Q

Every year a new vertebrate genome is sequenced, every week a microbial genome of ca. 2 million bp is sequenced-

A

This rate is increasing! As of April 2020, 11,531 eukaryotes, 35,744 viruses, and 246,954 prokaryotes!

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7
Q

The mapping or hierarchical approach

A

Divide the genome into segments with genetic and physical maps, then home in on details

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8
Q

The whole-genome or shotgun approach

A

entire genome is broken into random, overlapping segments that are then sequenced

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9
Q

Genetic Map

A

Genetic crosses and frequency of crossing over are used with polymorphic genetic markers to map the location of genes on chromosomes.

Humans have 24 genetic maps - 22 autosomal (non sex chromosomes, and the X and Y chromosomes

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10
Q

Sequence-tagged site

A

Unique genetic markers in the genome, very helpful for genetic maps

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11
Q

Physical Maps

A

More detailed information about genetic markers obtained from genome sequence data

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12
Q

Open Reading Frames (ORF’s)

A

Computer searches for start codons and stop codons to identify areas that are potential genes

Only ORF’s with more than 100 codons are likely genes

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13
Q

Genes with unknown functions

A

Over 35% of genes in any organism (including humans) have no deducible function!

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14
Q

The Human Genome

A

Sequenced in 2003, Aprox. 21,000 protein-coding human genes, Aprox. 22,000 other human genes, Greatest amount of genetic variation is in Africa.

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15
Q

Human Genome Variation

A

80,000 years ago, there were only 10,000 humans on the planet! Human genomes vary by at least 9 million bp

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16
Q

The genome of C. Elegans

A

C. elegans is a hermaphroditic roundworm (1 mm) that lives in soils throughout the world- from egg to adult in 3 days.
The entire genome (6 chromosomes) was sequenced in 1998.

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17
Q

Arabidopsis thaliana

A

First flowering plant genome to be sequenced in 2000.
Model organism for genetics and development studies.
Analysis of genes found 25,500- more than humans!
100 genes are similar to disease-causing genes in humans, including breast cancer and cystic fibrosis

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18
Q

Fugu

A

Fugu is an unusual vertebrate because its genome size is only 400 Mb.
Very few introns, and few gene deserts, regions with little genes.
Many genes in Fugu and humans are similar, so finding a gene in Fugu makes it easier to find in humans.

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19
Q

Bioinformatics

A

Is a marriage between biology with math and computer science. Can help to:
Find genes in a genome
Align sequences
Predict structure and function of genes
Figure out interactions between genes and gene products
Use genomes to figure out evolutionary relationships

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20
Q

GenBank

A

Database that contains millions of DNA sequences for every organism you can imagine

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21
Q

Discontinuous or Discrete Traits

A

Each trait has only a few distinct phenotypes

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22
Q

Continuous Traits

A

A wide distribution of phenotypes are possible

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23
Q

Nature Vs Nurture

A

Scientists have argued for decades about which is more important to phenotype: genetics or environment

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24
Q

Multifactorial Traits

A

Traits affected by a combination of genotype and environment

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25
Q

Polygene Hypothesis

A

For quantitative traits says that multiple genes control the traits. Should make sense when environments impact is limited

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26
Q

Quantitative Trait Loci

A

Chromosome regions with genes that affect quantitative traits

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27
Q

How do we measure traits?

A

VP (phenotype) = VG (genotype) + VE (environment)

We can measure a subset of the population called a sample
Must be large enough to eliminate chance differences between sample and population
Must sample at random to avoid bias

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28
Q

Mean (x), or average:

A

tells us the center of distribution of phenotypes = ∑xn/n

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29
Q

Variance

A

how much individual observations spread out around the mean

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30
Q

Standard Deviation

A

The square root of variance - provides the same information but in same units as measurements

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31
Q

Pleiotropy

A

Where one gene affects multiple traits

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32
Q

Correlation Coefficient

A

Measures the strength of association between two variables in the same experimental unit, usually individuals. To calculate correlation, we first need to calculate covariance.

The correlation coefficient ranges from –1 to 1

Absolute value (not considering sign) gives strength of correlation

1 is very strong- so increasing x always has an effect on y

0 is weak- increasing x has no effect on y

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33
Q

Covariance

A

Amount of variation of two characters that is shared in an individual

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34
Q

Regression

A

Tells us more precisely about the relationship of two variables, and predictions from data

Regression analysis can tell us how much of a trait is genetically determined

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35
Q

Slope

A

Tells us how much of an increase in x corresponds to an increase in y

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36
Q

ANOVA

A

Analysis of variance asks if two or more means or significantly different
If we reject the null hypothesis that differences are due to chance (usually p < 0.05), then we can say differences are due to differences in genetics or the environment

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37
Q

Heritability

A

Proportion of a populations phenotype that is due to genetics and not environment

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38
Q

Broad-sense heritability

A

Quantitative genetics are most interested to know how much VP is attributable to VG
H2B = VG/VP

Value can range from 0 to 1, with zero being no heritability and 1 being maximum heritability with minimal influence of environment

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39
Q

Narrow-sense heritability

A

geneticists want to know how likely parents are likely to resemble offspring, which is most affected by additive variation
H2N = VA/VP

Narrow-sense heritability can track phenotypes from generation to generation, and helps predict changes from selection (artificial or natural)

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40
Q

Limitation of Heritability Estimates

A
  1. Broad-sense heritability does not define all of the genetic contributions to a trait: it only measures proportion of phenotype that is due to genetics, not the genes that affect the trait
  2. Heritability does not indicate what proportion of a phenotype is genetic: heritability is based on variance of a population, not individuals
  3. Heritability is not fixed for a trait: depends on genetic makeup and environment of a population, which can shift often
  4. High levels of heritability for a trait does not imply that trait differences among populations is genetic: environment can have a major effect on phenotype even if heritability is high, so population differences may not be genetic
  5. Traits shared by members of a family do not imply high heritability: similar family environments can lead to similar phenotypes regardless of genetics
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41
Q

Calculations of heritability

A

Midparent value, or mean of mom/dad’s phenotype equals value for offspring if variation is due to additive genetic variation- gives a slope of 1

If slope is less than 1, gene interactions (epistasis) and environment are a factor

If slope is 0, environment is main factor

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42
Q

Evolution

A

Genetic changes in a population over time

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43
Q

Natural Selection

A

Individuals with certain traits leave more offspring than others

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44
Q

Artificial Selection

A

Only selected individuals are bred, causing genetic changes over time

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45
Q

friendly dogs & Williams syndrome

A

Hypersocial dog behavior is linked to mutations in GTF2I and GTF2IRD1 genes.
Deletions of these genes in humans leads to Williams Syndrome:
Affects 1 in 70,000 people
Elfin facial features
Cognitive difficulties
Tendency to love everyone

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46
Q

Dog size controlled by one gene

A

Size controlled by IGF-1 gene: insulin-like growth factor, a hormone. Same gene and mutation responsible for human dwarfism

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47
Q

Development

A

The irreversible process organisms undergo from single-celled zygote to multicellular organism.
Its an interaction of the genome, cell cytoplasm and environment, and involves a programmed sequence of events

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48
Q

Totipotent cell

A

Has potential to be any cell in the body

This is what the zygote begins as

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49
Q

Determination

A

Process where genetics “programs” a cell to become specialized (fate) - often done through induction, or chemical signaling

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50
Q

Differentiation

A

process in which determined cells undergo physical changes to become a specific cell type. e.g. Nerve cells, antibodies, etc.

controlled by gene expression- synthesis of specific proteins guides fate of the cell

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51
Q

Morphogenesis

A

“generation of form”, process or anatomical structure formation and cell shape and size changes

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52
Q

Genetic programs regulate 3 Developmental processes:

A

DETERMINATION
- Individual cells are fated to become….
DIFFERENTIATION
- Individual cells change to actually become….
MORPHOGENESIS
- Structures form by changes in cell #, shape, position

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53
Q

Model Organisms

A

Must have mutants that affect development, and involved genes must be mapped and cloned for study

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54
Q

The development controversy

A

Experiments with carrots in 1950’s: differentiated cells could be used to grow an entire new carrot, so DNA is NOT lost during development

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55
Q

Dolly - The first cloned sheep

A

Dolly the sheep was born after 277 eggs were used for SCNT (Somatic Cell Nuclear Transfer), which created 29 viable embryos. Only three survived until birth, and only one survived until adulthood.

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56
Q

Lymphotcytes

A

White blood cells involved in immune response

Small lymphocytes include B and T cells

B cells develop in bone marrow when activated by an antigen (foreign protein on virus or bacteria), they from plamsa cells that make antibodies after a few days

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57
Q

Clonal Selection

A

Cells with antibodies to an antigen are stimulated to proliferate and make more antibodies

58
Q

Immunoglobin’s

A

Antibody proteins, with 2 identical short or light (L) chains, and 2 identical long or Heavy (H) chains.

The two arms of the Y-shaped antibody contain the antigen-binding sites, which attach to antigens and stimulate clonal selection

59
Q

Hinge Region

A

allows antibody arms to move independently, and bind to separate antigen sites to help disable infecting agents

60
Q

Somatic Recombination

A

Random DNA arrangments during B cell development that join different gene segments and exclude others

61
Q

testis-determining factor (TDF)

A

Genes on the Y chromosome code for TDF, which causes testis formation. The absence of the Y chromosome defaults to ovaries formation instead

62
Q

Cancer

A

a disease where eukaryotic cells are transformed - divide uncontrollably and abnormally.
Such cells can invade surrounding tissues, or metastasize (spread) through the lymphatic system or blood to other regions of the body
Cancerous cells can undergo oncogenesis and lead to tissue masses called tumors (aka, neoplasm)

63
Q

Tumors

A

Malignant - Can spread to other parts of the body

Benign - Self contained and do not spread

64
Q

Cell Checkpoints

A

Regulatory molecules (cyclins and cyclin-dependent kinases) control these checkpoints

65
Q

Signal Transduction

A

Process of relaying a growth-stimulatory or growth-inhibitory signal after an extracellular factor binds to a cell

66
Q

Neoplastic Cells

A

(cancerous cell) divide uncontrollably because of mutations to genes for cell surface receptors, stimulatory factors, or inhibitory factors

67
Q

Familial Cancers

A

Some cancers seems to “run in the family”, and thus have a hereditary component - however, most cancers are sporadic (not hereditary)

68
Q

Viruses

A

Some viruses introduce their genes into the host, disrupting cell cycle controls

69
Q

Cancerous Cells

A

Gives rise to cancerous cells, and this is what causes tumors

70
Q

Mutagens

A

Like X-rays, smoking and chemicals increase the rate of cancer. Thus mutations in genes affect risk of cancer

71
Q

Chromosomal mutations

A

can lead to cancer - chromosomal breakage affects gene expression, crucial for control of the cell cycle

72
Q

Oncogene

A

a gene that cause unregulated cell proliferation - transmitted by RNA tumor viruses (all are retroviruses) into genome of host

73
Q

Retroviruses

A

Duplicate their RNA genomes through DNA intermediate using reverse transcriptase.
An example is HIV- human immunodeficiency virus, which can cause AIDS-acquired immunodeficiency syndrome

74
Q

Transducing Retroviruses

A

Pick up cellular (DNA) genes (often oncogenes) into their RNA genomes, and transfer them to new host genomes

Most transducing retroviruses can not self replicate- they need “helper viruses” if the cell is infected with viruses that have replication genes

75
Q

Carcinoma

A

Epithelial origin (breast, colon, pancreas, and others)

76
Q

Sarcoma

A

a cancer of the connective or supportive tissue (bone, cartilage, fat, muscle, blood vessels) and soft tissue

77
Q

provirus genome

A

When retroviruses invade a cell, the RNA is released. and reverse transcriptase make a double-stranded DNA copy of the RNA genome called provirus genome

78
Q

Nonocogenic retroviruses

A

Direct their own life cycle but do not change the growth properties of the cells they infect

79
Q

DNA Tumor Viruses

A

They can cause cancer bur they do not carry oncogenes like RNA tumor viruses

80
Q

Proto-oncogenes

A

Normal genes similar to viral oncogenes

When proto-oncogenes undergo mutation, they can become oncogenes that induce cancer in normal cells

81
Q

Growth Factors

A

Causes cell to grow and divide

82
Q

Protein Kinase

A

Enzymes that add phosphate groups to target proteins, thus altering their function
- protein kinases known to affect signaling pathways of cells, that are involved with growth factors

83
Q

Membrane-associated G proteins

A

Activated by growth factors to cell membrane receptors - involved in signaling cascade that activated transcription factors for specific genes

84
Q

Tumor Supressor Genes

A

in the 1960s, Henry Harris found that normal cells had tumor suppressor genes, that can suppress uncontrolled growth of cancerous cells

85
Q

apoptosis

A

Programmed cell death

86
Q

Retinoblastoma

A

Childhood cancer of the eye, before 4 years old. 90% treatable.
Hereditary form is worse- cancer appears earlier and usually involves BOTH eyes

87
Q

Alfred Knudson

A

1971: proposed a hypothesis (two-hit mutational model) to explain 2 forms of retinoblastoma

In the sporadic form, two mutations occur in eye cell - rare so it only happens in one eye

In hereditary form - one mutation is passed on by heredity - but 2nd mutation occurs in eye cell

88
Q

Mutator Gene

A

Any gene that increases the spontaneous mutation rates of other genes when it is in the mutant form

89
Q

Carcinogen

A

a natural or artificial agent (chemical, radiation), that increases a cell’s risk of becoming cancerous

90
Q

Direct-acting carcinogens

A

Bind to DNA and mutate it

91
Q

Procarcinogens

A

must be converted by the body’s metabolism to become carcinogenic
Both kinds of carcinogens induce point mutations- leading to cancer in some cases

92
Q

Cigarettes

A

contain @7,000 chemicals, including radioactive materials (polonium-210 & lead-210), cyanide, arsenic, and tar

If you smoke a pack or more of cigarettes a day = radiation exposure of > 300 chest x-rays/year

93
Q

Vaping

A

Smoking liquid forms of nicotine is NOT safe and highly addictive ( = cocaine, heroin)

Heavy metals from vaping devices (e.g., chromium) linked to brain damage and cancer

94
Q

Thymine Dimers

A

Caused by UV light, which disrupts A–T pairing, causes a bulge in DNA, disrupts DNA replication at bulge, and can lead to cell death (skin cancer)

95
Q

herpes simplex virus (HSV)

A

HSV-1 = usually oral herpes - 50-80% of adults in USA infected by age 20

HSV-2 = usually genital herpes - causes painful sores that last for several days or weeks- not correlated with cancer, but can increase chance of HIV

96
Q

Linked genes (syntenic)

A

Genes on the same chromosme

97
Q

Creighton, McClintock, and Stern

A

proved that Morgan’s idea of crossing over is correct

98
Q

Coupling

A

two wild-type alleles on one homolog, and two recessive alleles on the other

w+ m+ / w m

99
Q

Repulsion

A

has one wild-type allele and one mutant allele on each homolog

w+ m/ w m+

100
Q

Alfred Sturtevant

A

A student of Morgan’s, Defined a map unit (mu) as the interval in which 1% of crossing over takes place- aka, centimorgan (cM)

101
Q

Crossover frequency

A

frequency of physical exchange between chromosomes in between genes of interest

102
Q

Recombination Frequency

A

Frequency of recombination of genetic markers (alleles) in a cross - determined by offspring phenotypes

103
Q

Centromere

A

Usually central constriction of chromosomes

104
Q

Metacentric

A

Centromere about centered

105
Q

Submetacentric

A

Centromere positioned so one arm is longer than the other

106
Q

Acrocentric

A

Centromere close to the end that P arm is so tiny, it is hard to observe (called a satellite)

107
Q

Telocentric

A

centromere is on the end, so chromosome has only one arm

108
Q

Holocentric

A

Entire chromosome acts as a centromere

109
Q

Sets of Chromosomes

A

Diploid organisms have two sets of homologous chromosomes, polyploids have more than two

Aneuploid - ‘Unbalanced’ chromosome number, often resulting in few offspring,

Euploid - ‘balanced’ chromosome number, normal fertility

110
Q

Obligate Parthenogenesis (OP)

A

females reproduce exclusively by asexual means - female produces eggs with two set of genes

111
Q

facultative parthenogenesis (FP)

A

Females that normally reproduce sexually turn to asexual reproduction, usually in the lack of males - females second polar body behaves like a sperm to activate and fertilize ovum for diploid zygote

112
Q

Nondisjunction

A

Failure of homologous chromosomes (Meiosis I) or sister chromatids (Meiosis II) to separate and move to opposite poles during Anaphase. Results in Aneuploidy - abnormal condition where one or more chromosomes of a normal set are missing or present in large numbers

113
Q

Nullisomy

A

One pair of homologous chromosomes is lost

114
Q

Monosomy

A

Loss of a single chromosome

115
Q

Trisomy

A

Gain of a single chromosome

116
Q

Tetrasomy

A

gain of an extra chromosome pair

117
Q

Trisomy-21

A

Common aneuploid chromosome disorder occurs in 1,430 per million live births- probability increases with age of mother- father’s age factors in too if mother is over 35

Leads to mental retardation, epicanthal folds over the eyes, short and broad hands, and below-average height

118
Q

Fragile X syndrome

A

after Down’s syndrome, leading cause of mental retardation in the United States- occurs in 1 in 1,250 males and 1 in 2,500 female because it is X-linked

Caused by repeats of FMR1 allele resulting in methylation of DNA and constriction site

Leads to narrowing of small areas at end of chromosome, which can break, leading to deletion of key genes

119
Q

Monoploidy

A

Individual has only one set of chromosomes instead of two (haploid)

120
Q

Polyploid

A

Have multiple sets of chromosomes beyond normal diploid set

121
Q

Type of polyploidy

A

Autopolyploid - originated by unreduced gametes of the same species during meiosis (small percentage)- can result in aneuploid gametes (example- potato)

Allopolyploid: originated by hybridization between closely related species (large percentage- very common in ferns)- all gametes are euploid

122
Q

Chromosome mutation

A

variations from the normal (wild-type) condition in chromosome structure or number

123
Q

Four major types of chromosome mutations:

A
  1. Deletions- remove a section of DNA from the
    chromosome
  2. Insertions- add a section of DNA to the
    chromosome
  3. Inversions- flip a section of DNA around on the
    chromosome
  4. Translocations- move a section of DNA to a
    different place in the genome, usually a different
    chromosome
124
Q

Pseudodominance

A

where deletion of a dominant allele leads to unexpected expression of recessive phenotype because it is the only remaining copy of the gene

125
Q

Cri-du-chat Syndrome

A

Cri-du-chat syndrome is a heterozygous deletion of part of the short arm of chromosome 5

1 in 50,000 births results in this syndrome- children are mentally retarded, have a variety of physical abnormalities (including larynx to give weird cry), constant constipation, etc

126
Q

Duplications

A

A chromosomal mutation that results in the doubling of a segment of a chromosome.

  1. Tandem- adjacent to each other
  2. Reverse tandem- order of duplicated genes is
    opposite to those of the original
  3. Terminal tandem- duplicated segments arranged
    in tandem at end of chromosome
127
Q

Inversion

A

When a loop forms in a chromosome, a small piece may undergo breakage and reunion, and invert the order of genes (180 degrees)

128
Q

Paracentric inversion

A

does not include the centromere

129
Q

Pericentric Inversion

A

Includes the centromere

130
Q

Translocation

A

a chromosomal mutation with a move of parts of a chromosome to a different place in the genome

Nonreciprocal intrachromosomal translocation: movement within same chromosome

Nonreciprocal interchromosomal translocation: movement from one chromosome to another in a one-way direction

Reciprocal interchromosomal translocation: two-way movement from one chromosome to another

131
Q

Reciprocal translocation

A

breakage and reunion of a piece of non-homologous chromosomes

132
Q

Fusion

A

two non-homologous acrocentric chromosomes undergo reciprocal translocation to form a metacentric chromosome. Form a “trivalent” with non-fused acrocentric chromosomes- can result in aneuploid gametes

133
Q

Fission

A

a metacentric chromosome breaks into two acrocentric chromosomes (rare)

134
Q

Position Effect

A

location of the gene (in a chromosome fragment) changes its expression when it moves to a different part of the genome

135
Q

pronucleus

A

haploid nuclei of eggs or sperm

136
Q

Genomic Imprinting

A

phenomenon where a gene’s expression depends on the parental origin of a gene copy

137
Q

Epigenetics

A

coined by Conrad Waddington in 1942, a heritable effect resulting from alteration of DNA (but not in the DNA sequence!) or chromatin during gametogenesis (epi = above)

138
Q

Gene Silencing

A

a gene is not expressed (i.e., turned off) because of a mechanism that is not from the DNA itself (not a mutation)

139
Q

Transcriptional gene silencing

A

transcription is blocked because the gene occurs in heterochromatin- transcriptional enzymes cannot get access to perfectly normal gene

140
Q

Post-transcriptional gene silencing

A

mRNA from a transcribed gene is destroyed or blocked, so no translation occurs

141
Q

RNAi pathway-

A

where microRNA (miRNA) or small interfering RNA (siRNA) blocks translation of targeted mRNA

Used as a defense against viruses, during development, and to regulate gene expression

142
Q

DNA methylation-

A

addition of methyl groups —CH3 to CG dinucleotides of imprinted DNA areas

DNA methylase recognizes methyl groups on one strand of the double helix and adds them to the opposite strand

Genetics (3 decks)

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