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Final Flashcards

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Biology 101 flashcards
1
Q

Molecular genetics

A

Study of structure and function of genes and the regulation of their expression

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2
Q

Transmission genetics

A

“Classical genetics”

Study of how traits are transmitted from generation to generation

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3
Q

Population genetics

A

Study of heredity in a large group of individuals

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4
Q

Quantitative genetics

A

Study of polygenetic and multifactorial traits

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5
Q

Cytogenetics

A

Study of structure and function of cell, particularly the chromosomes

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6
Q

C value

A

Amount of haploid DNA in base pairs in organism

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7
Q

Genome

A

All the genetic material that an organism has

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8
Q

DNA

A

Deoxyribonucleic acid
Has H instead of OH at 2’ carbon
Contains thymine
Genetic material for all known prokaryotes and eukaryotes

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9
Q

RNA

A

Ribonucleic acid
Has OH at 2’ carbon
Contains uracil instead of thymine
Genetic material for some viruses

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10
Q

Antiparallel

A

Opposite

How two strands of DNA run in respect to each other

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11
Q

Double helix

A

Double-stranded DNA forms this

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12
Q

Nucleotide

A

Building block of DNA and RNA

Contains pentose sugar, nitrogenous base, and phosphate group

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13
Q

Major groove

A

Larger groove in DNA double helix

Results from angle of glycosidic bond

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14
Q

Minor groove

A

Smaller groove in DNA double helix

Results from angle of glycosidic bond

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15
Q

Nucleic acids

A

DNA and RNA (deoxyribonucleic acid and ribonucleic acid)

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16
Q

Phosphate group

A

-PO3 group

Present on nucleotides to allow for linkage between them (phosphodiester bond)

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17
Q

Deoxyribose sugar

A

Pentose sugar with H instead of OH on 2’ carbon

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18
Q

Ribose sugar

A

Pentose sugar with OH on 2’ carbon

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19
Q

Nitrogenous bases

A

Cyclic ring structure containing nitrogens

Pair with one another to form DNA helix

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20
Q

Phosphodiester bonds

A

Bonds between phosphate groups on nucleotides

Allows for linkage between nucleotides

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21
Q

Chromosomes

A

How DNA is packed in eukaryotes

Condensed to save space

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22
Q

Chromatin

A

DNA + protein in the nucleus

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23
Q

Histones

A

Proteins that help pack chromatin into nucleus
Positively charged: DNA is negatively charged
Consists of H1, H2A, H2B, H3, and H4

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24
Q

Nucleosome

A

DNA wound around histone core

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25
Q

Euchromatin

A

Chromatin that exhibits normal packing and unpacking in cell cycle
Contains genes that are actively being transcribed (loosely packed)
Typically devoid of repetitive sequences

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26
Q

Heterochromatin

A

Packed tightly

Not being actively transcribed

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27
Q

Epigenetics

A

A change in phenotype that doesn’t result from a change in the sequence of a gene
Change is heritable
Caused by switching on or off parts of genome in response to environment

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28
Q

Bidirectional replication

A

DNA replication proceeds in both directions due to the presence of 2 replication forks

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29
Q

Semiconservative replication

A

Parent strand is used as template and joins with new strand

Correct model of replication

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30
Q

Semidiscontinuous replication

A

Lagging strand of DNA is synthesized this way as a series of short fragments

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31
Q

Origin of replication

A

Place on DNA where replication begins

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32
Q

Replication bubble

A

Spot on DNA where replication is occurring

DNA strands are denatured, so DNA is temporarily single-stranded

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33
Q

Replication fork

A

Structure created during DNA replication

Consists of 2 denatured strands that can be synthesized off of

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34
Q

Leading strand

A

Strand of DNA that is synthesized off of in the 5’ to 3’ direction

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35
Q

Lagging strand

A

Strand of DNA that is synthesized off of in the 3’ to 5’ direction

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36
Q

Okazaki fragments

A

Sections of newly synthesized DNA

Formed on lagging strand

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37
Q

Helicase

A

Enzyme that breaks H-bonds between nucleotide bases in DNA replication

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38
Q

SSB protein

A

Protein that binds to single strands of DNA in replication, holding them apart

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39
Q

Primase

A

Enzyme that makes RNA primer in DNA replication

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40
Q

DNA polymerase

A

Enzyme that catalyzes phosphodiester bond formation between nitrogenous bases (dNTPs) in DNA replication

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41
Q

Ligase (DNA replication)

A

Enzyme that connects DNA strands in DNA replication

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42
Q

Topoisomerase

A

Enzyme that unwinds DNA in DNA replication

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43
Q

Transcription

A

Process of turning DNA into mRNA

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44
Q

Template strand

A

Strand to which RNA pol makes complementary RNA strand

Strand of DNA that is site of transcription

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45
Q

Centromere

A

Constitutive heterochromatin
Packed tightly: constricts chromosome
Mitotic spindle attaches to centromere in order to pull chromosomes apart during cell division

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46
Q

Telomere

A

Tandemly repeated DNA at the ends of linear chromosomes

Protects integrity of DNA from exonucleases (chew up ends of DNA: defense against foreign DNA)

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47
Q

RNA polymerase

A

Enzyme that transcribes RNA by linking together NTPs

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48
Q

Exons

A

Sequences that are expressed

Transcribed and translated

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49
Q

Introns

A

Euk genes only
Long insertions of non-coding sequences
Intervening sequences: transcribed, but not translated
Buffer against mutation and contain enhancer sequences

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50
Q

5’ capping

A

Methylated guanine nucleotide (5’ methyl G-cap) is added to 5’ end of mRNA
Protects RNA from exonucleases and ensures correct positioning of ribosome during translation

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51
Q

Polyadenylation

A 
End of transcription
Steps:
1. mRNA is cleaved at poly A site
2. mRNA is released
3. 50 to 250 adenine nucleotides are added to 3' end by poly A polymerase
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52
Q

Gene regulatory elements

A

Set of cis-acting (next to) sequence elements bound by trans-acting (from someplace else) factors
Contains core promoter, proximal elements (close to core promoter; enhancers or silencers), and distal elements (far away from core promoter; may be on other chromosome; enhancers or silencers)

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53
Q

Promoter

A

Region of DNA that initiates transcription of a particular gene

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54
Q

General transcription factors

A

Bind to core promoter, recruiting polymerase and causing basal transcription

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55
Q

Enhancers

A

Sequences of DNA that are bound by proteins called activators
When bound, transcription of gene is increased
Located further downstream or upstream from +1 site

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56
Q

Activators

A

Proteins that bind to enhancers, causing increased transcription of genes
2 major domains: DNA binding domain and transcription activation domain
Change shape, allow for binding to DNA

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57
Q

Repressors

A

Proteins that bind to silencers, causing decreased transcription of genes

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58
Q

Silencers

A

Sequences of DNA that are bound by proteins called repressors
When bound, transcription of gene is decreased
Located further downstream or upstream from +1 site

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59
Q

mRNA splicing

A

Modification of RNA in which introns are removed from exons

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60
Q

Alternative splicing

A

One gene can encode more than 1 protein because different combinations of exons are spliced together to create different proteins

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61
Q

Spliceosome

A

Removes introns from mRNA

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62
Q

rRNA

A

Ribosomal RNA

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63
Q

snRNA

A

Small nuclear RNA

Non-coding

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64
Q

Translation

A

Process of turning mRNA into proteins

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65
Q

Polypeptide

A

Polymers of amino acids that are connected by peptide bonds

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66
Q

Protein

A

Combination of polypeptides folded in a 3-D structure

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67
Q

Amino acids

A

Building blocks of proteins

Each different amino acid (20 in total) has a different R group that provide it different functions

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68
Q

Codon

A

Set of 3 mRNA nucleotides that code for an amino acid

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69
Q

Charged tRNA

A

tRNA loaded with an amino acid

Ribosome can transfer amino acid from tRNA to growing peptide strand

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70
Q

Anticodon

A

Triplet nucleotide sequence of tRNA that is complementary to that of mRNA

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71
Q

Genetic code

A

Set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells

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72
Q

Degeneracy

A

More than 1 codon occurs for each amino acid (3rd nucleotide might be different)
Allows for protection against mutation
Same as redundancy

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73
Q

Wobble

A

Base pairing between tRNA anticodon and mRNA codon doesn’t necessarily follow complementary base pairing rules at the 3rd nucleotide
Reason: energetic favorability

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74
Q

Open reading frame (ORF)

A

The codons of an mRNA that are read sequentially to specify amino acids

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75
Q

Ribosome

A

Site of translation

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76
Q

Polysome

A

Multiple ribosomes translating same RNA concurrently

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77
Q

Mutation

A

Change in nucleotide sequence

78
Q

Mutagen

A

Substance that induces mutation in DNA

Examples: radiation, intercalating agents, some drugs

79
Q

Nonsense mutation

A

Change from functional codon to stop codon

Often severe phenotypic effect, but effect depends on where mutation is and what amino acid is changed

80
Q

Missense mutation

A

A change in a codon so that a different amino acid is added to the polypeptide
Phenotypic change depends on amount of difference from original

81
Q

Frameshift mutation

A

Addition or deletion of 1 or more base pairs changes open reading frame
Missense or stop results

82
Q

Deletion

A

Loss of nucleotide(s) from sequence

83
Q

Neutral mutation

A

Change amino acid to another amino acid with similar chemical properties
Mild or no phenotypic effect

84
Q

Silent mutation

A

Change 1 codon for 1 amino acid to a different codon for the same amino acid

85
Q

Point mutation

A

Single base pair substitution

86
Q

Gain of function mutation

A

Causes gene product to have more activity

87
Q

Loss of function mutation

A

Results in partially or fully nonfunctional gene product

88
Q

Null allele

A

Fully nonfunctional allele

89
Q

Transposable elements

A

Segments of DNA that have the capacity to move in the genome

90
Q

Chromatin remodeling

A

Histone core is moved so that the gene is accessible: allows transcription of genes blocked by histone

91
Q

DNA methylation

A

CpG island is methylated, causing gene to be silenced
Methyl groups physically block transcriptional machinery
Can sometimes recruit histone deacetylases to modify histone tails

92
Q

Histone acetylation

A 
Histone acetyltransferases (HATs) cause masking of positive charge on histone tails, making DNA accessible
Heritable change
Process is reversible by histone deacetylases (HDACs), recruited by DNA methylation
93
Q

RNAi (RNA interference)

A
  1. miRNA is transcribed
  2. miRNA is processed into shRNA (short hairpin RNA)
  3. RISC (RNA interference silencing complex) recognizes shRNA and picks it up
  4. RISC complex binds to mRNA
  5. RISC complex cuts off mRNA’s poly A tail
  6. mRNA is degraded
94
Q

Hairpin RNA

A

RNA that makes a sharp hairpin turn

Can be used to silence gene expression through RNA interference

95
Q

RNA half-life

A

Point in time at which half of RNA is degraded

Depends on structure, proteins bound, and poly A tail length (too short, degraded)

96
Q

Aneuploidy

A

Number of chromosomes in individual’s cells isn’t a multiple of the normal haploid set
1 or more extra or missing chromosomes

97
Q

Insertion

A

Addition of a base pair

98
Q

Duplication

A

Doubling of part of chromosome

99
Q

Translocation

A

Piece of 1 chromosome is placed onto another chromosome

100
Q

Inversion

A

Segment of chromosome is taken out and re-inserted backwards

101
Q

Fragile sites

A

Narrow sites of some chromosomes

Prone to breakage

102
Q

Sister chromatid

A

Identical copy of a chromosome

103
Q

Homologous chromosomes

A

Chromosomes that aren’t identical, but code for the same genes

104
Q

Monohybrid cross

A

Cross between two individuals whose alleles differ for one gene

105
Q

Dihybrid cross

A

Cross between two individuals whose alleles differ for two genes

106
Q

Law of segregation

A

In meiosis I, homologous chromosomes end up at one pole or the other at random

107
Q

Law of independent assortment

A

In meiosis I, chromosomes don’t influence each other’s segregation

108
Q

Testcross

A

Cross of unknown genotype (homozygous dominant or heterozygous) with homozygous recessive individual
Allows for determination of unknown genotype

109
Q

Codominance

A

Heterozygote shows the phenotypes of both homozygotes simultaneously
Ex- roan horses (both red and white hairs)

110
Q

Incomplete dominance

A

Phenotype of heterozygote is intermediate to homozygotes

Ex- palomino horses (intermediate to chestnut and cremello)

111
Q

Epistasis

A

1 gene masks the expression of another gene

Polygenic phenomenon

112
Q

Haplosufficiency

A 
1 dose of gene product supports life
Autosomal recessive
Homozygous wt= healthy 
Heterozygous= healthy
Homozygous mutant= sick or dead
113
Q

X-linked

A

Trait carried on the X chromosome

More commonly seen in males than females

114
Q

Hemizygosity

A

Having unpaired genes

Ex- guys are this in respect to X-linked traits

115
Q

SRY (sex-determining region of Y) in humans

A

Becomes active at 6-8 weeks during development
Encodes Testes Determining Factor (TDF), which controls the development of testes (absence of this causes gonads to develop into ovaries)

116
Q

Barr bodies

A

Silencing of 1 X chromosome in females allows for the same level of expression for genes on the X chromosome in males and females
Entire chromosome isn’t completely inactivated- some parts are a little bit active

117
Q

Gene dosage

A

The amount of gene product present in an individual

118
Q

Pleiotropy

A

1 gene is responsible for multiple phenotypes

119
Q

Penetrance

A

The % of individuals with a particular genotype who show the expected phenotype

120
Q

Expressivity

A

Degree to which a phenotype is expressed

Severity of phenotype

121
Q

Phenotypic variation

A

Differences in phenotype between individuals

122
Q

Maternal effect

A

Mitochondria and mtDNA in egg cytoplasm are inherited in offspring
Phenotype of the offspring is determined by the genotype of the mother

123
Q

Extranuclear inheritance (mtDNA)

A

DNA found in mitochondria

124
Q

Polygenic trait

A

Trait that results from action by multiple genes

Most traits are these

125
Q

Multifactorial

A

Influence from many genes along with environment

126
Q

Discrete trait

A

Clearly defined by 1 or a few genes
No degrees of severity
Only a few traits follow this mode of expression

127
Q

Quantitative trait

A

Measurable in numeric terms
Controlled by multiple genes and environmental factors
Have continuous variation

128
Q

Continuous variation

A

Phenotypes are distributed along a continuum

Series of intermediate phenotypes that fall between 2 extremes

129
Q

Heritability

A

How much of the phenotypic differences are due to genetic factors
Expressed in a number ranging between 0-1 (0- none, 1- all)

130
Q

Quantitative trait loci

A

Loci that influence quantitative traits

131
Q

Genetic drift

A

Changes in allele frequencies due to random sampling
Reduces genetic diversity
Ex- settlers killing off millions of bison on the Great Plains

132
Q

Bottleneck effect

A

Population is drastically reduced in number, reducing genetic diversity
Not due to anything that would reduce selectively, like certain diseases

133
Q

Founder effect

A

Population is established from a small number of breeding individuals
Reduced genetic diversity

134
Q

Natural selection

A

Frequency of alleles that confer survival and reproduction increases in the population

135
Q

Gene pool

A

All of the alleles in a population

136
Q

Migration

A

Flow of alleles into and out of a population

137
Q

Gene flow

A

An individual migrates and contributes its alleles to the gene pool of the new population

138
Q

Selective mating

A

Mating of organisms in a non-random manner

139
Q

Genomics

A

Study of an entire genome(s)

140
Q

Functional genomics

A

Global analysis of function of sequences in a genome

141
Q

Comparative genomics

A

Comparison of entire genomes from different species, individuals, or groups

142
Q

Bioinformatics

A

Combination of biology and computer science

143
Q

Transcriptomics

A

Study of complete set of transcripts that are produced by a genome under a specific condition

144
Q

Reverse transcriptase

A

Enzyme that synthesizes DNA from RNA

145
Q

Orthologous genes

A

2 or more different genes in 2 different organisms that have the same or similar function
Result of speciation

146
Q

Paralogous genes

A

2 or more genes in an organism that have similar or identical function
Result of duplication

147
Q

Homologous genes

A

Paralogs and homologs

148
Q

Pharmacogenomics

A

Study of role of genetics in a drug response

149
Q

PCR

A

Amplify millions of copies of DNA molecule from very small starting portion of DNA
Many cycles of 3 steps: denature DNA using heat, anneal primers to DNA, extend strand using Taq polymerase

150
Q

cDNA

A

Complementary DNA: complementary to RNA

151
Q

Real-time PCR

A

Measure increase in amount of PCR product during thermal cycling reactions
Measure specific cDNA as it’s being amplified: use reporter probe

152
Q

Reporter probe in real-time PCR

A

Contains fluorescent marker and quencher
When quencher is close to fluorescent marker, no light is emitted
As polymerase makes strand, quencher is displaced from fluorescent marker, causing light to be emitted

153
Q

RNAseq

A

Method that provides sequences of all transcripts in a sample
Steps:
1. Extract RNA from cells of interest
2. Reverse transcribe into cDNA
3. Sequence cDNA using Next Gen technology

154
Q

Genetic engineering

A

Human manipulation of an organism’s DNA

155
Q

Transformation

A

Getting a host (ex- E. coli) to take up a cloning vector to make clones of the sequence of interest

156
Q

Clone

A

Identical copy

157
Q

DNA marker

A

Specific region of DNA that varies among individuals

Used to create a detailed map of the individual’s genome

158
Q

DNA polymorphisms

A

Changes in DNA sequence between individuals

159
Q

SNPs (single nucleotide polymorphisms)

A

Changes in DNA sequence at a specific nucleotide

160
Q

Copy number variants

A

Number of copies of genes present in a person’s genome

Cause changes between people

161
Q

RFLP

A

Method of identifying SNPs

SNP changes restriction enzyme site: different number of fragments observed in gel electrophoresis

162
Q

Shotgun sequencing method

A
  1. Extract DNA from human cells
  2. Cut DNA into small, overlapping fragments (contigs) using restriction enzymes (reaction is performed at suboptimal conditions- enzymes don’t cut at every site)
  3. Clone contigs to make genomic library
  4. Sequence each clone using Sanger sequencing
  5. Use computers to reassemble sequences of contigs by puzzling together overlapping sequences
  6. Deposit sequences into database, NCBI GenBank
163
Q

Human genome project

A

Project in 1990s that focused on sequencing whole human genome (hadn’t been done yet)

164
Q

Sanger method

A
  1. Cloning vector containing DNA of interest is amplified by PCR
  2. When polymerase randomly adds ddNTP with attached fluorescent probe, sequencing reaction stops
  3. Different sized segments of DNA are created
  4. Segments are separated by size using capillary gel electrophoresis (electrophoresis in a capillary tube)
  5. Detector identifies ddNTPs based on their unique fluorescence
  6. Sequence is recreated by reading ascending order of ddNTPs
165
Q

Next generation sequencing

A
  1. Extract DNA
  2. Cut into contigs
  3. Affix DNA to solid support (bead, chip, etc.)
  4. One by one, wash dNTPs across the DNA
  5. If known dNTP is incorporated by polymerase, then light is emitted
  6. Reassemble overlapping sequences
166
Q

Annotation

A

Identification and description of genes and their important sequences
Can be done using computer algorithms to predict open reading frames: look for promoters, start sites, and polyadenylation sites

167
Q

Haplotype

A

Set of SNPs that are close together on a chromosome

SNPs are inherited together: low recombination rates

168
Q

Cloning vector

A 
Plasmid used in cloning
Contains Ori (origin of replication), MCS (multiple cloning site), and gene for antibiotic resistance
169
Q

Ligase (cloning)

A

Enzyme that re-seals phosphodiester bonds between sequence and cloning vector

170
Q

Southern blotting

A
  1. Isolate DNA from organism of interest
  2. Cut DNA into small pieces using restriction enzymes
  3. Separate DNA fragments using gel electrophoresis
  4. Transfer DNA from gel to membrane/blot (DNA is in same position on blot as on gel)
  5. Incubate blot with labeled probe that is complementary to DNA of interest
  6. Visualize probe: see band on blot where DNA of interest is located
171
Q

Restriction enzyme

A

Cuts DNA at specific site, creating sticky ends

Used to create space in MCS for sequence of interest to be inserted

172
Q

Exonuclease

A

Cleaves sequence at its end

173
Q

Endonuclease

A

Cleaves sequence in its middle

174
Q

Transgene

A

Gene transplanted from one organism to another

175
Q

Restriction mapping

A

Using restriction enzymes that cleave at known sequences to obtain structural information about a piece of DNA (find out how large it is and the sizes of fragments making it up)

176
Q

Recombination hot spot

A

Region of the genome with increased recombination rates

177
Q

Recombination cold spot

A

Region of the genome with decreased recombination rates

178
Q

P value

A

Less than 0.05: fail to reject null hypothesis
Greater than or equal to 0.05: reject null hypothesis
Null hypothesis: statistical difference between observed numbers and expected numbers

179
Q

Central dogma of molecular biology

A

DNA is transcribed into RNA which is translated into amino acids

180
Q

FISH

A
  1. Solution of labeled probes is added to DNA sample in question while it is being denatured
  2. Sample is allowed to hybridize
  3. Probe will hybridize to the sample DNA if the specific sequence is present
    Used in detection of genetic disorders that result from copy number changes
181
Q

Spectral karyotyping (SKY)

A

Human karyotype is labeled with 24 uniquely labeled chromosome paints
Used to detect complex rearrangements, small translocations, and unknown chromosomes

182
Q

Array-based comparative genomic hybridization (Array CGH)

A

Patient’s DNA and normal DNA are differently labeled and co-hybridized to arrays of DNA clones which span the entire genome (comparison is expected to yield ratio of 1:1, indicating equal DNA copy numbers in both samples)
If yellow, normal copy number
If red, deletion in patient’s DNA
If green, duplication in patient’s DNA

183
Q

Whole exome sequencing

A

Analysis of the exons (coding regions) of thousands of genes simultaneously

184
Q

p and q

A

p= frequency of dominant allele (B)
q= frequency of recessive allele (b)
p+q=1

185
Q

Hardy-Weinberg equation

A

p^2 + 2pq + q^2 = 1
p^2= f(AA)
2pq= f(Aa)
q^2= f(aa)

186
Q

Map units (mu)

A

Map units=% recombination

Map units= (number of recombinants/total number of progeny)*100

187
Q

Progeny in lowest abundance result from…

A

Double crossover

188
Q

Progeny in highest abundance result from…

A

Parental

189
Q

How to tell which gene in a test cross is in the middle

A

DCO tells which gene is in middle: only one that isn’t switched (odd one out)

190
Q

Roughly equal number of offspring in testcross

A

No linkage of genes

191
Q

4 high numbers from 8 phenotypic classes in testcross

A

Odd trait out assorts independently and other two are linked

192
Q

2 parental (high #), 4 SCO (intermediate #), and 2 DCO (low #) in testcross

A

Odd trait out is in middle and all traits are linked

Genetics (20 decks)

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