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Genetics > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

3 reasons mutations spread

A
  • social (ex: found attractive)
  • selective advantage
  • small population
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2
Q

why is genetics one of biology’s unifying principles?

A

all organisms use genetic systems that have a number of features in common

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3
Q

why do we care about genetics?

A
  • we all possess genes/variants that influence our lives in significant ways
  • genetic selection impacts agriculture
  • pharmaceuticals
  • medical (inherited diseases)
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4
Q

divisions of genetics

A
  • molecular
  • transmission
  • population
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5
Q

molecular genetics

A
  • chemical nature of DNA
  • how information is encoded, replicated, and expressed
  • central dogma
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6
Q

transmission genetics

A

heredity and how traits pass from one generation to the next and the relationship of chromosome to heredity and gene mapping

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7
Q

population genetics

A

collection of genes in a population and the genetic variation over geography over time

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8
Q

unifying principle

A

all organisms use similar genetic systems

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9
Q

GENOME

A

complete set of genetic instructions for any organism

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10
Q

all genomes are composed of ________
(ex: ____ and _____)

A

nucleic acids
ex: DNA and RNA

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11
Q

examples of model organisms

A

fruit fly, mouse, bacteria, worms, plants, yeast

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12
Q

WHAT MAKES A GOOD GENETIC MODEL?

A
  • short generation time
  • large but manageable number of progeny
  • adaptability to lab environment
  • ability to be housed and propagated inexpensively
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13
Q

when paleobiologist study DNA thousands of years old why can they not get 100% of the DNA/full DNA traits of parents?

A
  • DNA decays overtime
  • there are some genes that are the same so you cannot code to one parent or the other
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14
Q

WHAT IS NEEDED FOR INHERITANCE?

A
  • information storage
  • information copying (replication)
  • information retrieval (translation)
  • ability to vary
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15
Q

3 PARTS OF THE CHEMICAL STRUCTURE OF DNA AND RNA

A
  • pentose sugar
  • nitrogenous base
  • phosphate group
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16
Q

pentose sugar

A
  • 5 carbons
  • DNA = deoxyribose
  • RNA = ribose
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17
Q

deoxyribose vs ribose

A
  • deoxyribose = H attached to 2’ C
  • ribose = OH attached to 2’ C
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18
Q

nitrogenous bases

A
  • adenine (A)
  • guanine (G)
  • cytosine (C)
  • thymine (T)
  • uracil (U)
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19
Q

purine and examples

A
  • double ring
  • adenine (A) and guanine (G)
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20
Q

pyrimidine and examples

A
  • single ring
  • cytosine (C), thymine (T), uracil (U)
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21
Q

pyrimidines are C U T from purines

A

pyrimidine(single ring) are C(cytosine) U(uracil) T(thymine) from purines(double ring)

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22
Q

nucleosides

A

nitrogenous bases are lined to the sugar by the 1’ carbon of the pentose sugar

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23
Q

nucleoside vs nucleotide

A

nucleoside: 2 pairs (base and sugar)
nucleotide: 3 pairs (base, sugar, phosphate)

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24
Q

where is the phosphate group attached to the pentose sugar?

A

attached to the 5’ carbon

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25
Q

purpose of the phosphate group

A

allows for two nucleotides to be linked creating a stream of information that DNA encodes (cleaved to create the phosphodiester bond)

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26
Q

polynucleotides

A

Covalent bonds between a phosphate group of one nucleotide and the 3’ carbon of the next nucleotide’s sugar

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27
Q

phosphodiester bonds

A

covalent bonds between a phosphate group of one nucleotide and the 3’ carbon of the next nucleotide sugar (5’ to 3’ linkage)

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28
Q

polarity of the DNA/RNA backbone

A

information is flowing through the 5’ to 3’ direction

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29
Q

complementary base pairs

A
  • A to T
  • G to C
  • A to U (RNA only)
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30
Q

number of hydrogen bonds in complementary base pairs

A
  • A to T = 2 hydrogen bonds
  • G to C = 3 hydrogen bonds
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31
Q

strong or weak: phosphodiester bond

A

strong

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32
Q

strong or weak: hydrogen bond

A

weak

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33
Q

which bond is stronger, A to T or G to C?

A

G to C because they have 3 bonds

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34
Q

how did Watson and Crick discover the molecular model of DNA?

A

used all available information about chemistry

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35
Q

STRUCTURE OF DNA

A
  • double helix (2 strands)
  • antiparallel strands (directionality)
  • base complementary (holds strands together)
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36
Q

_____ base pairs between each turn of the helix

A

10

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37
Q

in DNA what is the wider and thinner grooves called?

A
  • wider = major groove
  • thinner = minor groove
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38
Q

why are grooves important in DNA?

A

grooves are important for binding other molecules and the regulation of genes

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39
Q

1 C value

A

a single set of genes, HAPLOID content

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40
Q

2 C value

A

two copies of every base pair/gene (Mom and Dad), DIPLOID content

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41
Q

what does C mean (1C and 2C)?

A

C = content = total number of bases
–> there are millions of bases

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42
Q

1C or 2C: gametes (egg OR sperm)

A

1C

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43
Q

1C or 2C: sperm and egg combined

A

2C

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44
Q

what does “N” mean?

A

number of chromosome molecules in a cell

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45
Q

most cells are 2N and 2C meaning they are…

A

diploid (ex: 46 in humans)

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46
Q

egg and sperm cells are 1N and 1C meaning they are…

A

haploid (ex: 23 in humans)

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47
Q

how can several feet of DNA fit into a very small nucleus?

A

compact it!

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48
Q

to compact prokaryotes and bacteria…

A

supercoiled (like a phone line)

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49
Q

topisomerases

A

enzymes that break the double helix backbone and rotate the ends (using energy), needed for supercoiling

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50
Q

negative supercoiling

A

compact (turn) counterclockwise - easier

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51
Q

positive supercoiling

A

compact (turn) clockwise

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52
Q

chromatin

A

DNA with a protein scaffold

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53
Q

histones

A

net positive charge so that they attract to the negatively charged DNA (DNA wraps around it)

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54
Q

how is the DNA packaged?

how does it condense during cell division

A
  1. assembly of the nucleosome (DNA + protein)
  2. multiple nucleosomes are coiled together and stacked on top of each other
  3. chromatin is further packed by protein scaffolding forming a chromosome
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55
Q

when do chromosomes form?

A

only when the cell is dividing

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56
Q

karyotype

A

representation of all the chromosomes in the organism

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57
Q

2 types of chromatin

A
  1. euchromatin
  2. heterochromatin
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58
Q

EUCHROMATIN

A

hold active genes
(parts of the chromosome that are going to do something, so they are made accessible and less compact and uncoiled except during cell division, stains light)

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59
Q

HETEROCHROMATIN

A

holds inactive genes
(stains dark and more condensed)

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60
Q

2 types of heterochromatin

A
  1. constitutive heterochromatin
  2. facultative heterochromatin
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61
Q

constitutive heterochromatin

A

having the power to establish or give organized existence to something (maintain chromosome structure, telomeres and centromeres)

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62
Q

facultative heterochromatin

A

capable of but not restricted to particular function or made of life (has potential to be condensed… ex: X chromosome inactivation)

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63
Q

centromeres

A

located at the center of the chromosome, used by cells during cell division to ensure each daughter cell gets a copy of each chromosome

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64
Q

telomeres

A

located at the ends of the chromosomes, a repeated sequence that can be lost when the cell divides so important information is not lost

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65
Q

heteroplasmic cells

A

different kinds of mitochondria in the cell

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66
Q

homoplasmic cells

A

same kind of mitochondria in the cell
(good to have in case of possible mutations)

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67
Q

3 models of DNA Replication

A
  1. conservative
  2. dispersive
  3. semi-conservative
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68
Q

conservative

A

one double helix is unchanged by the process, the other is completely new

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69
Q

dispersive

A

each strand is a mix of old and new DNA (pieces dispersed)

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70
Q

semi-conservative

A

one strand of double helix is conserved the other is new

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71
Q

what is the model of DNA replication?

A

semi-conservative

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72
Q

4 RAW MATERIALS NEEDED FOR DNA SYNTHESIS

A
  1. template
  2. enzymes
  3. raw materials (substrates - A C T G)
  4. Mg 2+ ions
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73
Q

DNA polymerase

A

catalyzes the formation of phosphodiester bonds
(joins the 3’-OH group of the last base to the incoming 5’-phosphate)

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74
Q

phosphodiester bonds: strong or weak

A

covalent, strong

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75
Q

SYNTHESIS DIRECTION

A

5’ to 3’

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76
Q

characteristics of creating a new strand of DNA/RNA

A

complementary and antiparallel

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77
Q

replication fork

A

double stranded DNA exposure allowing for replication to occur in the 5’ to 3’ direction

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78
Q

leading strand

A

continuous coding strand

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79
Q

lagging strand

A

discontinuous coding strand

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80
Q

Okazaki fragments

A

short sections of DNA formed at the time of discontinuous synthesis of the lagging strand during replication of DNA

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81
Q

5 KEY ELEMENTS OF EACH REPLICATION FORK

A
  1. helicase to unwind DNA
  2. single stranded binding proteins to protect single stranded DNA
  3. gyrase to remove strain ahead of the form
  4. primase to synthesize RNA primer
  5. DNA polymerase
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82
Q

Key features of DNA replication in eukaryotes

A
  • occurs in the nucleus during S phase
  • initiated by RNA primers
  • occurs in 5’ –> 3’ direction
  • semiconservative
  • initiation at many points
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83
Q

origins of replication

A

initiations of replication at many points to have replication occur faster

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84
Q

what happens to histones during replication?

A

histones disassemble but stay in the cell to be reused and new histones are made for the new DNA

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85
Q

what direction does exonuclease activity occur in?

A

3’ to 5’

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86
Q

phases of the cell life cycle

A
  1. During G1, the cell grows
  2. cells may enter G0, a nondividing phase
  3. after G1/S checkpoint, the cell is committed to dividing
  4. in S, DNA duplicates
  5. in G2, the cell prepares for mitosis
  6. after the G2/M checkpoint the cell can divide
  7. mitosis and cytokinesis (cell division) take place in the M phase
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87
Q

5 Phases of the cell life cycle

A
  1. G1
  2. G0
  3. S
  4. G2
  5. Mitosis
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88
Q

G1 Phase

A

chromosome morphology changes from condensed to dispersed due to a change in the coiling of fibers

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89
Q

G0 Phase

A

neither growing or progressing
(muscle cells and neurons stay here)

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90
Q

S Phase

A

DNA untwists and replicates

91
Q

G2 Phase

A

DNA condenses

92
Q

Mitosis

A

formation of two cells from one cell, daughter cells

93
Q

5 STAGES OF MITOSIS

A
  1. Interphase
  2. Prophase
  3. Metaphase
  4. Anaphase
  5. Telophase
94
Q

Interphase

A
  • stage 1 of mitosis
  • nuclear membrane present, chromosomes relaxed
95
Q

Prophase

A
  • stage 2 of mitosis
  • chromosomes condense
  • 2 sister chromatids become detectable
96
Q

Metaphase

A
  • stage 3 of mitosis
  • chromosomes are arranged on metaphase plate
  • microtubules from chromosomes to kinetochore
  • used for karyotyping
97
Q

Anaphasse

A
  • stage 4 of mitosis
  • sister chromatids separate
  • chromosomes move toward opposite poles
98
Q

Telophase

A
  • stage 5 of mitosis
  • sister chromatids drive at opposite poles
  • nuclear membranes form
  • chromosomes relax and lengthen
99
Q

Meiosis

A

sexual reproduction, creates sex cells

100
Q

2 phases of meiosis

A
  1. Meiosis 1
  2. Meiosis 2
101
Q

Meiosis 1

A

prophase 1, metaphase 1, anaphase 1, telophase 1, cell division (NO separation of sister chromatids)

102
Q

Meiosis 2

A

prophase 2, metaphase 2, anaphase 2, telophase 2, cell division (centrosomes split to have haploid gametes)

103
Q

why are siblings so different?

A

during meisosis chromosomes cross over (recombinant) during prophase 1 and have independent assortment

104
Q

transcription

A

DNA into RNA

105
Q

RNA polymerase

A

catalyzes production of RNA using DNA as a template
(A U C G)

106
Q

RNA is syntheisized ___________, DNA is read ____________

A

5’ - 3’ , 3’ - 5’

107
Q

where does transcription occur

A

the nucleus

108
Q

DNA vs RNA: composed of nucleotides

A

both = yes!!

109
Q

DNA vs RNA: type of sugar

A
  • DNA = deoxyribose
  • RNA = ribose
110
Q

DNA vs RNA: nucleotides joined by phosphodiester bonds

A

both = yes!!

111
Q

DNA vs RNA: presence of free 2’-OH

A
  • DNA = NO
  • RNA = YES
112
Q

DNA vs RNA: bases

A
  • DNA = A G C T
  • RNA = A G C U
113
Q

DNA vs RNA: double or single stranded

A
  • DNA = usually double
  • RNA = usually single
114
Q

DNA vs RNA: secondary structure

A
  • DNA = double helix
  • RNA = many types
115
Q

DNA vs RNA: stability

A
  • DNA = stable
  • RNA = easily degraded
116
Q

messenger RNA (mRNA)

A

instructions to make a protein (each protein has a unique mRNA)

117
Q

transfer RNA (tRNA)

A

translates intrusions into protein “language”

118
Q

ribosomal RNA (rRNA)

A

machine that builds a protein

119
Q

small nuclear RNA (snRNA)

A

mostly modify mRNAs (lots and lots of them)

120
Q

structure of tRNA

A
  • stem/loop structure
  • section that recognizes AA
  • section that allow RNA to be recognized and position AA to make a peptide bond
121
Q

rRNA structure

A

2 subunits (large and small)

122
Q

collinearity of the central dogma

A

predictive relationship between the RNA and a protein

123
Q

KEY COMPONENTS NEEDED FOR TRANSCRIPTION

A
  1. DNA template
  2. the raw materials (ribonucleotide triphosphate) needed to build a new RNA molecule
  3. the transcription apparatus, consisting of the proteins necessary for catalyzing the synthesis of RNA
124
Q

RNA synthesis is _______________ and _______________ to the template strand

A

complementary and antiparallel

125
Q

RNA POLYMERASE

A

copies (transcribes) DNA to RNA

126
Q

3 main types of RNA polymerases

A
  • RNA Pol I
  • RNA Pol II
  • RNA Pol III
127
Q

RNA Pol I

A

transcribed rRNA

128
Q

RNA Pol II

A

transcribed mRNA

129
Q

RNA Pol III

A

transcribes tRNA

130
Q

RNA polymerase funnel and pore

A

where rNTPs (nucleotides) enter

131
Q

chromatin - remodeling complexes

A

reposition the nucleosomes allowing transcription factors and RNA polymerase to bind to promoters and initiate transcription

132
Q

promoter

A

sequence that transcription machinery recognizes and binds (specific sequence, not transcribed)

133
Q

coding region

A

the sequence that is copied (transcribed) from DNA to RNA

134
Q

terminator

A

specific sequences that indicate transcription should stop, generally transcribed

135
Q

genes can be turned on and off depending on:

A
  • time in development (TDF)
  • nutrients (ADH)
  • stress
136
Q

core promoter

A

on DNA, required for transcription, site where basal transcription machinery binds

137
Q

regulatory promoter

A

located upstream of the core promoter, transcription factors and regulatory factors can bind here, affects the rate of transcription

138
Q

enhancers

A

distal locations can also enhance transcription (can be upstream or downstream)

139
Q

initiation (transcription)

A

if the promoter (core and regulatory) and enhancers “say so”, a protein - coding gene is transcribed
(polymerase and other factors are bound)

140
Q

elongation (transcription)

A

keep adding nucleotides

141
Q

termination (transcription)

A

for RNA Pol II there is no specific termination sequence, can continue for 100s-1000s of base pairs

142
Q

gene

A

unit of information that encodes a genetic characteristic

143
Q

introns

A

non coding region of the DNA between 2 regions that can code

144
Q

introns must be _______ out by snRNPs (small nuclear ribonucleoproteins) in a splicesome

A

spliced

145
Q

what happens if there is an error is translation?

A

does NOT change the DNA, but could affect the protein

146
Q

5’ UTR

translatiion

A

does not code for a protein, ribosome binds here

147
Q

3’ UTR

A

not transcribed into a protein, affects stability of mRNA

148
Q

post-transcriptional modifications

A

1 addition of 5’ cap
2. addition of Poly-A tail
3. introns spliced out

149
Q

5’ cap

A

addition of methylate guanines to the 5’ end of RNA to increase stability

150
Q

Poly- A Tail

A

addition of adenines to the 3’ end after cleavage

151
Q

how can the Poly A Tail adjust the half life?

A
  • more As = longer half life
  • less As = shorter half life
152
Q

splicing

A

removal of introns (allowing for the DNA and RNA to be collinear)

153
Q

splicesome

A

large complex structure that comes in to remove introns and splice exons together

154
Q

the number of genes is _____ strongly correlated with organismal complexity, however _______ size and number is correlated to complexity

A

NOT, intron

155
Q

why would exons be put together with alternating splicing / cleavage? leaving some exons out?

A

different functions

156
Q

why not change the order of the exons? why can this not occur?

A

splicesome moves down a linear molecule and puts them back together in linear fashion, physically the splicesome could not change the order (but it can skip)

157
Q

proteins

A

functional molecules of the cell, function determined by structure based off AA

158
Q

how many AA?

A

20

159
Q

parts of an amino acid

A
  • amino group
  • carboxyl group
  • R group
160
Q

what part of the amino acids structure is different in each AA?

A

the R group

161
Q

primary structure of a protein

A

sequence of AA

162
Q

secondary structure of a protein

A

interactions between AA (a-helix, B-sheets)

163
Q

tertiary structure of a protein

A

structures after folding makes a 3D shape

164
Q

quaternary structure of a protein

A

more than one polypeptide

165
Q

the function of a protein is determined by __________________

A

its 3D shape

166
Q

codon

A

3 bases to encode an amino acid

167
Q

how many possible amino acid combinations?

A

64, 3 bases and 20 AA
(allows for redundancy)

168
Q

start codon

A
  • AUG - methionine
  • NOT ALWAYS THE FIRST CODON, YOU HAVE TO LOOK FOR IT IN THE SEQUENCE
169
Q

stop codons

A
  • UAA, UAG, UGA
  • NO tRNA FOR STOP CODONS, THIS IS WHAT CAUSES TRANSLATION OF THE SEQUENCE TO END
170
Q

degenerate

A

more than one codon for each AA

171
Q

wobble

A

typically the 3rd base of the codon can vary

172
Q

synonymus (wobble)

A

change in the DNA sequence does NOT change the AA

173
Q

non-synonumus (wobble)

A

change in DNA sequence CHANGES AA

174
Q

nonsense (wobble)

A

changes in DNA introduces a STOP CODON

175
Q

reading frame

A

code is read in three’s

176
Q

ribosome

A

the machinery the makes proteins (made up of a large and small subunit)

177
Q

4 Phases of Protein Synthesis

A
  1. tRNA charging (binding tRNA to AA)
  2. initiation: start of translation
  3. elongation: synthesis of polypeptide chain
  4. termination: ending of synthesis
178
Q

aminoacyl-tRNA synthetase

A

enzyme that attached an AA to a tRNA
(each is specific to a particular AA)

179
Q

5’ Cap

A

protection and recognition for the ribosome to bind in initiation of protein synthesis

180
Q

the _______ __________ scans the mRNA until it finds the start codon

A

initiation complex

181
Q

initiation complex

A

ribosome small unit, initiation factors, initiator tRNA

182
Q

ribosome reads mRNA moving _____________

A

5’ to 3’

183
Q

ribosome has 3 sites that can be occupied

A
  • Aminoacyl (A) site
  • Peptidyl (P) site
  • Exit (E) site
184
Q

Aminoacyl (A) site

A

where charged tRNAs enter the ribosome

185
Q

Peptidyl (P) site

A

where peptide bond is formed

186
Q

premature stop codon

A

mutation that moves the stop codon to be too early in the sequence

187
Q

removal of the stop codon

A

could make an unnecessary amount of a protein

188
Q

mutation

A

inherited change in genetic information, the descendants that inherit the change may be cells or organisms

189
Q

2 categories of mutations

A
  • somatic mutations
  • germ line mutations
190
Q

somatic mutations

A

occurs after conception occurring in any cell except germ cells and therefore not passed to offspring

191
Q

germ line mutations

A

occurs in germ cells and transmitted to offspring

192
Q

mutations: some are beneficial, some are detrimental, some are neutral. WHY?

A

dependent on the environment and location of the mutation in the gene

193
Q

is a plant or animal more affected by their environment (mutational changes)?

A

plants because they are not able to move

194
Q

2 classifications of mutations

A
  • physical nature of the variant
  • consequence of the variant
195
Q

base substitution

A

alteration of a single nucleotide

196
Q

base substitution types

A
  • transitions
  • transversions
197
Q

base substitution: transitions

A

substitution of purine for a purine OR substitution of a pyrimidine for a pyrimidine

198
Q

base substitution: transversions

A

substitution of purine for pyrimidine OR substitution of pyrimidine for purine

199
Q

purine (ex)

A

double ring carbon structures (A and G)

200
Q

pyrimidine (ex)

A

single ring carbon structures (C, U, T)

201
Q

missence

A

change in AA

202
Q

nonsense

A

add a stop codon

203
Q

silent

A

no change in AA

204
Q

neutral mutation

A

missence mutation that changes one AA for another chemically similar AA

205
Q

loss of function mutation

A

results in complete or partial absence of a normally functioning protein (nonsense-premature stop codon)

206
Q

lethal mutation

A

result is so drastic an organism cannot survive

207
Q

how can a lethal mutation pass on?

A

the biological purpose of life is to transmit DNA, so the mutation kills you after reproductive age

208
Q

indels

A

insertion/deletion of one or more bases (can cause a frameshift)

209
Q

what type of indel would be less consequential?

A

if it were to be in a multiple of 3 because it would either add or remove 1 AA, so the protein can sometimes still function

210
Q

expanding nucleotide repeats

A

mutations in which the number of copies of a set of nucleotides increases

211
Q

causes of mutations: replicative

A

the wrong base gets incorporated during DNA replication

212
Q

causes of mutations: strand slippage

A

newly synthesized strand loops out on the new strand in the addition of the nucleotide on the new strand or the template strand loops out resulting in the omission of one nucleotide on the new strand (common in repeat bases)

213
Q

causes of mutations: depurination

A

loss of a purine base from a nucleotide

214
Q

causes of mutations: deamination

A

loss of an amino (NH2) group from a base

215
Q

causes of mutations: mutagen

A

any environmental agent that significantly increases the rate of mutation above the spontaneous mutation rate

216
Q

what affect can UV have on replication?

A

produces thymine dimers that block replication

217
Q

common 4-step pathway for DNA Repair

A
  1. detection
  2. excision
  3. polymerization
  4. ligation
218
Q

common 4-step pathway for DNA Repair: step 1

A

detection!
The damaged section of the DNA is recognized

219
Q

common 4-step pathway for DNA Repair: step 2

A

excision!
make a nick and exonuclease removes error

220
Q

common 4-step pathway for DNA Repair: step 3

A

polymerization!
DNA polymerase replaces the nucleotides that were removed

221
Q

common 4-step pathway for DNA Repair: step 4

A

ligation!
ligase going over and filling in any “holes” / seals the nicks

222
Q

how many hydrogen bonds between A and T

A

2 H bonds

223
Q

how many hydrogen bonds between A and U

A

2 H bonds

224
Q

how many hydrogen bonds between C and G

A

3 H bonds

Genetics (10 decks)

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