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Biology 191 > Chapters 16-22 > Flashcards

Chapters 16-22 Flashcards

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1
Q

Where is the regulatory sequence, and what is located here?

A

generally in 5’ region. promoter is located here

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2
Q

What is the function of transcription factors?

A

affect RNA polymerase’s ability to bind can bind within regulatory region can help or hurt RNA polymerase

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3
Q

What are the two main motifs that recognize where to attach to DNA?

A

DNA binding motif leucine zipper motif

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4
Q

What is the DNA binding motif?

A

repeated structure in the protein EX. helix-turn-helix

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5
Q

What is the leucine zipper motif?

A

found repeatedly on proteins contains a zipper like protein

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6
Q

What is an operon?

A

grouping of proteins found only in prokaryotes genes necessary to make the enzymes necessary for a particular product

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7
Q

What is trp operon?

A

gene necessary to make the enzymes to make the amino acid tryptophan

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8
Q

What is the structure of trp operon?

A

coding region regulatory region

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9
Q

What is the regulatory region in a trp operon?

A

Contains a promoter

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10
Q

What sits on the promoter in trp operon?

A

RNA polymerase

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11
Q

What is an operator?

A

Binding site for a transcription factor

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12
Q

How does this operon work? When is it on, when is it off?

A

If tryptophan is absent the cell needs it - promoter is unoccupied and operon is on If tryptophan is present- promoter is occupied and the operon is off

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13
Q

What does the lac operon do?

A

produces the necessary enzymes to digest loctose

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14
Q

Is the lac operon a weak promoter or a strong promoter?

A

Weak promoter

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15
Q

What does CAP stand for?

A

Catabolite activator protein

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16
Q

What happens when glucose is low in a bacteria?

A

Bacteria must use a different sugar like lactose

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17
Q

What are the three things that happen in bacteria when glucose is low?

A

Then [cAMP] is increase, cAMP binds to CAP CAP binds to DNA allowing RNA polymerase to bind to lac operon

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18
Q

What is cAMP?

A

little molecule that is like ATP

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19
Q

What are the three genes within the coding region of a lac operon?

A

Z, Y, A

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20
Q

What are the three sections of the regulatory region in the lac operon?

A

Promoter operator CAP binding site

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21
Q

What happens if [glucose] is low and [lactose] is high?

A

RNA polymerase attaches to promoter and transcription occurs

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22
Q

What happens if [glucose] is low and [lactose] is low?

A

repressor attaches to operator

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23
Q

What must happen in order to for the lac operon to be on?

A

[glucose] low, and [lactose] higher

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24
Q

What are specific transcription factors?

A

they stick out of general transcription factors and attach to other parts of DNA called enhancers

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25
Q

What is development?

A

process that determines form and function of organisms

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26
Q

What are the three multicellular kingdoms?

A

Kingdom Fungi, Kingdom Viridiplantae, Kingdom Animalia

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27
Q

What is the kingdom fungi?

A

less complicated minimal development

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28
Q

What is Kingdom viridiplantae?

A

plant kingdom does have development- specialized cells flexible development

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29
Q

what is kingdom animalia?

A

animal kingdom most complex kingdom

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30
Q

What are the four model organisms?

A

Mouse- Mus musculus Fruit Fly- Drosophila Plant- Arabidopsis Insect- C. elegans

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31
Q

What is Mus musculus?

A

mouse vertebrate and mammal

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32
Q

What is totipotency?

A

up to 8-cell stage, any cell could produce a normal adult

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33
Q

What is Drosophila?

A

fruit fly has a short generation time and small and simple nutrient needs and enough complexity to be of interest goes through metamorphosis does 12 rounds of mitosis before any cytokinesis

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34
Q

What is metamorphosis?

A

different stages you go through as you grow EX, egg, larva, pupa, adult

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35
Q

What is it called when there are multiple rounds of mitosis before any cytokinesis?

A

syncytial blastoderm

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36
Q

What genes place appendages in correct place?

A

homeotic genes

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37
Q

What is Arabidopsis?

A

a plant mustard family easy to grow and small and self-pollinate

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38
Q

What is the development of the Arabidopsis?

A

Fertilized eggs under goes mitosis ball of cells differentiation into three layers this becomes three tissue systems ball changes shape into two cotyledons first root forms packaged into seed if conditions are right, undergoes germination grows into seedling

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39
Q

What are cotyledons?

A

1st leaves of a plant

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40
Q

What are meristems?

A

points of growth in plants the shoot and root

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41
Q

What are C. elegans?

A

round worm= nematodes 1 mm long and transparent always have over 959 cells

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42
Q

What are the 6 stages of vertebrate development?

A

Fertilization cleavage gastrulation neuralation organogenesis morphogenesis

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43
Q

What is the front of a sperm called?

A

acrosome or a modified lysosome

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44
Q

What is the use of an acrosome on sperm?

A

to digest its way through the stuff around the egg

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45
Q

What are the three steps of fertilization of vertebrate development?

A

Penetration activation nuclear fusion

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46
Q

What is penetration that happens during fertilization

A

the sperm gets through egg membrane by fusing with it

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47
Q

What happens during activation during fertilization?

A

egg cell membrane changes increase in protein synthesis cytoplasmic movement

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48
Q

What happens during cleavage during vertebrate development?

A

rapid cell division not getting bigger just getting more cells that are tinnier and tinnier

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49
Q

What is a blastula?

A

a hallow ball of cells 500-2000 cells. has fluid that accumulates in center of the ball (morula)

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50
Q

What happens during the gastrulation phase of vertebrate development?

A

lots of cell movement when tissue types are formed varies between animal groups in form

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51
Q

What does the endoderm cells become in the blastula?

A

lining of digestive and respiratory tracts

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52
Q

What does the ectoderm become in the blastula?

A

skin, nervous system, sense organs

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53
Q

What does the mesoderm form in the blastula?

A

skeleton, muscles, blood vessels, heart, blood, gonads, kidneys

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54
Q

When does gastrulation happen?

A

3 weeks after fertilization

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55
Q

What happens in the neuralation stage of vertebrate development?

A

beginning of the formation of the nervous system first steps or organogenesis

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56
Q

What happens in the organogenesis stage of vertebrate fertilization

A

making organs

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57
Q

When does organogenesis happen?

A

4th week after fertilization

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58
Q

What happens during morphogenesis in vertebrate development?

A

change in form like limbs cells dividing cells growing cells moving cells dying

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59
Q

What is induction?

A

one cell switches its developmental pathway because of an interaction with another cell

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60
Q

What must a cell be able to do in order to move?

A

cells must become less bound before it can move, then it must rebind itself to its new neighbors

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61
Q

What is determination and differentiation?

A

First cll can develop into anything as time goes on certain genes are turned off it is determined through the turning off of genes differentiation happens later when the cell forms into what it is becoming

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62
Q

What is a genome?

A

an entire genetic sequence of an organism

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63
Q

What is genomics?

A

study of genomes

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64
Q

What are some physical maps of genomes?

A

DNA sequence human genome project banding patterns on chromosomes restriction sites

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65
Q

What is the human genome project?

A

starts in 1990 attempt to map the human genome by 2001 the overall idea figured out

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66
Q

What is a genetic map?

A

genes are mapped onto the chromosomes can look for stop and start codons can look at linkage

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67
Q

How much of DNA actually codes for protein?

A

1 to 1.5%

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68
Q

What are the four types of DNA that does code for protein?

A

Single-copy genes segmental duplications multi-gene family Tandem cluster

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69
Q

What are single-copy genes?

A

25,000 of them 90,000 to 100,000 proteins made from them done by alternative splicing

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70
Q

What is segmental duplications?

A

gene group on more than one chromosome functional

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71
Q

What is multi-gene family?

A

collection of similar genes EX hemoglobin - 2 alpha 2 beta

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72
Q

What is a tandem cluster?

A

group of identical genes

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73
Q

What are the 6 types of DNA that does not code for protein?

A

Introns structural DNA simple sequence repeats segmental duplications pseudogenes transposable elements

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74
Q

What are introns?

A

intervening sequences of DNA snipped out of primary mRNA 24% of total DNA

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75
Q

What are the two controls for transcriptional regulation

A

Regulatory sequence on DNA Transcription factors

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76
Q

What is the structural DNA?

A

20% of DNA concentrated near centromere area does not uncoil or copy also found at ends of chromosomes-telomeres

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77
Q

What are simple sequence repeats?

A

3% of DNA 1-6 nucleotides long like stutters some are associated with mutations

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78
Q

What are segmental duplications?

A

chuncks of DNA found in more than one place does not make a message or protein

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79
Q

What are pseudogenes?

A

inactive genes a mutation happens and cannot work anymore 2% of DNA

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80
Q

What are transposable elements?

A

Transposons jumping genes ability to randomly move found in prokaryotes and eukaryotes stretch of DNA that can move

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81
Q

Who first discovered transposable elements?

A

McClintock found these in Indian Corn in 1950s

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82
Q

What is SNP?

A

single nucleotide polymorphism the fact that a single nucleotide in our genome is variable

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83
Q

What is comparative genomics?

A

genomes of different species are compared field of study more similar genomes = more common ancestor

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84
Q

How similar are drosophila and humans?

A

50% of Drosophila genes have a human counterpart

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85
Q

How are similar are humans and chimps?

A

have only 1.2% difference in nucleotide sequence

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86
Q

How similar are mice and humans?

A

both have 25,000 genes share 99% of genes

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87
Q

What is synteny?

A

degree of similarity between different organisms

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88
Q

What is proteomics?

A

study of cell’s proteins

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89
Q

What is bioinformatics?

A

integration of biology, math and computers

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90
Q

What is functional genomics?

A

Field looking at the function of genes instead of the structure

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91
Q

What are somatic cells?

A

cells of the body

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92
Q

What is teh basal lamina?

A

membrane that protects the organs, a-cellular

93
Q

What is metastasize?

A

When secondary tumors appear from cancer cells moving throughout the body When cancer cells go from a primary location to a secondary location

94
Q

What is epidemiology?

A

study of how to prevent cancer

95
Q

What do cancer cells contain on the chromosomal level?

A

highly abnormal chromosomes, reflecting genetic instability trasnlocation

96
Q

What is chromosomal painting?

A

a new version of karyotyping?

97
Q

How do tumors evolve?

A

by repeated rounds of mutation and proliferation

98
Q

What happens to the cancer cells after each evolutionary step?

A

gains a new mutation that enhances its ability to proliferate, survive, so that its progeny become the dominant clone in the tumor

99
Q

What are some competitive advantages of cancer cells?

A

reduced dependence on signals from other cells less prone to apoptosis cancer cells can proliferate indefinitely genetic instability abnormally invasive lack of cell adhesion molecules can survive in foreign tissues

100
Q

What are the two classes of cancer genes?

A

oncogene and tumor suppressor gene

101
Q

What is oncogene?

A

Dominant mutation gain of a function activating mutation enables oncogene to stimulate cell curvival and proliferation

102
Q

What is the tumor suppressor gene?

A

recessive mutation loss of function two inactivating mutations functionally eliminate the tumor suppressor gene, stimulating cell survival and proliferation

103
Q

What three kinds of genetic changes that can convert a proto-oncogene into an oncogene?

A

mutation i coding sequence gene amplification chromosome rearrangement

104
Q

What type of mutation in the coding sequence creates oncogene?

A

hyperactive protein made in normal amounts

105
Q

What gene amplification turns on the oncogene?

A

normal protein greatly overproduced

106
Q

What chromosome rearrangement creates oncogene?

A

nearby regulatory DNA sequence causes normal protein to be overproduced fusion to actively transcribed gene produces hyperactive fusion protein

107
Q

What is biotechnology?

A

moving genes for our own benefit

108
Q

What is genetic engineering?

A

the cutting of DNA -basic technique -cut into specific pieces -rearranged for a practical purpose

109
Q

What is the enzyme called that cuts DNA? And where does it cut it?

A

restriction endonucleases and cut at the restriction site

110
Q

Where was restriction endonucleases found at?

A

in bacteria

111
Q

Where does the restriction endonuclease cut at?

A

When a nucleotide sequence reads forwards and backwards the same

112
Q

Why does the Restriction endonuclease cut at a palindrome?

A

to create a sticky end

113
Q

What is a vector?

A

carries foreign DNA into another cell

114
Q

What are the three most common vectors and where do they carry too?

A

Plasmids- carry into bacteria and plants Animal virus- carry into animal cells Bacteriophage- virus that infects bacteria

115
Q

What is gel electrophoresis?

A

a method to separate molecules

116
Q

What is the end product of gel electrophoresis?

A

DNA, mRNA

117
Q

What is the process of gel electrophoresis with DNA?

A

-have a mixture made of DNA fragments -set up slap of gel with negative charge and positive on other side -load mixtures on negative side -submerge in liquid -turn on current -molecules move towards positive end

118
Q

What molecules are going to be closest to the positive side?

A

the smaller molecules

119
Q

What is gel electrophoresis used in?

A

crime scenes

120
Q

What is the process of getting a gene from one organism to another?

A

-cutting the DNA -mix the two DNA sources -get plasmids back into first organism -grow each organism separate -screen for the clone

121
Q

When cutting the DNA to put a gene from one organism to another, what must be done?

A

Have to do it to both organisms have to use the same restriction endonuclease

122
Q

How do you mix the two DNA sources in order to get a gene from one organism to another?

A

sticking together- recombinant DNA all fragments together are called a library

123
Q

What are two ways toe get the plasmids back into the first organism when transferring genes?

A

Gene gun- little pellets coated with DNA gets shot in and some get rid of DNA Solubilize wall of bacteria- plasmids get taken back in

124
Q

What are the 5 processes of hybridization or screening for the clone that contains the gene of interest

A

-make a copy of clones -add a solution that denatures the DNA from double to single stranded -add a solution that contains a probe -probe will bind to the colony that has the gene of interest -take correct colony and grow it for the gene product.

125
Q

What is a probe?

A

a single stranded radioactively label DNA of the gene of interest

126
Q

What is cDNA?

A

Complementary DNA

127
Q

What is cDNA used in?

A

used in a technique that drastically shortens the experiment of moving one gene from an organism to another

128
Q

What is the shorter process of moving one gene from an organism to another?

A

-extract mRNA from a cell that makes what you want -an enzyme called reverse transcriptase is used -take mRNA and go backwards -makes cDNA -put cDNA into a bacteria to make a product

129
Q

What is PCR?

A

polymerase chain reaction

130
Q

What is PCR used for?

A

used to make a lot of copies of a DNA piece quickly

131
Q

What is PCR used in?

A

-Crime scene -pre-natal DNA -fossils

132
Q

What do you need in order to do PCR

A

-original piece of DNA -DNA polymerase -nucleotides -short DNA primer -thermal cycler

133
Q

How do you do PCR?

A

Denaturation- double stranded DNA changes to single stranded Annealing- primer attaches Synthesis- When DNA is actually copied

134
Q

What is Southern Blotting and RFLP analysis used for?

A

to make a DNA fingerprint more commonly called DNA profiling

135
Q

How is DNA profiling done?

A

-cut DNA with restriction endonuclease -separate fragments by gel electrophoresis -take gel and transfer onto special paper -place paper in basic solution -apply to multiple probes -repeat until you can say that two are similar

136
Q

What does RFLP stand for?

A

Restriction fragment length polymorphism we all have different fragment lengths

137
Q

What are the uses of PCR?

A

DNA fingerprinting, identification of disease carriers, paternity testing

138
Q

What does STR mean?

A

short tandem repeat

139
Q

What are the medical reasons for using DNA sequencing?

A

If you know nucleotide sequence -> know amino acid sequence -> know 3D structure -> know how protein works -> know if there is a mutation -> find a pharmaceutical solution to mutation

140
Q

What are the forensic uses of DNA sequencing?

A

Can be used to identify remains

141
Q

What are some medical application off using DNA sequencing?

A

diagnosis of a disease, Human gene therapy, pharmaceutical products

142
Q

How can DNA sequencing help in diagnosing a disease?

A

using PCR to amplify DNA look for foreign DNA in cell Identify a carrier of a disease

143
Q

How can DNA sequencing help in Human gene therapy?

A

Placement in a person’s cells of a function allele

144
Q

What are some uses of DNA sequencing in plants?

A

Herbicide resistance in crops. drought resistant genes, frost resistant genes, increase nutritional value of a crop, N- fixation, Biopharming

145
Q

What are the results about adding herbicide resistance in crops?

A

Weeds are gaining resistance to herbicide neighboring farms may or may not like it

146
Q

Has animal bio-engineering worked?

A

NO

147
Q

What are some example of attempted genetically modified animals?

A

Salmon- AquAdvantage

148
Q

What are some bad things of genetically modified food/organisms?

A

might transfer genes into natural populations, people might be allergic to it might hurt organic farms increasing resistance of weeds to herbicides

149
Q

What is some environmental applications of genetic engineering?

A

bacteria can help break down oil from an oil spill e coli and yeast can make crude oil

150
Q

Who is Charles Darwin?

A

1809-1882 English 1861-1866- naturalist on HMS Beagle Compared artificial selection to natural selection

151
Q

Who were the two people that Darwin communicated with?

A

Thomas Malthus- 1798- essay on principle of population Charles Lyell- 1830- book that talked about age of earth

152
Q

What happened in 1842?

A

Darwin writes essay of 1842 butt does not publish it

153
Q

What happens in 1858?

A

Darwin gets a letter from Alfred Russel Wallace. Decided that Wallace and Darwin should present papers at the same meeting

154
Q

What happens in 1859?

A

Darwin published origin of species

155
Q

What did Darwin theorized?

A

World is not static but it is changing evolution is gradual natural selection is a process and it results in evolution

156
Q

What is genotype?

A

genetic makeup

157
Q

what is phenothpe

A

physical appearance

158
Q

what is population

A

individuals of one species that live together and are able to interbreed

159
Q

what is phenotype

A

physical appearance

160
Q

what is population

A

individuals of one species that live together and are able to interbreed

161
Q

What is gene pool

A

all genes in a population

162
Q

what is environment

A

total situation an organism lives in

163
Q

what is biotic

A

factors that are living in the environment

164
Q

What is abiotic

A

factors that arre nonlivinng in the envrionment

165
Q

What is natural selection?

A

differential perpetuation of genotypes

166
Q

Why is Natural selection necessary?

A

organisms are capable of sexual reproduction exists inheritable differences organisms are tested by environment

167
Q

What is the result of Natural selection?

A

microevolution

168
Q

What is microevolution

A

a result of natural selection that is a change in allele frequencies

169
Q

What type of natural selection is this?

A

Stabilizing Natural Selection

170
Q

What type of natu ral selection?

A

Directional

171
Q

What type of Natural Selection is this?

A

Disruptive

172
Q

What is adaptation?

A

Changes of organism to get use to environment

natural selection produces adaptations

173
Q

What is Micro Evolution?

A

Change in allele frequency

natural selection produces micro evolution

174
Q

What is co evolution

A

Evolution that uses two species

175
Q

What is Morphological variation?

A

Variation you can see

176
Q

What are Allozymes?

A

alternate forms of an enzyme that are coded for by the same locus

177
Q

How can you tell allozymes apart?

A

by gel eletrophoresis because they differ in size and or charge

178
Q

How do you quantify Allozymes?

A

H= Heteroozygosity

the percent of the loci that are in a heterozygous form in an individual (avergae)

P= polymorphism

The percent of the loci that are in a polymorphic form in a population (average)

179
Q

What is the percent of H in humans?

A

7%

180
Q

what is the percent of P in humans?

A

38%

181
Q

Where is most of the variability in DNA?

A

Non-coding

182
Q

What is the neutral theory?

A

Mutations that are neither positive nor negative

183
Q

What is evidence of the Neutral theory?

A

genetic codon- takes 3 nucleotides and makes 1 amino acid, less likely to have a mutation that changes protein all together

ABO blood types, no advantage to havinng the,

184
Q

Where are enzymes less variable?

A

At the active site, more neutral

185
Q

What is population geneticists?

A

study by looking at allele and genotype frequencies in populations and how they change

186
Q

What are the two most important agents of change that can change allele frequency?

A

Natural selection is the most important

migration is another one

187
Q

What are 4 basic assumptions of organisms?

A

Individuals are diploid, undergo meiosis

individuals mate randomly

no net mutation, no immigration, no natural selection

population is statistically large

188
Q

What is Panmixis?

A

Individuals mate randomly

189
Q

What happens if the 4 assumptions are true?

A

the distribution of ggenotypes and gametes will stay th esame generration to generation

190
Q

What is the Hardy-Weinberg equilibrium?

A

If there is no change there will be no resulting change

191
Q

How do you calculate genotype frequency?

A

Consider Locus A, a

Number of possible genotypes- AA, Aa, aa

number of AA individuals= N(AA)

total population size= N

frequency of genotype= f(AA) = N(AA)/N =.5

192
Q

How do you calculate allele frequency?

A

total number of alleles in a population at a locus= 2n or 2 times the total population

f(A)=(2*N(AA)+1*N(Aa))/2n

193
Q

If there is a mutation does it change allele frequency?

A

rates -0.001 to -0.00001 mutation per locus in a generation

194
Q

What is a mutation from A to a symbolized by?

A
195
Q

What is a mutation from a to A symbolized by?

A
196
Q

What are the reasons that random mating does not exist?

A

organisms often mate with a neighbor

organisms sometimes mate with an individual more like themselves

197
Q

what is the result with inbreeding?

A

increase of homozygosity

198
Q

Why are there not a lot of large population size?

A

Most are in a small group

Genetic Drift- Changes in allele frequency due to chance. Deals in small population size

199
Q

What are the two different species concepts?

A

Morphological species concept

Biological species concept

200
Q

What is the morphological species concept?

A

organism that look different enough are put in different species

201
Q

What is the biological species concept?

A

interbreeding individuals are in the same species

202
Q

What is speciation?

A

Appearance/production of a species

203
Q

What is geographical isolation?

A

a population has to become discontinuous

2 separate populations start with slightly different gene pools

experience different environments

leads to natural selection

204
Q

What is adaptive radiation?

A

When one species creates many

205
Q

What are reproductive isolating mechanisms?

A

biological properites of organisms that prevent interbreeding

206
Q

What are the three types of RIM?

A

Ecological RIM

Temporal RIM

Behavioral RIM

207
Q

What are ecological RIM?

A

Potentional mates do not meet each other

they are in different sup-sections of their habitat

208
Q

What are temporal RIM?

A

Reproduce at different times

frequent in insectts and plants

209
Q

What are Behavioral RIM?

A

Potential mates meet but don’t mate

have different signaling

frequent in animals

210
Q

What is hybridization?

A

interbreeding between two species

211
Q

Why are hybrids sterile

A

Genome of hybrid is AB

cannot create homologous pairs

212
Q

What are someways hybrids can reporduce?

A

if asexual reproductioin is possible

become polyploidy

213
Q

What is polyploidy?

A

more than 2 sets of chromosomes

214
Q

Where do polyploidy come from?

A

from a hybrid individual

error in meiosis or mitosis

215
Q

What happens if you get an odd polyploidy?

A

Triploid is not successful

216
Q

What are fossils?

A

any preserved sign of life?

217
Q

What does homologous fossils mean?

A

assumed to come from a common ancestor and are therefore similar

218
Q

What are analogous fossils mean?

A

Similarity are due to common function

219
Q

Why is ciochemical date used?

A

can look at DNA nucleotide or amino acid sequences

220
Q

What does biochemical dating do?

A

compare organisms and count number of differences or similarities betwen both fo them

221
Q

What is gradualism?

A

A group of organisms change gradually through time

222
Q

What is punctuated equilibrium?

A

alternation between rapid change and equilibrium

223
Q

What are some examples of rapid change?

A

genetic drift

polyploidy

developmental change

224
Q

What is extinction?

A

disappearance of some taxonomic

225
Q

what is taxonomic?

A

a named group

226
Q

What are some causes of extinction

A

both abiotic and biotic can cause it

227
Q

Is extinction continuously happening?

A

yes

228
Q

What are mass extinctions?

A

extinction that happens at higher rates

Biology 191 (5 decks)

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