Test 3 Flashcards
(184 cards)
1
Q
What is a phenotype?
A
differences or changes in function or outcome
2
Q
What is a Genotype?
A
Changes in gene sequence
3
Q
What are the two differences of mutations?
A
Purposefully (induced) Not Purposefully (Spntaneous)
4
Q
What are restriction enzymes?
A
They are endonucleases
5
Q
What do endonucleases recogize?
A
They recognize specific DNA sequences adn cleave DNA
6
Q
Are restriction enzymes common in prokaryotes or eukaryotes?
A
Prokaryotes
7
Q
What is the purpose of the restriction enzymes?
A
To degrade incoming DNA for protection
8
Q
What is type II restriction enzymes used in?
A
in vitro manipulation of DNA
9
Q
What does In vitro stand for?
A
in glass
10
Q
What does Type II restriction enzyme require?
A
It does not need ATP but does need Mg 2+
11
Q
How long are the sites of the type II restriction enzyme?
A
palindormes (4-8 bp long)
12
Q
When the DNA is cut what happens?
A
hydrolysis of phophodiester bonds in the sugar phosphate backbone
13
Q
What does the cut result in?
A
sticky ends
14
Q
What stops methylation ?
A
Methylase
15
Q
The length of recognition sequences determines the average number of cuts in a ___________________ DNA sequences?
A
Random
16
Q
What does Electrophorsis separate?
A
The charged molecules migrating in an electrical field
17
Q
What charged DNA migrates to the positive electrode?
A
Negative
18
Q
What size DNA fragments move slower in the agarose matrix?
A
Larger
19
Q
What can help the separated DNA can be visualized in the gel?
A
DNA binding fluorescent dye (ethidium bromide)
20
Q
Gel electrophoresis can also be used with what?
A
RNA and proteins
21
Q
What is nucleic acid hybridization?
A
Single stranded nucleic acid can base pair with complementary nucleic acids based on natural base pairing
22
Q
What is usually used in hybridzation?
A
labels
23
Q
What are the label?
A
DNA fragments called primers or probes
24
Q
what are the probes called?
A
oligonucleotide probes
25
Who created Southern blotting?
Dr. E. M. Southern
26
What type of blotting is used for RNA?
Northern
27
What type of blotting is used for protein
Western
28
What is cloning?
making many identical copies of something
29
What is molecular cloning?
Making many identical copies of a molecule
30
What is molecular cloning used for?
Transcription and translation
31
What usually happens in molecular cloning to the DNA fragments?
DNA fragment into a plasmid
32
What is the process of moving a fragment into a plasmid called?
cloning vector
33
Manipulations are done by what?
Restriction enzymes and DNA ligase
34
What are the engineered DNA fragments called?
recombinant
35
What is the product of the gene iac Z?
beta-galactosidase
36
What can Beta-galactosidase do?
It can cleave the substrate x-gal
37
What is a shuttle vector?
a vector that is replicated/functional in two different organism
38
Shuttle vectors allow what?
allows genetic manipulation of the plasmid
39
What is required for a shuttle vector?
origin of replication , selectable markers, screens
40
What are expression vectors used for?
production of proteins
41
What are reporter genes used for?
used to study gene expression
42
What is the purpose of translational fusion
to help determine locatlization of the protein in the cell
43
What happens when there is a direct disruption of gene?
Can cause loss of function
44
What is genomics?
Discipline of mapping, sequenceing analyzing, and comparing genomes
45
What are the 3 major steps of genome sequencing?
Shotgun sequencing
Alignment
Annotation and Interpretation
46
What was the first genome sequenced?
RNA virus MS2, 3,569 bases
47
What was the first cellulauenr genome?
Haemophilus influenzae (1995)
48
The first human genome was completed in what year?
2001
49
The first full genome sequenc was done by who?
J. Craig Venter in 1995
50
Using the shotgun stratrgy it is random sequencing using primers on the ______?
Vectors
51
Determination of the order of bases in a DNA molecule is called what?
Primary Structure
52
Sanger method is also called?
Chain Termination
53
Sanger method was developed by?
Nobel Laureate Fred Sanger
54
Where is DNA synthesized?
DNA is synthesized in vitro that is determined by the oligonucleotide primer.
55
What continues until a dideoxynucleodite triphosphate is incorpated?
Polymerization
56
What does dideoxynucleodite triphosphate lack?
lacks a hydroxyl group at the 3' position
57
What can and can not the ddNTPs do?
They are recognized and incorporated by DNApolymerase but does not allow for chain extension
58
Labeled ddNTPs (fluorescent) of primers (32P) allow for detection of what?
truncated products
59
The pyrosequencing method involves in vitro polymerization but the differences from sanger method?
It is recorded duringsynthesis due to enzymatic detection of pyrophosphate
60
What does ORFs mean?
Open reading frames
61
In Genome annotation the start codon preceded by what?
shine-delgarno sequence
62
What is comparative analysis?
To identified by the sequence similarity to genes found in other organisms where ther function has been characterized
63
What does comparative analyses allow for?
predictions of metabolic pathways and transport systems
64
Is annotation always correct?
NO
65
What has the smallest genomes?
parasites and endosymbionts
66
There is typically 1 ORF per what?
1000 bp
67
What are paralogs?
Genes with similarity due to duplication of an ancestral gene often have related but distinct function
68
What are orthologs?
Genes with similarity due to evolution/speciation of their hosts, usually have the same or similar function in their respective host
69
what does horizontal gene transfer happen?
the various methods of genetic exchange
70
What can horizontal dene transfer invovle?
It can involve transfer of plasmids or chromosomal DNA
71
What genes are subject to HGT?
Can include genes for drug resistance, pathogenicity
72
What type of descent is horizontal gene transfer?
Non-vertical descent
73
What are characteristics of the core genome?
It is shared by all strains
Includes necessary functions
Typically vertical descent
74
What are characteristics of the dispensable genome?
Only in some strains
Optional functions
Can include plasmids, prophages, transposons, insertion sequences, integrons, chromosomal islands
Veritcal and horizontal descent
75
What are chromosomal islands?
to be of "foreign" origin; large regions of DNA
76
Chromosomal islands are aquired by what?
HGT
77
What are some characteristics of the chromosomal islands?
Flanked by inverted repeats
| Base composition and codon usage differ
78
What did chromosomal island do?
Can encode genes with related functions
79
What can chromosomal islands contribute specialized functions that can be beneficial for what things?
```
Pathogenicity
Magnetotaxis
Thermophily
Degradation of novel compounds
Symbiosi of N-fixing root nodule bacteria with host plant
```
80
What is a metagenome?
the total gene content of organims inhabiting a given environment
81
What else is metagenomics known as?
environmental genomics
82
What else can metagenomics be done on?
cells or viruses
83
What is transcriptome?
All the RNA produced/present in the cell under a given set of conditions
84
What is proteome?
All the proteins produced/present in the cell under a given set of conditions
85
What is metabolome?
All the metabolites pre produced/present in the cell under a given set of conditions.
86
All transcriptome, proteome, and metabolome are what?
ambiguous and can be gualitative or quantitative
87
Proteins and metabolites can not be what?
amplified
88
What is the name of a technique?
Mass spectrometry
89
Why are igneous and metamorphic rocks not used in studying fossils?
Because they are heated too much to preserve record of life if it even existed
90
How old is the oldest sedimentary rock?
3.86 billions years old
91
What is it called for a stable isotope record?
Isotope fractionation
92
What type of isotope is incorporated?
Lighter over heavier
93
What are biomarkers?
molecules known only to be produced biologically
94
What is an example of microbial fossils?
Stromatolites
95
Ancient stromatolites are associated with what?
Light carbon and 2-methylhopanoids
96
What is the ancien earth atmosphere like?
highly reducing and hot
97
What was early life on earth like?
anaerobic and mainly thermophilic
98
What was Darwin's theory of life of surface origin?
Warm little pond but conditions may be too harsh
99
What was the theory of subsurface origin?
Hydrothermal vents on ocean floor which protected from harsh surface conditions
100
Why does the RNA world hypothesis work?
Can serve as templates for replication
Can be catalytic
Binds small molecules
101
What is the great oxidation event?
oxidation of iron
102
What created oxygen?
oxygenic photosynthesis by Cyanobacteria
103
What does the reactive between O2 with UV produce?
Produce a ozone shield
104
What is phylogenetics?
The evolutionary history of a group of organisms
105
What is taxonmy?
the science of identification, classification, and nomentclature.
106
In order teo understand phylogenetics led to what?
Five Kingdom System of classification
107
What is the five kingdom system of classification based on?
Morphology
108
In the five Kingdom system Monera is defined as what?
negatively
109
What is molecular evolution?
The process of the evolution of DNA, RNA and proteins
110
The evolution of the molecules may track the evolution of the orgamism only if it is transmitted what way?
vertically
111
What are the small subunits rRNA-based phylogeny championed by who?
Carl Woese
112
Why are rRNA genes argued to be the perfect organismal phylogenetics?
Universally distributed, functionally homologous, and slow evolving
113
What are rRNA used in phylogeny?
rRNA is present in all organism, and structurally and functionally conserved
114
What is phylogenetic tree?
Graphic illustration of the relationships among sequences
| Composed of nodes and branches
115
What is nodes?
Represent reconstructed divergence events
116
What are branches?
Define the order of descent and ancestry of the nodes
117
What do the branch length represents?
the number of changer that have occurred along that branch
118
What is monophyletic?
A group descended from one ancestor, most recent common ancestor and all decendents
119
What is polyphyletic?
A group that doesn't include a common ancestor
120
What does FISH stand for ?
Fluorescent in situ hybridization
121
What is phylogeny?
the evolutionary history of a group of organisms
122
What is taxonomy?
The science of identification, classification, and nomenclature
123
What is Systematics?
The study of teh diversity of organisms and their relationships.
Also links phylogeny with taxonomy
124
What is the polyphasic approach to taxonomy?
1. phenotypic analysis
2. genotypic analysis
3. phylogenetic analysis
125
What are the two different types of mechanisms for catabolismof organic compounds?
Respiration and Fermentation
126
What is respiration?
Exogenous electron acceptors are present to accept electrons generated from the oxidation of electron donors
127
What is fermentation?
Electron donor and acceptor are the same compound, yields little energy
128
What is the anabolic?
In the assimilative metabolism of an inorganic compound the reduced compounds are used in biosynthesis
129
What is catabolic?
the reduction of inorganic compounds called dissimilative metabolism because the reduced products are excreted
130
Does assimilative or dissimilative metabolisms have a much greater effect on the environment?
Dissimilative
131
What is dinitrification?
leads to teh loss of N from the ecosystem
132
What are some examples of different metals that Iron can respirate?
Mn, Se, Hg, As, Cr, U
133
When iron reducing bacteria can reduce U 6+ that is example of what?
Bioremediation
134
Who that swamp gas was combustible?
Alessandro Volta
135
What is methanogenesis?
A complex series of biochemical reactions that use novel coenzymes.
136
Where does autotrophy in methanogenes occur?
via the acetyl-CoA pathway
137
What does the C1 carries carry the carbon atom and gets oxidized from what?
CO2 to CH4
138
The steps to Methanogenesis?
1. CO2 activated by MF, reduced to formyl group H2
2. Formyl group transfered to MP, dehydrated, reduced to a methyl group
3. Methyl group is transferred to CoM
4. The methyl group is reduced to CH4 via e from F methyl reductase complex
139
What is the molecular approach?
```
Extract total community DNA
Amplify genes of interest
Library construction
DNA sequence analysis
Community genomics
```
140
What is extremophile?
an organism that thrives in and may even require physically or geochemically extreme conditions that are detrimental to the majority of life on Earth
141
Carbon from inorgnic sources?
Auto CO2
142
Carbon from organic sources
Organo
143
Energy from the sun
Photo
144
Energy from chemistry
Chemo
145
Organisms that obtain energy from the oxidation of inorganic compounds such as H2, Fe2+, H2S, S0, S2O3 2-, NH3, NO2 - are common from what kind of trophy?
Chemolithotrophy
146
Chemolithtrophy is known only what types nutrient cycling?
Bacteria and archaea
147
Carbon from inorganic molecules is known as?
Chemolithoautotrophs
148
Cabon from organic molecules is known as?
Mixotrophs
149
What is the key to understanding chemolithotrophy?
Thermodynamics
150
What relies on redox reaction?
Catabolic
151
If Gibb's free energy is negative what is the redox reaction?
exothermic
152
The reduction of CO2 into biomass is called what?
Carbon fixation or primary production
153
What are the different types of pathways?
1. Calvin Cycle
2. rTCA Cycle
3. 3-hydroxypropionate Pathway
4. 4-Hydroxybutyrate Pathway
5. Acetyl Co-A Pathway
154
What is hydrogen oxidation?
Hydrogen gas is derived from fermntation or from geologic processes (Can be aerobic or anaerobic)
155
In hydrogen oxidation is catalyzed by what enzyme?
hydrogenase
156
What does the hrdrogenase do?
Splits H2 into 2H+ and 2e-
157
In the ferrous iron oxidaiton what are the different rates of abiotic oxidation?
Fast at neutral pH
| Slow at acid pH
158
What does Rusticyanin do to Fe2+?
removes electrons from Fe2+ which flows directly to cytochromes and to TEA
159
Why are electrons need?
To maintain circumneutral pH in cytoplasm
160
Where is ammonia present?
in anaerobic water and produced by ammonification
161
What is nitrification is oxidation of what?
NH3 to NO3-
162
Ammonia oxidation is only catalyzed by what?
Only be certain bacteria and archaea
163
What is carbon fixation?
electrons from NAD9P)H are used to reduce CO2 into biomass
164
In oxygenic photosynthesis if H2O is the donor what is the waste?
O2
165
What is photophophorylation?
electrons are cycled through e transport components to createa PMF, driving ATP synthase activity
166
If there is another molecule that is the donor and O2 is not the waste that is called?
anoxygenic photosynthesis
167
what are the stacked membrane structures in the chloropasts called?
thylakoids
168
What are teh invaginations of the cytoplasmic membrane called?
Chlorosome
169
What are the photosynthetic membranes houses?
reaction centers
170
What do the reactions centers contain?
Chlorophylls
171
What do the chloropylls do?
use light energy to lower the reduction potential of electrons
172
What surround the reactions centers?
Antenn pigments, Chlorophylls, Carotenoids, and phycobilins
173
What do Chlorophylls, Carotenoids, and phycobilins do?
They absorb light and transfer enery to the reaction center of chlorophyll
174
What to antenna pigments do?
Allows cells to harvest light more efficiently, wspecially under low light conditions or protect the cells from photodamage under high light conditions
175
All phototrohs use some form of what?
Chlorophyll
176
What is a chlorophyll?
porphyrin
177
What is used in chlorophyll?
Mg instead od Fe
178
They are anchored into membranes by what?
Hydrophobic alcohol (phytol)
179
Where is chlorophyll found?
In Cyanobacteria
180
Where is bacteriochlorophyll found?
other bacteria
181
What are Carotenoids?
Always fund phototrophic organism
Typically Yellow, Red, Brown, Green
Energy absorbed
Prevent photo-ocidative damage to cells
182
How is ATP produced?
Produced by the process of cyclic photophosphorylation
183
Anoxygenic photosynthesis is what?
Purple Sulfur bacteria
184
Steps to Photophophorylation
1. Donation of electrons to PSII RC Chlorophyll form H2O
| 2. Excitation of RCII
