Micro Final Sec 2 Flashcards
(120 cards)
1
Q
Describe the function of a genome
A
Store and transmit all genetic info necessary for the organism to function, develop, and reproduce
2
Q
Briefly describe the size and nature (circular) of microbial genomes in comparison to eukaryotic genomes and the human genome
A
Microbial genomes: typically circular, range from 490-9,400 kb
Eukaryotic genomes: larger, linear, contian more noncoding DNA
3
Q
Define an operon
A
A set of genes controlled by a single promoter (cluster of genes; 2 or more)
4
Q
Describe the structure of DNA with respect to its constituent monomers (nucleotides) and its helical structure
A
Structure:
-Nitrogenous base (ATGC)
-Deoxyribose sugar
-Phosphate group
DNA Strands: antiparallel (5’ –> 3’ and 3’ –> 5’)
5
Q
Describe the bonds between adjacent nucleotides in a DNA chain
A
Base pairing
-A-T (2 hydrogen bonds)
-G-C (3 hydrogen bonds)
6
Q
Describe the hydrogen bonds between complementary bases
A
Base pairing
-A-T (2 hydrogen bonds)
-G-C (3 hydrogen bonds)
7
Q
Name the complementary base pairs and compare the two types of pairs with respect to their relative strength and number of H bonds
A
Base pairing
-A-T (2 hydrogen bonds)
-G-C (3 hydrogen bonds)
8
Q
Describe the polarity of DNA strands relative to one another in double stranded DNA
A
Antiparallel
9
Q
Describe how DNA strand polarity (5’, 3’) gets its name
A
from the numbering of the carbon atoms in the deoxyribose sugar molecule that makes up the backbone of the strand
10
Q
Describe the difference between RNA and DNA in terms of the 2’ position and be able to identify this in a diagram
A
RNA: has an OH on 2’ position
DNA: Has an H on 2’ position (more stable)
11
Q
Identify the electrostatic charge of DNA
A
Negative because of all the phosphate bonds (each phosphate is negative)
12
Q
Identify the enzymes that alter the supercoiling state of DNA
A
Topoisomerases
13
Q
Define DNA replication
A
Semiconservative, has three steps: initiation, elongation, and termination
14
Q
Name the main steps in DNA replication
A
Initiation: starts at the origin (ori), helicase unwinds DNA
Elongation: DNA polymerase III adds nucleotides in the 5’ –> 3’ direction
Termination: occurs at ter sites, Tus protein halts replication
15
Q
Define the functions of: initiator protein DnaA; helicase; DNA primase; DNA polymerase III, DNA polymerase I; DNA ligase: RNAse H
A
-DnaA: initiates replication by melting separate DNA strands
-Helicase: unzips DNA strands
-DNA primase: synthesizes RNA primers
-DNA Polymerase III: main replication enzyme
-DNA Polymerase I: replaces RNA primers with DNA
-DNA Ligase: seals Okazaki fragments (seals nicks on the backbone)
-RNAse H: Digest RNA primers so that they they can be filled with DNA
16
Q
Describe the polarity of DNA synthesis
A
DNA polymerase can only synthesize DNA in the 5’ to 3’ direction
17
Q
Distinguish between leading and lagging strands with respect to their polarity and the way they are replicated
A
Leading strand: continuously synthesized (5’–>3’)
Lagging strand: made in short Okazaki fragments (3’–>5’)
18
Q
Identify Okazaki fragments, know their approximate length, and describe how they are connected
A
-Short DNA segments that are created during DNA replication
-Connected by the DNA polymerase 1 and then the enzyme DNA ligase
-Part of lagging strand (1kb segment)
19
Q
Describe how DNA replication is terminated
A
At the ter site, a protein called Tus binds (creates trap), which stops the helicase and halts replication so it doesn’t just continue around and around the chromosome
20
Q
Define a plasmid, distinguish plasmids from chromosomes and describe what plasmids are used for
A
Plasmids are short (typically 3-20 kb), circular extrachromosomal DNA molecules that autonomously replicate
Used in molecular biology and genetics to carry genes of interest
–> replicates separately from chromosome
21
Q
Define transcription
A
-DNA –> RNA
-Accomplished by key Enzyme: RNA polymerase holoenzyme
–Include core polymerase and sigma factor
**Makes a copy of the encoded info
22
Q
Define translation
A
RNA –> Protein
Taking information from mRNA and converting it into polypeptide (into a protein)
23
Q
Define the functions and subunits of the RNA polymerase holo enzyme
A
–Core polymerase: catalyzes RNA synthesis
–Sigma factor: recognizes promoters (~10 and ~35 regions)
Subunits have alpha, beta, and sigma subunits
**It’s a multiimportant enzyme and the sigma factor has a special role to play
24
Q
Define the function of the sigma factor and describe when it dissociates from the RNA polymerase core
A
Sigma factor typically dissociates from RNA polymerase shortly after transcription initiation
25
Define a gene
A segment of DNA that encodes a protein (gets transcribed into RNA)
26
Define a promoter
a DNA sequence that is read by a sigma factor
Essentially says: start transcribing here
27
Describe how a sigma factor recognizes a promoter in a double stranded DNA helix
Sigma factor recognizes consensus sequences at the -10 and -35 positions (relative to the start of transcription, the +1 position)
Sigma factor is able to scan along the double helix and make chemical contact with the nitrogenous bases in major and minor grooves of the DNA (can identify sequences in a closed double helical structure)
28
Explain why bacterial cells use different sigma factors to direct the expression of different groups of genes
Many species have multiple sigma factors and each has its own matching consensus sequence
–each sigma factor recognizes a specific promoter sequence on DNA
29
Describe a consensus sequence
A sequence of DNA, RNA, or protein that represents aligned, related sequences
–> kind of like a promoter sequence
30
Describe the structure of RNA and distinguish it chemically from DNA, both in its ribose component and in its nitrogenous base
RNA is built of ribonucleotides
1) Nitrogenous base (uracil, no T)
2) Ribose sugar: like DNA but with OH at 2’ position; DNA has H)
3) Phosphate group: phosphodiester bonds just as in DNA
31
Explain why the 2' OH ribose makes RNA much less stable than DNA
The 2’-OH can occasionally attach the adjacent phosphodiester bond, breaking the RNA chain (self-cleaving)
–this happens well in warm temp and alkaline conditions
–DNA has no oxygen at the 2’ position (can’t self-cleave)
32
Describe the 3 principal components of a ribonucleotide and distinguish it from a deoxyribonucleotide
RNA is built of ribonucleotides
1) Nitrogenous base (uracil, no T)
2) Ribose sugar: like DNA but with OH at 2’ position; DNA has H)
3) Phosphate group: phosphodiester bonds just as in DNA
33
Describe the polarity of RNA
5’ –> 3’
34
Describe the relationship between promoters and sigma factors
Sigma factor recognizes sequences of promoter
35
Name and describe the 3 main steps in transcription
1) Initiation: RNA polymerase binds to promoter, opens DNA.
2) Elongation: RNA polymerase synthesizes RNA.
3) Termination: Ends via Rho-dependent or Rho-independent mechanisms.
36
Describe the steps in transcription initiation, distinguishing between the closed and open complex
1) RNAP “scans” for promoter sequences via sigma factor
2) Sigma factor binds to a promoter, forming the closed complex (DNA helix is “closed”)
3) RNAP unwinds DNA helix, making the open complex, and begins Synthesizing RNA. The sigma factor leaves once RNAP moves past the promoter
37
Explain how the complementary of bases allows for discrimination between correct and incorrect matches
Each base in DNA can only pair with its specific complementary base (lock and key mechanism) –> effectively filters out any mismatched bases that would disrupt the proper pairing and stability of the DNA molecule
38
Distinguish between the coding strand and template strand of DNA
1) Coding strand is the strand with the same sequence as the mRNA and runs 5’ to 3’
2) Template strand has the complementary sequence to the RNA and runs 3’ to 5’ –> used as the template to make mRNA used in coding strand
39
Define and distinguish between Rho-dependent and Rho-independent terminators with respect to the proteins involved and the DNA/RNA sequences involved
1) Rho-dependent terminators bind to a C rich sequence in mRNA and travel up RNA polymerase and cause it to fall off of the DNA and terminate transcription
2) Rho-independent terminators depend on a GC-rich region that forms a stem loop that is bound by a protein called NusA and causes RNAP to pause
40
Distinguish among the structures and functions of mRNA, rRNA, tRNA, and sRNA
mRNA: Carries genetic code.
rRNA: Component of ribosomes.
tRNA: Brings amino acids for translation.
sRNA: Regulates gene expression
41
Identify and define the major players in translation
-mRNA, containing the codons that specify the amino acid sequence
-Ribosomes, the rRNA-protein complexes that actually catalyze protein
formation
-Charged tRNA molecules that carry each of the 20 amino acids
-Elongation factors, proteins that help with translation
42
Describe how a tRNA molecule is able to decode a codon into the appropriate amino acid
-tRNA is a decoder molecule that converts the language of codons into an amino acid sequence (translates it)
-2 regions:
1) anticodon loop binds to its corresponding codon on mRNA
2) 3’ acceptor end is linked to the amino acid that corresponds to the anticodon loop
**When a tRNA has an amino acid attached to it, it’s called charged
43
Describe the function of an aminoacyl-tRNA synthetase, how it charges a tRNA, and how it ensures high fidelity
-Does the job of matching and attaching
-one for each of 20 amino acids
-Incredibly discriminatory, binding to their cognate tRNA molecule but to none of the others
44
Describe the organization of information in DNA and RNA into codons
Info organized into codons (3 nucleotide sequence in amino acids)
–> building blocks for protein synthesis
–> 4 nucleotides at each three positions
45
Define a reading frame
The way that codons are read in an mRNA sequence
46
Define the genetic code, including its generacy and universality
Composed of codons (3 nucleotide words that specify amino acids)
64 possible codons
–61 codons specify amino acids, other 3 stop codons
Universal: same in all species of life
Degenerate: each amino acid can be specified by multiple codons
47
Define and identify a start and stop codon
Start codon: AUG
Stop codon: UAG, UGA, or UAA
48
Describe the components of the ribosome in terms of their chemistry and their subunit division
Prokaryotic Ribosome (70S) Structure
- Small Subunit (30S) → 16S rRNA + 21 proteins (reads mRNA, aligns Shine-Dalgarno) –> first to bind
1 RNA molecule
- Large Subunit (50S) → 23S rRNA + 5S rRNA + 34 proteins (forms peptide bonds)
2 RNA molecules
- Composition: ~60% rRNA (structure + catalysis), ~40% proteins (stabilization).
- Function: Translates mRNA into proteins.
49
Describe how a ribosome becomes correctly positioned on mRNA and what components of the ribosome and mRNA interact to make this possible
Correctly positioned by an interaction between the 16S rRNA (part of the small subunit) and a sequence on the mRNA (RBS) –> happens before translation begins
50
Define a polysome and coupled transcription and translation and distinguish from transcription and translation in eukaryotes
1) Polysome: cluster of ribosomes attached to a single mRNA –> translates genetic info on mRNA into multiple polypeptide chains during protein synthesis (beads on a string)
2) Couple translation/transcription: happens at the same time –> key feature in prokaryotes (bacteria)
**In eukaryotes, transcription happens first, then translation
51
Define transertion
Where newly synthesized polypeptides (proteins) can begin the membrane insertion process before they’re done (translation and insertion into the membrane)
52
Describe the 3 tRNA-binding sites on the ribosome and distinguish among them with respect to their functions
1) The A (acceptor) site binds to
incoming charged tRNAs
2) The P (peptidyl-tRNA) site holds the
tRNA with the growing polypeptide
chain
3) The E (exit) site holds the tRNA that
was just stripped of its polypeptide
before it leaves the ribosome
53
Describe the 3 principal steps in translation
1) Initiation: the ribosomal subunits come together at the RBS, aligning the
ribosome so that the initiator tRNA is positioned correctly in the P site.
2) Elongation: amino acids (on tRNAs) come into the A site (guided by a correct
codon-anticodon match) and are added to the growing polypeptide chain
3) Termination: releases the completed protein at a stop codon and then recycles
the ribosomal subunits to begin again
54
Describe peptide bond formation and identify a peptide bond
The nitrogen of the amine group on the tRNA in the A site attacks the carbonyl carbon of the peptide in the P site, transferring the peptide to the tRNA at the A site
A peptide bond is a chemical bond that links amino acids together to form proteins
55
Describe the function of EF-Tu in ensuring fidelity in translation
Charged tRNA are brought to the A site by EF-Tu GTP
Only leaves if there is a correct match, EF-TU hydrolyzes
–this all occurs in elongation stage
–essentially responsible for bringing the correct amino acid to the growing polypeptide chain during translation elongation
–chaperone
56
Describe the function of EF-G in translocation
helps move messenger RNA (mRNA) and transfer RNA (tRNA)n through the ribosome during protein translation
–in elongation
57
Describe protein folding and the associated role of chaperones
Chaperones (e.g., GroEL-GroES) help proteins fold correctly based on finding their lowest energy conformation
–proper folding leads to it functioning
**essentially massage proteins to help
58
Describe the function of signal sequences of the SRP in the synthesis of membrane bound proteins or the secretions of proteins destined to be exported from the cell
Provides a specific amino acid sequences with signal sequences that target proteins to the membrane –> these are recognized by SRP and brought into membrane
59
Define transformation
Uptake of DNA by an organism
60
Define competence and give reasons why a bacterial cell might want to take up free DNA from its environment
Competence: ability of an organism to take up free DNA from its environment and internalize it and possibly incorporate it into its own genome if necessary
–Many reasons why a cell wants to do it: diversity, food, etc
61
Describe differences between Gram + and Gram - competence
Gram +: uses quorum sensing
Gram -: does not (competence machinery is different as well)
62
Define conjugation
Bacterial sex
63
Define the E.coli F plasmid (F factor) and explain how it is transferred
F plasmid has an origin of transfer on it and it also encodes machinery that allows DNA to be transferred from donor cell to recipient cell (uses mating pilus)
64
Explain what happens when the F plasmid is integrated into the E.coli chromosome
Origin of transfer becomes part of the chromosome that allows segments of the chromosome to be transferred like F plasmid
65
Describe the unique feature of Agrobacterium tumefaciens DNA transfer
Transfer DNA to plants and transform plant cells –> used in agricultural technology
66
Describe phage transduction
Process where a virus (bacteriophage) transfer genetic material from one bacterium to another
67
Define bacteriophage
A virus whose host is bacteria
68
Define restriction endonuclease
Proteins/enzymes that cleave DNA at specific sites on incoming “alien” DNA
69
Describe CRISPR and its function in bacterial "immunity" to invading DNA
CRISPR: provides a rudimentary “immune system” by specifically attacking certain foreign DNA molecules (bacterium immunity)
–Kind of like a bouncer from a club
70
Briefly describe how CRISPR can be used in biotechnology
Used to target genes for modification or deletion in eukaryotic systems (can target anywhere because of sequences of gRNAS)
71
Define and describe homologous recombination
The integration of one DNA molecule into another –> combining two DNA molecules into one
72
Define the role of the RecA protein in recombination
Recognizes homologous regions and brings them close to one another so that strand invasion can occur and the two DNA molecules can attach to each other
73
Distinguish between generalized recombination and site-specific recombination
Generalized transduction: why which any gene may be transferred from donor to recipient
Specialized transduction: where only genes closely linked to the phage chromosomal insertion site may be transferred (similar to F plasmid excision)
74
Briefly the describe the importance of recombination in bioengineering
Used all the time to add or subtract genes from organisms
75
Define a mutation in DNA
Change to the nucleotide coding sequence
76
Distinguish among point mutations, insertions/deletions, inversions, and reversions
Point mutations: single nucleotide base changes (can sometimes have effect on proteins)
Insertion/deletions: add/delete from nucleotide sequence
Inversions: stretch of DNA sequence flips around
Reversions: another mutation (mutated sequence) goes back to its original sequence
77
Distinguish between transitions and transversions
Transition: point mutation where a purine is substituted for another purine or pyrimidine for another pyrimidine
Transversion: purine to pyrimidine (like A going to C or T)
78
Define and recognize silent mutations, missense mutations, nonse mutations, and frameshift mutations
Silent mutation: point mutation that changes codon in coding sequence but does not change the amino acid (protein sequence is not changed at all)
Missense: changes codon and changes the specific amino acid (substituting one amino acid for another)
Nonsense: turns amino acid into a stop codon
Frame shift: insertions/deletions of nucleotides that change reading frame
79
Define a knockout mutation
Destroys the function of a gene
80
Describe how different chemical agents can cause DNA mutations
Intercalators - insert between bases in DNA helix —> cause misreading and introduces mutations
81
Describe spontaneous reactions that cause mutations
Cytosine deamination: That’s the loss of an amine group causing the nucleotides to mispair
82
Describe how UV light damages DNA
Causes formation of pyrimidine dimers -- distorts DNA structure and disrupts its normal functions
83
Describe different mechanisms for DNA repair: photoreactivation, nucleotide excision, base excision, methyl mismatch, recombination, and translesion bypass synthesis
Photoreactivation: cleaves pyrimidine dimers –> undoes damage done by UV light
Nucleotide excision: removes damage (removes damaged nucleotides from DNA strand)
Base excision: removes damaged bases from nucleotide (replaces with new ones)
Methyl mismatch: repair fixes replication error (fixes mistakes from DNA polymerase)
Recombination: uses other copy of a gene to repair the damaged gene (if given two copies of gene)
Trenslesion bypass synthesis: error prone method –> if DNA is extensively damaged, it will allow DNA synthesis to proceed where normal DNA synthesis can’t
84
Distinguish between error-proof and error-prone repair pathways
Error proof: the pressed way, as it restores the original sequence
Error prone: the last resort way –> preferable only to death, as errors may be introduced by the repair itself
85
Describe the mechanism of methyl mismatch repair
Based on the fact that the oldest gene in the cell (parent gene) is methylated. If, in replication, the original strand and new strand don’t match, it will use the methyl gene as the standard and will correct the newly synthesized strand so that it will match the methylated strand. Thus becoming methylated as well.
86
Define a mutator strain
Strain that is lacking one or more DNA repair pathways
87
Describe the SOS response and its relationship to error-prone DNA repair
SOS response is last resort (happens when there is extensive DNA damage and cell is at risk of losing integrity of its chromosome) to save its chromosome. It is error prone.
88
Describe the logic of having an error-prone DNA repair system if it can introduce mutations
Its mutate or die -- cell would rather mutate
89
Describe the utility of transposons as a way to screen for gene function
You can randomly inactivate genes when a transposon happens to hop into a gene –> used to screen mutagens
90
Describe how GC content can be a way of identify horizontal gene transfer events
Can tell about gene origins –> places with more/fewer GC base shows it may have originated from another molecule
91
Identify cellular energy intermediates (three)
Proton motive force
NADH
ATP
92
IDentify three carbon sources for catabolism
Polysaccharides
Lipids and amino acids
Aromatic compounds
93
Define fermentation and respiration and identify the important similarities and differences between them
Fermentation: incomplete breakdown (oxidation) of organic molecules using the breakdown products themselves as electron acceptors
Respiration: complete breakdown (oxidation) of organic molecules with electron transfer to a terminal electron acceptor
94
Which has more stored energy: an oxidized or reduced molecule
Reduced
95
Why does the triphosphate group of ATP contain high energy bonds
The phosphates have negative charges that repel each other and it’s very favorable to break said bond
–this breakage can be paired with unfavorable reactions in the cell to make them go
96
Identify 3 cellular electron carriers
ATP
NADH
FADH
97
Is carbon in glucose oxidized or reduced?
Oxidized
98
Distinguish EMP, ED< and PPP pathways with respect to their primary objective
EMP: most common form of glycolysis
–solely for energy generation
PPP pathway: building molecules (biosynthesis)
ED: splits the difference between PPP and EMP (used by E.coli)
99
List inputs/outputs of glycolysis (EMP) -- which molecules and how many
Input: glucose + 2 ATP
Output: 2 pyruvate, 4ATP, 2NADH
100
Distinguish between NAD+/NADPH and NADP+/NADPH in terms of what these energy intermediates are primarily used for in cells
NADP+ uses biosynthesis, other is for energy generation
101
Describe how NADH can be oxidized to regenerate NAD+ in the absence of oxygen
Fermentation
102
Define and distinguish among homolactic, heterolactic, ethanolic, and mixed acid fermentation
Homolactic: products-2 lactic acid, 2 NAD+
Heterlactic: lactic acid, ethanol, CO2, NAD+
Ethanolic: 2 ethanol, 2 CO2, 2 NAD+
Mixed-acid: Redox is balanced by making acetate, formate, lactate, succinate, ethanol, H2, CO2
103
Describe the TCA cycle in terms of its molecular inputs and outputs (idneity and number) and what the TCA cycle does to carbon compounds
Takes input of Acetyl-CoA to fully oxidize carbon dioxide
Outputs: 2 CO2, 3 NADH, ATP/GTP
104
Define and distinguish substrate level phosphorylation and oxidative phosphorylation
Substrate-level phosphorylation: produces ATP in glycolysis or TCA cycle
Oxidative phosphorylation: overall process of electron transport and ATP generation
105
Define ETS in terms of its 3 essential components, their order in the chain, and the overall function of an ETS within cells
NADH: quinone oxidoreductase
Mobile electron carrier (quinones)
Terminal oxidase (cytochromes)
Function: pumping protons
106
Describe the proton motive force in terms of it being an electrochemical gradient
Charges line up at high concentration (very localized) and wants to flow back into cell because of their gradient/charge
–cells harness PMF to generate ATP
107
Describe the function of the F1F0 ATPase: its power source and its cellular function
Consumes the proton motive force to make ATP – uses proton gradient as power source to spin
108
Identify 3 cellular functions or apparatuses that are powered by the proton motive force
Flagellar rotation
Antiporters
ATP generation
109
Explain how an ETS can connect oxidation of a carbon compound to ATP gneration
Take electrons from glucose, puts on NAD+ to make NADH, passed from NADH to ETS, pumps protons and establishes PMF which is then harnessed by F1FO to make ATP
110
Identify common terminal electron acceptors and compare them in terms of their reduction potentials (how good they are at taking electrons)
Nitrate – pretty decent electron acceptor
Sulfate – not good electron acceptor
Extracellular metals (Fe3+) – pretty good electron acceptor
111
Identify alternative, inorganic electron donors (food) that microbes use
H2, sulfur, ammonium
112
Define hydrogenotrophy and methyltrophy
Hydrogenotrophy : using H2
Methylotrophy: using one carbon compound
113
Identify the important outputs of photosynthesis
ATP and NADPH
114
Define photoexcitation and photolysis and describe how they relate to an electron transport system
Photoexcitation: uses energy embedded in light
This leads to photolysis – light driven separation of an electron from a donor molecule (its then transferred to ETS)
115
Describe the steps in photosynthesis
Chlorophyll aborbs light, electron separated from light, electron goes to ETS, ETS pumps H+ to make PMF go and drive ATP synthesis
116
Describe the function of the antenna complex and name the light absorbing pigment contained therin
Antenna complex holds chlorophyll molecules to maximize light absorption – like a satellite
117
Explain why the antenna complex is arranged in a circle around the reaction center (and define the reaction center)
Circular to maximize light absorption.
Reaction center: a protein complex where electron transfer to ETS occurs
118
Describe the oxygenic Z pathway in terms of its inputs, electron source, and outputs and in what organisms it is found
Takes electrons from water
Electrons used to pump H+ and make NADPH
Used by cyanobacteria and plants
119
Describe the function of bacteriorhodopsin and identify the light absorbing pigment therein
They are light-powered proton pumps and use retinal as their pigment
120
Describe the function of the Calvin cycle and define its inputs and outputs
Convert carbon dioxide into sugar. Autotrophs perform that
Inputs: carbon dioxide, ATP, NADPH
Outputs: glucose, ADP, and NADPH+
