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Micr exam 2 Flashcards

1
Q

Describe the function of a genome

A

all the genes in an organisms
function- to encode all the protiens and organisms needs

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2
Q

Briefly describe the size and nature (circular) of microbial genomes in comparison to eukaryotic genomes and the human genome

A

Microbial- circular, and small
Eukary- Larger, linear
Human- 46 chromosomes

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3
Q

Distinguish between monocistronic and polycistronic genes

A

mono- genes that are expressed or transcribed individually one promoter to one gene
Poly- Two or more Genes are transcribed together at the same time from the same promoter.

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4
Q

Define an operon

A

one promoter with multiple genes

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5
Q

Describe the structure of DNA with respect to its constituent monomers (nucleotides) and its helical structure; what holds the strands together?

A

DNA- deoxyribonucleotides
Two strands that wrap around each other held by hydron bonding between the nuclotide bases A-T C-G

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6
Q

dentify (in a diagram) and describe the three main components of a nucleotide

A

Nitrogous bases, sugar, phosphate group

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7
Q

Describe the bonds between adjacent nucleotides in a DNA chain

A

Phosphodiester bonds help together by phosphate group

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8
Q

Describe the hydrogen bonds between complementary bases

A

AT- Two bonds
CG- three bonds

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9
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

AT- Two bonds (weaker)
CG-Three bonds (Stronger)

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10
Q

Describe the polarity of DNA strands relative to one another in double-stranded DNA

A

one strand goes 5 to 3 and the other 5 to 3 antiparallel

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11
Q

Describe how DNA strand polarity (5’, 3’) gets its name

A

from the carbons in the ribo sugar 5’ has phosphate 3’ hydroxo unit

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12
Q

Describe the difference between RNA and DNA in terms of the 2’ position and be able to identify this difference in a diagram

A

in RNA there would be an additional hydroxyl group OH in DNA its just O

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13
Q

Briefly describe supercoiling and its relationship to DNA packing

A

When an helix wraps around itself to relieve strain needs to happen to be packed into the cyotplasm

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14
Q

Describe the difference between positive and negative supercoiling with respect to overwinding or underwinding of the DNA helix

A

POs- When the DNA helix is overwound
NEG- when the DNA Helix is underwound and twists DNA the opposite way

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15
Q

Identify the electrostatic charge of DNA

A

DNA is Neg- bc of all the phosphates are negative

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16
Q

Explain why most bacteria keep their chromosomes in a state of negative supercoiling

A

makes the DNA easier to unwind and you have to unwind the DNA to Do things like transcription and replication.

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17
Q

Identify the enzymes that alter the supercoiling state of DNA

A

Topoisomerases, change the supercoiling state by break a part of a strand and passing the other through then reconnecting

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18
Q

Define DNA replication

A

making a new copy of DNA from a template DNA

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19
Q

Explain what it means for DNA replication to be semiconservative

A

Each new strand has half of the original sequence of DNA

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20
Q

Name the main steps in DNA replication

A

Initiaion-
Englongation
Termination

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21
Q

Identify the loci on DNA where replication begins and ends

A

Loci- plural of loccus ,place, location
begins- Origin site, ori
Ends- Ter site , tus protiens

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22
Q

Define the functions of: the initiator protein DnaA; helicase; DNA primase; DNA polymerase III; DNA polymerase I; DNA ligase; RNAse H.

A

DNA A initiator- melts or separates the dna strands at ori site at the beginning on replication making space for helicase to load
Helicase- Unwind the DNA helix to make space for DNA primase
Primase- adds RNA primers to DNA so DNA polymerase can add on
DNA poly III- Main part, does most in replication elongates the RNA
DNA poly I-fills the gaps that are left after the RNA primers are removed
DNA Ligase- Seal the phosphdiester backbone when there are nicks or gaps left
RNAse H- digest RNA primers so they can be filled with DNA

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23
Q

Explain why DNA primase is needed in replication

A

makes RNA primer that can be elongated by DNA poly II

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24
Q

Describe the polarity of DNA synthesis

A

always 5’ to 3’

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25
Distinguish between leading and lagging strands with respect to their strand polarity and the way they are replicated
Leading- strand that can be consciously replicated 5' to 3' Lagging- can't be continuously replicated 5 to 3 so they have Okazaki fragments going in the opposite direction.
26
Identify Okazaki fragments, know their approximate length, and describe how they are connected
Fragments on the lagging strand that have to be replicated in smaller fragments 1,000 bases connected by DNA poly I
27
Describe how DNA replication is terminated
Ter sites opposite of Ori
28
Describe how interlinked replicated chromosomes (catenanes) are separated
By Topoisomerase XerCD
29
Define a plasmid, distinguish plasmids from chromosomes and describe what plasmids are used for
Plasmid- typically short circular piece of DNA that replicates on its own ,replicates separately form the chromosome Used to transfer genetic info from one cell to another or move genes
30
Define the central dogma of molecular biology
DNA replicates DNA is transcribed inot RNA, RNA is translateed into Protein
31
Definee transcription
Taking DNA and coverting it into RNA done by RNA polymerase
32
Define translation
Taking the info in a Mrna into a polypeptide into a protein
33
Define the functions and subunits of the RNA polymerase holoenzyme
Subunits- sigma factor RNA poly holo- one enzyme made of alpha subunit, beta subunits, omega subunit (chaperone)
34
Define the function of the sigma factor and describe when it dissociates from the RNA polymerase core
To detect the promoter, attaches to a DNA sequence tells promoter tells RNA polymerase where to transcribe the gene
35
Define a gene
a segment of DNA that encodes a protein or RNA
36
Define a promoter
DNA sequence that tells the sigma factor where a gene is to be transcribed every gene or operon needs one
37
Describe how a sigma factor recognizes a promoter in a double-stranded DNA helix
Is able to scan the DNA helix and connect with the bases and detect the major and minor groves
38
Explain why bacterial cells use different sigma factors to direct the expression of different groups of genes
39
Describe a consensus sequence
like a promoter sequence,
40
Describe the structure of RNA and distinguish it chemically from DNA, both in its ribose component and in its nitrogenous bases
DNA- 2' has an oxygen, ACGT RNA- 2' has a OH hydroxyl group. ACGU
41
Explain why the 2’ –OH of ribose makes RNA much less stable than DNA
Bc the hydroxyl group acts a nucleophyl and attacks the phosdideter and cleave
42
Describe the 3 principal components of a ribonucleotide and distinguish it from a deoxyribonucleotide
ribo- phosphate group. sugar, nitrogous base
43
Describe the polarity of RNA
5' prime end 3' end
44
Describe the relationship between promoters and sigma factors
Sigma- specifically recognize the sequences of Promoters
45
Name and describe the 3 main steps in transcription
Initiation elongation termination
46
Describe the steps in transcription initiation, distinguishing between the closed and open complex
47
Identify the directionality of RNA synthesis
5' to 3'
48
Draw complementary base pairing between DNA and RNA and deduce a complementary DNA or RNA sequence from a given template sequence
A- U
49
Explain how the complementary of bases allows for discrimination between correct and incorrect matches
Hydrogen bonding
50
Distinguish between the coding strand and template strand of DNA
coding- is the strand that has the same sequence as mRNA specify amino acids template- complementary to coding used to make mRNA strand
51
Define and distinguish between Rho-dependent and Rho-independent terminators with respect to the proteins involved and the DNA/RNA sequences involved
Dep- the protein is rho and binds to a C rich sequence in the mRNA and travels to RNA polymerase terminate transcription I- GC rich region forms stem loop in RNA
52
Distinguish among the structures and functions of mRNA, rRNA, tRNA, and sRNA
mRNA- messenger RNA, has coding sequence and takes DNA to ribosome to be decoded into protein sequence rRNA- Ribosomal RNa, strucuture and mechanism of ribosome tRNA- Transfer RNa, decodes codons has anticodon on one end and acid on other end sRNA- small rna, regulation of genes within cells
53
Identify and define the major players in translation
ribosomes, tRNAs, initiation and elongation factors, mRNA
54
Describe how a tRNA molecule is able to decode a codon into the appropriate amino acid
Anticodon on one end of tRNA and the aminoacid on the other side
55
Describe the function of an aminoacyl-tRNA synthetase, how it charges a tRNA, and how it ensures high fidelity
Have the right amino acids on the right tRNAs, job of aminoacyl tRNA syn, matches and charges the correct sequence with the tRNA
56
Describe the organization of information in DNA and RNA into codons
codons are 3 nucleotide "words" that specify the amino acid sequence.
57
Define reading frame
How the "words" are grouped
58
Define the genetic code, including its degeneracy and universality
64 codons ,61 encode specific amino acids 3 stop codons
59
Define and identify a start codon and stop codons
start- AUG, specifies methionine and the initiator tRNA Stop- 3, UAA, UGA, UAG, Tell ribosome to stop making protein
60
Describe the components of the ribosome in terms of their chemistry and their subunit division
Large sub- 50s subunit Small Sub-30s subunit 16s Rrna, first to bind both have rRNA
61
Describe how a ribosome becomes correctly positioned on mRNA and what components of the ribosome and mRNA interact to make this possible
small subunit of rRNA 16s rRNA interaste with ribosome binding site (Shine-Dalgarno) on the mRNA
62
Define a polysome and coupled transcription and translation and distinguish this from transcription and translation in eukaryotes
Polysome-Multiple ribosomes on the same mRNA Couples transcription and translation occur in the cytoplasm and can occur at the same time.
63
Define transertion
the insertion of a new protein into a new membrane combo of translation and insertion
64
Describe the 3 tRNA-binding sites on the ribosome and distinguish among them with respect to their functions
A site- acceptor site new charged tRNA come in to try to attach to the new chain if there a correct match. P site- peptidyl transfer site long peptide is stored and gets transferred into the new incoming amino acid. Esite- Exit Site, an empty uncharged tRNA leaves the ribosome
65
Describe the three principal steps in translation
Initiation, elongation, termination
66
Describe peptide bond formation and identify a peptide bond
67
Explain the function of initiation and elongation factors in translation
initiation factors help get the ribosome correctly positioned on the mRNA
68
Describe the function of EF-Tu in ensuring fidelity in translation
is a chaperon protein attached to the incoming charged tRNA only leaves if there is a match between the codon and anticodon
69
Describe the function of EF-G in translocation
Responsible for burning GTP so the the ribosome can move to the next codon and the empty tRNA can exit and the new tRNA can enter into the acceptor site
70
Describe protein folding and the associated role of chaperones
Proteins are long polypeptides they fold into specific 3d structures based on the lowest energy conformation. chaperone protein massage proteins to find optimal folded position
71
Describe the function of signal sequences and the SRP in the synthesis of membrane-bound proteins or the secretion of proteins destined to be exported from the cell
proteins end up in the membrane due through the signal recognition particle inserted inserted into the membrane through the insertion complex
72
Define transformation
uptake by a DNA organism
73
Define horizontal gene transfer and distinguish it from vertical gene transfer
Hor- Gene gets transferred from one organism to another that's on the same level as the organism Ver- Parent to offspring ,transfer of gene vertically
74
Define competence and give reasons why a bacterial cell might want to take up free DNA from its environment
Ability of an organism to take up free DNA from its environment and internalize it and incorporate it into its own genome - get a new gene - food
75
Define a transformasome and describe its function in competence
Gram positive organisms , complex in the cell envelope that import DNA and allows the cell to be transformed to take in DNA by secifically importing a strand
76
Describe differences between Gram + and Gram – competence
+- use quorum sensing - - does not, competence machinery is different
77
Define conjugation
Bacterial mating or sex
78
Define the E. coli F plasmid (F factor) and explain how it is transferred
origin of transfer than can encode machinery that allows DNA to be transferred from the donor cell directly to the recipient (pilis)
79
Explain what happens when the F plasmid is integrated into the E. coli chromosome
allows segments of the chromosome to be transferred
80
Describe the unique feature of Agrobacterium tumefaciens DNA transfer
able to inject DNA into plant cells, used in agriculture to move genes into plant cells
81
Describe phage transduction
3rd mechanism of horizontal gene transfer 1st- competence 2nd- conjugation
82
Define bacteriophage
a virus host is bacterium
83
Distinguish between generalized transduction and specialized transduction
gen- some of the host chromosomal DNA is accidently package into a phage particle Spec- integrating phages that sometimes will excise or leave the chromosome and take some chromosomal DNA
84
Define restriction endonuclease
Protein enzymes that cut DNA at very specific palindromic nucleotide sequences, used to protect themselves from harmful incoming DNA
85
Describe restriction sites in DNA and how they are used in molecular biology
Palindromic sequences of nucleotides used to cut DNA molecules
86
Describe CRISPR and its function in bacterial “immunity” to invading DNA
CRISPR spacers between repeats, DNA sequences that the bacteria recognizes it from a previous bacterium and wants to remember it to be able to defend itself from the sequence
87
Briefly describe how CRISPR can be used in biotechnology
Can be used to cut mammalian DNA sequences at defined sites
88
Define and describe homologous recombination
recombination is the integration of one DNA molecule into another making them one two DNA molecules having extensive regions of homology then able to be identified by the recA
89
Define the role of the RecA protein in recombination
to recognize the homologous regions and brings them close to each other so the strand invasion can occur
90
Distinguish between generalized recombination and site-specific recombination
Gen- Extensive regions of homology recognized by the RecA protein Site- Recombination of specific and short precise sequences found by recombinase enzymes
91
Briefly describe the importance of recombination in bioengineering
Make a new DNA molecule Give a gene a new bacterium/gene or take away a gene
92
Define a mutation in DNA
Change to the nucleotide coding sequence
93
Distinguish among point mutations, insertions/deletions, inversions, and reversions
Point- single nucleotide base changes Insertions/deletions: extra nucleotides being added or deleted from a nucleotide sequence Inversions: a stretch of DNA sequence flips around opposite orientation Reversion: another mutation goes back to its original sequence
94
Distinguish between transitions and transversions
transitions- pure mutation, a purine for a purine (A-G G-A), Pyrimidine for a pyrimidine (C-T T-C) transversions- mutation from purine to pyrimidine( A-C, A-T, G-C, C-G)
95
Define and recognize silent mutations, missense mutations, nonsense mutations, and frameshift mutations
Silent- Point mutation that changes a codon in a coding sequence but not the amino acid Missense- Changes the codon and the amino acid Nonsense- amino acid codon to a stop codon (ending the protein from continuing) Frameshift- Insertions or deletions of nucleotides not a multiple of 3 (2,5,7,10)
96
Define a knockout mutation
destroys a function of a gene
97
Describe how different chemical agents can cause DNA mutations
98
Describe spontaneous reactions that cause mutations
cytosine deamination-lose of an amine group causing nucleotides to mis pair EX G-A , G-T
99
Describe how UV light damages DNA
Causing cyclobutene pyrimidine dimers- links two thymine residues next to one another next to a dimer that destroys the helix
100
Describe different mechanisms for DNA repair: photoreactivation, nucleotide excision, base excision, methyl mismatch, recombination, and translesion bypass synthesis
photoreactivation- cleaves a dimer so that it becomes two thymine (undos UV damage) nucleotide excision- gets rid of thymine dimer and puts back correct base base excision- first cuts out damaged base and them inserted nucleotides methyl mismatch- helps mitigate errors made by the DNA polymerase by using methylation recombination- uses one DNA molecule being integrated into one translesion bypass synthesis- last resort SOS, allows DNA synthesis to proceed where normal DNA synthesis can not proceed
101
Distinguish between error-proof and error-prone repair pathways
Proof- restore the perfect DNA sequence the way it was Prone- SOS. translation bypass synthesis
102
Describe the mechanism of methyl mismatch repair
Uses methylated strand(parental strand) as the standard and correct the newly synthesizedA strand
103
Define a mutator strain
A strain that lacks one or more DNA repair pathways, accumulates mutations at a high rate
104
Describe the SOS response and its relationship to error-prone DNA repair
SOS response is the last resort, happens when there's extensive cell damage and the cell is in danger of losing its integrity of its chromosome, cant pass genetic information
105
Describe the logic of having an error-prone DNA repair system if it can introduce mutations
Choose mutation over death
106
Briefly describe non-homologous end joining
Broken DNA helices and they're put back together without consideration of its sequences, can introduce mutations
107
Define transposable element and name two examples
DNA molecule that is able to "jump" and insert itself into another DNA molecule EX: insertion sequences (IS), Transposon
108
Describe an inverted repeat
on either side of transposons or insertion sequences and they are sequences of DNA that match . facing one direction on one strand and visversa
109
Describe the utility of transposons as a way to screen for gene function
Use to randomly hop into a recipient DNA molecule, can randomly inactive genes
110
Describe how GC content can be a way of identifying horizontal gene transfer events

Micro Lec ExM 1 (2 decks)

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