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Microbiology > Exam 2 review > Flashcards

Exam 2 review Flashcards

1
Q

What is a genome?

A

complete set of genetic information

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2
Q

What is a gene?

A

functional unit

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3
Q

What is DNA replicaiton?

A

duplication of chromosome

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4
Q

What is gene expression?

A

going from DNA to protein

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5
Q

What is transcription?

A

going from DNA to RNA

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6
Q

What is translation?

A

going from RNA to protein

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7
Q

Information flows in which direction?

A

DNA——->RNA———->protein

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8
Q

What is the function of enzymes?

A

catalyze chemical reactions

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9
Q

What is molecular transport?

A

move small molecules into/out of cells

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10
Q

What is motility/mobility?

A

moves the cell

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11
Q

What is the function of sensors?

A

recognize extracellular conditions (nutrients, other cells, infectious agents, etc.)

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12
Q

What is the function of gene expression?

A

bind to DNA

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13
Q

What do proteins do for our body?

A

-produce enzymes
-molecular transport
-motility/mobility
-structure
-sensors
-gene expression

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14
Q

True or False
A:T nucleic acids base pairing have two hydrogen bonds.

A

True

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15
Q

True or False
G:C nucleic acids base pairing have one hydrogen bonds

A

False, there are three hydrogen bonds

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16
Q

How do antiparallel strands go?

A

5-3 and 3- 5

5PO4 attached to the 5th carbon and 3OH attached to 3rd carbon

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17
Q

What is replication?

A

DNA—–>DNA

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18
Q

What happens during initiation of DNA replication?

A

-proteins bind to origin of replication
-DNA gyrase and helicases

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19
Q

How do proteins bind to origin of replication?

A

-bacterial chromosomes/plasmids contain only one binding area
-eukaryotic cells multiple binding sites

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20
Q

What is the function of DNA gyrase and helicases?

A

-bind to origin of replication
-break and unwind DNA
-Primers (temporary bases are added) are added for replication

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21
Q

What is the function of DNA Polymerase?

A

-Synthesize DNA in the 5 to 3 direction
-Nucleotides added on the expanding 3` strand of the new DNA
-Can only add to pre-existing nucleotides (purpose of RNA primers)

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22
Q

What is step two of DNA replication?

A
  1. Synthesize DNA in the 5 to 3 direction
    Nucleotides added on the expanding 3` strand of the new DNA
    Can only add to pre-existing nucleotides (purpose of RNA primers)
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23
Q

What is step one of DNA replication?

A
  1. Synthesize DNA in the 5 to 3 direction
    Nucleotides added on the expanding 3` strand of the new DNA
    Can only add to pre-existing nucleotides (purpose of RNA primers)
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24
Q

What is step three of DNA Replication?

A

After helicase untwists and separates the strands, DNA polymerase binds to each strand. Scientists have identified several kinds of bacterial DNA polymerase. These vary in their specific functions, but all of them share one important feature—they synthesize DNA by adding nucleotides only to the hydroxyl group at the 3′ end of a nucleic acid. All DNA polymerases replicate DNA by adding nucleotides in only one direction—5′ to 3′—like a jeweler stringing pearls to make a necklace, adding them one at a time, always moving from one end of the string to the other. DNA polymerase III is the usual enzyme of DNA replication in bacteria.

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25
Q

What is step four of DNA replication?

A

An enzyme called primase synthesizes a short RNA molecule (4–15 nucleotides long) that is complementary to the DNA strand being copied. This RNA primer provides a 3′ hydroxyl group, which is required by DNA polymerase III.

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26
Q

What is step five of DNA replication?

A

Triphosphate deoxyribonucleotides form hydrogen bonds with their complements in the parental strand. Adenine nucleotides bind to thymine nucleotides, and guanine nucleotides bind to cytosine nucleotides.

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27
Q

What is step six of DNA replication

A

Triphosphate deoxyribonucleotides form hydrogen bonds with their complements in the parental strand. Adenine nucleotides bind to thymine nucleotides, and guanine nucleotides bind to cytosine nucleotides.

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28
Q

What is step seven of DNA replication?

A

Triphosphate deoxyribonucleotides form hydrogen bonds with their complements in the parental strand. Adenine nucleotides bind to thymine nucleotides, and guanine nucleotides bind to cytosine nucleotides.

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29
Q

What is step eight of DNA replication?

A

Primase synthesizes RNA primers, but in contrast to its action on the leading strand, primase synthesizes multiple primers—one every 1000 to 2000 DNA bases of the template strand.

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30
Q

What is step nine of DNA replication?

A

DNA polymerase III joins neighboring nucleotides and proofreads. In contrast to synthesis of the leading strand, however, the lagging strand is synthesized in discontinuous segments called Okazaki fragments, named for the Japanese scientist Reiji Okazaki (1930–1975), who first identified them. Each Okazaki fragment uses one of the new RNA primers, so each fragment consists of 1000 to 2000 nucleotides.

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31
Q

What is step ten of DNA replication?

A

Nucleotides pair up with their complements in the template—adenine with thymine, and cytosine with guanine.

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32
Q

What is step eleven of DNA replication?

A

DNA polymerase I replaces the RNA primers of Okazaki fragments as well as the RNA primer in the leading strand with DNA and proofreads the short DNA segment it has just synthesized.

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33
Q

What is step twelve of DNA replication?

A

DNA ligase seals the nicks between adjacent Okazaki fragments to form a continuous DNA strand.

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34
Q

What are the enzymes of DNA replication?

A

DNA gyrase, DNA helicase, RNA primase, DNA polymerase, Okazaki fragments, and DNA ligase.

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35
Q

What is the function of DNA gyrase?

A

Enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix.

Unique to PROKARYOTES

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36
Q

What is the function of DNA helicase?

A

Unwinds the double helix by breaking hydrogen bonds

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37
Q

What is the function of RNA primase?

A

Builds an RNA primer on leading and lagging strands

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38
Q

What is the function of DNA polymerase?

A

Adds daughter nucleotides on the parent strands

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39
Q

What is the function of Okazaki fragments?

A

Nucleic acid fragment produced during discontinuous synthesis of the lagging strand of DNA.

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40
Q

What is the function of DNA ligase?

A

Joins Okazaki fragments to form a continuous strand

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41
Q

What is the origin of replication?

A

Distinct region of a DNA molecule at which replication is initiated.

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42
Q

What is primer?

A

Fragment of nucleic acid to which DNA polymerase can add nucleotides (the enzyme can add nucleotides only to an existing fragment).

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43
Q

What is replisome?

A

The complex of enzymes and other proteins that synthesize DNA.

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44
Q

What are characteristics of RNA?

A

-Ribose instead of deoxyribose
-Uracil in place of thymine
-Usually shorter single strand
-Synthesized from DNA template strand
–RNA molecule is transcript
–Base-pairing rules apply except uracil pairs with adenine
–Transcript quickly separates from DNA

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45
Q

What are the 3 types of RNA?

A

-messenger RNA (mRNA)
-Ribosomal RNA (rRNA)
-Transfer RNA (tRNA)

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46
Q

What is RNA?

A

ribonucleic acid
-single stranded

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47
Q

What are the 5 steps of transcription?

A
  1. Sigma factor binding
  2. RNA polymerase splits the DNA
  3. RNA polymerase adds nucleotides (A, U, G, C)
  4. RNA polymerase links the nucleotides
  5. Hydrogen bonds between RNA & DNA are broken
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48
Q

What is transcription?

A

Process in which the genetic code from DNA is copied as RNA nucleotide sequences

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49
Q

RNA polymerase binds to sequence called a

A

promotor

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50
Q

What does the promoter do?

A

-Synthesizes in 5’ to 3’ direction
-Can initiate without primer

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51
Q

Where does transcription stop at?

A

a sequence called a terminator

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52
Q

RNA sequence is complementary, __________ to DNA template strand.

A

antiparallel

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53
Q

What strand is the DNA template?

A

minus strand

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54
Q

What strand is the RNA strand?

A

plus strand

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55
Q

RNA has the same sequence as (+) DNA strand except

A

Uracil instead of Thymine

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56
Q

What is genotype?

A

the actual set of genes in its genome

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57
Q

What is phenotype?

A

refers to the physical features and functional traits of an organism

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58
Q

What are the steps of transcription initiation, sigma factor?

A
  1. Initiation
    RNA polymerase binds to the promoter and melts a short stretch of DNA
  2. Elongation
    Sigma factor dissociates from RNA polymerase, leaving the core enzyme to complete transcription. RNA is synthesized in the 5’ to 3’ direction as the enzyme adds nucleotides to the 3’ end of the growing chain
  3. Termination
    When RNA polymerase encounters a terminator, it falls off the template and releases the newly synthesized RNA
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59
Q

What are the types of prokaryotic mRNA transcripts?

A

Monocistronic and polycistronic

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60
Q

What is monocistronic?

A

one gene

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61
Q

What is polycistronic?

A

multiple genes

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62
Q

What is translation?

A

process of decoding information in mRNA

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63
Q

What are the major components of translation?

A

mRNA, ribosomes (contain rRNA), tRNAs, and accessory proteins

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64
Q

What is genetic code?

A

every three nucleotides make up a codon which is one amino acid

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65
Q

How do ribosomes function in translation?

A

-Aligns and forms peptide bond between amino acids
-Locate punctuation sequences on mRNA molecule
==Begins at start site, moves along in 5′ to 3′ direction
-Maintain correct reading frame
Prokaryotic comprised of 30S and 50S subunits
==Made up of protein and ribosomal RNA (rRNA)

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66
Q

How does a tRNA get its amino acid?

A

Aminoacyl tRNA synthetase

ENZYMES

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67
Q

How are the polypeptide chains elongated during translation?

A

-peptide bind formed between amino acids
-ribosome advances one codon on mRNA
==tRNA exits E-site
==tRNA with growing protein occupies P site
==new tRNA occupies A-site
-the process repeats

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68
Q

What happens during the termination stage of translation?

A

-elongation continues until ribosome reaches stop codon
==not recognized by tRNA
==Enzymes break covalent bond joining to polypeptide to tRNA
-Ribosome falls off mRNA
==disassociates into component subunits (30s and 50s)
==subunits can be reused to initiate translation at other sites

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69
Q

what is an anticodon?

A

Sequence of three nucleotides in a tRNA molecule that is complementary to a particular codon in mRNA. The anticodon allows the tRNA to recognize and bind to the appropriate codon.

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70
Q

What is mRNA Polyribosome (polysome) reading frame?

A

Type of RNA molecule that contains the genetic information decoded during translation.
Multiple ribosomes attached to a single mRNA molecule.
Grouping of a stretch of nucleotides into sequential triplets that code for amino acids; an mRNA molecule has three potential reading frames, but only one is typically used in translation.

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71
Q

What is a ribosome?

A

Structure that facilitates the joining of amino acids during the process of translation; composed of protein and ribosomal RNA. The prokaryotic ribosome (70S) consists of a 30S and a 50S subunit.

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72
Q

What are ribosome binding sites?

A

Sequence of nucleotides in mRNA to which a ribosome binds; the first time the codon for methionine (AUG) appears after that site, translation generally begins.

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73
Q

What are rRNA start codons?

A

Type of RNA molecule present in ribosomes.
Codon at which translation is initiated; it is typically the first AUG after a ribosome-binding site.

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74
Q

What is a stop codon?

A

Codon that terminates translation, signaling the end of the protein; there are three stop codons.

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75
Q

What is tRNA?

A

Type of RNA molecule involved in interpreting the genetic code; each tRNA molecule carries a specific amino acid dictated by its anticodon.

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76
Q

What are components of translation in bacteria?

A

anticodon, mRNA Polyribosome (polysome) reading frame, ribosome, ribosome-binding site, rRNA start codon, stop codon and tRNA

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77
Q

What are the differences between Prokaryotes and Eukaryotes in transcription/translation?

A

Prokaryotes:
-All in the cytoplasm: No Nucleus!
-Translation begins as transcription is still occurring (simultaneous)
-Start codon codes for formylmethionine (f-Met)
==So do mitochondria & chloroplasts
-Multiple ribosomes (polyribosome) can be translating a strand of mRNA at the same time (quick)

Eukaryotes:
-Complete transcript is sent out of the nucleus where it is translated by ribosomes
-Start Codon is for methionine (Met)
-One ribosome translates a strand of mRNA before translation can begin again

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78
Q

How do Eukaryotes go through gene regulation?

A

Eukaryotic cells produce pre-mRNA

Capped with methylated guanine (5` end)

Poly A tail, ~200 adenine derivatives added (3` end)

Splicing introns out and exons together

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79
Q

What are the differences between prokaryotic and eukaryotic transcription and translation?

A

Prokaryotes:
-mRNA is not processed
-mRNA does not contain introns
-translation of mRNA begins as it is being transcribed
-mRNA is often polycistronic; translation usually begins at the first AUG codon that follows a ribosome-binding site

Eukaryotes:
-a cap is added tot he 5’ end of mRNA, and a poly A tail is added to the 3’ end
-mRNA contains introns, which are removed by splicing
-the mRNA transcript is transported out of the nucleus so that it can be translated in the cytoplasm
-mRNA is Monocistronic; translation begins at the first AUG

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80
Q

What is quorum sensing?

A

-cell/population density (expression at critical mass)
-biofilm formation

-“Sense” the density of cells within their own population
-Allows the expression of certain genes only when a certain mass has been reached
-Bacteria talk, via synthesized molecules

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81
Q

What is transduction?

A

transmission of information from the outside of a cell to the inside

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82
Q

What is phase variation?

A

involved switching genes on and off

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83
Q

__________ _________ is alteration of characteristics of surface proteins.

A

antigenic variation

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84
Q

What are the three main ways genes can be on or off?

A

Constitutive, inducible, and repressible

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85
Q

What is constitutive?

A

always on

-enzymes of the central metabolic pathways

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86
Q

What is inducible?

A

not routinely produced at significant levels

enzymes involved in the breakdown and transport of specific nutrients

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87
Q

What is repressible?

A

produced routinely, but can be turned off when they are not required

enzymes involved in building macromolecules (anabolic)

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88
Q

What are alternative sigma factors of bacterial gene regulation in transcription?

A

-sigma factors recognize specific promoters
-cells can produce specialized sigma factors to transcribe genes
-anti-sigma factors can inhibit transcription

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89
Q

What is an operon?

A

-consists of a promoter and a series of genes

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90
Q

What is an operator?

A

Controls the operon and is a regulatory element

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91
Q

What are repressors?

A

-protein that blocks transcription
-binds to the operator downstream of the promoter

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92
Q

What are activators?

A

-facilitates transcription (positive)
-protein binds to an activator binding site that helps RNA polymerase bind to the promoter

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93
Q

What is the lactose operon?

A

-includes genes involved in the transport and catabolism of lactose
-there are two events that activate the lac operon

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94
Q

What two events activate the lac operon?

A

-positive regulation by a protein called CAP
-deactivation of repressor molecule

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95
Q

What happens when both glucose and lactose are present?

A

-Caron catabolite repression (CCR) prevents expression of genes that metabolize lactose in presence of glucose.

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96
Q

What is the unique feature of gene regulation in eukaryotes?

A

RNA interference: RNAi
-microRNA (miRNA)
-short interfering RNA (siRNA)

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97
Q

What happens during regulation of genetic expression in eukaryotes?

A

RNA molecules can control translation
-Regulatory RNAs can regulate translation of polypeptides
==microRNAs bind complementary mRNA and inhibit its translation
==small interfering RNA. RNA molecule complementary to a portion of mRNA, tRNA, or DNA that binds and renders the target inactive
==Riboswitch: RNA molecule that changes shape to help regulate translation

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98
Q

What two mechanisms do bacteria have to adjust to new circumstances?

A

-regulation of gene expression
-genetic change

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99
Q

What are the two mechanisms of genetic change in bacteria?

A

-mutation
-horizontal gene transfer

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100
Q

What is mutation?

A

changes in existing nucleotide sequence

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101
Q

What is horizontal gene transfer?

A

movement of DNA from one organism to another

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102
Q

Changes are passed to progeny by _____ _______ _______

A

vertical gene transfer

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103
Q

Change in organism’s DNA alters __________

A

genotype

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104
Q

True or False

DNA has sequences of nucleotides

A

True

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105
Q

True or False

Bacteria are haploid

A

True

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106
Q

Change in genotype often changes observable characteristics or ________ that are influenced by environmental conditions.

A

phenotype

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107
Q

______________ __________ are genetic changes that result from normal processes

A

spontaneous mutations

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108
Q

____ ______ most common spontaneous mutation

A

Base substitution

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109
Q

What happens during base substitution?

A

-Incorrect nucleotide
-incorporated during
-DNA synthesis
-Point mutation is change of a single base pair

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110
Q

What are the three possible outcomes in base substitution?

A

-silent (synonymous) mutation
missense mutation
-nonsense mutation

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111
Q

What are silent mutations?

A

wild-type amino acid

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112
Q

What are missense mutations?

A

different amino acid
-resulting protein often does not function normally

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113
Q

What is a nonsense mutation?

A

specifies stop codon
-yields shorter, often non-functional protein

114
Q

How many hydrogen bonds do A-T have?

A

2 Hydrogen bonds

115
Q

How many hydrogen bonds do G-C have?

A

3 hydrogen bonds

116
Q

Base substitutions that inactivate a gene is termed a _____ or __________ mutation

A

null or knockout

117
Q

What environments are base substitutions more common in?

A

aerobic environments

118
Q

What is spontaneous mutations?

A

Deletion or addition of nucleotides
-3 pairs change one codon
-one or two pairs yields frameshift mutation

119
Q

What are transposons (jumping genes)?

A

pieces of DNA that can move from one location to another in a cell’s genome; process of transposition
-most have transcriptional terminators

120
Q

What is insertional inactivation?

A

gene into which transposon jumps is inactivated; function disrupted

121
Q

What are induced mutations?

A

result from outside influence
-agent that induces change in mutagen
-geneticists may use mutagens to increase mutation rate
-two general types:

==chemical agen
==radiation

122
Q

How do chemicals that modify nucleobases?

A

-change base-pairing properties; increase chance of incorrect nucleotide incorporation
-alkylating agents add alkyl groups onto nucleobases

123
Q

What are base analogs?

A

resemble nucleobases, but have different hydrogen-bonding properties
–can be incorporated into DNA by DNA polymerase
-wrong nucleotide is incorporated into complementary strand during DNA replication

124
Q

What are intercalating agents?

A

Increase frameshift mutations
-flat molecules that insert between adjacent base pairs in DNA strand.

125
Q

What do intercalating agents do?

A

-pushes nucleotides apart, produces space
-causes errors during replication

126
Q

True or False

Radiation can be used as a mutagen

A

True

127
Q

UV light cause _______ _______ (covalent bonds between adjacent thymines)

A

thymine dimers

128
Q

What is the function of thymine dimers?

A

-distorts molecule; replication and transcription stall
-mutations result from cell’s SOS repair mechanism

129
Q

_________ cause single-and-double-strand breaks in DNA

A

X-rays

130
Q

True or False

Mutations are rare because alterations in DNA generally repaired before being passed to progeny.

A

True

131
Q

During replication, _____ ________ sometimes incorporates wrong nucleotide.

A

DNA polymerase

132
Q

What are the two mechanisms of repair that takes place before DNA replication?

A

Proofreading and mismatch repair

133
Q

What is mismatch repair?

A

fixes errors missed by DNA polymerase

134
Q

What are the steps of mismatch repair?

A

-enzyme cuts sugar-phosphate backbone of new DNA strand
-another enzyme degrades short region of DNA strand with error
-DNA polymerase, DNA ligase fill in and seal the gap

135
Q

What happens when modified nucleobases lead to base substitutions?

A

-Glycosylase removes oxidized nucleobase
-Another enzyme cuts DNA at this site
-DNA polymerase removes short section; synthesizes replacement
-DNA ligase seals gap

136
Q

What is photoreactivation?

A

light repair

137
Q

How is photoreactivation used?

A

-enzyme uses energy form light
-breaks covalent bonds of thymine dimer
-only found in bacteria

138
Q

What is excision repair?

A

dark repair, no light involved

139
Q

How is excision repair used?

A

-enzyme removes damage
-DNA polymerase, DNA ligase fill in and seal the gap

140
Q

What is SOS repair?

A

last-ditch repair mechanism used when other systems fail

141
Q

When is SOS repair used?

A

Induced following extensive DNA damage that stalls DNA and RNA polymerases

142
Q

What are carcinogens?

A

cause many cancers; most are mutagens

143
Q

What is the Ames test?

A

measures effect of chemical on reversion rate of histidine-requiring Salmonella auxotroph
-uses direct selection on glucose-salts plate
-if chemical is mutagenic, reversion rate increases relative to control (more colonies grew)

144
Q

What are the 3 recombinant mutations of horizontal gene transfer?

A

Transformation, transduction, conjugation

145
Q

What is transformation?

A

a recipient cell takes up DNA from the environment. Involves uptake of short fragments of naked DNA by naturally transformable bacteria.

146
Q

What is transduction?

A

DNA is transferred from one cell to another via a replicating virus. Transfer of DNA from one bacterium into another via bacteriophages. Dead bacterial cells

147
Q

What is Conjugation?

A

bacterium containing a fertility plasmid forms a conjugation pilus that attaches and transfers plasmid genes to a recipient in reproduction of ciliates: Coupling of mating cells. Transfer of DNA material via sexual pilus and requires cell to cell contact

148
Q

What happens during transduction?

A

Phages infect bacterial cells
-Attaches to cell and injects its nucleic acid
-Phage enzymes cut bacterial DNA into small pieces
-Bacterial cell enzymes produce phage nucleic acid and a phage coat – components of new phage particles
-Phage particles are released from bacterial cell

149
Q

What is generalized transduction?

A

results when a fragment of bacterial DNA enters the phage protein coat
-produces a transducing particle

150
Q

What type of horizontal transfer involved the transfer of DNA via a virus?

A

Transduction

151
Q

What are the steps of transduction?

A
  1. phage injects its DNA
  2. phage enzymes degrade host DNA
  3. Cell synthesizes new phages that incorporate phage DNA and, mistakenly, some host DNA
  4. Transducing phage injects donor DNA
  5. Donor DNA is incorporated into recipient’s chromosome by recombination
152
Q

What are the steps of conjugation?

A
  1. donor cell attaches to a recipient cell with its pilus
  2. pilus draws cells together
  3. one strand of F plasmid DNA transfers to the recipient
  4. the recipient synthesizes a complementary strand to become an F+ cell with a pilus; the donor synthesizes a complementary strand restoring its complete plasmid
153
Q

What are the requirements in order for transformation to begin?

A

free DNA in the environment and a competent recipient

154
Q

What are the requirements in order for transduction to begin?

A

bacteriophage

155
Q

What are the requirements in order for conjugation to begin?

A

cell-to-cell contact and F plasmid, which is either in a cytosol or incorporated into chromosome of donor Hfr cell

156
Q

Which of the following represents the flow of information within a cell?

A

DNA > RNA > protein

157
Q

The molecule that seals the gaps between the pieces of DNA in the lagging strand is ___________________.

A

DNA ligase

158
Q

During transcription, RNA polymerase moves along the strand of DNA in which direction?

A

5’ to 3’

159
Q

Which of the following build(s) new strands of DNA?

A

DNA polymerase

160
Q

Transcription produces which of the following?

A

mRNA

161
Q

What results from the process of translation?

A

a polypeptide

162
Q

How is bacterial translation different from eukaryotic translation?

A

Bacteria can begin translation before transcription has terminated.

163
Q

Quorum sensing allows bacterial cells to…

A

engage in processes in a synchronous fashion.

create biofilms

deploy virulence mechanisms.

164
Q

Our human microbiota…

A

a. Educate our immune system
b. help us digest food
c. synthesize our vitamins

165
Q

In translation, which of the following act(s) as a decoder, reading mRNA codons and bringing the correct amino acid to the ribosome?`

A

tRNA

166
Q

A nucleotide base-pair substitution that changes an amino acid codon into a “stop” codon is a …

A

nonsense mutation

167
Q

What is the hallmark of all horizontal gene transfers?

A

Transfer of DNA between organisms of the same generation

168
Q

Which of the following is not a mechanism of genetic transfer between cells?

A

transcription

169
Q

When a transducing particle binds to and injects bacterial DNA into a recipient cell,

A

the DNA from the donor cell can recombine with the recipient host chromosome.

170
Q

The Lac Operon is…

A

an inducible operon

171
Q

Which of the following types of RNA molecule is/are part of the “machinery” of translation of the genetic code?

A

tRNA, rRNA

172
Q

Genes are _______ present in a cell, but _______ present in viruses.

A

Always
Always

173
Q

Ribosomes are ________ present in a cell, but _______ present in viruses.

A

Always, Never

174
Q

RNA polymerase is _______ present in a cell, but ________ present in viruses.

A

Always, Sometimes

175
Q

tRNA is _______ present in a cell, but _______ present in viruses.

A

Always, Never

176
Q

How are viruses different from eukaryotic cells?

A

They require a host in order to reproduce

177
Q

What is the function of the structural elements of a virus?

A

To package and protect the viral genome

178
Q

Which of the following represents the flow of information within a cell?

A

DNA > RNA > protein

mRNA acts as a messenger that carries information encoded by DNA to ribosomes, where proteins are synthesized.

179
Q

Which of the following is NOT a rationale for using mRNA intermediates in gene expression?

A

DNA lacks the necessary information for protein production.

DNA contains the information for protein production in its coding strand, which is acquired by mRNA during the process of transcription.

180
Q

Which of the following act(s) as a decoder, reading mRNA codons and bringing the correct amino acid to the ribosome?

A

tRNA

tRNA possesses an anticodon, which uses complementary base-pairing to bind the mRNA codon and provide the correct amino acid to the growing chain.

181
Q

What is the role of the A-site in translation?

A

to accept the next tRNA and its accompanying amino acid to the ribosome

The A-site contains the next mRNA codon, which is recognized by the appropriate amino-acylated tRNA. After accepting this tRNA, the peptide chain is transferred to the A-site momentarily before the ribosome translocates along the mRNA.

182
Q

You have designed a drug that irreversibly binds to the P-site of the ribosome. What is the outcome for a growing bacterial cell?

A

Protein translation would fail to initiate because of the inability of the initiator tRNA to bind within the ribosome.

If the P-site is occupied by the antibiotic, the initiator tRNA will no longer be able to bind the start codon, halting translation initiation.

183
Q

Which of the following statements best describes transcription?

A

the production of RNA from a DNA template

The template strand of DNA is read 3′ to 5′ by RNA polymerase using complementary base-pairing rules. This results in the synthesis of a single-stranded transcript that may be used in a variety of ways.

184
Q

What is the name of the DNA sequence to which RNA polymerase attaches to a gene and assists in transcription initiation?

A

the promoter

The promoter sequence is located upstream of the transcription start site. These sequences are recognized by RNA polymerase, promoting the binding of the enzyme upstream of the gene sequence itself.

185
Q

Which enzyme breaks the hydrogen bonds during replication?

A

DNA helicase

186
Q

How do stabilizing proteins work on the DNA?

A

They bind to the single-stranded DNA.

187
Q

In which direction does the replication fork move?

A

It moves ahead of the newly synthesized DNA.

188
Q

What ensures that the single strands of DNA do not come back together?

A

Stabilizing proteins

189
Q

What are the products of semiconservative replication for a double-stranded DNA molecule?

A

Two double-stranded DNA molecules, each consisting of one parental strand and one daughter strand.

190
Q

Why is DNA replication essential for a cell?

A

An organism must copy its DNA to pass genetic information to its offspring.

191
Q

What is the function of the parental DNA in replication?

A

It serves as the template for DNA replication.

192
Q

What is the inducer molecule in the lac operon?

A

Allolactose

193
Q

With which genetic region does the repressor protein interact?

A

The operator region

194
Q

When the cell is not in the presence of lactose,

A

the repressor proteins bind to the operator.

195
Q

What is the basic function of the lac operon?

A

To code for enzymes involved in catabolizing lactose.

196
Q

According to the animation, to what genetic element does the RNA polymerase bind?

A

The promoter

197
Q

Transcription produces which of the following?

A

mRNA, tRNA, and rRNA are all produced by transcription.

198
Q

According to the animation, which of the following makes mRNA from the information stored in a DNA template?

A

RNA polymerase

199
Q

Ribosomes contain which of the following?

A

rRNA

200
Q

Which of the following is involved in bringing amino acids to the ribosomes

A

tRNA

201
Q

Which of the following can be translated into protein?

A

mRNA

202
Q

With which nucleotide does adenine base-pair in a folded RNA molecule?

A

U

There are two hydrogen bonds formed between adenine and uracil in a folded RNA molecule. These interactions, as well as the hydrogen bonds between G and C, help stabilize the three-dimensional fold within an RNA molecule, which contributes to its function. It is important to note that thymine is only found in DNA—not RNA.

203
Q

What would be the sequence of the complementary DNA strand 5’ATCGGCTACG3’?

Based on the rules of complementary base pairing, the amount of guanine in a molecule of DNA will always be equal to the amount of cytosine. The same rule applies to adenine and thymine.

A

3’TAGCCGATGC’5

The base-pairing rules are A pairs with T and G with C. In order to hydrogen bond, the strands must run antiparallel, in opposite directions.

204
Q

Which molecule demonstrates the widest range of functions due to its ability to adopt multiple conformations?

A

RNA

The ability of RNA to fold into numerous three-dimensional conformations allows it to serve a variety of functions within the cell, including synthesizing proteins, regulating gene expression, and serving as a source of information for specific viruses.

205
Q

Which of the following lists the stages of the cell cycle in correct order?

A

interphase, prophase, metaphase, anaphase, telophase

The cell prepares to divide during interphase, including replicating its DNA. Then through mitosis and cytokinesis, the genetic material and the cell itself is divided, producing two identical daughter cells.

206
Q

Which of the following is not a correct description of a stage of mitosis?

A

In prophase, the DNA replicates and the cell prepares for division.

DNA replication and preparation for division takes place during interphase, which is represented by three distinct stages: G1, S, and G2.

207
Q

Which of the following build(s) new strands of DNA?

Enzymes are responsible for actually making new strands.

A

DNA polymerases

DNA polymerases build new strands of DNA by adding DNA nucleotides one at a time.

208
Q

Which statement about DNA replication is CORRECT?

The leading strand is newly sythesized DNA that can be synthesized without stopping.

A

The leading strand is built continuously, and the lagging strand is built in pieces.

The leading and lagging strands are the new strands of DNA made during DNA replication. The leading strand is built continuously, and the lagging strand is built in pieces.

209
Q

During DNA replication, which nucleotide will bind to an A nucleotide in the parental DNA?

Remember that thymine is replaced with uricil only in RNA.

A

T

210
Q

The molecule that seals the gaps between the pieces of DNA in the lagging strand is

Ligating the DNA ends to one another requires an enzyme (note: all enzymes end in “ase”).

A

DNA ligase

211
Q

Which statement about DNA replication is FALSE?

It is true that DNA polymerase builds both new leading and lagging strands by adding DNA nucleotides one at a time.

A

DNA ligase adds nucleotides to the lagging strand.

You’re right! This statement is FALSE. DNA ligase seals the gaps between segments of DNA in the lagging strand. It does not add nucleotides to the lagging strand.

212
Q

What characteristic of DNA allows two connected DNA polymerases to synthesize both the leading and lagging strands?

A

DNA is flexible

213
Q

What is the function of the connector proteins?

A

They link the leading strand DNA polymerase and the lagging strand DNA polymerase together.

214
Q

Which DNA strand is synthesized continuously?

A

Leading strand

215
Q

Which of the following are terms associated with Okazaki fragments?

A

Lagging strand, DNA ligase, and discontinuous

216
Q

Why is the DNA synthesis of the lagging strand considered discontinuous?

A

The synthesis is moving in the opposite direction from the replication fork.

217
Q

What are the steps in which the lagging strand is synthesized?

A
  1. DNA polymerase begins synthesizing the lagging strand by adding nucleotides to a short segment of RNA
  2. After each piece of the lagging strand is complete, it is released from DNA polymerase
  3. a different DNA polymerase replaces the RNA segments with DNA
  4. DNA ligase seals the gaps between the pieces, and eventually forms a continuous strand
218
Q

During the initiation step of translation, the fMet charged tRNA assembles in which site of the ribosome?

A

p site

219
Q

How does the ribosome know if the entering charged tRNA is correct?

A

The anticodon on the tRNA base pairs to the codon on the mRNA.

220
Q

Where would one find an uncharged tRNA molecule in a ribosome?

A

in the P and E sites

221
Q

What kind of bond is formed when two amino acids join together?

A

a peptide bond

222
Q

How is translation terminated?

A

When a protein called a release factor enters and binds to the A site

223
Q

What results from the process of translation?

A

a polypeptide

224
Q

How is bacterial translation different from eukaryotic translation?

A

Bacteria can begin translation before transcription has terminated.

225
Q

According to the animation, ribosomes move along the mRNA in which direction?

A

5’ to 3’

226
Q

How can viruses be distinguished from eukaryotic and prokaryotic organisms?

A

Viruses are acellular

Viruses are small, acellular, obligate intracellular parasites that consist of a small amount of genetic material enclosed in a protein shell

227
Q

What are the differences between DNA and RNA?

A

The RNA backbone is made up of ribose sugars and phosphate, while the DNA backbone is made up of deoxyribose sugars and phosphate; further, RNA uses uracil nucleotide whereas DNA uses thymine nucleotide

RNA is usually a single-stranded nucleic acid

228
Q

What effects does lysozyme have on bacteria?

A

lysozyme digests pptidoglycan, weakening their cell walls

229
Q

Where does transcription occur in eukaryotic cells?

A

in the nucleus

Transcription is the synthesis of RNA from a DNA template.

230
Q

What type of genome do viruses have?

A

Depending on the virus, viral genomes can be either DNA or RNA, either of which can be single stranded or double stranded

Viruses can have ssRNA, dsRNA, ssDNA, or dsDNA as their genomes, depending on the type of virus.

231
Q

What type of organisms do phages infect?

A

Bacteria

232
Q

What is the term used to describe viral nucleic acid surrounded by a protein “shell”?

A

Nucleocapsid

233
Q

Where does an enveloped virus get its envelope?

A

from a membrane of its host cell

234
Q

Which characteristics are used to classify viruses?

A

type of nucleic acid, presence or absence of an envelope, shape, and size

235
Q

What cellular structure protects bacteria from drying out?

A

Glycocalyx

236
Q

What type of microbe has lipid A?

A

Gram-negative bacteria

237
Q
A
238
Q

What can viruses infect?

A
  • plants
  • animals
  • bacteria
  • fungi
  • other viruses

A virus that infects bacteria won’t infect any other thing

239
Q

What are the differences between deasd and alive viruses?

A

Dead
1. inert
2. no cell compounds
3. no metabolism
4. no autonomy

Alive
1. Nucleic aicd
2. proteins
3. mutate
4. grow and multiple
5. react

Inert= onactive when not in a host
No autonomy= cannot survive on their own

240
Q

True or false

All viruses have a nucleic acid and a protein coat

A

True

241
Q

What is the structure of a virus?

A
  1. Nucleic acid
    • encodes virus genes
  2. protein coat
    * protective
    * enzymatic
  3. envelope (lipid bilayer)
    * matrix protein

Spikes attach to receptor sites on host cells. Phages attach by tail fibers.
Enveloped viruses have a lipid bilayer obtained from a host cell.
Enveloped viruses are more susceptible to disinfectant because damage to the envelope does not allow them to infect

242
Q

What are the 3 shapes of viruses?

A
  1. Icosahedral
  2. helical
  3. complex
243
Q

What is the description of a icosahedral shape?

A

20 flat triangles

244
Q

What is the description of a helical shape?

A

capsomeres arranged in helix

245
Q

What is the description of a complex shape?

A
  • phage
  • icosahedral nucleocapsid (head)
  • helical protein (tail)
246
Q

What are bacteriophages?

A
  1. infect bacteria
    * lytic
    * temperate
    * filamentous

bacteriophages enter and leave the bacteria via the F pilus
exit the host by lysing the cell

247
Q

What is lytic?

A

lyse the host cells and then end of infection

248
Q

What is temperate?

A

lytic or lysogenic

249
Q

What is filamentous?

A
  • rod shaped
  • requries an F-pilus
250
Q

What is horizontal gene transfer in bacteriophages?

A

Transduction
* generalized
* specialized

251
Q

What is generalized horizontal gene transfer?

A
  • Bacterial DNA that has been degraded can accidently packaged with new phage heads
  • Some viruses contain only fragmented bacterial DNA, these viruses cannot drive replication, but can incorporate into newly infected cell
252
Q

What is specialized horizontal gene transfer?

A
  • Bacterial DNA is excised with virus DNA when going from lysogenic to lytic
  • When incorporated into Phage it is defective, can also be incorporated into targets DNA
253
Q

What is a bacteriophage?

A

a virus that infects bacteria

254
Q

What is a capsomere?

A

proteinaceous subunit of a capsid

some capsomeres are composed of only a single type of protein, whereas others are composed of several different kinds of proteins.

255
Q

What is present in a viruses extracellular state?

A

virions have capsids-protein coats that provide both protection for viral nucleic acid and a means by which many viruses attach to their hosts’ cells.

256
Q

What is a capsid made of?

A

capsomeres

257
Q

What is a nucleocapsid?

A

nucleic acid surrounded by a capsid

258
Q

What are the three basic shapes of virions?

A

Helical, polyhedral, and complex

259
Q

True or False?

All viruses lack cell membranes

A

True

260
Q

True or False

Animal viruses have an envelope similar in composition to a cell membrane surrounding their capsids

A

True

261
Q

What is a virion called when it lacks an envelope?

A

non-enveloped or naked

262
Q

What are the 5 steps of the animal virus infection cycle?

A
  1. attachment (absorption)
  2. genome entry
  3. synthesis
  4. assembly
  5. release
263
Q

What happens in a lytic replication cycle?

A
  1. Attachment of the virion to the host cell
  2. Entry of the virion or its genome into the host cell
  3. Synthesis of new nucleic acids and viral proteins by the host cell’s enzymes and ribosomes
  4. Assembly of new virions within the host cell
  5. Release of the new virions from the host cell
264
Q

Where are most DNA viruses located?

A

Nucleus

265
Q

Where do most RNA viruses develop?

A

solely in cytoplasm

266
Q

During viral replication, how are enveloped viruses released?

A

by budding

can result in persistent infections

267
Q

How are naked viruses released?

A

exocytosis or lysis

268
Q

What are acute infections?

A
  • Rapid onset; short duration
  • Burst of virions released from infected host cell
  • Immune system gradually eliminates virus
269
Q

What are persistent infections?

A
  • continue for years or lifetime
  • may or may not have symptoms

Can be chronic or latent

270
Q

What is a chronic infection?

A

continuous production of low levels of virus particles

carriers may lack symptoms, but still transmit the virus

271
Q

What is a latent infection?

A

viral genome remains silent in host cell; can reactivate to cause productive infection

272
Q

What is a prion?

A

are proteinaceous infectious agents
* Linked to slow, fatal human diseases; animal diseases
* Usually transmitted only within a species
* Composed solely of protein; no nucleic acids

273
Q

What are the characteristics of prions?

A

Cellular PrP
* made by all mammals
* normal, functional structure has α-helices
Prion PrP
* Disease-causing form has β-pleated sheets
* Prion P r P causes cellular P r P to refold into prion P r P

274
Q

True or False

Normal sterilization procedures do not deactivate prions

A

True

275
Q

How are prions destroyed?

A

Prions destroyed by incineration or autoclaving in concentrated sodium hydroxide

276
Q

Short answer

Briefly describe the processes of transcription and translation. Note any differences in prokaryotic and eukaryotics transcription and translation

A

Transcription is the process of synthesizing an RNA molecule from a DNA template.
In both prokaryotic and eukaryotic cells, transcription involves the following steps:
a. Initiation: RNA polymerase binds to a promoter region on the DNA, marking the start of transcription.
b. Elongation: RNA polymerase moves along the DNA template, synthesizing an RNA strand complementary to one of the DNA strands.
c. Termination: Transcription ends when RNA polymerase reaches a termination signal, and the newly formed RNA molecule is released.
Translation is the process of synthesizing a protein using the information in an mRNA molecule.In both prokaryotic and eukaryotic cells, translation involves the following steps:
a. Initiation: The small ribosomal subunit binds to the mRNA and scans for the start codon (AUG). The large ribosomal subunit joins, and the first tRNA carrying the amino acid methionine (or N-formylmethionine in prokaryotes) is positioned at the start codon.
b. Elongation: The ribosome moves along the mRNA, and new tRNA molecules bring amino acids to the ribosome based on the codons in the mRNA. Peptide bonds form between the amino acids, and the ribosome advances.
c. Termination: Translation stops when a stop codon is encountered. Release factors bind to the ribosome, causing the release of the newly synthesized protein.

Transcription in prokaryotic cells, it occurs in the cytoplasm, while in eukaryotic cells, it occurs in the nucleus and involves mRNA modifications and complex gene regulation.

In prokaryotes, translation can begin before transcription is complete, using AUG as the start codon with N-formylmethionine. In eukaryotes, translation takes place in the cytoplasm after mRNA transcription, using AUG as the start codon with regular methionine.

277
Q

Short Answer

How does horizontal gene transfer occur? What is a major consequence of horizontal gene transfer?

A

Process in which a donor cell contributes part of its genome to a recipient cell, which may be a different species or genus from the donor. Cell to cell DNA movement. Must be kept by daughter cells.
* Homologuous recombination: exchange between two similar regions of DNA, highly conservative process
* Non-homologous: direct infection
* Transformation: involves uptake of short fragments of naked DNA by naturally transformable bacteria in the environment
*Transduction: Transfer of DNA from one bacterium into another via bacteriophages/ replicating virus
* Conjugation: transfer of DNA material via sexual pilus and requires cell to cell contact
A consequence of horizontal gene transfer is the emergence of resistant bacteria strains and the spread of human-related infections

278
Q

Short Answer

Compare and contrast silent, missense, and nonsense mutations

A

Silent: mutation produced by base-pair substitution that does not change the amino acid sequence, becuase of the redundancy of the gentic code
Missense: a substitution in a nucleotide sequence resulting in a different amino acid. What is transcribed makes sense but not the right sense
Nonsense: a substitution in a nucleotide sequence that causes an amino acid codon to be replaces by a stop codon
Comparison:
* Silent and missense mutations both involve changes in the DNA sequence, but silent mutations do not change the amino acid sequence, while missense mutations result in a different amino acid being incorporated.
* Nonsense mutations and missense mutations both result in changes to the amino acid sequence, but nonsense mutations introduce premature stop codons, leading to truncated proteins with impaired or no function.
Contrast
* Silent mutations have no impact on protein function, whereas missense and nonsense mutations can lead to functional changes.
* Missense mutations result in the replacement of one amino acid with another, while nonsense mutations lead to the premature termination of protein synthesis.
* Silent mutations typically involve codon changes that still code for the same amino acid, while missense and nonsense mutations often involve changes to different codons.

279
Q

Short Answer

Discuss lytic and lysogenic infections. Explain the medical significance of lysogenic conversion.

A

Are two difference ways in which bacteriophages can interact with their host bacteria. In a lytic infection, the bacteriophage injects its genetic material into the bacterial cell and takes over the host’s machinery for its own replication. In a lysogenic infection, the phage integrates its genetic material (prophage) into the host bacterial genome, becoming a part of the host’s DNA. Prophages can carry genes for antibiotic resistance. When integrated into bacteria, they can confer resistance to antibiotics, making infections harder to treat. This contributes to the spread of antibiotic-resistant bacteria.

280
Q

Describe the components and structure of viruses.

A

Have a nucleic acid, protein coat, and some have an envelope others are naked. Envelope is a bilayer. Either DNA or RNA. Three shapes: Icosahedral= 20 flat triangles, helical= capsomeres arranged in helix, and complex=phage, icosahedral nucleocapsid head and helical protein tail

Microbiology (15 decks)

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