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Microbiology > Chapter 6: Molecular information flow and protein processing > Flashcards

Chapter 6: Molecular information flow and protein processing Flashcards

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1
Q

gene

A

Functional unit of genetic information

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2
Q

genetic elements

A

Genes are part of genetic elements: large
molecules and/or chromosomes

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3
Q

Genome

A

all genetic elements

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4
Q

Informational macromolecules

A

nucleic acids and
proteins

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5
Q

Nucleotides

A

nucleic acid monomers
 D N A and R N A are polynucleotides
 Three components: pentose sugar (ribose or
deoxyribose), nitrogenous base, phosphate (PO43−)

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6
Q

DNA and RNA

A

DNA (genetic blueprint) and RNA (transcription
product)
 Messenger RNA (mRNA) is translated into
protein (amino acid sequence)

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7
Q

Nucleoside

A

has pentose sugar and
nitrogenase base, no phosphate

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8
Q

Properties of the Double Helix

A

 Nucleic acid backbone is a polymer of alternating phosphates and the pentose sugar deoxyribose
 Phosphodiester bonds connect 3′-carbon of
one sugar to 5′-carbon of the adjacent sugar
DNA is double-stranded and held together by hydrogen bonding between bases
 Two strands are antiparallel (5′-3′ and 3′ to 5′),
forming double helix
 Contains two grooves, major (where proteins bind)
and minor

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9
Q

Primary structure (DNA)

A

sequence of nucleotides
that encodes genetic information

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10
Q

complementary base sequences

A

Adenine pairs with thymine
 Guanine pairs with cytosine

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11
Q

Size and Shape of DNA

A

Size is expressed in number of nucleotide base pairs
 1000 base pairs = 1 kilobase pair = 1 kbp
 1 million base pairs = 1 megabase pair = 1Mbp
 E. coli genome = 4.64 Mbp
 Linear DNA length is several hundred times longer than cell, so supercoiling compacts DNA to
accommodate genome

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12
Q

supercoiled DNA mechanism

A
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13
Q

Supercoiled DNA components

A

 Topoisomerases insert and remove supercoils
 Negative supercoiling: twisted in opposite sense relative to right-handed double helix; found in most cells
 DNA gyrase: introduces supercoils into DNA via double-strand breaks
 Positive supercoiling: helps prevent DNA melting at high temperatures (e.g., some Archaea)

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14
Q

Central dogma

A

Genetic information flow can
be divided into three stages, DNA to RNA to
protein
 Gene expression transfers DNA information to
RNA.

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15
Q

Three main RNA classes involved in protein synthesis

A

 mRNA (messenger RNA): carry information to ribosome
 tRNA (transfer RNA): convert mRNA information to amino acid sequence
 rRNA (ribosomal RNA): catalytic and structural ribosome components

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16
Q

Synthesis of informational macromolecules steps

A
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17
Q

Eukaryotic genetic information flow

A

Each gene is transcribed individually into a single mRNA ( Monocistronic mRNA)
 Replication and transcription occur in nucleus
 RNAs must be exported outside nucleus for translation
Many different RNAs can be described from a short DNA region

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18
Q

Prokaryotes genetic information flow

A

Multiple genes may be transcribed in one m RNA (Polycistonic mRNA)
 Coupled transcription and translation occur producing proteins at maximal rate

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19
Q

How would a virus violate the
central dogma?

A

Viruses go backwards
contain RNA converted into DNA by reverse transcriptase

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20
Q

Chromosome

A

main genetic element in prokaryotes
 Other genetic elements include virus genomes, plasmids, organellar genomes, and transposable
elements
 Most Bacteria and Archaea have single circular chromosome carrying all/most genes
 Eukaryotes: two or more linear chromosomes

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21
Q

Kinds of genetic elements summary

A
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22
Q

Viruses and plasmid DNA content

A

Viruses contain either RNA or DNA genomes.
 can be single- or double-stranded
 can be linear or circular
 Plasmids: circular or linear double-stranded DNA that replicate separately from chromosome
Cell can survive without plasmid but survives better with it
Replicates separately from chromosomes

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23
Q

Transposable elements

A

 segments of DNA inserted into other DNA molecules that can move from one site to another site on the
same or a different DNA molecule (e.g., chromosomes, plasmids, viral genomes)
 found in prokaryotes and eukaryotes

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24
Q

Some features of the Escherichia coli K-12 chromosome

A

 About 5 Mbp in size
 Almost 4300 possible protein-encoding genes make up 88 percent of the genome
 Compact relative to eukaryotes, which contain extra DNA
 Many genes encoding enzymes of a single biochemical pathway are clustered into operons, transcribed to form single
mRNA and regulated as a unit
 Many genes for biochemical pathways are not clustered
 Thus, operons appear to be exceptions instead of the rule

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25
Q

plasmid description

A

found in many Bacteria and Archaea
 mostly non-essential but may influence host cell physiology (e.g., survival under certain
conditions)
 nearly all double-stranded DNA, mostly circular
 typically, less than 5 percent of the size of the chromosome
 present in different copy number (1 or a few to 100+ copies)

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26
Q

R plasmids

A

Widespread and well-studied
 Resistance plasmids; confer resistance to antibiotics or other growth inhibitors
 Several antibiotic resistance genes can be encoded on one R plasmid (e.g., R100)

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27
Q

what do plasmids code for

A

 In several pathogenic bacteria, virulence factors (e.g., ability to attach or produce toxins) are encoded by
plasmids
 Bacteriocins (proteins that inhibit or kill closely related species or different strains of the same species) can
be encoded on plasmids
 Rhizobia require plasmid-encoded functions to fix nitrogen
 Metabolism (e.g., hydrocarbon degradation)
 Important for conjugation (horizontal gene transfer)

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28
Q

Verticle transfer

A

From parents to offspring
Plasmids can also be transferred
vertically

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29
Q

Type of DNA replication

A

semiconservative: each of
the two resulting double helices has one new
strand and one parental (template) strand
 Precursor of each nucleotide is a
deoxynucleoside 5′-triphosphate
 Replication ALWAYS proceeds from the 5′
end to the 3′ end

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30
Q

types of DNA polymerase

A

 DNA polymerases catalyze polymerization of deoxynucleotides
 Five different DNA polymerases (DNA Pol I –V) in E. coli
 DNA Pol III is the primary enzyme in DNA replication
 DNA Pol I plays a lesser role in DNA replication
 Other repair DNA damage

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31
Q

Replication Enzyme mechanism

A

DNA polymerases can only add nucleotides to pre-existing 3′-OH and require a primer: short
stretch of RNA
 Primer made from RNA by primase
 Primer eventually removed and replaced with DNA

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32
Q

type of replication enzymes

A

Helicase
Single-strand binding protein
Primase
DNA polymerase III
DNA polymerase I
DNA ligase
Topoisomerase IV

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33
Q

Helicase

A

Unwinds double helix at replication fork

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34
Q

Single-strand binding protein

A

Prevents single strands from annealing

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35
Q

Primase

A

Primes new strands of DNA

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36
Q

DNA polymerase III

A

Main polymerizing enzyme

37
Q

DNA polymerase I

A

Excises RNA primer and fills in gaps

38
Q

DNA ligase

A

Seals nicks in DNA

39
Q

Topoisomerase IV

A

Unlinking of interlocked circles

40
Q

Initiation of DNA Synthesis

A

DNA synthesis begins at a specific location on the bacterial chromosome called the origin of replication (oriC).
●
The protein DnaA binds to oriC and opens up the DNA double helix.
●
Enzymes called DNA helicases then bind to the DNA molecule and begin to unwind the double helix, using energy from ATP. This creates two Y-shaped replication forks, which are the sites of DNA synthesis.
●
Single-strand binding proteins bind to the now-separated single strands of DNA to prevent them from coming back together.
●
Topoisomerases, such as DNA gyrase, help relieve stress on the DNA molecule as it unwinds by creating breaks in the DNA and then rejoining them, introducing negative supercoils.
●
The enzyme primase then synthesizes a short RNA primer, providing a free 3’-OH group for DNA polymerase to attach the first DNA nucleotide. The primase is sometimes referred to as a primosome.
●
Once the primer is in place, DNA polymerase III can begin adding deoxyribonucleoside triphosphates (dNTPs) to the 3’ end of the primer. This marks the beginning of DNA synthesis.

41
Q

Leading and Lagging Strands and the Replication Process

A

 DNA replication at replication fork
 occurs continuously on the leading strand 5’ to 3′ (always free 3’-OH)
 discontinuously on lagging strand—no 3’-OH
 Primase synthesizes multiple RNA primers

42
Q

 Leading and Lagging Strands and the Replication Process (after replication fork has been made)

A

DNA replication at replication fork
 Primase replaces by DNA Pol III and DNA synthesis until it reaches the previously synthesized DNA
 DNA Pol I removes the RNA primer and replaces it with DNA
 DNA ligase seals the nicks in the DNA

43
Q

replication rate

A

DNA Pol III adds 1000 bp per second

44
Q

Replication of Circular DNA

A

known as theta structure

45
Q

The Replisome

A

large replication complex of multiple proteins
 When replication forks collide at terminus of replication (opposite origin), replisome is finished
 DNA is partitioned; facilitated by FtsZ

46
Q

 Primosome

A

helicase and primase subcomplex within replisome

47
Q

Why do we need proofreading?

A

Mistakes Mutations Misfoldedprotein
Mutation rates are 10^-8 to 10^-11errorsperbp
Proofreading ensures high fidelity

48
Q

 Fidelity of DNA Replication:

A

During DNA replication DNA Pol I and III can detect a bp mismatch through double helix distortion
 Can remove the mismatched bp with 3’ - 5’ exonuclease activity
 Exonuclease proofreading occurs in prokaryotes, eukaryotes, and viral DNA replication systems

49
Q

Two key differences in RNA vs DNA chemistry

A

 ribose instead of deoxyribose
 uracil instead of thymine
 Typically, single-stranded
 Fold into secondary structure (complementary base pairing) that influences function

50
Q

Transcription mechanism

A

 Catalyzed by RNA polymerase
 Phosphodiester bonds between ribonucleotides
 Similar mechanism
 Uses DNA as template; only one strand transcribed
 no priming needed
 Transcription terminators mark end of transcription
 Highly regulated process allowing transcription at different frequencies depending on need

51
Q

Transcription binding

A
52
Q

 RNA Polymerases and the Promoter Sequence

A

 RNA polymerase has five different subunits
forming RNA polymerase holoenzyme
complex
 Sigma not as tightly bound, easily dissociates to yield
RNA polymerase core enzyme
 Core enzyme synthesizes RNA
 Sigma recognizes initiation sites on DNA called promoters to begin transcription
 Transcription occurs in opposite directions on DNA strands

53
Q

sigma factors

A

 Promoters are specific DNA sequences
 recognized by σ70
 sequences vary but two highly conserved regions: Pribnow box (−10 region, TATAAT) and TTGACA (−35)
 Strong promoters: promoters conforming most closely to consensus sequences more effective in binding RNA
polymerase
 Alternative sigma factors recognize different consensus sequences

54
Q

Transcriptional units

A

Transcriptional units: DNA segments transcribed into 1 RNA molecule bounded by initiation and
termination sites
 can result from 1 or 2+ (co-transcribed) genes
 Most genes encode proteins, but some encode untranslated RNAs (e.g., rRNA, tRNA)
 e.g., three types of rRNA: 16S, 23S, and 5S + one tRNA

55
Q

Operon transcription

A

Operons are transcribed into a single mRNA called a polycistronic mRNA containing multiple open reading frames, ( sequences that encode amino acids to make a polypeptide)

56
Q

Termination of Transcription

A

 Termination governed by specific DNA sequences
 Example: GC-rich sequence containing an inverted repeat and a central nonrepeating segment followed by
several adenines
 RNA forms stem-loop by intra-strand base pairing, RNA polymerase pauses, DNA and RNA dissociate
 Rho-dependent termination: Rho protein recognizes specific DNA sequences (Rho-dependent
termination site) and releases RNA polymerase from DNA

57
Q

No. of DNA pol of diffferent domains

A

Archaea contain one RNA polymerase
 Resembles eukaryotic polymerase
 Eukaryotes have 3 DNA polymerases

58
Q

binding sites for transcription for Archae

A

 Most important recognition sequence is 6–8 base pair “TATA” box
 18–27 nucleotides upstream of transcriptional start site
 recognized by TATA-binding protein (TBP) transcription factor
 B recognition element (BRE), upstream of TATA box, recognized by archaeal transcription factor B (TFB)
Binding of TBP to TATA and TFB to BRE enables RNA polymerase binding and
transcription initiation

59
Q

Less known about termination in Archaea

A

Some archaeal genes have inverted repeats followed by AT-rich sequence similar to bacterial terminators
 One suspected terminator lacks inverted repeats but has repeated thymine runs

60
Q

 Eta transcriptional termination protein found in Euryarchaeota

A

 Binds upstream of transcription bubble
 Collides with archaeal RNA polymerase and binds it off DNA

61
Q

coding and noncoding regions

A

 exons: coding sequences
 introns: intervening noncoding sequences
 found in tRNA and rRNA genes of Archaea
 RNA processing of primary transcript (original transcribed RNA) required to form mature RNAs for translation

62
Q

splicing in Eu and Arc

A

Eukaryotes: splicing occurs in nucleus via the
spliceosome (RNA + protein)
 Archaea: introns rare in protein encoding-genes but
need to be removed from tRNA- and rRNA-encoding
transcripts by special ribonuclease

63
Q

splicing definition

A

removing introns and joining exons

64
Q

splicing mechanisms

A
65
Q

steps in eu processing before splicing

A

 capping: addition of methylated guanine to 5′ end of mRNA in reverse orienation, needed to initiate translation
 polyadenylation: trimming 3′ end addition of 100–200 adenylate residues (poly(A) tail) to stabilize mRNA; must be
removed before mRNA can be degraded

66
Q

AA composition

A

Proteins are polymers of amino acids: organic
compounds containing both an amino (-NH2) and
carboxylic acid (-COOH) linked to and α-carbon
 Amino acids are linked by peptide bonds through
carboxyl carbon of one amino acid and amino nitrogen
of a second

67
Q

amino acid side chain

A

 Side chain abbreviated R is bonded to α-carbon
 Chemical properties of amino acids are related to their side chain (e.g., acidic, basic, nonpolar)
 Considerable variability
 Chemically related side chains show similar properties and are grouped into “families”

68
Q

different structures of proteins

A

Linear array of amino acids in a polypeptide called its primary structure
 Once formed, a polypeptide folds to form a more stable structure
 Secondary structure: from hydrogen bonding (alpha-helix or beta sheet)
 Tertiary structure: three-dimensional shape of polypeptide from hydrophobic and other interactions
 Quaternary structure: number and types of polypeptides (subunits) that make a protein

69
Q

Denaturation

A

loss of structure and biological properties

70
Q

tRNA structure and synthesis

A

 Transfer RNAs (tRNAs) carry amino acids to translation machinery
 Each contains an anticodon: three bases that recognize codon (three nucleic acids encoding an
amino acid)
 tRNA and correct amino acid brought together by aminoacyl-tRNA synthetases

71
Q

tRNA of different species

A

 Prokaryotes have ~60 different tRNAs
 Human cells have 100–110 different tRNAs
 Single-stranded
 Extensive secondary structure
 Contain bases modified post-transcription (e.g., pseudouridine, inosine, others

72
Q

General structure of Transfer RNA

A

Extensive double-stranded regions formed by internal base pairing
 Cloverleaf shape
 3′ end always has CCA added by CCA-adding enzyme instead of being encoded

73
Q

tRNA synthesis mechanism

A

 Recognition of tRNA by aminoacyl-tRNA synthetase is critical for translation fidelity
 Requires specific contacts
 Amino acid activated by ATP to form aminoacyl-AMP
 Amino acyl-AMP is attached to CCA stem of tRNA resulting in charged tRNA (aminoacyl-tRNA)
 Aminoacyl-tRNA leaves synthetase and will be bound ribosome

74
Q

codon

A

A triplet of nucleic acid bases (codon) encodes a specific amino acid
 64 possible codons
 specific codons for starting and stopping translation

75
Q

Degenerate code

A

Multiple codons encode a single amino acid (64 codons versus 22 natural amino acids);
lacks one-to-one correspondence

76
Q

Codon recognition

A

Codon recognition occurs by specific base pairing with complementary anticodon sequence on tRNA
 Some tRNAs recognize more than one codon
 Wobble: irregular base pairing allowed at third position of tRNA

77
Q

Codon bias

A

Multiple codons for the same amino acid are not used equally
 varies between organisms
 correlated with tRNA concentration

78
Q

Start and Stop Codons and Reading Frames

A

 Start codon: Translation begins with AUG, encodes N-formylmethionine in Bacteria and methionine
in Archaea and Eukarya
 Reading frame: Triplet code requires translation to begin at the correct nucleotide.
 Shine–Dalgarno sequence, or the ribosome-binding site (RBS), ensures proper reading frame in
Bacteria
 Stop (nonsense) codons: terminate translation (UAA, UAG, and UGA)
 Sometimes unusual amino acids selenocysteine and pyrrolysine can be encoded by stop/nonsense codons

79
Q

Open reading frame

A

AUG followed by a number of codons and a stop codon

80
Q

steps for protein synthesis

A

Three major steps: initiation, elongation, termination
 Uses mRNA, tRNA, ribosomes
 Requires multiple proteins
 Needs guanosine triphosphate (GTP) for energy

81
Q

Ribisomes

A

 Ribosomes: large complexes of proteins and RN
A where proteins are biosynthesized
 thousands of ribosomes per cell
 composed of two subunits (30S and 50S in
prokaryotes) to form 70S ribosome
 S = Svedberg units
 30S contains 16S rRNA + 21 proteins
 50S contains 5S + 23S rRNA + 31 proteins
 Translation factors (proteins) also essentia

82
Q

Initiation Complex (translation)

A

Initiation begins with free 30S ribosomal subunit
 Initiation complex (30S subunit, m RNA, formylmethionine t RNA, initiation factors (I F1, I F2, I F3) forms
 50S ribosomal subunit added = 70S ribosome
 Ribosome binding site: 3–9 nucleotides toward 5ʹ end of m RNA, complementary to sequences on 3ʹ end of
16S rRNA
 Base pairing holds ribosome-mRNA complex in frame

83
Q

initiation summary

A

two ribosomal subunits + formylmethionine tRNA + initiation factors assemble with mRNA
 begins at an AUG start codon

84
Q

elongation summary

A

 amino acids brought to the ribosome and added to the growing polypeptide
 occurs in the A (acceptor) and P (peptide) sites of ribosome

85
Q

Elongation mechanism

A

tRNAs interact at A (acceptor) and P (peptide) sites on 50S
 A site: incoming charged tRNA first attaches; loading assisted by elongation factor EF-Tu
 P site: growing polypeptide chain is attached to prior tRNA
 Growing polypeptide moves to tRNA at the A site as new peptide bond is formed
After elongation, tRNA holding peptide transferred to P site
 Ribosome advances 3 nucleotides (1 codon) along m RNA per translocation
 Amino acid-free tRNA pushed to E (exit site) and released from ribosome

86
Q

Polysomes

A

a complex formed by multiple ribosomes simultaneously translating a single mRNA
 Termination occurs at stop codon

87
Q

Termination of translation

A

 Termination occurs at stop codon
 Release factors (RFs): recognize stop codon and cleave polypeptide from tRNA
 Ribosomal subunits dissociate
 Subunits free to form new initiation complex and repeat process

88
Q

 Role of Ribosomal RNA in Protein Synthesis

A

 16S rRNA facilitates initiation via base pairing, holds mRNA in position on either side of A and P sites
 Also involved in ribosome subunit association and positioning tRNAs on ribosome
 Catalyzes peptide bond formation
 peptidyl transferase reaction catalyzed by 23S rRNA
 Involved in translocation
 Interacts with elongation factors

89
Q

 Freeing trapped Ribosomes and Trans-Translation

A

 ribosomes trapped if no stop codon at end of mRNA
 Release factor cannot bind, ribosome cannot be released = “trapped”
 Trans-translation: produces small RNA (tmRNA) that frees stalled ribosomes
 Mimics both tRNA (carries alanine) and mRNA (contains stretch that can be translated)
 Binds next to defective mRNA, allowing protein synthesis to proceed
 Also encodes degradation signal

Microbiology (6 decks)

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