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

Chapter 6: Molecular information flow and protein processing Flashcards

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
plasmid description
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)
26
R plasmids
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)
27
what do plasmids code for
 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)
28
Verticle transfer
From parents to offspring Plasmids can also be transferred vertically
29
Type of DNA replication
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
30
types of DNA polymerase
 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
31
Replication Enzyme mechanism
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
32
type of replication enzymes
Helicase Single-strand binding protein Primase DNA polymerase III DNA polymerase I DNA ligase Topoisomerase IV
33
Helicase
Unwinds double helix at replication fork
34
Single-strand binding protein
Prevents single strands from annealing
35
Primase
Primes new strands of DNA
36
DNA polymerase III
Main polymerizing enzyme
37
DNA polymerase I
Excises RNA primer and fills in gaps
38
DNA ligase
Seals nicks in DNA
39
Topoisomerase IV
Unlinking of interlocked circles
40
Initiation of DNA Synthesis
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
Leading and Lagging Strands and the Replication Process
 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
 Leading and Lagging Strands and the Replication Process (after replication fork has been made)
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
replication rate
DNA Pol III adds 1000 bp per second
44
Replication of Circular DNA
known as theta structure
45
The Replisome
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
 Primosome
helicase and primase subcomplex within replisome
47
Why do we need proofreading?
Mistakes Mutations Misfoldedprotein Mutation rates are 10^-8 to 10^-11errorsperbp Proofreading ensures high fidelity
48
 Fidelity of DNA Replication:
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
Two key differences in RNA vs DNA chemistry
 ribose instead of deoxyribose  uracil instead of thymine  Typically, single-stranded  Fold into secondary structure (complementary base pairing) that influences function
50
Transcription mechanism
 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
Transcription binding
52
 RNA Polymerases and the Promoter Sequence
 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
sigma factors
 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
Transcriptional units
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
Operon transcription
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
Termination of Transcription
 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
No. of DNA pol of diffferent domains
Archaea contain one RNA polymerase  Resembles eukaryotic polymerase  Eukaryotes have 3 DNA polymerases
58
binding sites for transcription for Archae
 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
Less known about termination in Archaea
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
 Eta transcriptional termination protein found in Euryarchaeota
 Binds upstream of transcription bubble  Collides with archaeal RNA polymerase and binds it off DNA
61
coding and noncoding regions
 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
splicing in Eu and Arc
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
splicing definition
removing introns and joining exons
64
splicing mechanisms
65
steps in eu processing before splicing
 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
AA composition
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
amino acid side chain
 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
different structures of proteins
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
Denaturation
loss of structure and biological properties
70
tRNA structure and synthesis
 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
tRNA of different species
 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
General structure of Transfer RNA
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
tRNA synthesis mechanism
 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
codon
A triplet of nucleic acid bases (codon) encodes a specific amino acid  64 possible codons  specific codons for starting and stopping translation
75
Degenerate code
Multiple codons encode a single amino acid (64 codons versus 22 natural amino acids); lacks one-to-one correspondence
76
Codon recognition
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
Codon bias
Multiple codons for the same amino acid are not used equally  varies between organisms  correlated with tRNA concentration
78
Start and Stop Codons and Reading Frames
 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
Open reading frame
AUG followed by a number of codons and a stop codon
80
steps for protein synthesis
Three major steps: initiation, elongation, termination  Uses mRNA, tRNA, ribosomes  Requires multiple proteins  Needs guanosine triphosphate (GTP) for energy
81
Ribisomes
 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
Initiation Complex (translation)
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
initiation summary
two ribosomal subunits + formylmethionine tRNA + initiation factors assemble with mRNA  begins at an AUG start codon
84
elongation summary
 amino acids brought to the ribosome and added to the growing polypeptide  occurs in the A (acceptor) and P (peptide) sites of ribosome
85
Elongation mechanism
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
Polysomes
a complex formed by multiple ribosomes simultaneously translating a single mRNA  Termination occurs at stop codon
87
Termination of translation
 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
 Role of Ribosomal RNA in Protein Synthesis
 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
 Freeing trapped Ribosomes and Trans-Translation
 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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