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Ali Microbiology > Genes and Genomes > Flashcards

Genes and Genomes Flashcards

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1
Q

What is the breakdown from genome to DNA (largest to smallest)?

A

genome, chromosomes (and/or plasimds), regulons, operons, genes, DNA

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2
Q

Name the purines and pyrimides. Which pairs with which?

A

Pyrimidines: Cytosine and Thymine

Purines: Guanine and Adenine

A-T

G-C

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3
Q

Eukaryote vs. Bacterial DNA

A

Ex. Human vs. E. Coli

Humans have wide repeat genomes, some introns, and some human pseudogenes (have similar make up to already known genes)

Bacteria has mostly genes with a few genome wide repeats

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4
Q

Operons

A

(Polycistronic mRNA)

Genes in tandem

Found in bacteria

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5
Q

Histone-like Protein

A

Maintain compacted/supercoiled DNA

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6
Q

Regulon

A

Genes and operons regulated together and functioning for a coordinated effort (eg. stress response)

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7
Q

Topoisomerase

A

Type 1: knicks DNA on 1 strand, only to relieve torsional stress to unwind and reduce the number of supercoials

Type 2: introduces negative supercoils

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8
Q

Why do archaea have a reverse DNA gyrase topoisomerase?

A

To introduce positive supercoils

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9
Q

Genome

A

Contains all genetic information within a chromosome

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10
Q

Information in Chromosome

A

Core genes

Housekeeping genes, transcription proteins, ribosomal proteins, cell division proteins

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11
Q

Information in Plasmids

A

Flexible genes

Useful in special conditions, antibiotic resistance, metal resistance, and metabolism of rare food sources

“expendable genes”

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12
Q

Rhizobium etli FCN42

A

has 6 plasmids

Fix nitrogen on legumes

This bacteria can cleave bond to provide N2 to soy beans

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13
Q

Agrobacterium tumafaciens

A

Can utilize opines (derivatives of amino acids)

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14
Q

Replication Begins

A

DNA melts at oriC

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15
Q

Steps of DNA Replication A through F

A

A - DnaA binds and melts DNA at AT rich region

B & C - DnaB and DnaC - helicase and loader unwind DNA

D - DNA dependent (binds to DNA) RNA polymerase (synthesizes RNA) synthesizes the one RNA primer on each leading strand

F - Replication Forck is formed with sliding clamp loader, clamp, and DNA pol 3

G - DnaG (primase) makes all the primers on the lagging strand

H - Rnase H removes primers, DNA pol 1 synthesizes new DNA and ligase fills the nicks

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16
Q

What primes the leading strand in DNA replication?

A

DNA dependent RNA polymerase

(Rifampicin sensitive RNA polymerase primes the leading strand)

THEN clamp binds DNA polymerase 3 to strand and replication fork forms

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17
Q

What direction is DNA synthesized in?

What about the template?

A

5 prime to 3 prime

Template is synthesized in 3 prime to 5 prime

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18
Q

What happens at the end of replication?

A

Fork trap

Rnase H cleaves primers

Gaps filled in by DNA polymerase 1

Ligase seals nicks

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19
Q

Replication is semi-conservative..What does this mean?

A

Each daughter cell received a newly synthesized strand and parental strand

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20
Q

What controls timing?

A

Methylation

New DNA is not yet methylated (by Dam)

Hemi-methylated DNA allows SeqA to bind at OriC and temporarily block replication

Different species methylate at different sequences correspond with restriction enzyme binding sites

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21
Q

DNA replication generates positive supercoils: What enzyme can relieve torsional stress?

A

Type 1 Topoisomerase

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22
Q

Which of the following is likely true of chromosomal DNA from both a bacterium and a eukaryote, assuming equal length:

A

The bacterium would have roughly 5 times the number of genes

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23
Q

List these in a decreasing number of genes: chromosome, genome, operon, regulon

A

Chromosome, regulon, operon, gene

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24
Q

True or False: DNA replication, transcription, and translation all occur at the same time.

A

True

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25
Q

Transcription Initiation

A
  1. Sigma factor (w/ holoenzyme) binds promotor
  2. DNA is unwound and transcription bubble forms
  3. Sigma factor is released and mRNA is transcribed
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26
Q

At the beginning of replication, where does DNA melt?

A

oriC

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27
Q

What enzyme primes the leading strand in DNA replication?

A

DNA dependent RNA polymerase

Rifampicin-sensitive RNA polymerase primes the leading strand

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28
Q

Primase (DnaG)

A

beings lagging strand replication

synthesizes lagging strand primers every 1000-1500 bp

RNA primers form 3 prime OH for DNA to attach

*There must be a 3 prime end for the DNA base to attach

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29
Q

What direction is DNA synthesized in?

A

5’ –> 3’

Template is read 3’ –> 5’

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30
Q

What does RNase H do at the end of replication?

A

Rnase H cleaves primers, gaps are filled in by DNA polymerase 1, and ligase seals in the nicks

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31
Q

Which enzyme relieves torisional stress generated from positive supercoils?

A
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32
Q

Central Dogma

A
  1. DNA replication: DNA dependent DNA polymerase
  2. Transcription: DNA dependent RNA polymerase
  3. Translation: Ribosome

Promoter –> transcription start –> Shine Dalgarno –> protein start/stop –> transcripition termination

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33
Q

Sigma Factors

A

Global regulators that promote transcription

Bring holoenzyme to -35 and -10 regions

Release from holoenzyme

Multiple sigma factors for different conditions

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34
Q

Transcription Elongation

A

Transcription begins at the +1 base (about 9th/10th base) after the last T in TATAAT

Consensus sequence is on the non-template strand (5’–>3’); complementary to template

The non-template is identical to trascription except T–>U

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35
Q

Types of RNA and Stability

A

mRNA: encodes protein, thousands of types, about 1500nt, half life of 3-5 minutes, no unusual bases

rRNA: synthesizes protein, three types, about 5S - 120nt, half life of hours, has unusual bases

tRNA: shuttles amino acids, 27 types, size of 80 nt, half life of hours, has unusual bases

sRNA: controls translation and transcription, 20-30 types, less than 100 nt size, variable half life, no unusual bases

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36
Q

tRNA

A

have specific T shape and T loop containing thymidine

3-base anticodon to bind mRNA (often contains Inosine which can bind to any base) –> this allows wobble base pairing

37
Q

Rho-dependent termination

A
  • Polymerase slows at pause site at 3’ site
  • Rho factor binds to mRNA at cytosine rich sequence (CCCCCC)
  • Slides along mRNA to polymerase
  • Releases polymerase and mRNA from DNA
38
Q

Rho-Independent Termination

A
  • GC rich inverted repeat
  • Uracil-rich region (UUUU) where RNAP is bound (allows RNA polym to be released b/c TU is weak bond)
  • mRNA breaks off of DNA, polymerase is released
  • No Rho factor to dissociate
39
Q

This is the +1 spot on the template strand: GCTTCCCG

What does the mRNA look like?

A

GCUUCCCG

40
Q

True or False: Transcription and Translation are coupled?

A

True

41
Q

How is translation initiated?

A

The ribosome binds at the Shine-Dalgarno sequence

5’ AGGAGGU (complementary to 16S 5’ ACCUCCU)

Binding is demonstrated using a radioactive oligonucleotide

42
Q

Shine Dalgarno

A

Very large protein polymerase of mostly rRNA

  • 2 subunits, 52 proteins, 3rRNAs
  • Can bind 1 mRNA + 3tRNAs
  • AGGAGGU
43
Q

3 steps of Ribosomal translation: mRNA –> protein

A
  1. Initiation: Shine-dalgarno sequence AGGAGGU, initation factors, start codon (AUG)
  2. Elongation: EF-Ts, EF-Tu, EF-G bring GTP energy, polymerization, movement of ribosome along mRNA, 16 AA per second
  3. Termination: releasing factors undock ribosome from mRNA, ribosoe recycling factor
44
Q

Translation Initiation

A

A. IF3 binds SSU and blocks LSU

B. IF1 facilitates fMet entering at p site

C. LSU (50S) binds

45
Q

fMet

A

N-formyl-methionine

Unique to bacteria (and mitochondria)

Eukaryotic cells can detect low concentration of fMet (10-12 M) –> bacterial invasion or cell death (release of bacterial or mitochondrial peptides)

46
Q

Translation Elongation

A

Specific tRNAs becomes “charged” with a specific AA

-aminoacyl-tRNA transferase (uses ATP)

tRNAs have specific “T” shape and 3-base anticodon bind to mRNA

47
Q

Elongation –> LSU

A
  1. tRNA at Acceptor site (A)
  • uses GTP
  • Codon and anticodon pair
  1. Polymerisation (P): Formation of peptide bond (covalent bond) by ribosome
  • peptidyltrasnferase
  • uses GTP
  1. Translocation and Exit (E)
  • Peptidyl “P” site –> E (exit) site
  • “A” Acceptor –> “P”
  • Uses GTP (EF-G-GTP)
48
Q

Translation Termination

A

Release factor binds

New Peptide and RF1 (RF2) is released - peptidyltransferase

Ribosome recycling factor (RRF) releases ribosome (uses GTP)

49
Q

Archaeal RNA polymerase core machinary is different than eukaryotes..T or F?

A

False, it is very similar to eukaryotes

Rifampicin binds the beta-subunit of bacterial RNA polymerase

50
Q

Would you expect rifampicin to affect Archaea?

A
51
Q

What is the fate of proteins that are translated?

A

Modified and/or folded

Secreted

Degraded

52
Q

Post-translational Protein Modification

A

N-formyl group (or entire fMet removed)

Phosphoryl/Methyl/Adenyl-groups added to amino acids

53
Q

What folds proteins?

A

GroEL-GroES complex

Uses ATP

Protein to be refolded fits into center of the barrel

54
Q

What two things determine protein structure?

A

Amino acid sequence

Chaperones (such as GroEL-GroES complex)

55
Q

Protein Secretion: out of the cytoplasm

A

some proteins with hydrophobic (membrane spanning) regions contain a Signal sequence for insertion into the membrane or secretion to periplasm

56
Q

Protein Secretion: out of the cell

A

Type 1 secretion system

57
Q

What are proteins degraded by?

A

Proteases

Proteasomes (many protease active sites, shown in red in picture)

Proteosomes are conserved across domains

58
Q

How long do arginine and lysin elarge compared to aspartic/gluatmic acid? What about house keeping proteins?

A

Arginine and lysine are short lived

Aspartic/glutamic acid are longer lived

Housekeeping proteins are long lived

59
Q

Are one or multiple mRNAs transcribed? What direction?

A

Multiple mRNAs = many mRNAs per DNA strand

5’–> 3’

60
Q

As soon as _____ is transcribed (on mRNA) ribosomes will bind and translate into proteins.

A

Shine Dalgarno

61
Q

Which way are the ribosomes moving?

A
62
Q

RNA polymerase reads which of the following?

A

DNA

63
Q

The Shine Dalgarno sequence can be recognized on which of the following:

Where is the binding site for the sequence found?

A

DNA and mRNA

mRNA

64
Q

Holoenzyme

A

Core polymerase (contains proteins required to elongate an RNA chain) + sigma factor (only needed for initiation of RNA synthesis)

Both of these make up RNA polymerase or DNA dependent RNA polymerase

65
Q

Sigma Factor

A

Part of RNA polymerase needed for initiation of RNA synthesis

Binds RNA polymerase through beta and beta-prime subunits and then helps the core protein detect the promotor

Located at -35 and -10 upstream of the transcription start site

66
Q

messenger RNA

A

average 1000-1500 bases in length,

RNA molecules that encode protein

67
Q

ribosomal RNA

A

forms the scaffolding on which ribosomes are built

forms the catalytic center of the ribosome

68
Q

Transfer RNA

A

ferry amino acids to the ribosome

69
Q

closed complex

A

occurs on an initial binding of RNA polymerase to promotor DNA

70
Q

Rifamycin B

A

antibiotic that selectively inhibits trascription initiation by RNA polymerase

71
Q

Actinomycin D

A

antibiotic that nonselectively inhibits trascription elongatoin

72
Q

True or False: All RNA’s have the same half life.

A

False. They vary within the cell

73
Q

Small RNA molecules

A

can regulate gene expression (sRNA), have catalytic activity (catalytic RNA), or function as a combination of rRNA and mRNA (rmRNA)

74
Q

Peptidyltransferase activity

A

ribosome activity

carried out by ribosomal RNA, not protein

The peptide elongates when the ribosome ratchets one codon length along the mRNA

75
Q

Translation termination

A

occurs upon reaching a stop codon

the ribosome pauses because it cannot find an appropriate tRNA

a release factor enters the A site and triggers peptidyltransferase activity thus freeing the completed protein from tRNA in the P site

76
Q

Ribosome release factor

A

binds to the A site along with EF-G to dissociate the two ribosomal subunits from the mRNA

77
Q

Why does RNA polymerase pause during transcription?

A

To allow the slower-translating ribosomes to stay close

This pause minimizes exposure of mRNA to degradative cellular enzymes

78
Q

What does tRNA rescue?

A

ribosomes stuck on damaged mRNA that lacks a stop codon

79
Q

N-terminal amino acid

A

can be removed by methionyl aminopeptidase or the formyl group only can be removed by methionine deformylase

help target membrane proteins to the membrane

80
Q

An inactive precursor protein

A

can be cleaved into a smaller active protein or other groups can be added to the protein (for example phosphate or AMP)

81
Q

When are protein modifications made?

A

After translation

82
Q

The signal recognition particle (SRP)

A

pauses the translation of a subset of proteins that will be placed into the membrane

83
Q

Type 1 secretion systems

A

are ATP binding cassette (ABC) mechanisms that move certain secreted proteins directly from the cytoplasm to the extracellular environment

84
Q

Twin arginine translocase

A

TAT

can move a subset of already folded proteins across the inner membrane and into the periplasm

85
Q

SecB

A

protein that can bind to certain unfolded proteins that will eventually end up in the periplasm, and pilots them to the SecYEG translocon

86
Q

open reading frame (ORF)

A

sequence of DNA predicted by various sequence cues to encode an actual protein

87
Q

Paralogs and orthologs

A

arise from gene duplications (paralogs) - exist in same genome but have different functions

arise from speciation events (orthologs) - occur in the genomes of different species but produce proteins with similar functions

88
Q
A

Ali Microbiology (8 decks)

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