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MICRB 265 > Topic 5 > Flashcards

Topic 5 Flashcards

1
Q

Nucleotides

A
  • comprised of 4 different nitrogenous bases (nucleobases) attached to a deoxyribose (5C)
  • this carries a phosphate at the 5’C
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2
Q

Nucleosides

A

lack a phosphate group

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3
Q

Nucleotides are connected via

A

phosphodiester bondsbetween 5’-phosphate groups and 3’hydroxyl groups

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4
Q

All linear DNA has

A

5’ and 3’ end (end of a sequence)

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5
Q

C/T vs. A/G

A
  • C/T : pyrimidines (6 membered rings)

- A/G : purines (fused 5/6 membered rings)

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6
Q

A/T vs. C/G base pairs

A
  • A/T : forms weaker interactions with only 2 hydrogen bonds

- C/G : forms stronger interaction with 3 hydrogens

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7
Q

Key to DNA’s functions

A

base pairing; it enables identical copies to be made and genetic information to be converted to RNA/protein

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8
Q

Why is RNA less chemically stable than DNA?

A
  • RNA contains 2’OH on its ribose that is absent in DNA

- tendency to be degraded (hydrolysis of phosphodiester bond)

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9
Q

How is T different from U

A

U lacks a methyl group

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10
Q

T or F. RNA is usually single-stranded but still uses base pairing

A

T!

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11
Q

Structure of prokaryotic chromosomes

A
  • chromosomes are usually circular but within cell; not a simple ‘relaxed circle’ as there is extensive supercoiling and many proteins are involved in structuring the chromosome
  • required to make DNA fit in the cell
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12
Q

Nucleoid

A

region of cell containing the chromosome (not membrane bound, but synonymous to the concept of the nucleus)

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13
Q

Exceptions to bacteria and archaea having one, circular chromosome

A
  • Vibrio cholerae has two (circular) chromosomes; one is 3 Mbp while other is 1 Mbp
  • Streptomyces have linear chromosomes!
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14
Q

Eukaryotes have multiple _______ chromosomes

A

linear; for ex: S. cerevisiae has 12 chromosomes that vary in size

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15
Q

Eukaryotes, including microbes, generally have ______ and ____ compact genomes than prokaryotes

A

larger and less (fewer genes per kbp of DNA); eukaryotic microbes have smaller and more compact genomes than higher eukaryotes

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16
Q

Why do eukaryotic microbes have more compact genomes than higher eukaryotes?

A

Eukaryotic microbes have fewer introns (non-coding gene segments removed during splicing) AND smaller introns per gene

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17
Q

What does “less compact genome” mean?

A

encoding fewer genes per kilobase of DNA; there’s more DNA that isn’t directly being converted into a protein sequence

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18
Q

Segments of genetic material that encode a functional protein or RNA product

A

Genes

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19
Q

Typical microbial genome is comprised of:

A
  • 85-90% protein-coding genes
  • 1-2% RNA coding genes (tRNA, rRNA, other functional RNAs)
  • 10% non-coding DNA (ex: regulatory sequences, junk DNA)
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20
Q

T or F. Genes can only run in one direction

A

F! either direction (can be encoded by either DNA strand) and they can also OVERLAP!

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21
Q

Genes are often organized into

A

functionally-related clusters - function of surrounding genes can offer insight into a gene’s function

genes of a related function can also be scattered around chromosome

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22
Q

Microbial genome

A
  • very dense and compact; most of a genome is making a protein
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23
Q

Endosymbionts vs. Parasites

A

E - can only live within the cells of another organism
P - require another organism

**don’t have to adapt to different conditions as host is regulating environment; just need bare essentials to survive; not much regulation

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24
Q

Mycoplasma

A
  • parasite (CAN live freely)

- 0.5 Mb genome (~500 genes); smallest genome capable of independent life?

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25
Q

T or F. Free-living bacteria/archaea have larger genomes.

A

T! E.coli (4.5 Mb)vs Mycoplasma (0.5 Mb)

Some bacteria with complex life cycles (regulation, etc.) have genomes as large as ~15 Mb!!!

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26
Q

Core and Pan genomes

A

Used when comparing a number of different genomes (members of a given species)

  • Core: genes present in all members; usually conserved genes important for biology of that lineage
  • Pan: all genes present in any member; includes rare genes that encode highly specialized functions
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27
Q

Genomes of closely-related lineages often exhibit significant

A

synteny: homologous genes arranged in the same order in their genomes

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28
Q

Unique genes of a particular genome are often found in blocks of genes

A

large blocks = genomic island
small blocks = genomic islet

** often represent horizontally acquired genes; in many cases, the genes have a related function that confers that lineage with unique properties

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29
Q

Viruses that infect bacteria (archaea also infected by these)

A

Bacteriophages

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30
Q

Temperate phages

A

bacteriophage that can integrate into bacterial genomes where they become a part of the genome called a prophage ; can be stable or transient (temporary)

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31
Q

Prophages

A
  • content can vary form strain to strain
  • can carry cargo genes that have nothing to do with phage biology (can provide the bacterial host with useful new genes)
  • many important bacterial toxins are encoded by prophage
  • plays a big role in genome evolution and function evolution for bacteria/prokaryotes
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32
Q

Genome diagrams

A
  • show key features of genome, including location of genes
  • key info/strain name shown in middle
  • often include some specialized information that relate to interesting features of the specific organism (eg. virulence genes) or that relate to the particular study
33
Q

Plasmids (some have multiple and some none at all)

A
  • typically circular DNA (can be linear) molecules that are replicated in the cytoplasm
  • encode ‘non-essential’ accessory genes (genes important under certain conditions such as antibiotic resistance genes); not part of core physiology of microbe
  • vary in size from ~1 kbp to 1 Mbp, but typically less than 5% size of genome
  • can vary in copy number (how many per cell from 1 to >100)
  • genes to ensure that their replication is using host DNA replication machinery
34
Q

How do asexual microbes evolve/adapt efficiently?

A

they are not genetically stagnant – they mutate, exchange genes, etc.

35
Q

Gene names

A
  • 4 letters; first 3 describe function and 4th designates a specific gene
    ex: btuC (B 12 uptake gene C)
  • italicized (first three lower case and end with upper case letter)
  • PROTEIN NAMES ARE NOT THE SAME (BtuC)
36
Q

Mutant

A

an organism whose genome carries a mutation

37
Q

Wild-type strain

A

strain isolated from nature and/or one being used as the parental strain in a study; term can also be applied to a single gene

38
Q

Genotype

A

the complete genetic makeup of an organism

39
Q

Phenotype

A

an observable characteristic of an organism; there can be many different sorts of phenotypes: metabolic, virulence, morphology, etc.

40
Q

Genomic locus

A

specific position on the chromosome

41
Q

How do we denote mutations in bacterial genetics?

A

we add numbers to gene name (ex: hisC –> hisC 1 italicized)

** done far less now since mutations are generally sequence and so naming using the specific mutation is more common

42
Q

Mapped mutations

A

can be described using nucleotide or amino numbers
Convention: WT base or amino acid, then number, then mutant base or amino acid (ex: HisC (A77K) residue 77 mutated from an alanine to lysine)

43
Q

shown using the delta symbol

A

deletion mutations

44
Q

Phenotype names

A

have three letters where first letter is capital; strains are shown with a +/- for that phenotype (ex: His+ strain can make histidine, whereas His- is a histidine auxotroph which means they must acquire histidine from environment in order to grow as His is essential for life )

45
Q

In some instances, mutants can be isolated by

A

selection - mutant grows, but parent doesn’t or grows significantly worse (eg: antibiotic resistance)

selection is highly efficient – can identify single mutant with a desired phenotype out of millions (or more) of cells

46
Q

Point mutations

A

mutations to a single base pair within a protein-coding sequence; can be:

  • silent
  • missense
  • nonsense
47
Q

Silent mutations

A

do not change amino acid sequence, different codon but same amino acid
(DNA changed but AA -> protein remains unchanged and so function is unchanged)

48
Q

Missense mutations

A

most common; lead to a change in that amino acid to a different amino acid; won’t kill protein function completely

49
Q

Nonsense mutations

A

lead to a change in that amino acid to a stop codon leading to a premature end to the protein sequence; TRUNCATION

50
Q

Other mutations are not simple substitutions (Point) from one bp to another, but instead result in DNA being added or lost

A

Deletion: DNA lost

Insertion: DNA added to a specific location; can be as small as a single bp or can be as large as thousands bp

51
Q

Deletions/Insertions within protein coding regions often result in a

A

frameshift mutation ; shifts and scrambles downstream sequence; highly disruptive!

52
Q

Reversion

A

mutant that acquires another mutation to “revert” back to wild-type
term often applied to phenotype
**Genotype still different but phenotype is rescued by a suppressor mutation

53
Q

Suppressor mutation

A

mutations that compensate for the effects of a prior mutation; can be a different gene - “fixes problem” created by initial mutation

54
Q

Horizontal gene transfer

A

acquiring new genetic material from foreign DNA via the environment, a virus (phage) or another organism plays an even bigger role (on the whole)

55
Q

Foreign DNA can enter prokaryotic cell in 3 major ways:

A

Transformation, Transduction, and Conjugation

56
Q

When foreign DNA gets inside the cell, this DNA can:

A
  1. be degraded/lost (can be eaten too as it is a good E source)
  2. replicate as a separate entity (plasmids, phage)
  3. be integrated into the chromosome (recombination, transposition)
57
Q

Genetic recombination

A

physical exchange of DNA between genetic elements; homologous recombination (important for DNA repair mechanism)

58
Q

Foreign DNA with homology to a region of host chromosome can be …

A

inserted into host genome at that location in place of (or in addition to) the native DNA sequence
HR

59
Q

Key player in HR

A

RecA - binds a single-stranded DNA and searches for homologous double-stranded DNA = mediates strand invasion ; DNA strand from one source (ex: chromosome) fused to DNA strand of another (ex: foreign DNA)

60
Q

Mobile genetic elements found in almost all species

A

Transposable elements ; contain transposase gene flanked by inverted repeats

61
Q

Transposases enzymes are able to:

A

recognize the inverted repeats/cleave DNA to free “transposable elements”, cleave another DNA (eg chromosomal DNA) and insert transposable element into that DNA

**Process is called transposition)

62
Q

Many transposable elements are conservative (cut and paste mechanisms - move from one place to another), whereas, others work via a…

A

replicative mechanism: transposon remains at its locus and a copy is produced an inserted elsewhere

63
Q

This is used extensively in the lab to generate mutant strains

A

Transposons ; can insert randomly into genome, inactivating genes

64
Q

Transformation

A

Process by which free DNA is incorporated into a recipient cell and brings about genetic change

65
Q

A cell capable of taking up free DNA is said to be

A

competent; some bacteria/archaea are naturally competent while others are not; competence often tightly regulated

66
Q

In many competent organisms, DNA from environment is capture by

A

pili, which retracts bringing DNA through outer membrane/cell wall
One strand of DNA typically degraded and other strand passed through cytoplasmic membrane and into cell via multi-protein competence system

67
Q

Bacteriophage infections

A
  • virus DNA protected by virions (protein coats)
  • virion binds cells
  • inject DNA
68
Q

Lytic pathway of bacteriophage infections

A
  • phage DNA replicated and new particles produced using host resources
  • viruses then lyse host cell, released to infect new cell
69
Q

Lysogenic pathway of bacteriophage infections

A
  • viral DNA integrated into host DNA - prophage

- can be induced, triggering the lytic cycle

70
Q

Phages can be: (2)

A
  • purely lytic (only operate via lytic pathway)

- temperate (can operate via the lytic or lysogenic pathway)

71
Q

Process in which a virus (phage) transfers DNA from one cell to another

A

Transduction

72
Q

Two types of transduction (2):

A

Generalized:

  • during the lytic cycle, some host cell DNA is accidentally packaged into a viral particle
  • this DNA injected into new cell in place of phage DNA

Specialized:

  • when a prophage is induced, its DNA is excised from genome and packaged into phage particles
  • sometimes some neighbouring DNA is also packaged by mistake
  • this DNA can then be injected into a new cell by that phage particle
73
Q

HGT that requires cell-cell contact

A

Conjugation

74
Q

Conjugation is typically mediated by plasmids called

A

conjugative plasmids - F plasmid (originally identified in E. coli)

75
Q

F plasmid

A
  • fertility
  • large (~100 kbp)
  • strains with this plasmid are called F+; donor cells
  • F- lack plasmid and are recipient cells
  • DNA transfer only from donor to recipient (unidirectional)
  • only between F- and F+; two of each won’t mate
76
Q

These code many tra (transfer) genes that are involved in the conjugative transfer process

A

F plasmids

77
Q

Some tra genes encode conjugative pilus

A

produced by F+ cells, attach to F- cells only

**F plasmid encode genes that prevent attachment

78
Q

T or F. Much acquired DNA will not be evolutionarily useful and will ultimately be lost

A

T, ex: transposon or recombination-mediated processes; random processes/errors during DNA replication or DNA repair

MICRB 265 (6 decks)

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