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
2
Q
Nucleosides
A
lack a phosphate group
3
Q
Nucleotides are connected via
A
phosphodiester bondsbetween 5’-phosphate groups and 3’hydroxyl groups
4
Q
All linear DNA has
A
5’ and 3’ end (end of a sequence)
5
Q
C/T vs. A/G
A
- C/T : pyrimidines (6 membered rings)
- A/G : purines (fused 5/6 membered rings)
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
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
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)
9
Q
How is T different from U
A
U lacks a methyl group
10
Q
T or F. RNA is usually single-stranded but still uses base pairing
A
T!
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
12
Q
Nucleoid
A
region of cell containing the chromosome (not membrane bound, but synonymous to the concept of the nucleus)
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!
14
Q
Eukaryotes have multiple _______ chromosomes
A
linear; for ex: S. cerevisiae has 12 chromosomes that vary in size
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
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
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
18
Q
Segments of genetic material that encode a functional protein or RNA product
A
Genes
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)
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!
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
22
Q
Microbial genome
A
- very dense and compact; most of a genome is making a protein
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
24
Q
Mycoplasma
A
- parasite (CAN live freely)
- 0.5 Mb genome (~500 genes); smallest genome capable of independent life?
25
T or F. Free-living bacteria/archaea have larger genomes.
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!!!
26
Core and Pan genomes
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
27
Genomes of closely-related lineages often exhibit significant
synteny: homologous genes arranged in the same order in their genomes
28
Unique genes of a particular genome are often found in blocks of genes
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
29
Viruses that infect bacteria (archaea also infected by these)
Bacteriophages
30
Temperate phages
bacteriophage that can integrate into bacterial genomes where they become a part of the genome called a prophage ; can be stable or transient (temporary)
31
Prophages
- 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
32
Genome diagrams
- 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
Plasmids (some have multiple and some none at all)
- 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
How do asexual microbes evolve/adapt efficiently?
they are not genetically stagnant -- they mutate, exchange genes, etc.
35
Gene names
- 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
Mutant
an organism whose genome carries a mutation
37
Wild-type strain
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
Genotype
the complete genetic makeup of an organism
39
Phenotype
an observable characteristic of an organism; there can be many different sorts of phenotypes: metabolic, virulence, morphology, etc.
40
Genomic locus
specific position on the chromosome
41
How do we denote mutations in bacterial genetics?
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
Mapped mutations
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
shown using the delta symbol
deletion mutations
44
Phenotype names
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
In some instances, mutants can be isolated by
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
Point mutations
mutations to a single base pair within a protein-coding sequence; can be:
- silent
- missense
- nonsense
47
Silent mutations
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
Missense mutations
most common; lead to a change in that amino acid to a different amino acid; won't kill protein function completely
49
Nonsense mutations
lead to a change in that amino acid to a stop codon leading to a premature end to the protein sequence; TRUNCATION
50
Other mutations are not simple substitutions (Point) from one bp to another, but instead result in DNA being added or lost
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
Deletions/Insertions within protein coding regions often result in a
frameshift mutation ; shifts and scrambles downstream sequence; highly disruptive!
52
Reversion
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
Suppressor mutation
mutations that compensate for the effects of a prior mutation; can be a different gene - "fixes problem" created by initial mutation
54
Horizontal gene transfer
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
Foreign DNA can enter prokaryotic cell in 3 major ways:
Transformation, Transduction, and Conjugation
56
When foreign DNA gets inside the cell, this DNA can:
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
Genetic recombination
physical exchange of DNA between genetic elements; homologous recombination (important for DNA repair mechanism)
58
Foreign DNA with homology to a region of host chromosome can be ...
inserted into host genome at that location in place of (or in addition to) the native DNA sequence
**HR**
59
Key player in HR
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
Mobile genetic elements found in almost all species
Transposable elements ; contain transposase gene flanked by inverted repeats
61
Transposases enzymes are able to:
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
Many transposable elements are conservative (cut and paste mechanisms - move from one place to another), whereas, others work via a...
replicative mechanism: transposon remains at its locus and a copy is produced an inserted elsewhere
63
This is used extensively in the lab to generate mutant strains
Transposons ; can insert randomly into genome, inactivating genes
64
Transformation
Process by which free DNA is incorporated into a recipient cell and brings about genetic change
65
A cell capable of taking up free DNA is said to be
competent; some bacteria/archaea are naturally competent while others are not; competence often tightly regulated
66
In many competent organisms, DNA from environment is capture by
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
Bacteriophage infections
- virus DNA protected by virions (protein coats)
- virion binds cells
- inject DNA
68
Lytic pathway of bacteriophage infections
- phage DNA replicated and new particles produced using host resources
- viruses then lyse host cell, released to infect new cell
69
Lysogenic pathway of bacteriophage infections
- viral DNA integrated into host DNA - prophage
| - can be induced, triggering the lytic cycle
70
Phages can be: (2)
- purely lytic (only operate via lytic pathway)
| - temperate (can operate via the lytic or lysogenic pathway)
71
Process in which a virus (phage) transfers DNA from one cell to another
Transduction
72
Two types of transduction (2):
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
HGT that requires cell-cell contact
Conjugation
74
Conjugation is typically mediated by plasmids called
conjugative plasmids - F plasmid (originally identified in E. coli)
75
F plasmid
- 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
These code many tra (transfer) genes that are involved in the conjugative transfer process
F plasmids
77
Some tra genes encode conjugative pilus
produced by F+ cells, attach to F- cells only
| **F plasmid encode genes that prevent attachment
78
T or F. Much acquired DNA will not be evolutionarily useful and will ultimately be lost
T, ex: transposon or recombination-mediated processes; random processes/errors during DNA replication or DNA repair
