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Micro 265 Fall 2023 > 3.1 -Microbial Genomes > Flashcards

3.1 -Microbial Genomes Flashcards

1
Q

What do all cells store their genetic information as?

A

DNA
-DNA –> RNA –> protein –> build cellular aspects
a. DNA to RNA = transcription
b. RNA to Protein =translation

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2
Q

What happens at the first step of cell division?

A
  • DNA is copied or replicated
  • and one copy is given to one daughter cell and the other copy is given to the other daughter cell.
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3
Q

What is transcirption?

A
  • genetic information is copied to RNA
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4
Q

what is translation?

A
  • open reading frames from mRNA are converted to proteins.
  • mRNA is the code for proteins
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5
Q

What role does rRNA serve?

A
  • not converted to protein
    -serves in cellular functions as RNAs.
  • they don’t all act as intermediates, some actually do stuff in the cell.
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6
Q

what is DNA?

A
  • is a polymer comprised of strings of nucleotide, monomers.
  • has sugar, phosphate and base.
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7
Q

what is a nucleotide?

A
  • comprised of phosphate, sugar and nucleobase.
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8
Q

what is a nucleobase?

A
  • they are nitrogenous bases that are attached to sugars.
  • A,T, G, C, U
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9
Q

what is a nuceloside?

A
  • it is a nitrogenous base linked to a sugar, there is no phosphate involved in it.
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10
Q

what is the basic nucleotide structure?

A

-sugar carries phosphate at 5’ carbon.
- sugar carries one of the four base at the 1’ carbon
- the sugar is deoxyribose.
- there is repeated units of phosphate, sugar, base

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11
Q

what are the nucleotides connected

A
  • by phosphodiester bonds between the 5’ phosphate groups and the 3’ hydroxyl (OH)
  • one base has the ability to recognize the other base.
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12
Q

what do all linear DNA have?

A
  • have a 5’ end and a 3’ end
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13
Q

In what direction do the two complementary run in?

A

They run anti-parallel to form a helix via the interaction of their nucleobases

  • this helps form a double strand.
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14
Q

DNA base pairs

A
  • 4 bases pairs
  • A -adenine
  • C - cytosine
  • G - guanine
  • T- thymine (DNA)
  • U -Uracil (RNA)
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15
Q

What are C and T ?

A
  • C and T are pyrimdines
  • they have a 6 membered ring
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16
Q

what are G and A?

A
  • they are purines
  • it is a five-membered ring attached to a six memebered ring.
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17
Q

Does A/T have a stronger interaction than C/G?

A
  • no
  • AT has a weak interaction with 2 hydrogen bonds (less stable)
  • GC has a stronger interaction with 3 hydrogen bonds (more stable and harder to break)
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18
Q

what does base pairing allow?

A
  • is the key to DNA’s function: it
    enables identical copies to be made and genetic
    information to be converted to RNA/protein
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19
Q

Compare RNA and DNA

A
  • RNA:
    a. 2’-hydroxyl group (OH) on its
    sugar (ribose)
    b. RNA less chemically stable (2’-OH can attack the sugar phosphate backbone - hydrolysis of the phosphodiester bond)
    c. can act as an enzyme
    d. has uracil - no methyl group
    e. single stranded - uses base pairing
  • DNA:
    a. no hydroxyl group on sugar,
    (deoxyribose)
    b. more chemically stable
    c. cannot act as an enzyme
    d. has thymine - has methyl group
    e. double stranded uses base pairing
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20
Q

Prokaryotic chromosomes

A
  • they are usually circular
  • there is extensive supercoiling
  • many proteins are involved in the structuring of the chromosome
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21
Q

what is a nucleoid?

A
  • region of cell containing the chromosome (not membrane
    bound, but similar to the concept of the nucleus)
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22
Q

steps of how the DNA is supercoiled

A
  1. relaxed circle that is double-stranded
  2. the DNA becomes supercoiled, as it twists.
  3. structuring is guided by the proteins that interact with the DNA. The DNA is not so compact since has to be accessible for transcription.
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23
Q

what is one thing that is similar that bacteria and archaea have in terms of genome?

A
  • almost always has one circular chromosome.
  • the ends are joined together, does not have to be circular.
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24
Q

what is Vibrio Cholerae?

A
  • a bacterium that has 2 circular chromosomes.
  • both chromosomes are replicated individually
  • both have their ended joined together.
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25
Q

what is streptomyces?

A
  • antibiotic producer
  • has linear chromosomes
    -ends are not joined together, though in a circular fashion.
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26
Q

what type of chromosomes for eukaryotics have?

A
  • have multiple linear chromosomes

ex. saccharomyces cereviase has 16 chromosomes but they vary in size.

27
Q

Eukaryotic vs Prokaryotic genome

A
  • Eukaryotic = larger and less compact genomes (fewer genes per Kb of DNA)
    a. eukaryotes are complex organisms and their genomes get larger and are much more spread out.
  • prokaryotic = smaller and more compact genomes
28
Q

Eukaryotic Microbes and Higher Eukaryotics

A

Eukaryotic microbes have more compact genomes than higher eukaryotes, in part
because they have fewer introns (noncoding gene segments removed during splicing) per gene

29
Q

what are genes?

A
  • are segments of genetic material that encode a functional
    protein or RNA product
30
Q

what is a prokaryotic gene comprised of?

A
  • 85-90% -protein-coding genes
  • 1-2% - RNA genes – noncoding RNA (tRNA, rRNA, other functional
    RNAs)
    -10% -non-coding DNA (E.g., regulatory sequences, junk DNA)
31
Q

In what direction can genes run in?

A
  • genes can run in either direction and can overlap.
  • they can start and stop in either direction.
  • gene overlap : The reason is genes overlap possibly due to chromosome rearrangements so that lead two separate genes to be linked together; alternatively, overlapping genes may result in the generation of a new gene or gene mutation
32
Q

what are genes organized in?

A
  • functionally related clusters
    a. function of surrounding genes can offer insight into a gene’s function
33
Q

what are endosymbionts?

A
  • cells that can only live within the cells of another organism
34
Q

what are parasites?

A
  • they require another organism.
  • they can have very small genomes.
35
Q

what is a mycoplasma?

A

-a parasite that can live freely
- has a 0.5Mb genome
- it is the smallest genome capable of independent life

36
Q

what is a free-living bacteria?

A
  • they have larger genomes.
37
Q

Does the complexity of a bacteria affect its size?

A
  • yes
  • some bacteria with complex life cycles have genomes as large as 15Mb.
    a. lots of regulation, different needs for different stages.
38
Q

What happens is prokaryotic genomes?

A
  • genome size increases = number of genes also increases
39
Q

Are all function essential in genomes?

A

-No, only some functions are essential.

-ex. translation, DNA replication

40
Q

what do genes that encode specialized functions for adapting to different
environments or operating in different lifestyles do?

A
  • they increase in larger genomes.
  • the bigger genome the more closer to the line.
41
Q

Change in gene composition?

A
  • an increase in genome = composition of gene will change
  • genes decide when or where they will turn on.
  • only need one set of protein to translation of RNA to protein.
  • diff type of gene and what % of composition change.
42
Q

what are core and pan genomes?

A
  • is basically what genomes are composed of.

-used to describe gene states within the gene.

  • when comparing a number of different genomes
43
Q

what is a core genome?

A
  • genes present in all members. usually conserved genes important for the biology of that lineage.
44
Q

what is pan genome?

A
  • all genes present in any member. Includes rare genes that encode highly specialized functions.
  • anything in genome 1, genome 2, genome 3
  • pan means anything.
  • pan-genome increases = core genome decreases or becomes shorter or shrinker
45
Q

Example of Core and Pan genomes

A
  • There are many different lineages of
    Salmonella that have different ecologies
    & virulence properties
  • they share a lot of common genes.
  • Different lineages also encode many
    unique genes that give them their unique
    properties
  • ex. the Typhi serovar is human adapted
    and encodes unique genes to help it
    infect & persist within humans
46
Q

what doGenomes of closely-related lineages often exhibit significant)?

A

synteny

47
Q

what is synteny?

A
  • homologous genes arranged in the same order in their genomes.
48
Q

where are unique genes of a particular genome often found in?

A
  • They are found in blocks
    a. large blocks –> genomic islandb. small blocks–> genomic islet
49
Q

what is a genomic island?

A
  • large blocks
50
Q

what is a genomic islet?

A
  • small blocks
51
Q

What do genomes acquire?

A
  • horizontal genes.
  • genes have a related function that confers that lineage with unique properties.
52
Q

Explain the diagram of Salmonella Pathogenicity Island

A

-this has any genes encoded.
- the sit gene helps get more iron.
- the arrows in a genome will be in different directions, this tells you which direction is the gene going. (forward or stop)

53
Q

what are bacteriophages?

A
  • they are also known as phages
  • they are viruses that infect bacteria
    a. archaea are also infected by similar viruses. (contribute to genetic diversity)
54
Q

what is a prophage?

A
  • some bacteriophages known as temperate phage, can integrate into bacterial genome where they become a part of a genome.
  • these can be stable or transient
55
Q

Do prophage have diversity?

A
  • yes they vary from strain to strain
56
Q

what are carry genes?

A
  • prophages carry them
    -it provides the bacterial host with useful new genes.
  • they exist for a long period of time.
57
Q

How are bacterial toxins encoded?

A
  • they are encoded by prophages.
    -specific growth for specific condition
58
Q

Explain the steps of the formation of a prophage

A
  • viral DNA is integrated into a host DNA
  • this then forms a prophage.
  • the prophage is then replicated with the host DNA at the cell division, resulting in two cells.
59
Q

what extra characteristics do bacteria and archaea have?

A
  • plasmids –> assecory genes are carried by them
60
Q

What are plasmids?

A
  • they are typically circular DNA molecules that are replicated in the cytoplasm.
  • they encode non-essential assessory genes.
61
Q

why are accessory genes important?

A
  • genes are important under certain conditions such as antibiotic resistant genes.
  • they also allow for specialized metabolism.
62
Q

what is usually the size of plasmids?

A
  • they vary in size from 1kbp to 1Mbp, but typically less than 5% size of a genome.
63
Q

Can plasmids vary in copy number? (how many per cell)

A
  • they vary form 1 to > 100

Micro 265 Fall 2023 (9 decks)

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