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Microbiology > Week 7 Review > Flashcards

Week 7 Review Flashcards

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Biology 101 flashcards
1
Q

What is the central dogma? How do DNA replication, transcription, and translation relate to it?

A

The central dogma is the process where DNA gets replicated during DNA replication and an RNA copy is made in the transcription process. That RNA gets translated into proteins

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2
Q

What are the differences between RNA and DNA?

A

DNA
Sugar: deoxyribose
Strands: ds (double-stranded)
Base pairing: A-T, C-G
Life: years

RNA
Sugar: ribose
Strands: ss (single-stranded)
Base pairing: A-U, C-G
Life: minutes

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3
Q

What are the 3 Kinds of RNA from most to least?

A

Ribosomal RNA
Structure and function of ribosomes

Transfer RNA (tRNA)
“Adaptor” molecule: links nucleotide base sequence to aa sequence

Messenger RNA (mRNA)
Encodes for proteins

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4
Q

Why are bacterial genes transcribed together?

A

Bacterial genes are arranged in operons and are clusters that relate in function

These genes get transcribed together via a promoter, that acts as a single on-and-off switch to transcribe all the genes together

Bacterial genes are constantly dividing about every 20mins so bacterial genes transcribe together to maximize efficiency.

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5
Q

Compare and contrast DNA replication and transcription. (Hint: purpose, templates and products, enzymes used, bases)

A

One strand of DNA serves as the template

Free nucleotides are added in the 5’ to 3’ direction

Nucleotides added by base pairing with the DNA template strand

In RNA, uracil (U) is added instead of thymine

Transcription product is a single-stranded product

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6
Q

What are the steps in transcription?

A

Initiation
- RNA polymerase binds to the promoter sequence
- Promotor: start of gene/operon
- DNA unwinds

Elongation:
- RNA pol adds nucleotides to the 3’ end of a new strand
- Moves 5’ to 3’

Termination:
- RNA pol stops at a specific DNA sequence
- RNA and RNA pol released

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7
Q

What is a codon and how does it relate to the Genetic Code?

A

Codon: a set of 3 nucleotides of mRNA that specify one amino acid
- Specific codons signal start and stop in translation

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8
Q

What are the different types of codons?

A

Initiation: AUG (common), GUG (rare)
Stop:(nonsense): UAA, UGA, UAG

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9
Q

What is the reading frame?

A

The sequence between initiation and stop codons

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10
Q

Why is the genetic code said to be degenerate?

A

Some codons code for the same amino acid

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11
Q

Do prokaryotes exhibit codon preference?

A

Prokaryotes exhibit codon preference or codon bias
- some codons are preferred over others because the G/C content is different

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12
Q

What is the major structure of tRNA? What is an anticodon?

A

tRNA carries anticodon that base pairs with complimentary codon found on an mRNA
- An anticodon is a sequence of three nucleotides forming a unit of genetic code in a tRNA molecule

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13
Q

What is the role of ribosomes in translation?

A

Synthesizing proteins by translating the genetic code transcribed in mRNA into an amino acid sequence
- Control orientation of activated tRNAs (have amino acid attached) to codons
- Forms peptide bonds between amino acids from tRNA

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14
Q

What are the steps of translation?

A

Initiation:
Transitional complex forms and tRNA brings the first amino acid in the polypeptide chain to bind to start codon on mRNA

Elongation:
tRNAs bring amino acids one by one to add to the polypeptide chain

Termination:
The release factor recognizes the stop codon, the translational complex dissociates, and the completed polypeptide is released

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15
Q

Why is translation simultaneous with transcription in prokaryotes?

A

They happen simultaneously due to location, as prokaryotes don’t have a nucleus so they don’t need to migrate for translation to occur.

In eukaryotes, transcribing occurs in the nucleus and then migrates into the cytoplasm for translating

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16
Q

What are the requirements for translation?

A

mRNA w/ ribosome binding site (RBS)
Ribosomes
tRNA’s

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17
Q

How are eukaryotic mRNAs processed from longer transcripts?

A

In Eukaryotes, transcription occurs in the nucleus and then migrates into the cytoplasm where translation occurs

18
Q

Why are genes regulated?

A

Only some proteins are expressed and at different amounts

Adaptation to environmental conditions will alternate the level of RNA available for translation

Save energy and resources

19
Q

How is expression regulated?

A

Constitutive expression
- enzymes made at the same level regardless of need

Transcriptional expression
- Controlled by other proteins (repressors/activators) that respond to the environment
- Controls initiation of transcription

20
Q

How are genes transcriptionally regulated?

A
  • Operon are protein with related functions transcribed together in a block
  • The promoter signals the start of transcription
  • The structural genes are proteins with related functions
  • The operator is where the repressor binds
  • Regulatory genes make repressors that are constitutively expressed
21
Q

What are the main types of control of initiation of transcription? Compare and contrast repressible and inducible operons.

A

Repressible operons: transcription of structural genes, represses (stops) an activity
Ex: trp operon
- Transcription of E, D, C, B, and A represses trp synthesis
- The net effect is off

Inducible operons: transcription of structural genes, induces (starts) an activity
Ex: lac operon
- Transcription of Z, Y, A induces lac breakdown
- The net effect is on

22
Q

How do the trp and lac operon operate?

A

Trp: represses
- Tryptophan binds to the repressor and changes the repressor’s shape
- The repressor binds to the operator and blocks RNA polymerase
- No transcription of trp structural genes

  • In the absence of trp, the repressor does not bind to the operator and allows RNA polymerase to transcribe structural genes

Lac: induces
- Structural genes: involved in lactose breakdown (lac Z: hydrolysis, lac Y: transport, lac A: unknown)
- If lac is not present, no need to transcribe genes that break lac down

Lactose present:
- Lac binds to the repressor and changes the repressor’s shape
- The repressor can no longer bind to the operator, so RNA polymerase is free to transcribe genes

23
Q

Where do mutations arise?

A

Spontaneous, arising from DNA replication errors

Requency may increase with mutagenic agents

24
Q

What if any are the changes in phenotypes?

A

The enzyme becomes inactive

25
Q

How are mutations fixed in DNA replication?

A

Some of the mistakes are corrected immediately during replication through a process known as proofreading, and some are corrected after replication in a process called mismatch repair.

26
Q

Describe the main types of mutations.

A

Single base pair: a base substitutes for another base
- Substitution or point mutations

Frameshift: deletion or insertion of DNA sequence
- A few base pairs
- Alters the order of triplet codons relative to the start
- Often leads to non-functional proteins

27
Q

What are the different types of base pair mutations?

A

Silent: changes base that does not change amino acid, protein sequence

Nonsense: changes base to stop codon

Missense: changes base to a new codon for another amino acid

28
Q

What are the different types of frameshift mutations?

A

Deletion and insertion

29
Q

What are inversions?

A

When a segment breaks off and reattaches within the same chromosome, but in reverse orientation

30
Q

What is the source of spontaneous mutations?

A

DNA replication errors

31
Q

Name and describe the different sources of chemical and radiation mutagens.

A

Chemical:
Base pair mutagens: chemical conversion of a nitrogenous base into another

Nucleoside analogs: structures are similar but base pairing differs

DNA Intercalating: insertion of a compound into DNA

Radiation:
Ionizing radiation
- X-rays and gamma rays “ionize” atoms and form free radicals that seal electrons and cause breaks in the DNA
- Single-strand break or double-strand break

Ultraviolet radiation
- UV light causes dimer formation (covalent bond between Ts that arent originally there), kinks DNA
- Stalls replication or transcription
- DNA polymerase replicates dimer incorrectly

32
Q

What is the evolutionary significance of mutations? What is the rate?

A

Mutation rate: probability gene will mutate

Spontaneous rate: 10^-6 per gene

Evolutionary adaptation leads to genetic variation

Most are lethal mutations, few are beneficial

Mutagen: 10^-5 to 10^-3 per gene (increases rate of mutation)

33
Q

How are mutagens identified? What are the two main types?

A

Direct:
Positive
Select cells that gain function

Indirect:
Negative
Select cells that lose function

34
Q

What are the steps involved in replica plating?

A

Press sterile velvet cloth onto a medium containing histidine (plate) to pick up cells from bacterial colonies

Transfer the cells to 2 plates: one medium continuing histidine and another one lacking histidine

Incubate

Compare growth on plates to identify auxotrophic mutants that grow on medium containing histidine but do not grow on medium lacking histidine

35
Q

Purpose and steps for Ames test.

A

Purpose: to determine if a mutagen is carcinogenic (causes cancer)

Two cultures of Salmonella auxotrophs (requiring histidine)

Add mutagen to experimental sample only

Add rat liver extract to mimic metabolism in animals

Growth in media lacking histidine (needs to grow)

Look for revertants, can grow with or without histidine again

36
Q

Contrast vertical and horizontal gene transfer.

A

Vertical:
Parent to child

Horizontal:
Between those of multiple generations
Exchange genetic information not from a parent cell

37
Q

Name and describe the different types and steps of genetic recombination involving horizontal gene transfer.

A

Transformation: involves uptake of short fragments of naked DNA by naturally transformable bacteria
- Linear or circular from surroundings
- Requires competent cells (cells willing to take up DNA)

Transduction: involves the transfer of DNA from one bacterium into another via bacteriophages (viruses)
- Protein coat + DNA or RNA

Conjugation: involves the transfer of DNA material via sexual pilus and requires cell-to-cell contact

38
Q

Be able to describe Griffith’s experiment and its results.

A

For the control group, he injected the rough strain (nonvirulent) into a mouse and it lives

In experiment 1 he injected heat-killed smooth strain into the mouse and it lives

In experiment 2 he injected rough strain AND heat-killed smooth strain into the mouse and it dies

In experiment 3 he recovered the smooth strain (virulent) from the dead mouse in experiment 2

The results show that DNA from the heat-killed strain transferred over to the rough strain, proving DNA transformation

39
Q

How is competence determined in nature and artificially?

A

Artificially: treated in lab
Chemical treatment: CaCl2
Electrical current: electroporation

Nature: some cells are naturally competent (willing to take up DNA)
Depending on species and conditions take up DNA

40
Q

What are F+, F-, Hfr?

A

F+ is the donor cell
F- is the recipient cell
Sometimes F+ becomes Hfr (F+ inserts itself into chromosome)

Microbiology (16 decks)

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