Microbiology Quiz 2

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Which of the following usually requires active transport to bring molecules across and why? Which of these do not require active transport and why?

Outer membrane 

Cell wall

Cytoplasmic membrane

Cytoplasmic membrane requires active transport - Due to the tightly sealed phospholipid bilayer and the sealed bilayer that stops hydrophilic/charged molecules from crossing, molecules need be moved against their concentration gradient. This requires energy to move them across.

Cell walls (peptidoglycan) does not require active transport. The cross linked NAG-NAM layers allow for small molecules to diffuse across without active transport.

Outer Membrane does not requires active transport - The outer membranes has porins with open channel proteins that allow small hydrophilic molecules to pass right through via passive diffusion.

If a cell did not have the genes for the pentose phosphate pathway (PPP), it would not be able to make what building block any why?

Histidine | Histidine is the one amino acid whose biosynthesis requires a PPP product. Its carbon skeleton is built starting from PRPP (phosphoribosyl pyrophosphate), which is made directly from ribose-5-phosphate. No PPP → no ribose-5-phosphate → no PRPP → no histidine.

Which reactions incorporate inorganic phosphate into cellular molecules? (Choose all that are correct.)

ADP + Pi > ATP

ATP > ADP + Pi

NAD+ + 2 > NADH

Phosphoenol pyruvate +ADP + Pi > ATP + Pyruvate

ADP + Pi > ATP

Phosphoenol pyruvate +ADP + Pi > ATP + Pyruvate

What are the differences between aerobic and anaerobic respiration?

1. Terminal Electron Acceptors | Aerobic respiration uses oxygen as the final electron acceptor, meanwhile anaerobic respiration uses something other than oxygen (nitrate (NO₃⁻), sulfate (SO₄²⁻), tetrathionate, fumarate, CO₂, ferric iron, etc) as it’s final electron acceptor.

2. Energy Yield | Aerobic respiration produces much more ATP than anaerobic respiration due to oxygen having the highest positive reduction potential of all common electron acceptors.

3. Where it happens | Aerobic respiration requires oxygenated environments while anaerobic respirations occur in anoxic environments.

What shared machinery do aerobic and anaerobic respiration use?

Both use glycolysis, the TCA cycle, an electron transport chain, and ATP synthase/chemiosmosis.

Which of the following are energy forms that are used for active transport? (Choose all that are correct.)

Periplasmic binding proteins

Transmembrane ion gradient

Oxygen

Lactose

ATPase

Transmembrane ion gradient, ATPase

What is the correct order of the steps of nitrogen assimilation using NH3?

A.NH3 is converted into NH4+

B.NH4+ is reacted with 2 oxoglutarate to create Glutamate

C.NH3 is transported across the cytoplasmic membrane

D.2 oxoglutarate is produced in the TCA cycle

C → A → D → B

The most abundant class of macromolecule by weight in the cell is the lipids. (True or false?)

False | Protein is the most abundant macromolecule by weight in a cell (roughly half the dry weight). Lipids are a smaller fraction — mostly confined to membranes. Order is generally protein > RNA/nucleic acids > lipids > carbohydrates/DNA.

The 3’ end of an mRNA is signaled by ...

The transcription terminator

The start point of the pgk gene open reading frame is the __________ codon and the end is the __________ codon.

Start, Stop

A polycistronic mRNA has only one of which of the following. (Choose all that are correct.)

Genes

Ribosome binding sites

Promoters

Transcriptional terminators

Start codons

Promoters and Transcriptional Terminators

Which of the following are true about the ribosome binding site? (Choose all that are correct.)

It is complementary to the 16S rRNA of the ribosome

It signals where the ribosome should bind

It is also called promoter

It is near to the first start codon

Is also called the Shine Dalgarno sequence

It is complementary to the 16S rRNA of the ribosome

It signals where the ribosome should bind

It is near to the first start codon

Is also called the Shine Dalgarno sequence

RNA polymerase binds to promoter DNA. True or false, explain

False | sigma factor binds the promoter, not RNA polymerase. In bacteria, RNA polymerase (the core enzyme) can't recognize a promoter by itself. It needs a detachable subunit called the sigma factor (σ) to find and bind the promoter. The sigma factor is the part that actually recognizes and contacts the promoter DNA sequence.

What is the sec system?

The sec system, or the secretory system, is the main pathway bacteria use to move proteins out of the cytoplasm either across the cytoplasmic membrane to the outside, or inserted into the membrane itself. Any protein that needs to end up beyond the cytoplasm generally gets there through Sec.

What proteins would you expect the sec system to use?

Peptidoglycan transpeptidase, Porin and Periplasmic binding proteins

Sigma 70 interacts with both promoter DNA and RNA polymerase. (True or false?)

True

DNA PolIII makes few errors in part because it has proofreading ability. (True or false?)

True

Horizontal gene transfer is when the genetic material of one microbe moves to another, and can occur via transformation, conjugation or transduction. (True or false?)

True

During natural transformation, __________ while during conjugation, __________.

1. DNA is carried by phages, DNA is exchanged directly cell to cell

2. Naked DNA is taken up by cells, DNA is exchanged directly cell to cell

3. Naked DNA is taken up by cells, DNA is carried by phages

4. DNA is carried by phages, Naked DNA is taken up by cells

5. DNA is exchanged directly cell to cell, Naked DNA is taken up by cells

2. Naked DNA is taken up by cells, DNA is exchanged directly cell to cell

During Oswald Avery’s experiment, the live rough cells took up heat-killed smooth cell DNA by __________.

Transformation

Which of the following are components of the replisome? (Choose all that are correct.)

DnaA

DNA polymerase III

Primase

DnaB

Single stranded binding protein (SSB)

DNA polymerase III

Primase

DnaB

Single stranded binding protein (SSB)

Which would have a larger effect on the resultant proteins when it happens within a gene?

A point mutant or Insertion

Insertion because it can alter an entire codon chain, while a point mutant only changes a single letter

Name all types of mutations found in prokaryotes

Point mutation, Small deletion, Small insertion, Large deletion

What are the steps of nitrogen assimilation using NH3

1. NH3 is transported across the cytoplasmic membrane

2. NH3 is converted into NH4+

3. 2-oxoglutarate is produced in the TCA cycle

4. NH4+ reacts with 2-oxoglutarate to create glutamate

Note: Technically steps 2 and 3 can happen in either order because they occur independently of one another.

Siderophores bind ...

Iron

Assuming the same carbon/energy source (e.g. glucose), would a fermentation or respiration be predicted to produce more ATP?

Respiration creates more ATP then fermentation

Which of the following are true about bacterial translation? (Choose all that are correct?)

1. Happens at the same time as transcription because there is no nuclear membrane 

2. Only happens for polycistronic mRNAs

3. Ribosomes can start translating as soon as a ribosome binding site is produced

4. More than one ribosome can be bound to an mRNA as once

5. Translation is not a good target of antibiotics

1. Happens at the same time as transcription because there is no nuclear membrane
   4. More than one ribosome can be bound to an mRNA as once
   5. Translation is not a good target of antibiotics

Bacterial mRNAs have a __________ half life.

Short

A polycistronic mRNA has more than one of which of the following. (Choose all that are correct.)

Genes

Ribosome binding sites

Promoters

Transcriptional terminators

Stop codon

Genes, Ribosome binding sites, Stop codon

A promoter that is a good match to consensus would be highly transcribed. (True or false?)

True

What are functions of DnaA?

Separates the two DNA strands in the origin of replication, Binds to DnaB to build the replisome, Binds to the DnaA-box in the origin of replication

Why does an incoming piece of transformed DNA require an origin of replication?

Because otherwise it will not be copied and passed to daughter cells

A high fidelity DNA Polymerase makes more errors than a low fidelity one. (True or false?)

False

Mutagens help experimentally obtain mutants because ...

They increase the frequency of mutations

Streptococcus pneumoniae is naturally competent, which means ... (Choose all that are correct.)

It has an unusually high mutation rate

It uses flagellar motility

It is able to take up DNA from the environment

It does not require special treatment to make it take up DNA

It infects mice

It is able to take up DNA from the environment

It does not require special treatment to make it take up DNA

DnaB function

Helicase that separates the two DNA strands in front of the replication fork

Primase Function

Synthesizes a primer for DNA Polymerase to extend

DnaA function

Binds to the origin of replication and separates the two strands

Single stranded protein function

Coats the single stranded DNA and keeps it from re-anneling.

DNA Polymerase III function

The enzyme that actually copies the DNA to make the new strand