Microbiology Test 2
Explain the molecular events that take place during the termination of bacterial translation.
- Begins when stop codon (UAA, UAG, UGA) enters A site. - Release factor enters A site. - Release factor adds a water to carboxyl terminus. - Complex dissociates and ends translation.
Understand how nitrogen and phosphorus can be incorporated into organic molecules (including sources of nitrogen and phosphorus and important enzymes).
- Nitrogen assimilation is when organic nitrogen compounds like amino acids, ammonia, or nitrate are formed from inorganic nitrogen compounds from the environment. - Nitrogen fixation is when nitrogen gas (N2) forms ammonia. - Phosphorylation is the transfer of inorganic phosphates. - Phosphorus assimilation occurs when phosphates hydrolyze organic molecules to release inorganic phosphates.
Explain the molecular events that take place during the initiation phase of bacterial transcription.
- RNA polymerase holoenzyme binds to promoter region of DNA. Sigma factor helps position it correctly. - RNA polymerase unwinds DNA. - First 10 ribonucleotides are made into RNA. - Sigma factor is released and elongation begins.
Explain the molecular events that take place during elongation phase of bacterial transcription.
- happens in locally unwound transcription bubble. - RNA polymerase responsible for unwinding and rewinding DNA as it transcribes. Only 20 base pairs are unwound at once. - Nucleotides are added according to base pairing rules. uracil replaces thymine.
Explain the molecular events that take place during the initiation of bacterial translation.
- occurs when 30S ribosomal subunit recruited to mRNA. 16S rRNA binds mRNA. - complex moves 5' to 3' until it reaches start codon (AUG)/Met. - Initiation factors bind to Met-tRNA. - Complex combines with mRNA-ribosome complex to make initiation complex. - Initiation factors are released and 50S ribosomal subunit binds active.
Explain the molecular events that take place during termination phase of bacterial transcription.
- the termination signal is a sequence in DNA that indicates to RNA polymerase it should stop elongating the RNA.
Name 2 types of fermentation that use pyruvate as a carbon source and their outputs.
1. Lactic acid fermentation: pyruvate-->lactate 2. ethanol fermentation: pyruvate-->ethanol+CO2 3. mixed acid fermentation: pyruvate-->ethanol + mixtures of other acids
List the four unifying themes of fermentation.
1. NADH is oxidized to NAD+ 2. O2 isn't required. 3. Pyruvate (or pyruvate-derivative) as an electron acceptor 4. No ETC (no large ATP yield)
Explain the mechanism of peptidoglycan synthesis.
1. UDP-NAG is formed. 2. UDP-NAM is formed and amino acids added to create UDP-NAM-pentapeptide. 3. NAM-pentapeptide is added to bactoprenol phosphate in the cytoplasm, creating Lipid I. 4. NAG is added to Lipid I in the cytoplasm, creating Lipid II. 5. Bactoprenol shuttles new peptidoglycan subunit across the membrane from the cytoplasm to periplasm. 6. Peptidoglycan subunit is added to the growing polypeptide chain. 7. Bactoprenol shuttles back across the membrane to the cytoplasm. This step must have bactoprenol so that it can lose a phosphate. 8. Transpeptidation
Outline the molecular events that take place during the bacterial cell cycle.
1. period of growth 2. chromosome replication and partitioning. - Each new cell needs a chromosome. a. origin of replication lines up in the middle of the cell. b. replisome forms. c. chromosome replication begins. d. cell elongates. e. chromosomes pushed to sides of cell. ParB binds to the chromosome. ParA binds to ParB and pulls the chromosome toward the pole. 3. cytokinesis a. FtsZ accumulates in the middle of the cell and forms the z-ring. b. The z-ring pinches the 2 cells. The cell wall position is dictated by the z-ring. c. The cell constricts and septum forms. d. PBPs (Penicillin-binding proteins) are the enzymes that are involved in the peptidoglycan cell wall synthesis. e. Autolysin is a type of PBP that degrades peptidoglycan. It is localized to a specific area of the cell.
Explain the molecular events that take place during initiation phase of bacterial replication.
1. proteins are recruited to origin of replication. - DnaA is the first protein to bind the oriC and denature DNA. - DnaA recruits DnaB-DnaC complexes. - DNA helicase helps unwind and unzip DNA more. - DNA gyrase is the enzyme that relieves tension of unwinding DNA and makes little cuts to relieve tension. - SSB proteins bind each DNA strand and keep them separate, preventing winding back up. 2. DNA primase makes RNA primers, which is a short RNA chain that starts replication by providing the necessary 3'-OH. - DNA polymerase needs a free 3'-OH to add nucleotides to.
Describe the three functions of ribosomal RNA (rRNA).
1. ribosome structure 2. 16s rRNA needed for initiation of translation 3. 23s rRNA catalyzes peptide bond formation
Explain the molecular events that take place during elongation phase of bacterial replication.
3. DNA polymerase III synthesizes DNA from 5' to 3'. - Deoxynucleotides are only added to the 3' end of DNA strand. The DNA strand is made of 2 antiparallel strands. - Leading strand is 5' to 3' and made continuously at replication fork. - Lagging strand is 3' to 5' and made discontinually at replication fork (Okazaki fragments) 4. RNA primers removed form lagging strand and replaced with DNA. - Exonuclease Activity where there is enzymatic and cutting activity of DNA or RNA. (5' to 3' exonuclease removes primer and 3' to 5' exonuclease removes mismatched nucleotide) 5. Okazaki fragment on lagging strand connected by DNA ligase. - DNA ligase is the enzyme that closes small nicks or breaks in DNA by breaking phosphodiester bonds.
Explain the molecular events that take place during termination phase of bacterial replication.
6. Replisome reaches termination sequence and dissociates from DNA
Know how bacteria can increase the efficiency of gene expression as compared to eukaryotes.
Bacteria do not have a nucleus. their ribosomes are in the cytoplasm and can start synthesizing the protein as the mRNA strand is formed. In eukaryotes, the mRNA strand has to be transported into the cytoplasm for the ribosomes to bond with the mRNA strand. In bacteria, there are only 2 steps to gene expression, while there are three steps for eukaryotes. 2) Bacteria can express more than one operon at a time. In eukaryotes, only one operon can be expressed at a time.
Know why aerobic respiration yields less ATP in bacteria than in eukaryotes.
Bacterial cells have less complexes and are branched, so they make less ATP.
Discuss how bacterial cells get their characteristic shapes.
Coccoid (spherical) - new peptidoglycan cell wall only forms at the septum. - FtsZ determines septum location and gets other PBPs and other enzymes to make cell wall. Rod-shaped - Peptidoglycan cell wall made all along cell wall. - MreB dictates location. - Peptidoglycan synthesis becomes confined to the septum and depends on FtsZ.
State the functions of replisome components: DNA polymerase I.
DNA repair enzyme that repairs bases, nucleotides, and double-strand breaks
Briefly describe how microbes can use complex carbohydrates (like disaccharides and polysaccharides) in catabolic reactions.
Disaccharides and polysaccharides can be broken down by hydrolysis or phosphorolysis. Hydrolysis is when ATP is added to water. Phosphorolysis is when an ATP molecule can give phosphates to other molecules.
Enteric bacteria are the normal bacterial members of the gut microbiome in humans. Enteric bacteria are considered facultative anaerobes. What is the advantage of being a facultative anaerobe?
Facultative anaerobes can change whether they use respiration or fermentation. It will use the most advantageous process in the presence or absence of oxygen.
List the theoretical maximum number of ATP generated by glycolysis, Krebs Cycle, and ETC.
Glycolysis- 2 ATP Krebs Cycle- 2 ATP ETC - 30-32 ATP
List the inputs and outputs of glycolysis and the TCA/Krebs Cycle.
Glycolysis: - Inputs: 1 glucose, 2 NAD+, 4 ADP (+2 ATP) - Outputs: 2 pyruvate, 2 NADH, 4 ATP (Net 2 ATP) TCA/Krebs Cycle: - Inputs: 1 Acetyl CoA, 3 NAD+, 1 FAD, 1 ADP - Outputs: 2 CO2, 3 NADH, 1 FADH2, 1 ATP
Discuss how microbiologists helped determine DNA is the genetic material.
Griffith found 2 strains of S. pneumoniae. The R strain was not harmful, while the S strain killed the mouse. Other scientists experimented with the R and S strains. The R cells could not grow on the plate. When R and S cells were combined, they grew on the plate. They had 3 experiments: R+S+DNase (destroys DNA), R+S+RNase (destroys RNA), R+S+protase (destroys protein). The R cells did not grow when DNase was added, so they found that DNA was required genetic material.
Compare anaerobic respiration of glucose to aerobic respiration.
In both anaerobic and aerobic respiration, sugar is oxidized, electron carriers (NADH and FADH2 are reduced, and they make ATP. Differences are that the ETC ends with O2 as the terminal acceptor in aerobic respiration, while the ETC ends with a different terminal acceptor in anaerobic respiration. In anaerobic respiration, there is no oxygen. In aerobic respiration, oxygen is required. Anaerobic respiration also makes less ATP.
Bacteria can be classified by the temperature range in which they grow best. under which temperature classification would most human pathogens fall? Why?
Mesophiles because the temperatures in which they thrive is 20-42*C, which is the range that human temperature falls in.
What cytoskeletal proteins are required in the process of bacterial cells getting their characteristic shapes?
MreB and CreS determine the shape of the cell. MreB directs cell wall synthesis by making hoops inside the cell membrane. CreS accumulates on one side of the cell in some species. This bends the cell. FtsZ determines where the cell is going to pinch in and make two cells.
What molecule carries the electrons from the oxidation of glucose to the complexes of the electron transport chain (ETC) to make ATP?
NAD+/FAD
Explain how nutrient availability is related to the different phases of bacterial growth.
Nutrient availability is determined by the environment. During the lag phase, there is the most nutrients because the bacterial cells are not dividing due to the stress they are enduring because of changing environments. Therefore, the nutrients that was available is used up in the exponential phase because the bacteria are dividing rapidly. When there is no more nutrients, the bacterial cells try to conserve their energy in the stationary phase. Finally, the bacterial cells die in the death phase because there is no nutrients available. However, bacteria can evolve and use toxic waste or another source of energy to enter a long-term stationary phase and eventually enter the exponential phase once the nutrient conditions improve.
Explain how the proton motive force generates ATP.
Proton motive force (PMF) is the force arising from a proton gradient and membrane potential. PMF powers ATP synthase, which generates ATP. NADH turns into NAD+ while hydrogen moves up the gradient, forming a proton gradient. 1 NADH makes 2.5 ATP and 1 FADH2 makes 1.5 ATP.
Name the enzyme that synthesizes mRNA from a DNA template during transcription.
RNA polymerase
Why are bacteria that oxidize glucose for energy able to donate electrons to NAD+, while bacteria that oxidize sulfur and ammonia are not?
Something that oxidizes ammonia can't transfer electrons as much because it is a better acceptor than donor. Bacteria that oxidizes glucose can easily donate electrons because it is a better electron donor than acceptor.
The drug Taxol works by preventing formation and degradation of microtubules and filaments made of microtubule homologs. If you treated a bacterium with Taxol, what outcome would you expect?
Taxol would prevent cell replication because the microtubules would not be able to pull apart the chromosomes.
Compare and contrast the Sec and Tat systems for protein secretion.
The Sec System moves unfolded proteins across the membrane, while the Tat system moves folded proteins across the membrane. In the Sec system, signal peptides in the polypeptide bind to the signal recognition molecule, which brings the whole ribosome to the membrane. In the Tat system, the chaperones bind to the signal peptide and bring the protein to the tat complex.
Describe the structure and basic function of the Type II Secretion System (T2SS).
The Type II Secretion System is in proteobacteria. Pseudopilus pushes proteins through the outer membrane and secretes degredative enzymes.
Describe the structure and basic function of the Type III Secretion System (T3SS).
The Type III Secretion System consists of "injectosomes". It extends through the plasma membrane, outer membrane, and host cell membrane. It secretes proteins for pathogenesis and attacks eukaryotic cells.
Why is it important for the origin of replication to be oriented in the middle of a dividing bacterial cell?
The origin of replication determines chromosome division. If the origin of replication is not in the middle of the cell, one of the daughters will have less chromosomes, while the other will have more genes.
Describe the structure and basic function of the Type VI Secretion System (T6SS).
The type VI secretion system secretes toxins. The inner core is ejected and punctures a hole in the outer and target cell membranes. It is supposed to attack bacterial and eukaryotic cells, delivering effectors.
Enteric bacteria are the normal bacterial members of the gut microbiome in humans. Enteric bacteria are considered facultative anaerobes. At the molecular level, how might bacteria 'switch' between catabolic pathways (switch from aerobic to anaerobic respiration)?
They can sense oxygen regulation and alter by changing genes.
Know the difference between a 1-step and 2-step secretion system.
a 1-step secretion system is one where secretion occurs through a complex that spans the periplasmic space. (Type III and VI). A 2-step secretion system is one where 1) translocation into periplasmic space by sec or tat system. 2) secretion across outer membrane. (Type II)
Define halophile.
a bacteria that lives in highly-salt concentrated conditions.
Explain the molecular events that take place during the elongation of bacterial translation.
a. aminoacyl-tRNA enters the A site of the ribosome. b. Growing polypeptide chain is transferred from tRNA on the P site to the tRNA on the A site by making a peptide bond. c. Ribosome moves down one codon on mRNA. - Empty tRNA enters E site and exits ribosome. - Growing polypeptide chain in P site. - A site open to receive next tRNA.
Define replisome.
acts as the DNA copy machine that contains helicases to unwind the DNA duplex, polymerases to copy the DNA duplex, and nucleases and ligases to process the discontinuous stretches of DNA on the lagging strand.
Define thermophile.
bacteria that grow best at temps above 45 celsius
Define mesophile.
bacterial species that lives between 20C and 40C
State the functions of replisome components: SSB proteins.
bind each DNA strand and keep them separate (prevents winding back up)
Define promoter.
binding site for RNA polymerase. It is important because enzymes take up physical space. It needs to have enough room to assemble. Promoter region is not transcribed or translated.
Define persister.
certain bacterial cells that are resistant to antibiotic and are slow-growing. They can resume their growth once the stress is taken off of them.
State the functions of replisome components: DNA ligase.
enzyme that closes small nicks or breaks in DNA by breaking phosphodiester bonds
State the functions of replisome components: DNA gyrase.
enzyme that relieves tension of unwinding DNA and makes little cuts to relieve that tension
Define cell cycle.
forming one new cell through division by three phases: period of growth, chromosome replication and partitioning, and cytokinesis.
List the function of sigma factor.
initiate transcription
State the functions of replisome components: DNA primase.
makes RNA primers, which are short RNA chains that start replication by providing the necessary 3'-OH
List the function of rho factor.
mediates termination of transcription at distinct sites.
Define polycistronic mRNA.
messenger RNA molecule that contains information transcribed from 2 or more genes
Define monocistronic mRNA.
messenger RNA that codes for a single protein
Define chaperone.
proteins that help folding--can unfold and refold the protein correctly
Define coding region.
sequence of nucleotides that specifies the amino acid sequence. It begins with start codon (AUG) and ends with stop codon.
Define terminator.
sequence that stops RNA synthesis. It is not transcribed or translated.
Know several environmental factors that can affect microbial growth.
starvation, stress, temperature, oxygen concentration, solutes and water, or pH can affect microbial growth.
Define template strand.
strand of DNA that is the template from which the mRNA is made
State the functions of replisome components: DNA polymerase III.
synthesizes DNA from 5' to 3'
Define replication fork.
the Y-shaped structure where replication occurs after DNA unwinds. There are 2 replication forks that move in opposite directions away from the origin of replication (bidirectional replication)
Define origin of replication.
the area where replication begins on the DNA strand
Define exponential phase.
the phase of bacterial growth where bacteria are dividing rapidly. There is a lot of nutrients available.
Define lag phase.
the phase of bacterial growth where cells make material but aren't dividing. The bacteria are under stress from environmental movement.
Define stationary phase.
the phase of bacterial growth where cells stop dividing because there is no more nutrients. The cells try to conserve their energy.
Describe how trigger factor and GroES/GroEL help proteins fold.
trigger factor helps proteins fold by wrapping around the site where the growing polypeptide chain comes out of the ribosome. It protects the hydrophobic amino acids so they don't clump together. GroES and GroEL is a 2-pieced protein that works like a trash can. It gives the protein a place away from the cytoplasm where it can fold by itself.
State the functions of replisome components: helicase.
unwinds and unzips DNA more
Define operon.
ways bacteria organizes genes that are similar to each other in functions or processes.
