Exam 2 Study Guide Flashcards
define thermodynamics
a science that analyzes energy changes in a collection of matter called a system (e.g., a cell); all other matter in the universe is called the surroundings
List the laws of thermodynamic and describe their relevance in the chemical reactions.
- First law of thermodynamics: energy can be neither created nor destroyed, total energy in the universe remain constant; however energy may redistributed either within a system or between the system and its surroundings
- Second: physical and chemical processes proceed in such a way that the disorder of the universe increases to the maximum possible
What does “life obeys the laws of thermodynamic” mean?
obeys the laws of physics and chemistry
define the standard reduction potential (E0)
equilibrium constant for an oxidation-reduction reaction, a measure of the tendency of the reducing agent to lose electrons
Why do aerobics generate the highest amount of energy ATP and how does this play a role in the ETC?
o Anaerobes generate less ATP because the terminal electron acceptors in aerobes have more positive electron potentials. Aerobes have less positive because they do not use O2 .
o The electron acceptor has a smaller distance than between NADH and O2.
o This results in a shorter ETC in anaerobes and fewer protons transported to the periplasmic area.
( This explains why facultative aerobes try to use O2 as much as possible )
Compare E’0 of aerobic and anaerobic respiration
• The standard electron potential is aerobic respiration has more positive E0, and anaerobes have less positive E0. This is because there is a greater distance between the electron carrier and acceptor in aerobes. This often results in a lower yield of ATP in anaerobes.
True or False: A redox pair with more negative reduction potential will spontaneously donate electrons to a pair with more positive potential.
true
True or False: The first electron carrier in an ETC has the most negative E’0
true
True or False: ETC are associated with plasma membranes or mitochondrial/chloroplast internal membranes
True; they are in the plasma membrane of prokaryotes and mitochondria/chloroplasts of eukaryotes
All molecules found in ETC are capable of transferring both electrons and protons
false
Describe the flow of electron in respiration. What happened to the electron in each of the above processes (final electron acceptor?)
o In respiration, as electrons pass through the electron transport chain to the final electron acceptor, a proton motive force (PMF) is generated and used to synthesize ATP
o The final electron aerobic acceptor is O2
o The final electron anaerobic acceptor is NO 3-, SO4 2-, CO2, Fe 3+, or SeO4 2-
Describe the flow of electron in fermentation. What happened to the electron in each of the above processes (final electron acceptor?)
o Uses an endogenous electron acceptor
o Does not involve an ETC nor a PMF
Describe how enzymes are involved in chemical reactions
o Carry out reactions at physiological conditions
o Speed up the rate of a reaction to reach equilibrium quicker
o Can act as catalysts
describe enzyme’s involvement in activation energy and E0
energy required to form transition state complex, an enzyme speeds up the reaction by lowering E0
define apoenzyme
protein component of an enzyme
define cofactor
nonprotein component of an enzyme
define prosthetic group
A tightly bound cofactor that remains at the active site of an enzyme during its catalytic activity
what is the significance of cofactors?
Used for catalytic activity
how is enzymatic activity regulated or inhibited?
- Enzymes can regulated and inhibited through competitive inhibitors, which is a molecule that inhibits enzyme activity by binding the enzyme’s active site
- Enzymes can be regulated be using competitive inhibitors to fight the substrate that is supposed to bind to the enzyme. The main difference between them is that a substrate that binds with an enzyme will form a product, but a competitive inhibitor will not make a product.
- Enzymes can also be altered through noncompetitive inhibitors, which do not bind to the activation site. Instead, they bind to another site on the enzyme, making the enzyme change shape and causing the substrate to not be able to bind to the enzyme.
- Both of these processes are useful in controlling microbial diseases
How does Sulfanilamide use competitive inhibition to control enzymes involved in synthesis of folic acid?
Sulfanilamide (sulfa drugs) resemble PABA, which is used in the formation of the coenzyme folic acid. Sulfa drugs compete with PABA for the enzyme that is involved in folic acid synthesis. This in turn inhibit growth of microbes. It does not affect humans because we do not produce folic acid, but rather get it from our diet
what is the role of prosthetic group?
a tightly bound cofactor that remains at the active site of an enzyme during its catalytic activity
compare and contrast ribozymes and enzymes?
Ribozymes are an RNA molecule with catalytic activity, while an enzyme is a protein catalyst with specificity for the reaction catalyzed and its substrates
what are ribozymes and enzymes made out of?
Ribozymes are made of RNA molecules, while enzymes are made of either only proteins or proteins (apoenzyme) and a nonprotein factor (cofactor)
what is the use of ribozymes?
Ribozymes are used in the formation of a peptide bond between amino acids during protein synthesis. They are also used in catalyzing self-splicing, which they cut themselves into pieces and join back together.
Ribozymes in Tetrahymena spp.
slicing pre-RNA
ribozymes in numerous fungi
splicing mitochondrial rRNA and mRNA
ribozymes in plants and algae
splicing of chloroplasts rRNA, tRNA, and mRNA
ribozymes in viruses (like T4 and delta)
splicing of viral mRNA
posttranslational regulation
occurs after an enzyme has been synthesized, there are several mechanisms to alter the enzyme after it has been made, some are reversible like allosteric and covalent modification
allosteric modification
most regulatory enzymes are allosteric enzymes, they are a small molecule called an allosteric effector. It binds to the regulatory site and causes the shape of the enzyme to change. A positive effector can increase the activity of the enzyme, but a negative effector decreases the enzyme
covalent modification
A mechanism of enzyme regulation in which the enzyme’s activity is either increased or decreased by the reversible covalent addition of a group such as phosphate or AMP to the protein.
List and describe effects of environmental factors on enzymatic activities
when an enzyme is exposed to too much heat, high pH, or high salinity, the molecule can break down and become denatured. This causes the enzyme to be nonfunctional
What chemical intermediate links pyruvate to TCA cycle?
Pyruvate dehydrogenase complex (PDH) oxidizes and cleaves pyruvate to form one NADH, one CO2, and acetyl CoA, which is the chemical intermediate
List the three chemoorganotrophic fueling processes.
- Oxidize hydrogen
- Sulfur oxidizing (hydrogen sulfide), sulfur, and thiosulfate
- Nitrifying
Define chemiosmotic hypothesis
- the most widely accepted hypothesis to explain oxidative phosphorylation
- electron transport chain organized so protons move outward from the mitochondrial matrix as electrons are transported down the chain
- proton expulsion during electron transport results in the formation of a concentration gradient of protons and a charge gradient
- the combined chemical and electrical potential difference make up the proton motive force (PMF)
Compare light vs dark reactions in photosynthesis.
- Light reaction: light energy is trapped and converted to chemical energy
- Dark reaction: the energy produced in the light reactions is used to reduce CO2 and synthesize cell constituents
Dna A
initiation of replication, binds origin of replication
Dna B
helicase breaks hydrogen bonds holding two strands of double helix together; promotes DNA primase activity, involved in primosome assembly
DNA gyrase
relieves supercoiling of DNA produced as DNA strands are separated by helicases, separates daughter molecules in final stages of replication
SSB proteins
bind single stranded DNA after strands are separated by helicases
Dna C
helicase loader, helps direct Dna B protein to DNA template
DNA primase
synthesis of RNA primer, component of primosome
DNA polymerase 3 holoenzyme
complex of about 20 polypeptides, catalyzes most of the DNA synthesis that occurs during DNA replication, has 3’ to 5’ exonuclease activity
DNA polymerase 1
removes RNA primers, fills gaps in DNA formed by removal of RNA primer
Ribonuclease H
removes RNA primers
DNA ligase
seals nicked DNA, joining DNA fragments together
Tus
termination of replication
topoisomerase 4
separation of chromosomes upon completion of DNA replication
What are the important features of Chemoorganotrophs?
An organism that uses organic compounds as sources of energy, electrons, and carbon for biosynthesis. Nearly all microorganisms are chemoorganotrophs
Can chemoorganotrophs use the same compound as a C source, energy source, and as a source for reducing power?
Yes, all chemoorganotrophs can use organic carbon for their sources of energy
what are some examples of chemoorganotrophs?
most non photosynthetic microbes, like most pathogens, fungi, and many protists
what is meant by CO2 fixation?
The process by which inorganic carbon is converted to organic compounds by living organisms
list the three pathways used by microbes to fix CO2
o Calvin-Benson Cycle
o Reductive TCA cycle
o Reductive acetyl-CoA pathway
carbon sources
o Autotrophs: CO2 sole or principle biosynthetic carbon source
o Heterotrophs: reduced, preformed, organic molecules from other organisms
energy sources
o Phototrophs: light
o Chemotrophs: oxidation of organic or inorganic compounds
electron sources
o Lithotrophs: reduced inorganic molecules
o Organotrophs: organic molecules
photolithoautotroph
o Carbon source: CO2
o Energy source: light
o Electron source: inorganic e- donor
o Representative organisms: Purple and green sulfur bacteria, cyanobacteria, diatoms
photoorganoheterotroph
o Carbon source: organic carbon
o Energy source: light
o Electron source: organic e- donor
o Representative organisms: Purple nonsulfur bacteria, green nonsulfur bacteria
chemolithoautotrophs
o Carbon source: CO2
o Energy source: inorganic chemicals
o Electron source: inorganic e- donor
o Representative organisms: Sulfur-oxidizing bacteria, hydrogen-oxidizing bacteria, methanogens, nitrifying bacteria, iron-oxidizing bacteria
chemolithoheterotroph
o Carbon source: organic carbon
o Energy source: inorganic chemicals
o Electron source: inorganic e- donor
o Representative organisms: Some sulfur-oxidizing bacteria (e.g., Beggiatoa spp.)
chemoorganoheterotroph
o Carbon source: organic carbon
o Energy source: organic chemicals, often same as C source
o Electron source: organic e- donor, often the same as C source
o Representative organisms: Most nonphotosynthetic microbes, including most pathogens, fungi, and many protists
how is proton motive force generated?
During respiration, electrons pass through the electron transport chain to the final electron acceptor generating a type of potential energy called the proton motive force (PMF) The PMF is used to synthesize ATP from ADP and phosphate
how is the proton motive force utilized?
the PMF is used to perform work when protons flow back across the membrane, down the concentration and charge gradients, and into the mitochondrial matrix or the cytoplasm of bacterial and archaeal cells. This flow is exergonic and is often used to phosphorylate ADP to ATP. PMF is also used by many secondary active transport systems to directly move nutrients into the cell and to rotate the bacterial flagellar motor without the need for ATP hydrolysis
oxidative phosphorylation
The synthesis of ATP from ADP using energy made available during electron transport initiated by the oxidation of a chemical energy source
substrate level phosphorylation
The synthesis of ATP from ADP by phosphorylation coupled with the exergonic breakdown of a high-energy organic substrate molecule
Which phosphorylation is associated with glycolysis, Krebs cycle, and electron transport system?
oxidative phosphorylation
Define and give examples of amphibolic pathways
Metabolic pathways that function both catabolically and anabolically
examples:
o Embden-Meyerhof pathway
o pentose phosphate pathway
o TCA cycle
List possible molecules that are used as final electron acceptor in anaerobic respiration.
NO 3-, SO4 2-, CO2, Fe 3+, or SeO4 2-
Compare respiration and fermentation.
- Respiration is exogenous, goes through glycolysis and TCA, has a final electron acceptor (different in aerobic and anaerobic), goes through the ETC, has to have a constant supply of an electron acceptor, generates a PMF to synthesize ATP from ADP
- Fermentation is endogenous, only goes through the glycolysis, there is no final electron acceptor because the by product accepts the electrons, does not have an ETC, ATP is synthesized almost exclusively through substrate level phosphorylation
Why does anaerobic respiration and fermentation make less ATP than aerobic respiration?
Anaerobic respiration makes less ATP because the final electron acceptors are less positive, are there is a smaller difference in the standard reduction potential, fermentation has less ATP because it does not have an ETC, and glucose is only partially catabolized
Do any of the eukaryotes perform fermentation?
Fungi and protists
compare respiration and fermentation on ATP synthesis and the pathways involved
- In respiration, electrons are moved across the ETC, which creates a proton gradient. When protons are transferred it creates a charge that can be used to make ADP into ATP
- In fermentation, ATP is formed through substrate level phosphorylation and use ATP synthase in the reverse direction. They make ATP from ADP and P and ATP synthase pumps protons out of the cel
- Important pathways in respiration include glycolytic pathways and the TCA cycle
- Pathways in fermentation are lactic acid and alcohol
compare respiration and fermentation on the role of ETS
Respiration uses the ETC, while fermentation does not
compare respiration and fermentation on electron carriers and acceptors
Respiration has electron carriers and acceptors because it utilizes an ETC, but there is not an ETC in fermentation. The biproducts of fermentation accept the electrons
compare respiration and fermentation on the number of ATP produced
- There is a maximum amount of 32 ATPs in respiration
- There is a maximum of 2 ATP molecules in fermentation
list the end products of fermentation: lactic acid
• Lactic acid: reduction of pyruvate to lactate
o Homolactic fermenters: use Embden-Meyerhof pathway and directly reduce almost all their pyruvate to lactate
o Heterotactic fermenters: use pentose phosphate pathway to form products other than lactate like ethanol and CO2
list the end products of fermentation: alcohol
pyruvate is decarboxylated to acetaldehyde, and reduced to ethanol
list the end products of fermentation: mixed acid fermentation
will yield acetic, lactic, succinic, and formic acids, and ethanol
list the end products involved in fermentation: butanediol
major end products are butanediol, but also lactic, formate, and ethanol
What are the environmental impacts of sulfur-oxidation?
extraordinarily flexible metabolically. For example, some bacteria and archaea can grow by oxidizing sulfur with oxygen as the electron acceptor However, in the absence of , they switch from chemolithotrophy to anaerobic respiration and oxidize organic material with sulfur as the electron acceptor. use their carbon source but will grow heterotrophically if they are supplied with reduced organic carbon sources such as glucose or amino acids.
What are the environmental impacts of Nitrification?
nitrifying bacteria, like soil and aquatic bacteria, carry ecological significance by oxidizing ammonia to nitrate
What are the environmental impacts of denitrification?
soil microbes use nitrate (NO3 -) as an electron acceptor is anoxic soils, this depletes the nitrogen in soil and reduces crop yields, which makes farmers use nitrogen fertilizers which can contaminate wells, groundwater, and rivers. However, in sewage, it decreases the levels of NO3 – and pollution of the plant. Lastly, it links the carbon cycle to other cycles such as the nitrogen cycle and the sulfur cycle, which is the basis of interaction between microbes and their habitats.
chemolithotrophs
a microorganism that uses reduced inorganic compounds as a source of energy and electrons
What are the environmental impacts of chemolithotrophs?
- These microbes donate electrons to their ETC by oxidizing inorganic molecules rather than organic nutrients
- Because they make consume a large amount of inorganic material, they make important contributions to several biochemical cycles such as nitrogen, sulfur, and iron cycles
anoxygenic phototroph
does not oxidize water to produce O2, other molecules besides water are used as an electron source and O2 is not produced, bacteriochlorophylls are used as pigments, only one photosystem, and there are mechanisms to generate reducing power
What types of bacteria are anoxygenic phototrophs?
Proteobacteria (purple sulfur and non-sulfur bacteria), chlorobi (green sulfur bacteria), chloroflexi (green non-sulfur bacteria), firmicutes (heliobacteria), and acidobacteria
oxygenic phototroph
oxidizes water to form oxygen, photosynthesis in plants, protists, and cyanobacteria, oxygen is released into the environment when light energy is converted to chemical energy, its pigment is chlorophylls, has two photosystems
what is the significance of bacteriorhodopsin?
Bacteria and archaea are capable of chlorophyll-independent phototrophy. These microbes depend on rhodopsin. They are now known as archaerhodopsin, many live in the ocean, are chemoorganoheterotrophs, can live nutrient depleted areas
What type of photoautotroph is cyanobacteria?
Uses oxygenic photosynthesis; the most abundant photosynthetic organism on earth and is a major contributor to the functioning of the biosphere.
True or False: Both organic and inorganic compounds may be used as electron acceptor in anaerobic respiration
true
True or False: Only inorganic compound may be used as electron acceptors in aerobic respiration
false
Lipid Metabolism: How do lipids enter the central pathway to metabolism and be consumed as energy source (beta-oxidation pathways)?
Lipids are entered into the central pathway to metabolism through Acetyl CoA. Fatty acids enter into the cycle through glycolysis
Protein Metabolism: what is meant by deamination?
- Proteins enter into the central pathway of metabolism through glycolysis and the Krebs cycle
- Deamination is the removal of amino groups from amino acids, which must occur to transport amino acids across the cell; it is the first step of amino acid catabolism to be used in TCA or glycolysis
Describe the Calvin-Benson Cycle.
- Basically the reverse of the pentose phosphate cycle
- Occur in the chloroplast stroma of eukaryotic autotrophs, but is also associated with carboxysomes in cyanobacteria, nitrifying bacteria, and thiobacilli
- There are three phases to the Calvin-Benson cycle called the carboxylation phase, reduction phase, and the regeneration phase.
- In carboxylation, ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the addition of CO2 to a 5-carbon ribulose (1,5-biphosphate), which forms a 6 carbon intermediate that splits into a 3 carbon phosphoglycerate (PGA).
- In the reduction phase, PGA is reduced to glyceradldehyde 3-phosphate by two reactions of Embden-Meyerhof pathway, which uses NADPH instead of NADH.
- In the regeneration phase, RuBP is reformed to repeat the cycle. This part of the cycle also produces carbohydrates like fructose, 6-phosphate, and glucose 6-phosphate, which are precursor molecules
- To make the molecules mentioned above, the cycle must start with CO2 and operate 6 times and reform RuBP 6 times
- The incorporation of CO2 into the cycle requires 3 ATP and 2 NADPH
What are the two enzymes used in the Calvin-Benson cycle?
o ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO)
o glyceraldehyde 3-phosphate dehydrogenase
True or False: Calvin cycle is used by both prokaryotes and eukaryotes.
True, it is used by eukaryotic autotrophs and most aerobic bacterial autotrophs
Griffith transformation experiment demonstrated that a cellular component transformed nonpathogenic bacteria into pathogenic bacteria. Name this compound.
- Griffth and his colleagues used pneumococci bacteria in mice
- They found that if the bacteria had an enzme that attacked DNA, the bacteria was virulent. If the bacteria had RNA blocked, it was not. This suggested that DNA was carrying information for transformation
Briefly explain how Hershey-Chase experiment ruled out protein as being the genetic material.
• Hershey-Chase wanted to determine if protein or DNA was the genetic carrier. They performed experiments with a T2 bacteriophage using radioactive 32P on the DNA and 35S on the protein coat. They were put into host bacteria, and then into a blender and centrifuged. Most of the supernatant had 35S, while 32P was not in the pellet but in the bacteria.
semi-conservative replication
the two strands of DNA are separated, there is an old stand, which was taken off of the DNA and a new strand, which is synthesized from the old strand. Only one new strand is made
antiparallel
strands of DNA are antiparallel, the backbones run in opposite directions; one strand is in the 5’ – 3’ direction and the other is in the 3’ – 5’ direction
complementary strand
the 5’ end of one strand is aligned with the 3’ end of another
major/minor grooves
major grooves are large spaces in helix curves and minor grooves are smaller spaces. Major grooves are effective in proteins being able to grab and unwind the DNA
OriC
DNA is supercoiled and needs to be relaxed. OriC opens up the DNA to allow replication in both directions in the 5’ – 3’ direction
Helicase
unwinds the helix with the aid of topoisomerases such as DNA gyrase, the strands are kept separate by SSBs
Topoisomerase
apart of the replisome; an enzyme used to relax the DNA; change the topology of DNA molecules by transiently breaking one or both strands, play an important role in replication and transcription
primer
needed to start the process of replication, each primer is needed for an okzaki fragment in the 3’ – 5’ direction, but only one is needed in the opposite; short RNA strand and can initiate RNA polymerase
ssDNA binding proteins
keep DNA strands apart once they have separated
Describe proofreading process in replication.
- The ability of enzymes to check their products to ensure that the correct product is made. For instance, DNA polymerase checks newly synthesized DNA and replaces an incorrect nucleotide with the correct one prior to further synthesis.
- Is not 100% efficient
What are the enzymes involved in proofreading?
o Carried out by DNA polymerase 3
o Topoisomerases
o Holoenzyme
coding/complementary strand
Refers to the matching of two strands of DNA or RNA based on the base-pairing rules; AT and GC are base pairs
What coding strand is complementary to mRNA?
mRNA contains the same complementary features as DNA, with the exception of T, which is replaced with U, but is still complementary with A
transcription in prokaryotes:
the sigma factor binds to DNA and flags down RNA polymerase. Sigma factor recognizes the promoter and enables RNA polymerase to bind to DNA. RNA polymerase then participates in elongation and produces a complementary strand to DNA. There are two kinds of termination in prokaryotes; rho dependent where rho stops the RNA and there is loop. Then there is intrinsic where there are many Us in a segment that slows down RNA polymerase. mRNA makes a stem and loop that causes RNA polymerase to pull away
transcription in eukaryotes
o Similar process, except that it needs to be processed before it can be functional mRNA
There is removal of pieces (splicing) that are not needed. Exons are kept and introns are removed. This does not always give the same give the same result or the same mRNA pieces, this is alternative slices
o then a guanine cap is added and a poly A tail is added post-transcriptionally, which allows RNA to come out of the nucleus and into the cytoplasm
differences in bacterial and eukaryotic transcription
- eukaryotes have 3 major RNA polymerases
- promoters differ from those in bacteria by having combinations of many elements.
- RNA polymerase II is a large aggregate, containing 10 or more subunits. catalyzes production of heterogeneous nuclear RNA (hnRNA) which undergoes posttranscriptional modification to generate mRNA
describe ribosome structure in eukaryotes and prokaryotes
- Prokaryotes are 70S, made with 30S and 50S subunits
* Eukaryotes are 80S, made with 40S and 60S subunits
what is the role of ribosomes in protein synthesis?
mRNA is moved into the ribosomes that bears a message for protein synthesis and make a polypeptide
tRNA
small RNA that binds an amino acid and delivers it to the ribosome for incorporation into a polypeptide chain during protein synthesis.
rRNA
RNA present in ribosomes; contributes to ribosome structure and also directly involved in the mechanism of protein synthesis.
mRNA
Single-stranded RNA synthesized from a nucleic acid template (DNA in cellular organisms, RNA in some viruses) during transcription; mRNA binds to ribosomes and directs the synthesis of protein.
Describe the role of chaperones in polypeptide folding,
Chaperones are small proteins that bind to a growing polypeptide after it leaves the ribosomes
Indicate if the following portions of a gene is located upstream or downstream of the coding region?
- promoter
- +1 nucleotide
- terminator
- trailer
- upstream
- upstream
- downstream
- downstream
Which portions of a gene are transcribed, but not translated?
promoter
positive control mechanism
Control of transcription by an activator protein. When the activator is bound to the activator-binding site, the level of transcription increases.
negative control mechanism
Regulation of transcription by a repressor protein. When bound to the repressor-binding site, transcription is inhibited.
repressors
A protein that can bind to a repressor-binding site and inhibit transcription
co-repressors
A small molecule that binds a transcription repressor protein, thereby activating the repressor and inhibiting the synthesis of a repressible enzyme.
inducers
A small molecule that stimulates the synthesis of an inducible enzyme
Explain how attenuation regulatory mechanism works for tryptophan operon
- Transcription of the trp operon will be inhibited by attenuation when a bacteria if deficient in other amino acids besides tryptophan, which will start to accumulate in the cell. When the bacterium can accumulate large amounts of other amino acids, tryptophan will be low, so attenuation will cause tryptophan to be synthesized.
- Can be coupled with repression
What is the significance of having alternative sigma factors for Escherichia coli?
• To help direct RNA polymerase activity, also helps to bind to multiple sequences in order to perform multiple cellular tasks, such as flagella and chemotactic proteins with sigma 28
alternative sigma factors
direct the core RNA polymerase to transcribe distinct sets of inducible genes or operons and is thereby a mechanism for global regulation
What are the important features of genetic code?
- Universal
- 3 base pairs makes 1 amino acid
- 61 code for amino acids, 3 are stop codons
- AUG is always first, UGA, UAA, and UAG are stop codons
What is meant by code degeneracy/redundancy?
• The presence of more than one codon for each amino acid.
List and define different forms of mutagen
A chemical or physical agent that causes mutations
- base analogues
- DNA modifying agents
- intercalating agents
base analogues
Molecules with minor chemical differences from normal DNA nucleotides that can substitute for them during DNA replication, leading to mutations. Also used as antiviral agents
DNA modifying agents
mutagens that change a base’s structure and therefore alter its base-pairing specificity; some will preferentially affect certain kinds of base pairing causing a certain kind of DNA damage
intercalating agents
Molecules that can insert between the stacked bases of a DNA double helix, thereby distorting the DNA and inducing frameshift mutations
Embden-Meyerhof pathway
most common pathway for glucose degradation to pyruvate, glycolysis
o Makes 2 ATP
o Phosphorylation, taking a phosphate group and putting it on to ADP to make ATP
o Substrate level phosphorylation takes PEP (also used in PTS) to get a high energy Phosphate to produce ATP and is used as an energy source
o One glucose becomes 2 pyruvate
o Oxidation step makes NADH
pentose phosphate pathway
o Amphibolic, needed for biosynthesis
o Produces NADPH for biosynthesis
o Provides precursors for making nucleic acids, gives 5 carbon sugars for it (like deoxyribose)
o Does not really produce ATP
Enter-Doudoroff pathway
o Also turns glucose in pyruvate
o Only makes 1 ATP
o Makes NADPH
How is anabolism and catabolism intertwined in glycolysis and TCA cycle.
- With anabolism, glucose is in an oxidation-reduction reaction and it is used to extract electrons (oxidized) and another molecule will pick up the electron and become reduced
- Catabolism is involved because it completes the oxidation of glucose and taking into different pathways such as glycolysis
What is the significance of glycolysis and TCA cycle in providing skeleton carbon to the cell?
the carbon skeletons produced from glycolysis and the TCA cycle are significant because they are needed for biosynthesis for chemical building blocks like amino acids. This eventually leads to macromolecules
RNA Polymerase
o The holoenzyme begins transcription and elongates the DNA and reads it
o The complementary copy of RNA is being made. Replaces T with U in the RNA strand
o mRNA is made
o endonuclease activity
DNA polymerase
o Endonuclease activity, in the 5’ to 3’ direction o Reads the complementary strand o Unwinds the DNA o Has to start with a primer o Produces Okazaki fragments o It is used for proofreading
Describe and explain the significance of tRNA charging, attachment of an amino acid to a tRNA as a (proof-reading step in translation).
• tRNA carries the amino acid and brings it to the ribosome
• when the codon and anticodon match, the tRNA goes to get the corresponding amino acid
• tRNA has to be activated/charged, which means to adding an amino acid to tRNA
o aminoacyl-tRNA synthase is an enzyme that adds an amino acid to tRNA, and it must bring the right amino acid that corresponds with the anticodon
has to add the right amino acid because the codon and amino acid will bind, so you must proofread before translation
Describe the role of chaperones in polypeptide folding, and molecular chaperones in protein secretion across the membrane
- Chaperones are small proteins that bind to a growing polypeptide after it leaves the ribosomes
- Can refold a denatured protein after heat has degraded it
protein secretion mechanisms in gram negative and positive
- gram-positive and gram-negative bacteria have different problems secreting proteins based on the differences between the structure of their walls
- Both G+ and G- use the Sec-dependent pathway for transporting proteins across the membrane
- Other secretion pathways also exist, but all systems require energy
SEC dependent pathway
o translocate proteins from cytoplasm across or into plasma membrane
o Attached to pre-protein is signal peptide which: delays the folding, chaperone proteins keep preproteins unfolded, and removed once pre-protein emerges from plasma membrane
Type 1 (ABC) protein secretion method
o ubiquitous in prokaryotes
o transports proteins from cytoplasm across both plasma membrane and outer membrane
o sends information from the outside to the inside
o energy for this comes from PMF
Type 3 protein secretion method
o secretes virulence factors of Gram-negative bacteria from cytoplasm, across both plasma membrane and outer membrane, and into host cell
o can inject an exotoxin
o has an extension that can inject things into another cell
o virulence factor, and contributes to pathogenicity
Type 4 protein secretion method
o unique because they secrete proteins and transfer DNA during conjugation
o like type 3, injects plasmids with a pili
o virulence factor
o share plasmids with another cell and can contribute to antibiotic resistance and pathogenic genes
What is the role of Dnaj and Dnak in protein secretion process?
- DNAj and DNAk protects cells from heat shock and high temperatures
- Bind and hold on to the protein in an amino acid shape and holds this shape until it binds to a cell and then can reform the 3-dimensional shape
- Can aid and pass through the cell membrane and delay the folding
- Consume ATP to protect and properly fold the DNA
promoter
site where RNA polymerase binds to initiate transcription
upstream region
region of the DNA strand that is above the gene that is to be regulated
downstream region
region of the DNA that is after the gene that is to be regulated
TATA box
10 base pairs upstream of transcriptional start site; A base sequence in bacterial promoters that is recognized by RNA polymerase and is the site of initial polymerase binding.
-35 region
RNA polymerase recognition site
CAP binding site
catabolic activity protein; alter the binding of polymerase. Determines whether RNA polymerase will bind to the promoter region
what is an operon?
unique to bacteria; they control several genes under one mechanism
Lactose operon
o Inducible operon
o With a strand of DNA, there is an operator region, which is where the inducible molecule, the lac repressor, binds to the strand. This repressor inhibits transcription
o When there is no lactose, this repressor is active and binds to the operator region to prevent RNA polymerase from binding and initiating transcription
If there is no lactose, no transcription will occur
o When there is lactose, allolactose (corepressor) binds to the lac repressor and inhibits it. It prevents the lac operon from binding, which allows for RNA polymerase to bind and transcribe the gene
Tryptophan operon
o Repressible
o Tryptophan is always needed, it is an amino acid
o If there is not tryptophan in the system, then transcription occurs, and RNA will bind to the promoter
o When there is a lot of trp, there will be a corepressor that binds to the site and blocks transcription and prevents RNA polymerase
o When the repressor protein is active, it binds to the operator region, and causes RNA polymerase to not be able to transcribe
compare the trp and lac operons
o Trp is repressible and lac is inducible
o Lac has negative and positive control; trp has positive control
DNA binding proteins
o Topoisomerases: relive the rension generated by rapid unwinding of the double helic
o DNA gyrase: A topoisomerase enzyme that relieves tension generated by the rapid unwinding of DNA during DNA replication or transcription.
o Primosome: In bacteria, a complex of proteins that includes the enzyme primase, responsible for synthesizing the RNA primers needed for DNA replication.
o SSB: keeps strands apart
o RNA polymerase: An enzyme that catalyzes the synthesis of RNA using a DNA molecule as a template
DNA binding domains
o Leucine zipper: alpha helices with leucines
o Zin finger: several amino acids bonded to a zinc molecule
o Helic turn helix: an alpha helix with a turn and another alpha helix, can hold DNA, CAP
what are riboswitches?
A site in the leader of an mRNA molecule that interacts with a metabolite or other small molecule, causing the leader to change its folding pattern. In some riboswitches, this change can alter transcription; in others, it affects translation.
how can riboswitches stop transcription prematurely?
riboswitches are regions on mRNA where an effector molecule can bind, and this molecule determines whether mRNA is synthesized. Depending on the folding of the mRNA, the riboswitch can turn DNA on or off.
how can attenuation stop transcription prematurely?
• Attenuation prevents transcription by acting as a corepressor in the trp operon. In a addition, attenuator sequences form stem-loops that can slow RNA polymerase. For example regions 1 and 2 pause just before termination. Regions 3 and 4 is the terminator loop. Lastly, if a loop forms in regions 2 and 3, this prevents the formation of the other loops.
how can riboswitches control translation?
• Riboswitches that control translation have an effector binding element at the 5’ end of mRNA, which alters the folding pattern. This folding pattern prevents the shine Delgarno and 16S RNA from binding to start ribosome binding to make a polypeptide
how can small RNAs (sRNA) control translation?
small RNAs are used as antisense RNA ad uses the coding strand to make a copy. This copy can be used and bind to mRNA as a way to prevent ribosomes from binding to mRNA and prevent translation. (mRNAs normally make a copy from the complementary strand)
Briefly discuss the regulation of gene expression in eukaryotes and archaea
- Although archaea live in similar habitats as bacteria, their gene expression is similar to how eukaryotes function
- Gene regulation is monitored at replication, transcription, and post-translation, but most occurs is transcription because it is costly to make, and the cell does not want to waste products to make mRNA unless the final product is completed.
What are the important features of Two-Component Regulatory and Phosphorelay Systems?
- They are both global regulatory systems, used in environmental stresses
- Two-component signal transduction systems involve a simple relay where the sensor kinase transfers a phosphoryl group directly to the response regulator.
Two-component signal transduction
A regulatory system that uses the transfer of phosphoryl groups to control gene transcription and protein activity. It has two major components: a sensor kinase and a response regulator protein.
o Link events going on outside the cell to events in the cell
o Sensor kinase spans the plasma membrane to open to the extracellular environment and the cytoplasm
o Then the response regulator has a conformational change to interact with molecules
o Can control transcription to repress or activate
phosphorelay systems
A set of proteins involved in the transfer of phosphate from one protein in the set to another. It is often used to regulate protein activity or transcription
o Proteins participate in the transfer of phosphoryl groups
o Important in quorum-sensing
frame-shift mutation
Mutations arising from the loss or gain of a base or DNA segment, leading to a change in the codon reading frame and thus a change in the amino acids incorporated into protein
point shift mutation
A mutation that affects only a single base pair
define global regulatory system and give examples
Regulatory systems that simultaneously affect many genes, operons, and pathways
examples:
- two-component
- alternate sigma factors
- second messengers
- catabolite repression
- stringent response
Describe how Ames test detects carcinogens.
- Based on the observation that carcinogens are mutagens
- The test determines if a substance increases the rate of mutation
- If the substance is a mutagen, then it is likely to be a carcinogen
- It does not directly test for carcinogenicity
- Tester stains of s. typhimurium are plated with the tested bacteria. Once the initial colonies exhausted the efforts of histidine, only revenants that have mutated ad can synthesize histidine grow on the plate. The more colonies there are, the more mutagenicity there is
what is meant by DNA repair?
when significant effects damage certain proteins will aid in fixing the genome
mismatch repair
A type of DNA repair in which a portion of a newly synthesized strand of DNA containing mismatched base pairs is removed and replaced, using the parental strand as a template
excision pair
A type of DNA repair mechanism in which a section of a strand of damaged DNA is excised and replaced, using the complementary strand as a template. Two types are recognized: base excision repair and nucleotide excision repair
direct repair
A type of DNA repair mechanism in which a damaged nitrogenous base is returned to its normal form (e.g., conversion of a thymine dimer back to two normal thymine bases)
recombinational repair
A DNA repair process that repairs damaged DNA when there is no remaining template; a piece of DNA from a sister molecule is used
why does DNA need to be repaired?
• Mutations can have very bad effects on microbes, therefore DNA replication is important to be able to function and repair any changes that have been made
Where in bacteria, archaea, and eukaryotes the components of ETC are located?
- Bacteria and archaea have ETC in the plasma membrane
* Eukaryotes have ETC in the mitochondrial/chloroplasts
Define and give examples of horizontal gene transfer (HGT)
- Horizontal gene transfer: The process by which genes are transferred from one mature, independent organism to another. In bacteria and archaea, transformation, conjugation, and transduction are the major mechanisms by which HGT can occur
- Examples: conjugation, transduction, transformation
what is the significance of HGT?
main mechanism in which bacteria and archaea evolve, DNA transfer among genera and domains of life, survive environmental stressors, virulence factors, expand ecological niche
chemical work
synthesis of complex molecules; build polymers
transport work
take up nutrients, elimination of wastes, maintenance of ion balances
mechanical work
cell motility and movement of structures within cells
reducing power
molecules that serve as a ready supply of electrons for a variety of chemical reactions; Molecules such as NADH and NADPH that temporarily store electrons. The stored electrons are used in anabolic reactions such as CO2 fixation and the synthesis of monomers (e.g., amino acids).
standard reduction potential (E’0)
A measure of the tendency of an electron donor to lose electrons in an oxidation-reduction (redox) reaction. The more negative the reduction potential of a compound, the better electron donor it is.
endergonic
A reaction that does not spontaneously go to completion as written; the standard free energy change is positive, and the equilibrium constant is less than one.
exergonic
A reaction that spontaneously goes to completion as written; the standard free energy change is negative, and the equilibrium constant is greater than one.
Electron Transport Chain
o Used in oxidation and reduction reactions (glucose is oxidized and the electron carriers are reduced)
o first electron carrier having the most negative E’o
o the potential energy stored in first redox couple is used to form ATP
o first carrier is reduced and electrons moved to the next carrier
o examples of electron carriers: NAD< NADP, FAD, CoQ, cytochromes
phosphorylation
phosphate is added to a molecule
photophosphorylation
The synthesis of ATP from ADP using energy made available by the absorption of light
oxidative phosphorylation
The synthesis of ATP from ADP using energy made available during electron transport initiated by the oxidation of a chemical energy source.
substrate level phosphorylation
The synthesis of ATP from ADP by phosphorylation coupled with the exergonic breakdown of a high-energy organic substrate molecule. (PEP from PTS)
Proton Motive Force (PMF)
The potential energy arising from a gradient of protons and a membrane potential that powers ATP synthesis and other processes.
charge gradient
electrical potential energy formed from proton expulsion during electron transport
ATP synthase
An enzyme that catalyzes synthesis of ATP from ADP and Pi, using energy derived from the proton motive force
chromosome
The bodies that have most or all of the cell’s DNA and contain most of its genetic information (mitochondria and chloroplasts also contain DNA).
chromatin
The complex of DNA and proteins, including histones, from which eukaryotic and some archaeal chromosomes are made
histone
A small basic protein with large amounts of lysine and arginine that is associated with eukaryotic DNA in chromatin. Related proteins are observed in many archaeal species, where they form archaeal nucleosomes
nucleosome
A complex of histones and DNA found in eukaryotic chromatin and some archaea; the DNA is wrapped around the surface of the beadlike histone complex
monocistronic transcription
An mRNA containing a single coding region
polycistronic transcription
An mRNA that has more than one coding region; formed when an operon is transcribed
phosphorelay system
o A set of proteins involved in the transfer of phosphate from one protein in the set to another. It is often used to regulate protein activity or transcription
o Used in sporulation of B. subtillis
telomers
Complexes of DNA and proteins at the ends of eukaryotic chromosomes.
regulon
A collection of genes or operons that is controlled by a common regulatory protein
modulon
individual genes are under control of their own regulators, responsible for the need of glucose over other sugars and CAP
protoplast fusion
promotes genetic variability o Protoplasts (lack cell wall) are put in a solution with enzymes that degrade cell walls. Protoplasts of cells fuse together during coincubation. The cell wall is regenerated with osmotic stabilizers. This allowed for recombination of chromosomes from two different cells. This is a mutagenic process
polysome
a complex of several ribosomes translating a single messenger RNA
rolling circle replication
o Happens with circular DNA
o Some viruses use these processes and for plasmids
o A double layer of the DNA, cut one of the strands and separates
o As that piece is cut and pulled away, nucleotides are added to it in the 5’-3’ direction
o As it is pulled away, the other strand is also being synthesized until it is fully resynthesized
o There is unlimited pulling and replication
o Can have multiple copies of that DNA, could be unlimited, in regular replication only 2 copies can be made
Shine-Delgarno Sequence
o A segment in the leader of bacterial mRNA and some archaeal mRNA that binds to a sequence on the 16S rRNA of the small ribosomal subunit. This helps orient the mRNA on the ribosome
denitrification
The reduction of nitrate to gaseous products, primarily nitrogen gas, during anaerobic respiration
nitrogen fixation
The metabolic process in which atmospheric molecular nitrogen (N2) is reduced to ammonia; carried out by nitrogen-fixing bacteria and archaea
type 5 protein secretion pathway
A pathway in Gram-negative bacteria that translocates proteins across the outer membrane after they have been translocated across the plasma membrane by the Sec system.
type 2 protein secretion pathway
- only in proteobacteria
- Proteins for secretion enter from the periplasm and the pseudopilus acts like a piston to push the proteins through the outer membrane.
- Typical cargo for a T2SS includes degradative enzymes like proteases, lipases, and cellulases.
