MCB3020 Asghari Exam 2

First Law of Thermodynamics

energy can neither be created nor destroyed, it can only be transformed or redistributed.

Total energy in universe remains constant

Second Law of Thermodynamics

entropy (disorder) in the universe is constantly increasing

Standard reduction potential (Eo)

a measure of a reducing agent's tendency to lose electrons

more negative Eo is better electron donor

Why does aerobic growth generate the highest amount of ATP? How does this play a role in electron transport system

because oxygen is the terminal electron acceptor with greatest Eo

ETC moves electrons from carriers with more negative Eo to carriers with a more positive Eo

Compare Eo of aerobic and anaerobic respiration

aerobic is more efficient because oxygen is terminal electron acceptor, creating the most ATP

Describe how enzymes are involved in chemical reactions

biological catalyst that speeds up rate of reaction by lowering activation energy

Apoenzyme

protein component of the holoenzyme

Cofactor, significance?

non protein component of haloenzyme

can be prosthetic group which firmly attach to enzyme or can be loosely attached coenzyme

How are enzymatic activities regulated or inhibited

via changes in temperature, pH, or saturation of substrate molecule

Compare and contrast ribozymes and enzymes

ribozyme is RNA molecule wtih catalytic activity

enzyme is a protein with catalytic activity

Allosteric Regulation VS Covalent Modification (ways to regulate enzyme activity)

AR: small molecule binds reversibly to regulatory site away from catalytic site, causing conformational change in enzyme, altering its activity

CM: chemical groups are added to or removed from the enzyme, affecting its activity

Effects of environmental factors of enzymatic activities? How?

Saturation: increases as concentration of substrate increases. at point of saturation, adding more substrate will not increase the rate of reaction

Temperature: every enzyme has optimal temperature, any deviation decreases rate of reaction. Increase in temp impacts H bonds and function

pH: every enzyme has optimal pH, any deviation decreases rate of reaction. change also alters ionic properties and function

*may become denatured if temp or pH deviate too much*

Fermentation vs Respiration

F: inefficient method of producing energy, involves only *substrate-level phosphorylation*. Yields less ATP, endogenous electron receptor is reduced and then regenerated.

R: efficient method of producing energy that involves *oxidative phosphorylation*. involves the oxidation of glucose and passage of electron down ETC. Energy released is used to pump protons, creating PMF

Why does anaerobic respiration and fermentation make less ATP than aerobic?

because fermentation relies on SLP to produce ATP and respiration produces less ATP because it uses something other than Oxygen as the terminal electron acceptor

Ex of eukaryotes that perform fermentation

They DO perform fermentation

ex: humans ferment lactic acid in muscles when oxygen levels are low

ex: single celled yeasts ferment ethanol

Important features of chemoorganotrophs.

Can they use the same compound as C source, energy source, and as source for reducing power? Ex?

They are organisms that derive their energy and electrons from organic molecules

Chemoorganoheterotrophs use same compound for all sources

Role of chemolithoautotrophs in acid mine drainage and in geochemical recycling?

they oxidize ferrous iron to ferric iron and sulfide ions to sulfate ions. They combine with pyrite in cole mines which leaches metals from the mines, turning river acidic

GR: they consume such large amounts of inorganic material that they make important contributions to the N, S, and Fe cycles

CO2 fixation means what?

process by which inorganic carbon dioxide is converted to complex organic molecules

3 Pathways used by microbes to fix CO2

- Calvin Cycle

- reductive TCA cycle

- acetyl- CoA pathway

- 3-hydroxypropionate cycle

Compare respiration and fermentation: ATP synthesis, pathways, ETS, Electron donor, electron carriers, electron acceptors, and amount of ATP produced

*ATP Synthesis*: both synthesize ATP from ADP but respiration is more efficient

*Pathways*: Respiration = passage of electrons down ETC and creation of ATP with oxidative phosphorylation. Fermentation = passage of electrons to endogenous acceptors and creation of ATP through SLP

Glucose = electron donor in both respiration and fermentation

*Electron carriers and acceptors*: Aerobic Respiration acceptor = oxygen

anaerobic respiration terminal acceptor is not oxygen

Fermentation uses endogenous acceptors (NAD+) which must be regenreated

Proton Gradient

Proton Motive Force

PG: electrons move down ETC and protons are pumped across membrane from lower concentration to higher concentration

PMF: gives the proton gradient its potential energy, protons move down their concentration gradient across membrane

Different forms of Phosphorylation

which is associated with glycolysis, Krebs cycle, and electron transport system?

Substrate-Level Phosphorylation: involves creation of ATP using energy from another high-energy compound

Oxidative Phosphorylation: involves creation of ATP from scratch, using PMF that is established as electrons are passed through ETC

Amphibolic Pathways

pathway that can be simultaneously catabolic and anabolic.

Ex: TCA cycle, glycolysis, pentose phosphate pathway

Define and Compare 3 common routes of glucose conversion to pyruvate

1- Embden-Meyerhof Pathway: most common glycolytic pathway, aka glycolysis

2- Pentose phosphate pathway: amphibolic pathway that involves the oxidation of glucose followed by synthesis of 5 carbon pentose sugars that can be used for synthesis of DNA and RNA

3- Entner-Doudoroff pathway: alternative that combines some elements of both glcolytic pathway and pentose-phosphate pathway. Yields a net of 1 NADH, 1 NADPH, and, 1 ATP

How are anabolism and catabolism intertwined in glycolysis and TCA cycle? What is the significance of glycolysis and TCA cycle in providing skeleton carbon to the cell?

glycolysis and TCA cycle can produce intermediaries that serve as carbon skeletons in anabolic pathways

pathways are assumed to be amphibolic

Energy in Proton Motive Force can be used in/for:

ATP synthesis, the concentration of molecules in active transport, or to power the rotation of bacterial flagella

Molecules used as final electron acceptors in anaerobic respiration

(uses something other than oxygen)

can be organic or inorganic compound

SO4, NO3, Fe, CO2, SeO4, fumarate, etc

List several possible end products of fermentation

lactic acid

propionate

isopropanol

acetate

butanol

ethanol

butyrate

2,3-butanediol

assimilatory nitrate reduction

reduction of nitrate to nitrite via nitrate reductase and then further reduction of nitrite to ammonium

aerobic

de-nitrification

reduction of nitrate to nitrogen gas, can be devastating to soil fertility because nitrogen gas is unusable to most organisms

nitrification

oxidation of ammonia to nitrate, two step reaction requiring two genera of microorganisms. one converts ammonia to nitrite and the other converts nitrite to nitrate

sulfur-oxidation

sulfur oxidizing bacteria use anaerobic respiration with sulfite to produce ATP via SLP and Oxidative phosphorylation

Different forms of photoautotrophs (oxygenic photosynthesis vs anoxygenic photosynthesis)

Oxygenic: eukaryotes and cyanobacteria, produces oxygen byproduct

Anoxygenic: bacteria and archaeans, does not producs oxygen byproduct

What is the significance of bacteriorhodopsin?

is an alternative pigment to chlorophyll, acts directly as proton pump, instead of relying on an ETC to generate PMF

Compare light vs dark reaction

Light: light energy is converted to chemical energy in form of ATP and NADPH

Dark: (Calvin Cycle) the reducing power of ATP and NADPH is harnessed and the energy is put into long-term storage molecules such as glucose, sucrose, and starch

semi-conservative replication

DNA replication is semi-conservative

means that one is the strands of daughter DNA molecule is "new" while the other is "old". It means that the daughter strand always has the correct template

antiparallel

one DNA strand runs from 5' to 3' left to right and the other runs 3' to 5' left to right

complementary strand

a nucleic acid strand that exhibits complementary base pairing with another strand

major/minor grooves

the twisting arrangement of the two strands of DNA forms grooves, they play important role in facilitating interaction of other molecules, such as enzymes with genetic material.

compare DNA polymerase vs RNA polymerase

similarities:

- synthesize nucleic acids

- use DNA as template

- synthesize new strand of nucleotides from 5' to 3'

differences:

- DNA polymerase- synthesizes DNA

adds thymine as comp pair to adenine

used in DNA replication

requires a primer before synthesis can begin

-RNA polymerase- synthesizes RNA

adds uracil as comp pair to adenine

used in *transcription*

does not require a primer

endonuclease/exonuclease activities

ENDO: cleave the bonds of DNA from within the molecule

EXO: cleaves nucleotides at the ends of the molecule

significance of 3'-5' exonuclease activity

3' to 5' exo activity gives DNA polymerase III the ability to proofread

What event occurs during initiation of replication with regards to OriC, helicase, topoisomerase, primer, ssDNA, binding proteins

replication begins at specific sites on DNA called *Origins of Replication* (ORI)

here is where the proteins attach to DNA and open "replication bubbles" that expand laterally which allows DNA replication to proceed at replication forks

unwinding proteins such as *helicase* unwind the DNA at replication fork into single strands. *Single-strand binding protein* stabilizes the DNA while synthesis occurs

The superocoiled tension has to be relieved before DNA replication can occur via the enzyme *topoisomerase* . this occurs ahead of the replication bubbleby breaking and joining DNA strands

DNA synthesis cannot start from scratch because DNA only adds nucleotides to a 3' carbon. RNA synthesis can start from scratch. *Primase* = RNA polymerase that adds primer to allow replication to begin

DNA *ligase* eventually replaces the RNA primase and "glues" the DNA fragments together via phosphodiester bonds

Proofreading

list enzymes involved

DNA Polymerase III

allows it to go back and identify, remove, and fix incorrect base pairs to avoid spontaneous mutations

not 100% effective

What is meant by coding strand, complementary strand? mRNA is complementary to which strand?

coding strand = strand with same sequence as the mRNA (with Thyamine instead of Uracil)

mRNA strand is complementary to the template DNA strand because the RNA Polymerase reads it directly during transcription

coding strand is directly translated during protein synthesis

During which process is a DNA:RNA hybrid is formed

during transcription when mRNA strand is formed from template DNA strand

Compare the transcription process/mRNA synthesis in prokaryotes, eukaryotes and Archaea. Compare RNA polymerase activity in different domains.

DIfferences:

- *site and timing*: occurs in nucleus of eukaryotes, the final mRNA transcript has to be exportedfrom nucleus before it can be transcribed. Occurs in the cytoplasm of prokayotes, mRNA can be immediately translated. transcription and translation are often simultaneous in prokaryotes

- *different RNA poly. enzymes*: eukaryotes have 3 RNA polymerases, RNA poly. II is huge molecule to produce heterogenous nuclear RNA that is modified to make mRNA

- *different promoter sequences*: Eukaryotic promoters are larger and more diverse. In Bacteria, the Pribnow Box is found in promoter sequence, plays a role in initiating transcription. Eukaryotes and Archaea have TATA box to serve the same purpose

- Eukaryotes undergo RNA splicing and post-transcriptional modification while prokaryotes do not.

Ribosome structure and its role in protein synthesis, role of different RNA molecules?

made up of RNA and proteins and consist of a small and large subunit. Play a structureal role in maintaining these subunits

They are the site of polypeptide synthesis. Prokaryotes have 70S ribosomes and euaryotes have 80S ribosomes that are larger and of slightly different content than prokaryotic

significance of tRNA charging (proof-reading step for translation)

occurs when an enzyme (aminoacyl tRNA synthetase) transfers the correct amino acid to the appropriate tRNA molecule, forming an ester linkage.

This is an important step because it is essential that the tRNA brings the correct animno acid to the growing polypeptide chain

role of chaperones in polypeptide folding and molecular chaperones in protein secretion across the membrane

chaperones are proteins that bind to polypeptide and ensure correct folding, with the help of ATP input

able to facilitate protein folding but can also cause proteins to unfold. It allows the proteins that have folded incorrectly to correct itself.

Sec-dependent protein secretion

used by both G- and G+

proteins are translocated across or into the plasma membrane while carrying an attached signal peptide that delays folding of the polypeptide until it emerges from the plasma membrane

ABC secretion pathway

used by G- only

involves protein subunits that form a contiguous channel across plasma and outer membranes which allows proteins to cross with ease.

very common in prokaryotes

type IV protein secretion

used by G- only

transports DNA and proteins from one cell to another during bacterial conjugation

role of DNAj and DNAk in protein secretion process?

they are molecular chaperones that play a role in ensuring proteins are properly folded

promoter

area in DNA where RNA polymerase binds and begins to unwind the DNA to initiate transcription

operator

the "switch" sequence on the DNA that controls transcription of an entire set of genes in an operon

upstream region

relative term to describe a portion on the DNA strand that is more toward the 5' end

downstream region

relative term used to describe a portion on the DNA strand that is more toward the 3' end

TATA box

highly conservative region of the promoter, found in the DNA of eukaryotes and archaeans

-35 region

region of DNA about 35 bases upstream of the leader sequence where RNA polymerase typically binds

CAP binding site

area on the promoter where catabolite activator protein (CAP) binds, making it easier for RNA polymerase to bind and begin transcription

operon

compare the 2 forms

groupings of functionally related genes that appear in bacterial cells, all controlled by a single promoter sequence. A single switch is called an operator, controls the transcription of the entire operon

-inducible operon- normally turned off, gene expression is turned on whene the operons are on

-repressible operons- are normally turned on and can be regulated by turning gene expression off

compare lactose and tryptophan operons

lac operon- produces enzymes needed for lactose catabolism. Is an inducible operon under both positive and negative control. Turned on when lactose is present but glucose is absent

trp operon- produces the enzymes needed for tryptophan anabolism, repressible operon under negative control. Can be turned off when tryptophan is present in the environment

positive and negative control mechanism

negative control- *presence* of control molecule in the repressor binding site *inhibits* transcription and removal of repressor from binding site promotes transcription

positive control- *presence* of a control molecule in activator binding site *promotes* transcription and the removal of the activator from activator binding site inhibits transcription

difference between repressors, corepressors, and inducers

repressor- control molecule that inhibits transcription when it binds to the repressor binding site on an operon

co-repressor- molecule that activates an otherwise inactive repressor molecule, allowing it to bind to itts repressor binding site

inducer- molecule that inactivates an otherwise active repressor or activator protein

Explain how attenuation regulatory mechanism works for tryptophan operon

attenuation is a process that turns the trp operon off when tryptophan levels are high.

There are 4 regions on the mRNA that can form complementary base pairing that essentially turns transcription on and off

significance of having alternative sigma factors for E. Coli

allows E. coli to respond to different environmental conditions by producing different alternate sigma factors for that " turn on" different genes

important features of genetic code

it is universal

it is redundant, multiple codons can code for the same amino acid

it is not ambiguous, a codon can code for one and only one amino acid

figure 12.44 diff protein secretion mechs in prokaryotes

riboswitch

a site on the leader sequence of an mRNA molecule that interacts with a small molecule or metabolite causing a change in folding pattern of the leader, which alters transcription or translation

involved in a special kind of transcription attenuation

regulation of gene expression in eukaryotes and archaea

can be regulated in multiple stages, including DNA replication, transcription, and post-translation.

most occurs at level of transcription due to the high energy cost, the cell would waste energy if it produced mRNA without using it to make the final gene product

this can be done by organizing genes in operons that are controlled by a single region of the DNA (operons are rare in eukaryotes)

What are the important features of Two-Component Regulatory/Signal Transduction and Phosphorelay Systems

both are ways to control global regulatory systems

-Two-Component: link gene expression to events occurring outside of the cell ( temp, osmolarity, and oxygen level changes). Involves two proteins, a sensor and a response protein. Sensor-kinase protein is embedded on *cytoplasmic membrane* and senses environmental change then passes the signal to the response-regulator protein that receives a *phosphoryl* group and binds to DNA and can act as an activator or repressor

- Phosphorelay- essentially signal transduction systems involving more signal relay steps and more proteins

mutagens and their different forms

chemical or physical factors that produce a stable, heritable change in the DNA nucelotide sequence.

chemical - base analogs, intercalating agents, etc

phyiscal - UV rays or X rays

point mutation

type of mutation that causes a change in a single nucleotide with another nucleotide

frame-shift mutation

mutation caused by the insertion or deletion of nucleotides that are not in groups of three, throwing off the reading frame and significantly impacting the final polypeptide

global regulatory mechanisms

simultaneously control an even larger number of genes or multiple operons and simultaneously affecting multiple genes and metabolic pathways.

under the control of regulatory mechanisms

SOS response

the calle "last-ditch" effort to survive after experiencing significant damage to DNA, allows the cell to survive but in a highly mutated form

how does AMES test detect carcinogens?

uses bacteria that have mutations in genes involved in histidine synthesis to determine whether a given chemical is carcinogenic. Since they cannot synthesize histidine they require it from their environments for growth, testing the substabce's ability to create mutations that allow the bacteria to revert and synthesize histidine again. If reversion occurs in a large number of colonies, it may be carcinogenic

DNA repair

list different forms of DNA repair mechanisms

a collection of processes in which a cell identifies and corrects damage to its genome, necessary because cells are often exposed to chemical or physical mutagens that do damage to their DNA

proofreading, excision repair, mismatch repair, direct repair, and SOS response

Where are the components of ETC located in bacteria, archaea, and eukaryotes?

Eukaryotes: located along the inner mitochondrial membrane

Prokaryotes: on the cell membrane

post-transcriptional modifications

alteration of the pre-mRNA before the final mRNA molecule is exported from the nucleus in eukaryotes. Involves the excision of introns and addition of a poly-A tail and guanine cap

post-translational modifications

alteration of the product of translation before it becomes a mature polypeptide.

Ex: addition of functional groups, removal of portion of polypeptide, or folding of polypeptide

Horizontal Gene Transfer (HGT)

significances?

transmission of genetic information between organisms in a manner other than traditional sexual or asexual reproduction

What are the role of plasmids and viruses in HGT

plasmids are small, circular, extrachromosomal bits of bacterial DNA that can be transferred from one bacterium to another via HGT. for example conjugation involves transfer of genetic material through direct contact

viruses can mediate horizontal gene transfer as well. In transduction, genetic information is transferred between bacterium via virus

chemical work

the production of complex molecules from simpler ones

transport work

involves the elimination of waste, take-up of nutrients, and maintenance of ion balances within the cell

mechanical work

involves cell movement (motility) and the movement of intracellular structures

entropy

a measure of a system's disorder

reducing power

a molecule's power to reduce another molecule by donating an electron

standard reduction potential

Eo

a measure of a reducing agent's tendency to lose electrons. More negative Eo = better electron donor

the greater the difference between the Eo values for the acceptor and donor, the more energy is released

endergonic vs exergonic reaction

endergonic absorb/require energy

exergonix releases energy

ETC, ex of components / electron carriers

components include coenzyme Q and cytochromes which use iron to transfer electrons

activation energy

energy required for a reaction to proceed through its high-energy transition state, reduced by enzymes

ribozymes

an RNA molecule with catalytic activity

allosteric regulation of enzymes

occurs when the binding of a molecule to the enzyme changes the shape of its active site and thus impacts the enzyme's ability to act as a catalyst

covalent modification of enzymes

enzyme function can be regulated by covalent attachment of another molecule to the enzyme

autotrophs

phototrophs

chemotrophs

organotrophs

lithotrophs

chemolithotrophs

phosphorylation

addition of a phosphate group onto an organic molecule, thereby affecting its activity

substrate-level-phosphorylation

uses enzymatic transfer of a phosphate group to another molecule.

ex:

enzymatic transfer od a phosphate group to ADP produces a small amount of ATP during glycolysis and the TCA cycle

oxidative phosphorylation

uses the reducing power of NADH and FADH2 to create a PMF which can be harnessed by ATP synthase to phosphorylate ADP