MCB3020 Exam 2 SG

Thermodynamics

Study of relationship among heat, work, temperature, and energy

First law of thermodynamics

Energy can’t be created or destroyed, therefore, the total energy in the universe is constant

Second law of thermodynamics

Entropy (disorder) in the universe is constantly increasing. The universe as a system is constantly moving towards a state of disorder

What is meant by “life obeys the laws of thermodynamics?”

Life is able to persist in an ordered fashion because it uses energy from the environment and releases heat, thereby increasing disorder in the universe as a whole

Metabolism

Sum of all chemical rxns within the cell

Catabolism

Involves breaking down complex molecules into their smaller subcomponents

Anabolism

Involves synthesis of complex molecules from their simpler subunits

Photolithoautotrophs

Derive energy from light

Electrons from reduced inorganic molecules

Carbon from CO2

Photolithoautotrophs examples

Cyanobacteria, purple and green sulfur bacteria

Photoorganoheterotrophs

Derive energy from light

Electrons from organic molecules

Carbon from reduced organic molecules

Photoorganoheterotrophs examples

Purple and green NONsulfur bacteria

Chemolithoautotrophs

Derive energy from oxidation of inorganic molecules

Electrons from reduced inorganic molecules

Carbon from CO2

Chemolithoautotrophs examples

Sulfur-oxidizing bacteria, methanogens, nitrifying bacteria, iron-oxidizing bacteria

What do methanogens produce as metabolic byproduct?

Methane gas

Chemolithoheterotrophs

Derive energy from oxidation of inorganic chemicals

Electrons from reduced inorganic molecules

Carbon from reduced, pre-formed organic molecules

Chemolithoheterotrophs examples

Some sulfur-oxidizing bacteria

Chemoorganoheterotrophs

Derive energy from oxidation of organic chemicals

Electrons from organic molecules

Carbon from reduced, pre-formed organic molecules

All above components usually come from the same sources

Chemoorganoheterotrophs examples

Most nonphotosynthetic microbes (i.e. fungi, pathogens, protists, archaea)

Standard reduction potential (E0)

Measure of a reducing agent’s tendency to lose electrons

A compound with a more negative E0 is a better electron… , and a compound with a more positive E0 is a better electron…

Donor; acceptor

The greater the difference between the E0 for the electron acceptor and donor, the…

More energy is released from a set of redox reactions (delta G is more negative)

How do electrons move in the ETC?

From electron carriers with more negative E0 to electron carriers with more positive E0

Why is aerobic respiration more efficient than anaerobic respiration?

Because oxygen is the terminal electron acceptor with the greatest E0, generating the greatest amount of energy

A redox pair with a more negative reduction potential will spontaneously donate electrons to a pair with more positive potential (T/F)

True

The first electron carrier in an ETC has the most negative E0 (T/F)

True

The more positive the reduction potential, the greater is the affinity for electrons (T/F)

True

Respiration

An efficient method for producing energy that involves the oxidation of an organic molecule (e.g. glucose), and the passage of an electron down an ETC

What energy source does the ETC directly generate?

Proton motive force

Fermentation

Inefficient method of producing energy that involves only substrate-level phosphorylation

Substrate-level phosphorylation

Enzymatic transfer of a phosphate group from a high-energy substrate to ADP, forming ATP

Fermentation yields (more/less) ATP than oxidative phosphorylation in respiration, which produces ATP indirectly

Less

In fermentation, … is reduced and… is oxidized

Endogenous electron receptor; glucose

Electron carrier molecules in cellular respiration

NADH and FADH2

Electron carrier molecules in photosynthesis

NADPH

What are coenzyme Q (CoQ) and cytochromes?

Electron carriers in ETC

Holoenzyme

The protein component and the nonprotein component in enzymes

Holoenzyme protein component

Apoenzyme

Holoenzyme nonprotein component

Cofactor; can be a prosthetic group

Prosthetic group

Cofactor firmly attached to enzyme; if not a prosthetic group, it can be a loosely attached coenzyme

Cofactors

Often necessary for enzymes to function properly

What are the best-studied riboenzymes?

Those that are involved in self-splicing; they are able to cut themselves then join segments back together

Where has self-splicing been observed?

Unicellular eukaryotes, fungi, plants, algae, viruses

Allosteric regulation

Allosteric effector binds reversibly to regulatory site away from catalytic site, causing a conformational change and altering its activity

Covalent modification

Chemical groups added to or removed from the enzyme, affecting its activity

Why does a change in temperature affect enzymatic activity?

It impacts enzyme’s H bonds, impacting its structure/function

Why does a change in pH affect enzymatic activity?

It impacts the enzyme’s ionic properties, thus altering its function

Metabolic channeling

Localizing enzymes and metabolites within the cell via compartmentalization to produce significant variations in metabolite concentrations within cell

How do gram negative bacteria compartmentalize?

Contain certain materials and rxns within periplasmic space

How do euks compartmentalize?

Rxns within organelles

Pyruvate oxidation yields…

2 carbon acetyl-CoA molecule (chemical intermediate that enters TCA cycle)

Examples of how euks perform fermentation

Humans ferment lactic acid in muscles when O2 levels are low; yeasts ferment ethanol

3 fueling processes for chemoorganotrophs

Aerobic respiration, anaerobic respiration, fermentation

CO2 fixation

Process by which inorganic CO2 is converted to complex organic molecules, like glucose

Pathways for CO2 fixation

Calvin cycle, reductive TCA cycle, 3-hydroxypropionate cycle, acetyl-CoA pathway

For CO2 fixation, most autotrophs use the…

Calvin cycle

How do respiration and fermentation differ based on number of ATP produced?

Both methods synthesize ATP from ADP, but respiration is more efficient (38 ATP per glucose vs 2 ATP per glucose)

How do respiration and fermentation differ based on pathways?

Respiration involves passage of electrons down ETC and creation of ATP via oxidative phosphorylation; fermentation involves passage of electrons to endogenous acceptors and creation of ATP through substrate-level phosphorylation (glycolysis)

How do respiration and fermentation differ based on role of ETC?

ETC is involved in respiration but not fermentation

How do respiration and fermentation differ based on electron carriers and acceptors

Aerobic (anaerobic) respiration uses oxygen (something other than oxygen) as terminal electron acceptor; fermentation uses endogenous electron acceptors that must be regenerated (e.g. NAD+)

Oxidative phosphorylation

Creation of ATP from scratch, using proton motive force established as electrons passed through ETC

ATP creation is glycolysis and Krebs cycle

Substrate-level phosphorylation

ATP creation in ETC

Oxidative phosphorylation

Chemiosmotic hypothesis

As electrons transported down mitochondrial ETC, protons move from matrix to intermembrane space; this creates proton gradient used to make ATP via ATP synthase

Amphibolic pathway

Pathway that can be catabolic and anabolic

Amphibolic pathway examples

TCA/Krebs cycle, glycolysis, pentose phosphate pathway

Embden-Meyerhof pathway

Most common glycolytic pathway

Pentose phosphate pathway

Amphibolic; involves oxidation of glucose → synthesis of 5-C pentose sugars used as intermediaries for synthesis of RNA/DNA; can occur aerobic or anaerobic and alongside other pathways

Entner-Doudoroff pathway

Combines elements from glycolytic and pentose phosphate pathways; yields net 1 NADH, 1 NADPH, and 1 ATP per glucose; rare

Why are glycolysis and TCA cycle considered amphibolic?

Can produce intermediaries that serve as carbon skeletons in anabolic pathways

Terminal electron acceptors in anaerobic respiration examples

SO4²-, NO3-, Fe³+, CO2, SeO4²-, fumarate, other organic acceptors (e.g. humic acids)

End products of fermentation

Lactic acid, propionate, isopropanol, acetate, butanol, ethanol, butyrate, 2,3-butanediol

Sulfur-oxidizing bacteria

Use anaerobic respiration with sulfite (SO3²-) to produce ATP via substrate level phosphorylation and oxidative phosphorylation

Nitrification

Oxidation of ammonia (NH3) to nitrate (NO3-); two-step rxn requiring two genera of microbes

How are two genera of microbes used for nitrification?

One converts ammonia to nitrite → another converts nitrite to nitrate (usable form of nitrogen)

Denitrification

Reduction of nitrate to nitrogen gas; devastating to soil fertility because N2(g) is unusable to organisms

Thiobacillus ferrooxidans is a…

Chemolithotroph; oxidizes ferrous iron to ferric and sulfide ions to sulfate

What turns the Ohio river red and acidic?

Thiobacillus ferrooxidans, who combine with pyrite in coal mines of Appalachian Mountains to leach metals from mines

Chemolithotrophs consume such large amounts of… that they have a huge…

Inorganic material; ecological impact

Photoautotrophs

Derive energy from sunlight and make their own food

Oxygenic photosynthesis

Photosynthesis that produces O2 as byproduct; by euks and cyanobacteria

Anoxygenic photosynthesis

Photosynthesis that does not produce O2 as byproduct; by bacteria besides cyanobacteria and archaeans

Chlorophyll

Primary pigment found in most photosynthetic organisms

Bacteriorhodopsin

Alternative pigment to chlorophyll that acts directly as proton pump instead of relying on ETC to generate proton motive force

What is the final electron acceptor in anaerobic respiration?

Either an organic or inorganic compound

What type of respiration uses only inorganic compounds, like O2, as terminal electron acceptors?

Aerobic

Beta oxidation

Process of breaking down fatty acids into 2-C fragments, which are then converted into acetyl-CoA that is fed into Kreb’s

How are lipids used in glycolysis?

Lipids are hydrolyzed to form glycerol and fatty acids → glycerol is fed into glycolysis

Two major stages of photosynthesis

Light and dark (carbon-fixation/Calvin cycle) rxns

Light rxns

Light energy converted to chemical energy as ATP and NADPH

Dark rxns (carbon-fixation/Calvin cycle)

Reducing power of ATP and NADPH is used and put into long-term storage molecules (e.g. glucose, sucrose, starch)

Photosynthesis is rare in what domain?

Archaea; only Halobacteria species

Where does the Calvin cycle occur?

Stroma of chloroplasts

Three stages of Calvin cycle

Carboxylation, reduction, regeneration of RuBP (the CO2 acceptor)

Carboxylation phase

Rubisco attaches CO2 to 5-C sugar called RuBP → unstable 6-C compound formed → immediately splits into two 3-C compounds, 3-PGA

Reduction phase

3-PGA phosphorylated by ATP and reduced by NADPH to form intermediate → intermediate phosphorylated into G3P, a 3-C sugar and the end product of Calvin cycle → G3P used to make starch and sucrose

Regeneration of RuBP, the CO2 acceptor

Majority of G3P used to regenerate RuBP

For every 6 G3P molecules produced… is used to make sugar

1; the rest is recycled

The net synthesis of 1 G3P molecule requires… turns of the Calvin cycle

3; because fixation of 3 CO2 molecules is required

2 enzymes specific to Calvin cycle

RuBisCO and glyceraldehyde 3-phosphate dehydrogenase

Major and minor grooves

Formed by twisting arrangement of two DNA strands; plays an important role in facilitating interaction of other molecules with genetic material