BIOL 265-61 Exam 2 Preparation

Important concepts from CH5, ...

Metabolism

The sum of all chemical reactions occurring in a living cell. These reactions can release energy (catabolism) or require energy (anabolism).

Anabolism

An endergonic reaction that builds from simple molecules to larger, more complex molecules. Often involves dehydration synthesis → releases WATER.

Catabolism

An exergonic reaction that breaks complex molecules into much smaller, simpler molecules. Usually hydrolytic and uses WATER to break CHEMICAL BONDS.

ATP breakdown: ___________________________.

ATP → ADP + Pi + Energy

The cell’s main energy-transfer molecule consists of: ____________________________________.

Adenine + Ribose + 3 Phosphate Groups

The Collision Theory

Explains how chemical reactions occur:

• Particles must collide

• They must have enough energy

• They must have the correct orientation

Activation Energy (Ea)

The minimum energy required to start a chemical reaction.

Reaction Rate

How frequently successful collisions occur.

It will increase when:

• Temperature increases → Molecules move faster and collide more often.

• Concentration increases → Molecules are closer and collide more often.

• Pressure increases → Molecules (especially gases) are closer and will collide more often.

Enzymes

Catalysts that speed up a chemical reaction without being permanently changed.

Enzyme Specificity

An enzyme works with a particular substrate or type of reaction. The active site has a shape that matches the substrate, however, enzymes and substrates are flexible and will adjust (slightly) if needed.

Turnover Number

The maximum number of substrate molecules an enzyme active site can convert into product per second when the enzyme is fully saturated.

(Typically ~1 to 10,000).

Enzyme Example: Oxidoreductases

Catalyze oxidation-reduction reactions.

Enzyme Example: Transferases

Transfer functional groups from one molecule to another.

Enzyme Example: Hydrolases

Breaks chemical bonds by hydrolysis.

Apoenzyme

The protein portion of an enzyme. By itself, it is inactive when a co-factor is required.

Cofactor

Nonprotein component required for enzyme activity.

Coenzyme

An organic co-factor. Many are derived from vitamins.

Holoenzyme

Complete, active enzyme.

NAD⁺

Electron carrier; mainly catabolism.

NADP⁺

Electron carrier; mainly anabolism.

FMN

Electron carrier (comes from B2).

FAD

Electron carrier (also comes from B2)

CoA

Fat metabolism + Krebs Cycle (comes from B5)

Denaturation

Loss of the enzyme’s normal 3D shape. If active site shape changes: Substrate cannot bind properly (enzyme loses activity).

Changes in __________ concentrations can interfere with the bonds that maintain the enzyme’s structure.

H⁺ or OH^-

Saturation

All available active sites are occupied.

Competitive Inhibition

Competes with the substrate for the active site. Resembles the substrate enough to fit into the site, but does not produce the normal product.

Noncompetitive Inhibition

Binds to another location on the enzyme: the allosteric site.

(Inhibitor changes the enzyme’s shape → active site malfunctions → reaction decreases).

Allosteric

A molecule binds to a site other than the active site and changes enzyme activity.

Feedback Inhibition

A cellular control mechanism where the end product of a biochemical pathway binds to an enzyme early in that same pathway to slow down or stop further production.

Ribozymes

RNA molecule that acts as a catalyst. They are involved in RNA cutting/splicing and protein synthesis at the ribosome(s).

Oxidation

The loss of electrons, an increase in oxidation state, or the gain of oxygen (and loss of hydrogen).

Reduction

The gain of electrons, a decrease in oxidation state, or the loss of oxygen (and gain of hydrogen).

Oxidation and reduction ________________ because if one molecule loses electrons, another molecule must receive them. Together, they form a ______________.

Always occur together; redox reaction

Glucose is an important energy source because: __________________________________________________________.

It releases a large amount of energy (which can be used to produce ATP) when it is oxidized. Glucose is gradually oxidized, allowing the cell to capture energy instead of releasing it all at once as heat.

Phosphorylation

Adding a P group to a molecule.

Mechanisms of ATP Generation: Substrate-level phosphorylation

Phosphate is transferred directly to ADP.

Mechanisms of ATP Generation: Oxidative phosphorylation

Electron transport chain generates energy used

to make ATP.

Mechanisms of ATP Generation: Photophosphorylation

Light energy is used to generate ATP.

Key difference between oxidative phosphorylation and photophosphorylation: _________________________________________________________.

…

Electron Transport Chain (ETC)

A series of electron carriers that transfer electrons and release energy.

Chemiosmosis

The process that uses the energy from the electron transport chain to make ATP.

It is part of oxidative phosphorylation and produces most of the ATP during aerobic respiration.

___________ is required for aerobic resperation because it accepts the electrons at the end of the ETC.

Oxygen

What is the major difference between aerobic respiration and anaerobic respiration?

Aerobic respiration requires oxygen to completely break down glucose. Meanwhile, anaerobic respiration occurs without oxygen and breaks down glucose incompletely.

Fermentation

Most important purpose: Regenerate NAD⁺ so glycolysis can continue. Allows glycolysis to continue when the cell cannot use aerobic or anaerobic respiration.

Lactic Acid Fermentation

Pyruvate + NADH → Lactic acid + NAD⁺
Important point: NAD⁺ is regenerated.

Homolactic Fermentation

Produces primarily/only lactic acid.

Heterolactic Fermentation

Produces lactic acid + other products, such as other acids or alcohols.

Lipid Metabolism

Fat → Lipase → Glycerol + Fatty acids

Protein Metabolism

The sum of the biochemical processes that control the synthesis, breakdown, and transformation of proteins and amino acids in the body.

Deamination

• Removes the amino group (-NH₂) from an amino acid

• Produces NH₄⁺ (ammonium ion)

• The remaining organic molecule can be converted into a substance that enters the Krebs Cycle

Decarboxylation

Removal of COOH.

Desulfurization

Removal of SH.

Fermentation Test

Tests whether a microorganism can ferment a specific carbohydrate.

Acid Production → pH indicator changes color.

Gas Production → bubble appears in Durham tube.

Oxidase Test

Detects the enzyme Cytochrome C Oxidase, which is involved in the electron transport chain.

H₂S is what some bacteria produce by breaking down ________________ compounds and is _______________________.

Sulfur-containing compounds; useful for distinguishing similar organisms

What is considered to be a microbial interaction?

Some microorganisms can use the waste products of other microorganisms as nutrients.

Autotrophs

Make their own organic compounds from simple inorganic substances.

Photosynthesis

Conversion of light energy → chemical energy, used to convert CO₂ into reduced organic compounds (sugars).

Carbon Fixation

Incorporation of carbon from CO₂ into organic compounds.

Type of Photosynthesis: Oxygenic Photosynthesis

Includes plants, algae, and cyanobacteria. Uses H₂O as the hydrogen/electron donor and produces O₂.

6 CO₂ + 12 H₂O + light → C₆H₁₂O₆ + 6 H₂O + 6O₂

Type of Photosynthesis: Anoxygenic Photosynthesis

Performed by some bacteria (such as purple/green sulfur bacteria) and uses H₂S as the hydrogen/electron donor. Produces sulfur (S) instead of O_2.

6 CO₂ + 12 H₂S + light → C₆H₁₂O₆ + 6 H₂O + 12 S

Chlorophyll

Absorbs light energy.

Photosystems

Groups of pigments and proteins that capture light.

ETC

Transfers excited electrons and pumps H⁺.

Plants, algae, and cyanobacteria primarily use ___________. Other photosynthetic bacteria use _________________.

Chlorophyll a; bacteriochlorophylls

Cyclic Photophosphorylation

Uses Photosystem I only.

Leaves chlorophyll → moves through carriers → returns to chlorophyll.

Produces: ATP, no NADPH, and no O₂.

Noncyclic Photophosphorylation

H₂O → PS II → electron transport chain → PS I → NADPH

Produces: ATP, NADPH and O₂.

Light-Independent Reactions

CO₂ + ATP + NADPH → reduced carbon compounds → sugars

The overall energy pathway can be simplified to:

Electron donor → Electrons transferred to NAD⁺/NADP⁺/FAD →

Electron transport chain (in respiration) → Final electron acceptor →

H⁺ gradient → Chemiosmosis → ATP.

Cells can build simple sugars into larger carbohydrates. Glycogen synthesis:

Glucose → glucose-6-phosphate → ADPG → glycogen

UDP-N-acetylglucosamine (UDP-NAc)

An important starting material for making peptidoglycan, which forms bacterial cell walls.

Amination

Adding an amine group (—NH₂) to an organic acid produces an amino acid. Organic acid + amine group → amino acid.

Transamination

The amine group is transferred from an existing amino acid to another organic acid. Amino acid → transfers —NH₂ → another organic acid.

The amino acids are joined together through __________________, which requires energy.

Dehydration Synthesis

Nucleotide

A molecule made of a nitrogenous base, a five-carbon sugar, and one or more phosphate groups.

Nucleotides are used to make: ____________________________.

Nucleic acids that include DNA and RNA.

Catabolism

Breaks molecules down and releases energy.

Anabolism

Builds molecules and requires energy.

Catabolism and Anabolism are connected through _____________________________.

Common Metabolic Intermediates

_________________ function in both catabolism and anabolism. The Krebs cycle is an important example.

Amphibolic Pathways

Krebs cycle intermediates can be used to make ____________________________________________.

Amino acids and other cellular molecules

____________________ regulates metabolic pathways.

Feedback Inhibition

High ATP → ____________.

Slows glycolysis

Low ATP/high energy demand → _______________.

Increases glycolysis

Microbial Growth

An increase in the number of cells, not the size of the individual cells.

The ability of a microorganism to survive and grow depends on its _____________________.

Metabolic Charcteristics

Three important temperatures for microorganisms: _________________________________________________________.

Minimum growth temperature, optimum growth temperature, and maximum growth temperature.

Psychrophiles

“Cold-loving” organisms (opt. 15^.C, can grow at 0^.C).

Psychrotrophs

“Cold-tolerant” organisms (opt. 20-30^.C, can grow at 0^.C).

Mesophiles

“Moderate-temperature loving” organisms (opt. 25-40^.C; most pathogens).

Thermophiles

“Heat-loving” organisms (opt. 50-60^.C; hot springs or hot soil).

Hyperthermophiles

“Extreme heat-loving” organisms (opt. 80^.C or higher; archaea or volcanic hot springs).

Bacteria grow best in a pH between _______________.

6.5 and 7.5 (very few grow at ~pH4)

Acidophiles

Can grow at a very acidic pH. Some can survive at pH 1.

Yeast and molds tolerate a wider pH range than bacteria. Their optimum is ___________.

~pH 5-6.

Buffer

Helps maintain a stable pH.

Note: Phosphate salt is an especially useful buffer.

A microbial cell is approximately _______________.

80-90% water

Hypertonic Environment

Has a higher solute concentration outside the cell.

Water moves OUT of the cell → cell loses water → plasmolysis

Plasmolysis

Shrinkage of the cell’s cytoplasm because water leaves the cell.