Anabolism

- biosynthesis: synthesis of cell molecules and structures

- endergonic - require energy to move forward

Catabolism

- break the bonds of larger molecules to release energy

- exergonic - release energy

What is an enzyme?

- Biological catalyst

- is a protein

- endo (in membranes, cytosol, organelles) & exo (excreted

- speeds up the rate of metabolic reaction by lowering Activation Energy Barrier (not by changing the thermodynamic properties of the reaction)

- not consumed or altered during course of the reaction (can function over and over again)

- have substrate specificity

How do enzymes catalyze the reactions?

- by lowering the Activation Energy Barrier

- enzymes do not affect the change in free energy; instead they speed up reactions that would occur eventually (reach the transition state with less additional energy than without the enzyme present)

How can the active site lower the Activation Energy Barrier of a reaction?

- orienting substrate correctly

- straining substrate bonds 

- covalently bonding to a substrate

- providing a favorable microenvironment (acidic, basic, hydrophobic, hydrophilic) for the reaction to occur

1. Key-lock fit

2. Induced fit

1. perfect fit between a substrate and an enzyme (no temporary changing of a shape)

2. after binding to a substrate, then shape of an enzyme is changed to accommodate the substrate more tightly

1. Substrate

2. Enzyme + substrate

3. Active site

4. Regulatory (Allosteric) site

1. the reactant upon which an enzyme acts on

2. enzyme-substrate complex

3. region on enzyme where substrate binds (complementary to a substrate)

4. region on enzyme (different than active site) where allosteric regulatory molecule (activator or inhibitor) binds affecting enzyme's shape and function (regulatory feedback mechanisms)

1. Simple enzymes

2. Conjugated enzymes (holoenzyme)

1. consist of protein alone

2. contain protein and some other non-protein molecule

→→Apoenzyme: protein portion on an enzyme (nonfunctional enzyme)

→→Cofactors: non-protein helpers to an enzyme

1. Exoenzymes

2. Endoenzymes

1. transported extracellularly; break down large food molecules or harmful chemicals

2. retained and functions intracellularly; most enzymes of metabolic pathways

Factors that affect enzyme activity -- Environmental (Temperature & pH)

- each enzyme has optimal temperature at which it works best

- has an optimal pH (for most it is 6-8)

- heat, low or high pH, or certain chemicals can cause enzyme denaturation (weakening of bonds that maintain the shape of an enzyme and unfolding → prevents the substrate from attaching to the active site)

1. Competitive inhibitors

2. Noncompetitive inhibitors

1. compete with substrate for active site -- some antibiotics compete with substrate for the active site thus shutting down the metabolic process

2. bind to allosteric site but alter 3D structure of the active site (ex: toxins, poisons, pesticides; or in the case of NEGATIVE FEEDBACK regulation, the regulatory molecule is the product of the enzymatic reaction)

Competitive inhibition of enzymes

- a molecule that resembles the substrate occupies the active site, preventing the substrate from binding

- enzyme cannot act on the inhibitor and is effectively shut down

Noncompetitive inhibition of enzymes

- some enzymes have two binding sites (active site, regulatory site)

- regulated by the binding of molecules other than the substrate to the regulatory site

- often, the regulatory molecule is the product of the enzymatic reaction

- provides negative feedback that slows enzyme activity once a certain concentration of product is reached

Feedback inhibition

- the end product of a metabolic pathway shuts down the pathway

- cell is prevented from wasting chemical resources by synthesizing more product than is needed

Types of Enzymes

- oxidoreductases: transfer electrons from one substrate to another and dehyrogenases transfer a hydrogen from one compound to another

- transferases: transfer functional groups from one substrate to another

- hydrolases: cleave bonds on molecules with the addition of water

- lyases: add groups or remove groups from double-bonded substrates

- isomerases: change a substrate to its isomeric form

- ligases: catalyzes the formation of bonds with the input of ATP and the removal of water

Oxidation-Reduction reactions (REDOX)

- transfer of electrons during catabolic chemical reactions releases energy stored in organic molecules

-this released energy is ultimately used to synthesize ATP

- reduction = gain of electrons

- oxidation = loss of electrons

What are the 4 stages of harvesting energy from glucose?

1. Glycolysis: Glucose breaks down → 2 molecules of pyruvate

2. Pyruvate oxidation: pyruvate breaks down → 2 molecules of Acetyl CoA

3. Citric acid cycle: completes the breakdown of Acetyl CoA

4. Oxidative phosphorylation: synthesis of majority of ATPs

NAD+ (Nicotinamide Adenine Dinucleotide)

- electron carrier

- oxidized form

- low in Ep

- e- recipient; oxidizing agent in cell respiration

- by accepting e- becaomes reduced to NADH

NADH

- reduced form

- rich in Ep

- stores the Ep released by respiration until the ETC is activated; passes the electrons to the ETC

- oxidation back to NAD+ releases the stored energy used to regenerate ATP

Phosphorylation

- the energy captured in the electron carrier is used to phorylate (add inorganic phosphate to) ADP or another compound

- store energy in a high energy molecule

- ATP (Adenine: nitrogen base; Ribose: 5-carbon sugar; Three phosphate groups bonded to the ribose)

Substrate-Level

- ATP made directly in glycolysis (2 ATP) and the citric acid cycle (2 ATP)

- accounts for 10% of the total ATP generated by cellular respiration

- requires an enzyme (kinase) to transfer the phosphate group to a molecule

Oxidative

- 28-34 ATP

- phosphorylation that occurs with ETC 

- accounts for 90% of the total ATP generated by cellular respiration

- requires oxygen and a proton gradient to add a phosphate group to ADP

Oxidation of Pyruvate to Acetyl CoA

- 3 step biochemical pathway

- carbon is removed from pyruvate (3 C) as CO2, leaving 2 of the original carbons attached to Coenzyme A (complex is called Acetyl CoA)

- 1 NADH molecule is produced/pyruvate

- Occurs inside mitochondria

- Only occurs with oxygen

Citric Acid Cycle = Krebs Cycle

- 8 step biochemical pathway that converts all of the remaining carbons from the original glucose into CO2

- yields 1 ATP per Acetyl CoA

- traps high energy electrons in 3 NADH, and 1 FADH2 per Acetyl CoA

- occurs inside mitochondrial matrix of eukaryotes

- only occurs with oxygen

Citric Acid Cycle (cont.)

- the acetyl group of Acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate

- the next seven steps decompose citrate back to oxaloacetate, making the process a cycle

- the NADH and FADH2 produced by the cycle transfer electrons extracted from food to the ETC

Oxidative phosphorylation (ETC + chemiosmosis)

- high energy electrons trapped in NADH and FADH2 (in glycolysis, pyruvate oxidation, and the Krebs cycle) and donated to ETC are used to produce ATP indirectly through chemiosmosis

- accounts for the most of the extracted energy

- occurs in the inner membrane (cristae) mitochondria of eukaryotes

- only occurs with oxygen

Electron Transport Chain

- series of enzyme-catalyzed redox reactions

- gradually removes Ep from NADH (electrons are transferred to each enzyme in series; protons (H+) follow along)

- ultimately transfers 2 electrons to oxygen (O2- picks up two protons (H+) to balance the charge; creates a molecule of water)

- NADH & FADH2 deliver electrons (H+ follow)

Electron Transport Chain II

- electrons are passed (in redox reactions) through a number of protein carriers including cytochromes 

- final electron (and H+) accepter is O2 and they form H2O

- gradual energy release

- some of this energy will drive active transport of H+

- ETC generates no ATP directly

Chemiosmosis

- couples ETC with ATP synthesis by using the imbalance of H+ (proton gradient) from the ETC

→→at the end of ETC: because of active transport of H+ (proton pump) there is more H+ in intermembrane space than in matrix

→→H+ then moves back (to matrix) across the membrane (by facilitated diffusion down con. gradient), passing through the transport protein, ATP synthase

- REsult: synthesis of 28-34 ATP (ADP + Pi = ATP)

Accounting of ATP Production by Cellular Respiration

- Energy flow: Glucose → NADH → e- transport chain → proton-motive force → ATP

- 1 NADH generates up to 2.5 - 3 ATP

- 1 FADH2 generates up to 1.5 - 2 ATP

- a total of 32-38 ATP made (28-34 ATP by oxidative phosphorylation + 4 ATP by substrate phosphorylation)

Anaerobic Respiration

- uses ETC with a final electron acceptor other than O2

Fermentation

- use glycolysis to generate ATP → only substrate-level phosphorylation (and not ETC)

- glycolysis results in an excess of NADH that must be oxidized back to NAD+ (in order to be used back in glycolysis)

Nitrate and nitrite reduction systems

- found in E. coli

- nitrate reductase catalyzes the removal of oxygen from nitrate reducing it to nitrite and water

- a test for this reaction in one of the physiological tests used in identifying bacteria

Dentrification

- enzymes that further reduce nitrite to nitric oxide, nitrous oxide, and even nitrogen gas

- found in Pseudomonas and Bacillus

- important step in recycling nitrogen in the biosphere

1. Alcoholic fermentation

2. Acidic fermentation

1. occurs in yeast or bacterial species that have metabolic pathways for converting pyruvic acid to ethanol

2. pathways extremely varied

→→Hemolactic fermentation: lactic acid bacteria reduce pyruvate to lactic acid only

→→Heterolactic fermentation: glucose is fermented to a mixture of acetic, lactic, succinic, formic acids, as well as CO2

Fermentation vs. Respiration

- all use glycolysis (net ATP = 2) to oxidize glucose and harvest chemical energy of food

- cellular respiration produces 32-38 ATP per glucose molecule; fermentation produces 2 ATP per glucose molecule

- in all three, NAD+ is the oxidizing agent that accepts electrons during glycolysis

- the processes have different final electron acceptors: an organic molecule (such as pyruvate or acetaldehyde) in fermentation and O2 in cellular respiration

Glycolysis

- a 10-step biochemical pathway where Glu (6 C) is split into 2 molecules of pyruvate (3 C). To begin the process 2 ATP must be invested.

- Energy released from the reactions is captured in the form of 4 ATP molecules and high energy electrons are trapped in the reduction of 2 NAD+ to NADH. Occurs outside of mitochondria, in the cytoplasm.

- Occurs with/without presence of O2.

Pyruvate oxyidation

- In three-step a carbon is removed from pyruvate (3 C) as CO₂, leaving 2 of the original carbons attached to Coenzyme A. The complex is called Acetyl Co A. In this process, 1 NADH molecule is produced

Krebs Cycle

- A 8-step biochemical pathway that converts all of the remaining carbons from the original glucose into CO₂, and yields 1 ATP, and traps high energy electrons in 3 NADH, and 1 FADH₂ per Acetyl Co-A

Oxidative phosphorylation (ETC + chemiosmosis) 

- high energy electrons trapped in NADH and FADH2 (in glycolysis, pyruvate oxidation, and the Krebs cycle) are used to produce ATP through chemiosmosis. O2 is the final acceptor of high energy electrons.