Chapter 3 - Cell Metabolism

Metabolism

the total of all reactions that occur in a living cell; most reactions in living cells are involved in energy storage and usage

Catabolic Reactions

reactions that break down large molecules into smaller molecules (proteins into amino acids)

Anabolic Reactions

reactions that synthesize large molecules from small molecules (amino acids bonding to form proteins)

General Equation for Chemical Reactions

A + B → C + D, where A and B are reactants and C and D are products

Condensation Reaction

a reaction where A-OH + H-B combine to form A-B + H2O

Hydrolysis Reaction

a reaction where A-B + H2O breaks down into A-OH + H-B

Phosphorylation Reaction

a reaction in which a phosphate group is added to a molecule (ADP + PO4 → ATP + H2O); the enzyme kinase participates in this reaction

Dephosphorylation Reaction

a reaction in which a phosphate group is removed from a molecule (ATP + H2O → ADP + PO4); the enzyme phosphatase participates in this reaction, and energy is released and captured by the cell for metabolic activities

Kinase

the enzyme that participates in phosphorylation reactions

Phosphatase

the enzyme that participates in dephosphorylation reactions

Oxidation

a reaction in which electrons are removed from atoms

Reduction

a reaction in which electrons are accepted by atoms

Oxidation/Reduction (Redox) Reactions

reactions in which electrons are removed from one atom (oxidation) and accepted by another (reduction); when hydrogen ions are released from a molecule, they carry electrons, which always carry a small supply of energy (H2 → 2H+ + 2e-)

Energy

the capacity to perform work

How is energy produced?

it is the outcome of many metabolic reactions

What does energy do?

it drives numerous physiological processes (body movements, heart contractions, protein sythesis)

Two broad categories of energy

kinetic and potential

Kinetic energy

energy that is actively working. in this case, molecules are randomly moving

Examples of kinetic energy

thermal energy and electrical energy

Potential energy

stored energy, this energy can be converted into kinetic energy

Examples of potential energy

chemical energy and nuclear energy

Two laws of thermodynamics

- the law of conservation of energy

- the law of entropy

Law of conservation of energy

law states that energy can neither be created nor destroyed. based on this law, the amount of total energy in a system remains constant. even though energy in the system can be converted from one from to another

Example of the law of conservation of energy

chemical reactions can release energy in the form of heat

Law of entropy

in natural processes, energy spreads out. this move towards "disorder" increases over time. a measure of this disorder is known as entropy

Example of the law of entropy

ice melting in a glass of water

Energy changes in chemical reactions

exergonic reactions and endergonic reactions

Exergonic reactions

energy releasing reactions

reactants --> products + energy

Why are exergonic reactions SPONTANEOUS

the reactants have more energy than the products

Example of exergonic reactions

catabolic reactions

Endergonic reactions

require an input of energy to occur

Reactants + Energy ---> Products

Why are endergonic reactions not spontaneous?

the products have more energy than the reactants

Example of endergonic reactions

anabolic reactions

In cells what is it sometimes necessary to do?

for couple reactions can be used to drive anabolic reaction. this process is known as ENERGY COUPLING

Examples of energy coupling?

synthesis of polysaccharides and glycolysis

Synthesis of polysaccharides

ATP powers the reactions that link monosaccharides together

For reactant molecules to complete a reaction and form products, the reacting molecules must go through what?

a transition stage

Transition stage

in graphic form it is often classified as a distinctive "hump"

Activation energy

is the extra energy that is needed to help the reacting molecules get over this hump and complete the reaction

How is activation energy created?

created as molecules collide with each other, thus, creating enough energy to get over the "hump"

Enzymes

speed up biological reactions by reducing the amount of activation energy needed for a reaction to occur

Factors affecting the rates of chemical reactions

- reactant and product concentrations

- temperature

- height of activation energy barrier

Reactant and product concentrations

- increased reactant concentration, increased rate of forward reaction

- increased product concentration, increased rate of reverse reaction

Temperature

can either speed something up (heat) or slow things down (cold)

Height of the activation energy barrier

- decreased height-increased reaction rate

- increased height-decreased reaction rate

General features of enszymes

- they are CATALYSTS

- they function by lowering the activation energy barrier

- they are SPECIFIC for a particular SUBSTRATE

- enzymes are not chemically altered in the reaction they regulate

- enzymes regulate processes that either breakdown large molecules or build up large molecules

- optimal pH and optimal temperature for enzyme activity

Catalyst

a substance that speeds up a chemical reaction (in this context, an enzyme)

Activation energy in an enzyme

the energy barrier that must be overcome for a reaction to occur; enzymes function by lowering this barrier

Substrate specificity

enzymes are specific for a particular substrate, which reacts with the active site of that specific enzyme (Amylase-Starch)

Active site

the location on an enzyme where a substrate binds; enzyme-substrate interactions here are reversible

Enzyme-substrate interaction

a reversible interaction between an enzyme's active site and its specific substrate

Chemical stability of enzymes

enzymes are not chemically altered in the reactions they regulate

Enzyme regulation of reactions

enzymes regulate processes that either break down large molecules (catabolic) or build up large molecules (anabolic)

Optimal pH

the pH level at which an enzyme functions most efficiently

Optimal temperature

the temperature at which an enzyme functions most efficiently

Induced fit model

a model of enzyme activity in which the active site of the enzyme attaches to the substrate and undergoes a conformational change that strengthens the connection between enzyme and substrate; this process is reversible (Previously known as the "lock and key" model.)

Conformational change

a change in shape that occurs in the enzyme's active site upon binding to a substrate, strengthening the enzyme-substrate connection

Enzyme activation

enzymes are typically turned on by increased levels of their specific substrate

Factions that affect the rates of enzymes-catalyzed reactions

- catalytic rate

- substate concentration

- enzyme concentration

- affinity

Catalytic rate

refers to the rate at which enzymes can generate product molecules. this rate varies from enzyme to enzyme

Substrate concentration

enzymes reaction rate increases as the supply of substrate increases

Enzyme concentration

enzyme reaction rate increases as the supply of enzymes increases

Affinity

a measure of how strong an enzyme is attracted to its substrate and how tightly they bind together

Regulation of enzyme activity

- allosteric regulation

- covalent regulation

- feedback regulation

Allosteric regulation

in this situation, a modulator molecule will attach to the REGULATORY SITE of an enzyme. this leads to a structural; change in the active site; the enzyme cannot attach to its substrate

Covalent regulation

these occur when a covalent bond forms between the enzyme and a chemical group

Where are covalent regulations most commonly found?

most common group involved in is the phosphate groups

What is the function of covalent regulations?

the attachment can alter the overall activity of the enzyme

How is a covalent regulation broken?

they remain intact until it is broken (usually by another enzyme)

Examples of covalent regulation

protein kinase and phosphatase

Feedback regulation

certain enzymes in a metabolic pathway regulation can serve as rate-limiting enzymes

What is the primary goal of feedback regulation?

is to maintain a constant rate of product production based on the metabolic needs of body cells and tissues

Negative feedback control

in this situation, the last product of a pathway is a modulator that acts as an allosteric regulator

Positive feedback control

in this process, an intermediate compound regulates a later enzyme in the pathway

Adenosine Triphosphate (ATP)

a ribonucleic acid that serves as a stored form of energy for cells

Condensation reaction

generates ATP and requires an input of energy to occur

Hydrolysis reaction

removes a phosphate group from ATP and releases energy

What are condensation and hydrolysis reactions classified as?

coupled

What does the classification coupled mean?

they must work together to maintain sufficient energy production for cellular activity

How is ATP generated in living cells?

- oxidative phosphorylation

- substrate level phosphorylation

Oxidative phosphorylation

the oxidation of sugar (typically glucose) to release energy. this energy is used by cells to synthesize ATP. in this case, energy is released through the breakdown of sugar (A CATABOLIC REACTION) and this energy is used to drive the production of ATP via ANABOLIC REACTION

What is the link between catabolic and anabolic reactions?

electron carrier (such as NADH)

Electrons carry...

A small amount of energy

What is the small amount of energy that electrons carry used for?

they can be used to drive the anabolic reaction that builds ATP

Substrate level phosphorylation

enzymes transfer a phosphate group from a substrate to ADP to generate ATP

Oxidative phosphorylation stages

1. glycolysis

2. Kreb's cycle

3. oxidative phosphorylation

What happens to the energy generated via the oxidation in oxidative phosphorylation?

it is coupled to the energy requiring steps of ATP production. this ATP is then sued to drive cellular activities

What stage glycolysis?

stage 1

Glycolysis

is a collection of reactions that utilize 10 different enzymes to split GLUCOSE into 2 molecules of PYRUVATE

Where does glycolysis occur?

entirely in the cytosol of the cell

How many ATP molecules are required for glycolysis?

2 ATP

How much ATP is produced at the end of glycolysis?

4 ATP, but it also generates 2 molecules of the electron carrier NADH

NADH

used in oxidative phosphorylation

What is produced by glycolysis?

essentially no energy for metabolic cellular activity. however, the energy and NADH produced in glycolysis can later be used to generate substantial supplies of ATP

What is important to notice about glycolysis?

there are numerous enzymes involved in this process

What process is glycolysis?

anaerobic

The linking step

once pyruvate is produced, it must be modified before it can enter the mitochondria and continue the process of oxidative phosphorylation

What role does oxygen play in glycolysis?

plays a small role by acting to carry pyruvate across the mitochondrial membrane and into the mitochondrial matrix

Mitochondrial matrix

region between the double membrane

Acetyl CoA (The Linking Step)

links glycolysis to the Kreb's cycle; no ATP is generated, but 2 additional NADH molecules are produced, and carbon dioxide is produced via decarboxylation