Ch. 10: Intro to Metabolism

how chemical reactions can proceed how enzymes can increase the likelihood that reactions take place how chemical reactions facilitated by enzymes play their roles in metabolic processes

what is metabolism

total of all biochemical reactions in the cell and is divided into 2 parts

• most reactions involve enzymes

• 2 parts: catabolism and anabolism

function of catabolism

• fueling reactions

• energy-conserving reactions

• provide reducing power

• generate precursors

function of anabolism

• synthesis of complex organic molecules

  • requires energy

What are two key features of microbial metabolism in terms of nutrition and ecological function?

1. Microbes exist in all five major nutritional types.

2. They cycle essential elements (CHONPS).

example of elemental cycling

nitrogen cycle

• 4 steps are solely done by microbes

  • microbes are still part of the other four steps

what are the energy units?

• calorie (cal)

• joules (J)

• kilocalorie (kcal) or Calorie, big “C”

calorie (cal)

energy needed to raise 1 gram of water up 1 ºC

joules (J)

1 cal of heat = 4.1840 J of work

kilocalorie (kcal) / Calorie (C)

• 1000 calories = 1 Calorie or Kilocalorie

  • 1 kcal/C is enough energy for a person weighing 70kg to go up 35 steps

what is the unit for standard free energy change

ΔGº

what kind of reaction is it when ΔGº’ is negative?

• exergonic

  • products have less energy than reactants

• reaction proceeds spontaneously

• releases energy

what kind of reaction is it when ΔGº’ is positive?

• endergonic

  • products have more energy than reactants

• reaction will not proceed spontaneously

• requires energy

What are the nucleoside triphosphates involved in metabolism?

ATP, GTP, CTP, UTP

ATP (adenosine 5’-triphosphate) is the…

• main energy currency of the cell

• ATP + H₂O → ADP + Pi + H⁺

• ATP: gamma phosphate (3 P)

• ADP": beta phosphate (2P)

• AMP: alpha phosphate (1P)

GTP (Guanosine 5’-triphosphate) is involved in…

protein synthesis

CTP (cytidine 5’-triphosphate) is involved in…

lipid synthesis

UTP (uridine 5’-triphosphate) is involved in…

peptidoglycan synthesis

What does it mean that ATP has a high phosphate transfer potential?

It can donate a phosphoryl group to other molecules, activating them for metabolic reactions

Why can ATP transfer its phosphate group to other molecules?

Because high-energy phosphorylated compounds (like ATP) have a large amount of free energy

What is substrate-level phosphorylation (SLP)?

A metabolic process where a phosphate group is directly transferred from a high-energy compound to ADP, forming ATP

What is required for biochemical reactions involving phosphate transfer?

Enzymes — they catalyze the reactions

redox reactions are made up of

oxidizing and reducing reactions

which is the oxidized form in a conjugate redox pair?

electron donor (reducing agent)

oxidized form + e- → reduced form

which is the reduced form in a conjugate redox pair?

electron acceptor (oxidizing agent)

oxidized form + e- → reduced form

unit for standard redox potential (E’₀)

volts

is a more negative E₀ a better electron donor or acceptor?

more negative E₀ → better electron donor

• reductant/reducing agent

• is oxidized

is a more positive E₀ a better electron donor or acceptor?

more positive E₀ → better electron acceptor

• oxidant/oxidizing agent

• is reduced

what is the first rule of redox pairs

the reduced member of the pair that is more negative donates electrons to the oxidized member of the pair that is more positive

what is the second rule of redox pairs

the greater the difference in redox potential (E’0) between the redox pairs that serves as the electron donor and acceptor, the greater amount of energy available (G0) in the oxidation-reduction reaction

~~ greater difference in redox potential between donor acceptor means there is a greater amount of energy available

direction of reaction if ∆Gº is < 0 and Eº_cell > 0

spontaneous in forward direction

favors products

direction of reaction if ∆Gº is > 0 and Eº_cell < 0

spontaneous in reverse direction

favors reactants

direction of reaction if ∆Gº and Eº_cell are both 0

no net reaction: system at equilibrium

comparing 2 redox pairs

• solve for standard redox potential

• nernst equation?

  • faraday’s constant?

n = # of electrons

F = Faraday’s constant

flip oxidation (oxidized form) half reaction

Faraday’s constant

23 kcal/volt or 96.5 kJ/volt

a negative ∆G or change in free energy means…

the reaction is exergonic

the products have less energy than the reactants

the first electron carrier is…

the most negative E’_º

where is ETC found in eukaryotes

in the mitochondria (cristae) or chloroplast

where is ETC found in prokaryotes

cell membrane

do electrons lose or gain energy whilst moving through the molecule

lose

what is the ETC used in

oxidative phosphorylation

what are protons

hydrogen ions that help in the reduction process

what are the main electron carriers?

• NADH and NADPH

• FAD and FMN

• CoQ/ubiquinone

• cytochromes

• nonheme iron-sulfur proteins

what do NADH and NADPH carry

2 electrons and 1 proton

what do FAD and FMN carry

2 electrons and 2 protons

what is FAD and FMN also known as

flavoproteins (Fp)

what is CoQ (ubiquinone// UQ)

lipid-soluble electron carrier

what does CoQ (ubiquinone) carry?

carries 2 electrons and 2 protons

• lipophilic and embedded in membrane

what carries e- in CoQ/ubiquinone

quinone

What do cytochromes carry and what group do they contain?

They carry 1 electron at a time and contain iron in a heme group.

What do nonheme iron-sulfur (FeS) proteins carry and what group do they lack?

they carry 1 electron at a time and do not contain a heme group

• aka ferredoxin

what are the types of biochemical pathway structures

linear, cyclic, branching

which biochemical pathway is most common vs least common?

branching are most common while linear is least common

what are the components of biochemical pathway structures

substrates (or reactants), intermediate, and end product

• they can have more than one product

How do biochemical pathways interact with each other?

overlapping/feeding into each other

• complex networks

What are dynamic pathways in metabolism?

they monitor changes in metabolite levels (flux)

what do enzymes do?

carry out reactions at physiological conditions (# of substrates, temperature, pH, etc); speed up the rate

• classified by the type of reaction they catalyze

do enzymes alter the equilibrium?

no

what kind of catalysts are enzymes?

biological

what do enzymes temporarily bind to?

reactant/substrate

• not a covalent bond because it would not release

• can be H, hydrophilic or ionic bond

composition of enzymes

one or more polypeptides (apoenzyme), may also be with nonprotein components (cofactor) forming the holoenzyme

what are cofactors

nonprotein components that assist enzymes

what are the 2 types of cofactors

• prosthetic group

• coenzyme

prosthetic group

usually covalently bonded to enzyme

coenzyme

• usually loosely attached (H-bond, etc…)

• deactivate/activates enzyme easily

what are involved in the mechanism of enzyme reactions

enzymes, transition-state complex, activation energy

in a typical exergonic reaction, how do the energies in reactants vs products compare

reactants have more energy than products

why is an enzyme needed in an exergonic reaction

to provide energy for reaction to proceed forward

transition-state complex

transient (temporary) binding of substrates

activation energy (Ea)

enzymes speed up reactions by lowering Ea

How do enzymes lower Ea?

• increase concentrations of substrates at active/catalytic site

• orient substrates properly

  • Induced fit model for enzyme-substrate interaction

induced fit model for enzyme-substrate interaction

enzyme changes shape slightly to fit the substrate better, stabilizing transition state and lowering Ea

what is the relationship between reaction rate and substrates

direct relationship: reaction rate increases as substrate increases

• plateaus at saturation; rxn rate cannot increase further, max enzyme activity reached

What causes enzyme activity to change?

• Substrate concentration (Km)

• pH

• temperature (denaturation)

what is a competitive inhibitor

• inhibitor and substrate both competing for the same site

• substrate binding is blocked

• ex: PABA/SFA

what is a noncompetitive inhibitor?

• inhibitor and substrate competing for different sites

  • Referred to as allosteric site

• substrate can bind, but reaction is blocked

What is an allosteric site?

Where the noncompetitive inhibitor will bind

Why does the noncompetitive inhibitor bind to an allosteric site?

inhibit reaction or change the form of the active site to prevent the substrate from binding

what is a ribozyme?

RNA molecule that acts as an enzyme

examples of ribozyme function

• catalyze peptide bond formation

• self-splicing RNA molecules

• involved in self replication

why must metabolism be regulated?

To maintain homeostasis and prevent (or at least the accumulation of) waste, so it does not become toxic

How is metabolism regulated?

• Conservation of energy and materials

• Maintenance of metabolic balance

What are the 3 major mechanisms of regulating metabolism

• Metabolic channeling

• Gene expression – transcriptional and translational

• Post-translational regulation (irreversible or reversible)

what is metabolic channeling also known as

compartmentalization

• different metabolic processes are separated into specific areas of a cell — either by physical space or by organizing enzymes close together

Is allosteric regulation irreversible or reversible?

reversible

what does allosteric regulation consist of

allosteric effector and regulatory site

most regulatory enzymes use allosteric regulation

allosteric enzymes typically have mulitiple subunits and possess both active sites and allosteric (regulatory) sites

what binds to the regulatory site

positive and negative effectors

what is positive effector

changes the site to substrate CAN bind and increases enzyme activity

what is negative effector

changes the site so substrate CANNOT bind and decreases enzyme activity

Is covalent modification of enzymes reversible or irreversible?

reversible

How does covalent modification of enzymes occur

Through addition and/or removal of a chemical group

• Ex: phosphoryl (ATP/ADP), methyl (DNA), adenylyl

What enzymes are involved in feedback/end-product inhibition

Pacemaker enzyme and isoenzymes

What does the pacemaker enzyme do

Catalyzes slowest or rate limiting step of a pathway

• Tends to be one of the first enzymes

What can each end-product regulate

• inhibits the enzyme at the start of its own branch

• Initial pacemaker enzyme

what do isoenzymes do

2 isoenzymes bind to the same substrate but differ in regulation

• versatility in controlling metabolism and adapting to varying physiological needs

what is E’_º

standard redox potential

what does it mean to be the most negative standard redox potential

• the substance is more likely to be oxidized (lose electrons)

• better reducing agent (more readily donating electrons)

lyase

dissociates molecules

breaks covalent bonds without using anything

A → B + C

ligase

joins 2 molecules together, forms covalent bonds

A + B → AB

isomerase

rearranges bonds of a molecule

a reactant forms one of its isomers

A → B

transferase

transfers a functional group from one molecule to another

A + BX → AX + B