Metabolism

Jin Changjiang

Email: jincj@ustc.edu.cn

General biology:

Enzymes

• Enzymes are large biological molecules responsible for the thousands of metabolic processes that sustain life

• They are highly selective catalysts, greatly accelerating both the rate and specificity of metabolic reactions, from the digestion of food to the synthesis of DNA.

• Most enzymes are proteins, although some catalytic RNA molecules have been identified.

• Enzymes adopt a specific three-dimensional structure, and may employ organic (e.g. biotin) and inorganic (e.g. magnesium ion) cofactors to assist in catalysis.

Thermodynamics

"Lock and key" model

Two zinc ions that are needed for the enzyme to catalyze its reaction are shown as purple spheres, and an enzyme inhibitor called S-hexylglutathione is shown as a space-filling model, filling the two active sites.

Human glyoxalase I

Factors that Affect Enzymes

Factors Affecting Enzyme Function

• Enzyme concentration• Substrate concentration• Temperature • pH• Salinity• Activators• Inhibitors

catalase

• Enzyme concentration – as enzyme = reaction rate

• more enzymes = more frequently collide with substrate

– reaction rate levels off• substrate becomes limiting factor• not all enzyme molecules can find substrate

enzyme concentration

reac

tio

n r

ate

• Substrate concentration – as substrate = reaction rate

• more substrate = more frequently collide with enzyme

– reaction rate levels off• all enzymes have active site engaged• enzyme is saturated• maximum rate of reaction

• Temperature– Optimum T°

• greatest number of molecular collisions• human enzymes = 35°- 40°C

– body temp = 37°C

– Heat: increase beyond optimum T°• increased energy level of molecules disrupts bonds in

enzyme & between enzyme & substrate– H, ionic = weak bonds

• denaturation = lose 3D shape (3° structure)– Cold: decrease T°

• molecules move slower • decrease collisions between enzyme & substrate

Enzymes and temperature

• Different enzymes function in different organisms in different environments

37°Ctemperature

reac

tio

n r

ate

70°C

human enzymehot spring

bacteria enzyme

(158°F)

How do ectotherms do it?

• pH– changes in pH

• adds or remove H+

• disrupts bonds, disrupts 3D shape – disrupts attractions between charged amino acids – affect 2° & 3° structure– denatures protein

– optimal pH?• most human enzymes = pH 6-8

– depends on localized conditions– pepsin (stomach) = pH 2-3– trypsin (small intestines) = pH 8

720 1 3 4 5 6 8 9 10 11

pepsin

trypsin

• Salt concentration– changes in salinity

• adds or removes cations (+) & anions (–)• disrupts bonds, disrupts 3D shape

– disrupts attractions between charged amino acids – affect 2° & 3° structure– denatures protein

– enzymes intolerant of extreme salinity• Dead Sea is called dead for a reason!

Compounds which help enzymes

• Activators– cofactors

• non-protein, small inorganic compounds & ions– Mg, K, Ca, Zn, Fe, Cu– bound within enzyme molecule

– coenzymes• non-protein, organic molecules

– bind temporarily or permanently toenzyme near active site

• many vitamins– NAD (niacin; B3)– FAD (riboflavin; B2)– Coenzyme A

Mg inchlorophyll

Fe inhemoglobin

Compounds which regulate enzymes

• Inhibitors– molecules that reduce enzyme activity– competitive inhibition– noncompetitive inhibition– irreversible inhibition– feedback inhibition

Competitive Inhibitor

• Inhibitor & substrate “compete” for active site– penicillin

blocks enzyme bacteria use to build cell walls– disulfiram (Antabuse)

treats chronic alcoholism• blocks enzyme that

breaks down alcohol • severe hangover & vomiting

5-10 minutes after drinking

• Overcome by increasing substrate concentration– saturate solution with substrate

so it out-competes inhibitor for active site on enzyme

Competitive inhibition

Non-Competitive Inhibitor

• Inhibitor binds to site other than active site– allosteric site – allosteric inhibitor

• regulation of enzyme function– keeps enzyme inactive

• some anti-cancer drugsinhibit enzymes involved in DNA synthesis

– stop DNA production– stop division of more cancer cells

• cyanide poisoningirreversible inhibitor of Cytochrome C, an enzyme in cellular respiration

– stops production of ATP

– causes enzyme to change shape• conformational change• active site is no longer

a functional binding site

Irreversible inhibition• Inhibitor permanently binds to enzyme

– competitor• permanently binds to active site

– allosteric• permanently binds to allosteric site • permanently changes shape of enzyme• nerve gas, sarin, many insecticides (malathion,

parathion…)– cholinesterase inhibitors

» doesn’t breakdown the neurotransmitter, acetylcholine

Allosteric regulation• Conformational changes by regulatory

molecules – inhibitors

• keeps enzyme in inactive form

– activators • keeps enzyme in active form

Conformational changes Allosteric regulation

The top-level classification of enzymes

• EC 1 Oxidoreductases: catalyze oxidation/reduction reactions • EC 2 Transferases: transfer a functional group (e.g. a methyl or

phosphate group) • EC 3 Hydrolases: catalyze the hydrolysis of various bonds • EC 4 Lyases: cleave various bonds by means other than hydrolysis

and oxidation • EC 5 Isomerases: catalyze isomerization changes within a single

molecule • EC 6 Ligases: join two molecules with covalent bonds.

Metabolic pathways

A B C D E F G enzyme

1

enzyme

2

enzyme3

enzyme4

enzyme5

enzyme6

• Chemical reactions of life are organized in pathways– divide chemical reaction into

many small steps• efficiency

– intermediate branching points

• control = regulation

A B C D E F G

Efficiency• Organized groups of enzymes

– if enzymes are embedded in membrane they are arranged sequentially

• Link endergonic & exergonic reactionsWhoa!

All that going onin those littlemitochondria!

allosteric inhibitor of enzyme 1

Feedback Inhibition• Regulation & coordination of production

– product is used by next step in pathway– final product is inhibitor of earlier step

• allosteric inhibitor of earlier enzyme• feedback inhibition

– no unnecessary accumulation of product

A B C D E F G enzyme

1

enzyme2

enzyme3

enzyme4

enzyme

5

enzyme6

X

Feedback inhibition

• Example– synthesis of amino

acid, isoleucine from amino acid, threonine

– isoleucine becomes the allosteric inhibitor of the first step in the pathway

• as product accumulates it collides with enzyme more often than substrate does

Cooperativity

• Substrate acts as an activator– substrate causes conformational

change in enzyme• induced fit

– favors binding of substrate at 2nd site– makes enzyme more active & effective

• hemoglobinHemoglobin 4 polypeptide chains can bind 4 O2; 1st O2 binds now easier for other

3 O2 to bind

Metabolic RegulationMetabolic Regulation Is Achieved by Is Achieved by Controlling the Activity of EnzymesControlling the Activity of Enzymes

Thousands of reactions mediated by an equal number of enzymes are occurring at any given instant within the cell.

Metabolism has many branch points, cycles, and interconnections.

This metabolic regulation is achieved through controls on enzyme activity so that the rates of cellular reactions are appropriate to cellular requirements.

Metabolism proceeds by discrete steps

• A metabolic pathway has many steps– That begin with a specific molecule and end

with a product– That are each catalyzed by a specific enzyme

Enzyme 1 Enzyme 2 Enzyme 3A B C D

Reaction 1 Reaction 2 Reaction 3Startingmolecule

Product

Glycolytic enzymes and their functions in the metabolic pathway of glycolysis

烯醇化酶

变位酶

己糖激酶

醛缩酶

丙糖磷酸异构酶

• One reason for multiple steps is the limitied reaction specificity of enzymes.

• Another reason for multiple steps in metabolic pathways is to control energy input and output.

• Finally, multiple steps provide opportunities to establish control points.

metabolic pathways are regulated

• The flow of material through a metabolic pathway, or flux, depends not only on the supply of substrates and the removal of products but also on the activities of the enzymes that catalyze individual reactions.

Properties of Metabolic Pathways

• Irreversible (overall): reversibility of individual steps

• Separate Anabolic and Catabolic Pathways

• First Committed (Exergonic) Step: others close to equilibrium

• Regulation (usually first committed step): often rate-limiting

Features of Metabolic Pathways

A ——> B ——> C ——> D ——> E

(1)Sequences and Energetics

(2) Enzymes and Mechanisms

(3) Control Mechanisms (Regulation)

(4) Compartmentation

Compartmentation and interorgan metabolism

Vesicle trafficking systems

http://t.cn/hoJcx

Steps of vesicle trafficking

The 2013 Nobel Prize in Physiology or Medicine

• James E. Rothman is the Fergus F. Wallace Professor of Biomedical Sciences at Yale University and Chairman of the Department of Cell Biology at Yale University Medical School.

• Randy W. Schekman, professor of molecular and cell biology at the University of California, Berkeley.

• Thomas Südhof, MD, professor of molecular and cellular physiology at the Stanford School of Medicine, Neuroscientist.

The three scientists were awarded the prize "for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells."

There is unity in diversity

• DNA and/RNA is/are genetic material. • The cell is the basic unit of life.• Living things acquire materials and energy• All living things came from ONE organism, so we are all

alike but different.• Similarities exists when common ancestors are recent,

diversity occurs when genetics and environment interact and natural selection occurs.

• Evolution is "descent with modification", according to Darwin, accounting for Unity and Diversity.