General Biology II (101-DCN) Winter 2010 Professor...

General Biology II (101-DCN)

Winter 2010

Professor: Christian Levesque

Course Notes – Unit A

Campbell & Reece (2008)

Table of content

General introduction to this course pack: A quick guide on how to take notes efficiently #..#. 2

I. Chemistry and life ###############################.... 4

II. Organic chemistry: the chemistry of life #####################..... 10

III. Membrane structure and function #######################...... 27

IV. Enzymes and metabolism ###########################... 31

C. Levesque, John Abbott College 101-DCN Winter 2010 Unit A

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General introduction to this course pack: A quick guide on how to take notes efficiently

Taking notes is one of the most important skills to develop as a student. There are several reasons to take lecture notes:

• Taking notes forces you to be an active student (i.e., to listen carefully in order to understand the concepts covered in class)

• As you take notes, writing down the information stimulates your brain in a way that increases your retention of the information

• Taking notes is a way to make sure you have all the essential information at hand to prepare for the exams

• Notes provide indications as to what is important when studying for a test

• Notes are much easier to study from than a textbook The key to be able to take notes efficiently (and more generally to be a successful student) is to be an active student. Here are a few points to consider to take notes efficiently: Before the lecture

1. Be prepared: when possible, read the notes (if you have a course pack) and/or the appropriate sections in the textbook before coming to class. Make sure you have an idea of what will be covered in class. You should also revise your notes from the previous lecture.

During the lecture

2. Pay close attention to what is said in class – much of the learning experience happens here,

not later at home.

3. Based on your understanding (you’ll understand a lot better if you follow steps 1 and 2), identify the essential information or the main ideas (see How to identify the main ideas below).

4. Summarize this information in writing (be concise, avoid unnecessary words like “a” and “the”,

use abbreviations and symbols as much as possible). Remember: the goal here is to understand what is discussed in class, not to try to record exactly everything the professor says.

After the lecture

5. Revise your notes as soon as possible after the lecture (preferably within 24 hours, since at that time you will still remember most of the lecture). Make sure you review your notes before the next lecture. This will greatly improve your understanding, your retention of the information, and probably even your interest in the course.

While revising your notes, try to be an active reader, i.e.:

• review regularly

• recite – repeat key concepts

• reflect – connect ideas together (pay special attention to the structure of the course and notes; this greatly helps your brain to efficiently map different concepts and to see the connections between them). Remember that there is no learning without understanding!


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How to identify the main ideas? (point 3 above)

• The most obvious way to identify what’s important is to be prepared for the lecture (point 1 above) and to pay close attention to what is said during the lecture (point 2 above). Based on your understanding of the material, you should be able to identify the main ideas / concepts.

• Pay special attention to what is said at the beginning and at the end of the lecture. Listen carefully to the introduction: by knowing the outline of the course, you will be prepared to anticipate what is important. Most professors will also summarize the key ideas at the end of the lecture.

• Professors usually give clues to what is important. Here are some clues professors will use:

• Emphasis / repetition

• Writing material on the blackboard

• Using word signals (e.g., “the most important concept#”, “there are two reasons for this#”) How does that apply to General Biology II? In my General Biology II class, you are provided with partial course notes. The notes contain most of the essential information, and this information is organized following a logical structure. There are three main reasons why I prepare these notes. The first one is that they save a lot of time in class. You can focus on understanding instead of note-taking. But you also need to be prepared to take notes efficiently, and this is the second reason why I prepare these notes: they provide a framework around which you can organize your notes logically. And the third, and maybe most important advantages of using these notes, is that they provide insight into how the main ideas and concepts are logically organized and connected. Here are three specific points to consider when using these notes:

• You should briefly read the notes before class. This will make it easier for you to follow what we’re discussing in class. Remember that you will have insight into how the main ideas and concepts are logically organized and connected. This will greatly improve your ability to identify and understand the important points.

• You should read the corresponding chapters in the textbook.

• You have to write down any additional information discussed in class (i.e., highlight or summarize important ideas, add terms or definitions covered in class, examples that will improve your understanding and retention of the material, etc.), following the same logical structure. Remember that even though the notes contain most of the essential information, there is important information discussed in class that is not included in the partial notes.

Finally, remember that the key to good note taking is to be an active student!


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UNIT A The complexity and unity of life • The Earth harbours the most complex thing in the known universe: life • Life is the most structurally and functionally complex system on Earth (and in the known universe) • A cell is much smaller than a grain of sand, or a speck of dust. Yet, its complexity is unrivalled. It

takes books and books to explain just the basic structural organization and functioning of a cell • Yet, there is unity in life. Organisms seemingly as different as a human being and a mushroom

share the same basic organisation. They obtain and process their food, manufacture their proteins, grow and reproduce using the same basic processes, with subtle differences

• Our goal in General Biology II is to understand these basic processes

I. Chemistry and life

• The natural world is organized into a hierarchy of structural levels – Additional properties emerge at each successive level

• e.g., molecules perform functions that individual atoms can't perform • e.g., organelles are not alive; cells are

• In this course, we will see how emergent properties exist at the lowest levels of biological organization (subcellular level)

– These properties are the underlying machinery responsible for the functioning of higher levels of organization

• e.g. fixation of a CO2 molecule in a chloroplast vs seasonal changes in CO2 concentration in the atmosphere

Elements and compounds • Organisms are composed of matter

• i.e., anything that takes up space and has mass • Matter is made up of:

– Elements in pure form • Element = substance that cannot be broken down to other substances by chemical

reactions, e.g., – Compounds

• Substance consisting of two or more elements in a fixed ratio, e.g., • A compound has characteristics different from those of its elements (emergent

properties) Elements that are essential to life • About 25 of the 92 natural elements are essential to life • C, H, O, N make up 96% of living matter • ~ 4% consists of Ca, P, K, S • Trace elements are those required by an organism in minute quantities

• e.g., iodine


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An element’s properties depend on the structure of its atoms

• Each element consists of unique atoms – Smallest unit of matter that still retains the properties of an element

Subatomic particles

• Atoms are composed of subatomic particles • Relevant subatomic particles:

– Neutrons (no electrical charge) – Protons (positive charge) – Electrons (negative charge)

• Atoms of the various elements differ in number of subatomic particles • An element’s atomic number is the number of protons in its nucleus

– Defines the element (e.g., only C has 6 protons) • An element’s mass number is the sum of protons plus neutrons in the nucleus

– Differs between isotopes of the same element (e.g., 12C, 13C, 14C) • Atomic mass, the atom’s total mass (in g per mole), can be approximated by the mass

number – The mass of 1 proton or 1 neutron is ~1.7 X 10-24g = 1 dalton = an atomic mass unit

(amu)

• All atoms of an element have the same number of protons but may differ in number of neutrons • Isotopes are atoms of an element that differ in number of neutrons

– Stable isotopes do not decay (e.g., 12C, 13C) – Radioactive isotopes decay spontaneously, giving off particles and energy (ionizing

radiation) • Half-life: time it takes to decay ½ of a certain amount of radioactive isotope

• Some applications of stable isotopes in biological research are:

– Tracing atoms through metabolic processes – Tracing atoms through ecosystems

• Some applications of radioactive isotopes in biological research are:

– Dating material • e.g., radiocarbon dating

– Tracing atoms through metabolic processes – Diagnosing medical disorders

Introduction to chemical bonds

• Biological material includes molecules / compounds • 2 or more atoms of the same / different elements attached through covalent bonds

• Other weak chemical bonds are important in biology (e.g., hydrogen bonds)

• The formation of chemical bonds is related to the behaviour of electrons

• Energy is the capacity to cause change • Potential energy is the energy that matter has because of its location or structure • The electrons of an atom differ in their amounts of potential energy • An electron’s state of potential energy is called its energy level, or electron shell


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• The chemical behaviour of an atom is determined by the distribution of electrons in electron shells

• The periodic table of the elements shows the electron distribution for each element

• Valence electrons are those in the outermost shell, or valence shell • Chemical behaviour of an atom is mostly determined by valence electrons

– Elements with a full valence shell are chemically inert – Atoms with incomplete valence shells can share or transfer valence electrons with

certain other atoms – # of unpaired electrons in valence shell = atom's valence = bonding capacity (e.g., C

has a valence of 4) • These interactions usually result in atoms staying close together, held by

chemical bonds • Covalent bonds • Ionic bonds • Hydrogen bonds • van der Waals interactions

Covalent bonds

• A covalent bond is the sharing of a pair of valence electrons by two atoms – Forms a molecule ( 2 or more atoms held together by covalent bonds)

• Single bond: sharing of 1 pair of valence electrons • Double bond: sharing of 2 pairs of valence electrons • Atom's valence = its bonding capacity

– e.g., C has a valence of 4

• In a nonpolar covalent bond, the atoms share the electrons equally – e.g,

• In a polar covalent bond, one atom is more electronegative (attracts shared electrons more strongly), and the atoms do not share the electrons equally

– Causes partial positive & negative charges in molecule – e.g,

Ionic bonds

• Atoms sometimes strip electrons from their bonding partners • e.g., transfer of an electron from sodium to chlorine • After the transfer of an electron, both atoms have charges (ions) • Oppositely charged ions can form ionic bond • Compounds formed by ionic bonds are called ionic compounds, or salts • Salts, such as sodium chloride (table salt), are often found in nature as crystals (maintained by

strong ionic bonds) • When salt (ions) is dissolved in water, ions are shielded by H2O

� ionic bonds become weak


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Weak chemical bonds

• Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules • Weak chemical bonds are also important • Reinforce shape of large molecules • Help molecules adhere to each other and interact • Hydrogen bonds

– A hydrogen bond forms when a hydrogen atom covalently bonded to one

electronegative atom is also attracted to another electronegative atom – In living cells, the electronegative partners are usually O or N – Explains most of the unusual properties of water

• Van der Waals interactions

– If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge

– Van der Waals interactions are attractions between molecules that are close together as a result of these charges

– e.g., interactions between millions of setae of gecko lizard and wall surface Molecular shape and function

• The shape of a molecule is determined in part by weak chemical bonds • The shape of a molecule is usually very important to its function • Molecular shape determines how molecules recognize and interact with each other with

specificity • Molecules with similar shapes can have similar biological effects

Properties of water

• Water plays a unique role in biology – Water is the most important type of habitat on Earth – Life appeared in water – The first terrestrial organisms “captured” their environment inside their body – All organisms still live “in water” – Life as we know it requires water

• Most of the chemical reactions responsible for life occur in water • Why is water so important for life on Earth?

– Water has unique properties • Most of these unusual properties are due to:

• the polar nature of water • the presence of hydrogen bonds between water molecules

1. Strong cohesion and adhesion

• Water molecules "stick together" • Capillary action in plants:

– Water adheres to plant vessels, counteracting gravity – important for capillary action – H2O evaporated from plant’s leaves “pulls” the water up to the leaves from roots


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2. High surface tension • H2O molecules at the surface of water are attracted to other H2O molecules - and attracted

much less to air molecules above • Forms a film strong enough to support some organisms (water striders, small plants)

3. High specific heat • Specific heat: amount of heat that has to be absorbed or lost to change the temperature of 1g

of water by 1°C • Liquid water requires much more energy to increase its temperature than most other

compounds (due to H bonds) • ► Water moderates temperature changes in the environment...

– Coastal regions have milder climates – Aquatic environments have relatively stable temperatures

• ... and in organisms (all of which contain a large amount of water)

4. High heat of vaporization (evaporation) • Heat of vaporization: amount of heat a liquid must absorb for 1g to be converted to gas • Water evaporation (liquid � gas) requires a lot of heat (H-bonds need to be broken) • Evaporation cools the water left behind (evaporative cooling)

– Sweat, breathing, evaporation from plants (transpiration) cool organisms – Bodies of water can be cooled by evaporation (moderation of temperature variations) – As moist tropical air moves towards the poles, water vapour releases heat as it

condenses into rain 5. High heat of fusion (freezing)

• In frozen water H-bonding becomes complete • H-bond formation releases heat � slows the process and moderates temperature changes • Water releases heat when it turns into ice

► It is warmer near water as winter starts and cooler in the spring as ice melts 6. Ice is less dense than liquid water

• Liquid water becomes denser as it cools – maximum density at 4°C • In frozen water, molecules arrange in an optimal configuration (with all molecules with H-

bonds)

• This structure takes a lot of space → Ice is less dense than liquid water • Ice floats and insulates water below • Lakes and oceans don’t freeze solid • Water below the ice stays at ~4°C all winter – allows survival of many species • The deep ocean = largest habitat (by volume) on Earth has a temperature of ~4°C

7. Water is an important biological solvent

• Because water is polar, it is a good solvent for many polar molecules – Polar molecules or ions are hydrophilic – water can contact them – Non-polar molecules (e.g., oil) are hydrophobic

• Insoluble in water


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8. Water dissociation and pH • Water dissociates: A hydrogen atom shared by 2 H2O molecules can shift from 1 molecule to

the next

– H2O + H2O ⇔ H3O+ + OH-

– Or: H2O ⇔ H+ + OH-

• In pure water: [H+] and [OH-] = 10-7M (1 ten millionth mole H+ or OH- per liter of water) • pH = -log [H+] • In pure water, pH = 7

• Acid: substance that increases [H+] of a solution

– e.g., HCl → H+ + Cl- (strong acid, i.e., dissociates completely) – e.g., H2CO3 ↔ HCO3

- + H+ (weak acid, i.e., reversibly releases and accepts H+)

• Base: substance that decreases the [H+] of a solution – directly by accepting H+

• e.g., NH3 + H+ ↔ NH4+ (weak base)

– indirectly by dissociating to form OH-, which combines with H+ to form H2O • e.g., NaOH → Na+ + OH- (strong base)

• Chemical processes in cells are sensitive to pH

– e.g., protein structure (and function) can be modified by pH change • pH needs to be controlled in organisms (usually pH ~7)

• Buffers: substances that minimize pH changes in a solution

• e.g. in water (human blood, lakes, oceans#): CO2 + H2O ↔ H2CO3 ↔ HCO3

- + H+ – What happens if acid is added?

• Strong vs weak acids

– Acid: • e.g., HCl → H+ + Cl- (strong acid, i.e., dissociates completely) • e.g., H2CO3 ↔ HCO3

- + H+ (weak acid, i.e., reversibly releases and accepts H+) – Acid dissociation constant (Ka) indicates the strength of an acid (concentration of

dissociation products vs acid at equilibrium

• pKa = – log Ka • pKa < – 2 : strong acids • pKa = – 2 to 12 : weak acid • pH = pKa – log [AH]/[A-]


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II. Organic chemistry: the chemistry of life Organic molecules

• Chemical compounds whose molecules contain carbon – Exclude:

• Simple oxides of C (CO, CO2) • Carbonates (H2CO3...) • Cyanides • Allotropes of C (pure forms of C, with different structures: graphite, diamond)

Why is C so important?

• Carbon can form diverse molecules by bonding to up to four other atoms – Tetravalence of C allows to build large, complex molecules

• In organic molecules, C bonds most frequently with H, O, N

• The architecture of organic molecules varies widely – Skeleton varies in:

• length • shape (straight, branched, ring) • presence / absence of double bonds

– e.g., hydrocarbons (molecules made only of C and H)

– Atoms of other elements can be bonded to the C skeleton at available sites • e.g.,

– The spatial arrangement of atoms in organic molecules creates different molecules

• Isomers: compounds that have the same number of atoms of the same elements (same formula) but different structures (hence different properties)

– Structural isomers: differ in structure – Geometric isomers: differ in arrangement of atoms about a double

bond – Enantiomers: differ in spatial arrangement around an asymmetric C

(mirror images – optical isomers) – L: left (levo) – D: right (dextro)


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– Remember that molecular structure and properties (functions) are inseparable (molecules have emergent properties that depend on specific arrangement of their atoms)

• e.g., thalidomide – 'R' isomer reduces morning sickness in pregnant women

– 'S' isomer is now known to cause birth defects

– The drug (a mixture of both) was prescribed in 1960's and 1970's • Thousands of birth defects

– Chemical groups can be bonded to the hydrocarbon skeleton of organic molecules

• These chemical groups are key to the functioning of organic molecules – May participate in chemical reactions – May have an effect on molecular shape (and therefore function)

• e.g., estradiol and testosterone differ in only 2 functional groups � completely different functions (development of ♀ and ♂ features)


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Campbell & Reece (2008), Fig. 4-10


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Overview: the molecules of life

• All living things are made up of four classes of large biological molecules: – Carbohydrates – Lipids – Proteins – Nucleic acids

• In cells, small organic molecules are joined to form macromolecules = large molecules composed of thousands of covalently connected atoms

Polymers

• Polymer: long molecule consisting of many similar building blocks • Building-block molecules are called monomers

• Three of the four classes of life’s organic molecules are polymers: • Carbohydrates • Proteins • Nucleic acids

• Polymerization is done by dehydration reaction (condensation)

– Two monomers bond together through the loss of a water molecule • Enzymes speed up the dehydration process

• Polymers are disassembled to monomers by hydrolysis (essentially the reverse of the dehydration reaction)

• Each cell has thousands of different kinds of macromolecules • Macromolecules vary among cells of an organism, vary more within a species, and vary even

more between species • An immense variety of polymers can be built from a small set of monomers

Survey of the four main classes of organic molecules

• All living things are made up of four classes of large biological molecules: – Carbohydrates – Lipids – Proteins – Nucleic acids

Carbohydrates

• Carbohydrates include sugars and the polymers of sugars – Main functions: fuel and structural molecules

• The simplest carbohydrates are monosaccharides, or single sugars • Monosaccharides can be used to build disaccharides and polysaccharides


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• Monosaccharides have molecular formulas that are usually multiples of CH2O – e.g., Glucose (C6H12O6), the most common monosaccharide

• Monosaccharides vary in: – The location of the carbonyl group (as aldose or ketose) – The number of carbons in the carbon skeleton – The spatial arrangement of atoms (isomers)

• e.g., enantiomers of glucose: • D-glucose (dextrose): biologically active • L-glucose: not metabolized by cells in glycolysis

Campbell & Reece (2008), Fig.5-3

• Though often drawn as linear skeletons, in aqueous solutions many sugars form rings


• Disaccharides are formed when a dehydration reaction joins two monosaccharides – Covalent bond formed btw monosaccharides: glycosidic linkage

• e.g., sucrose, maltose, lactose

• Polysaccharides (polymers of sugars) have storage and structural roles • The structure and function of a polysaccharide are determined by:

– the type of sugar monomer – the positions of glycosidic linkages


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• Polymers of glucose: – Cellulose: major component of plant cell wall

• 1-4 linkages of β glucose monomers • Cellulose is the most abundant large organic compound on Earth!

• 1017 g cellulose produced per year

• Why is cellulose a stable structural molecule? • Few organisms have the enzymes required to hydrolyze the β linkages

of cellulose • No caloric value for most animals ('insoluble fibres') • Important role as: paper, cotton, wood (with lignin) • Some prokaryotes have the enzymes required to hydrolyze the β

linkages of cellulose • Many herbivores have mutualistic relationships with these microbes

• e.g., in rumen of cows: prokaryotes hydrolyze cellulose from hay, grass � glucose � converted to other nutrients

• e.g., in digestive tract of termites (eat wood) • Some fungi also have the enzymes required to hydrolyze the β linkages

of cellulose • e.g., Oyster mushrooms (Pleurota ostreatus)

– Starch: storage polysaccharide

• 1-4 linkages of α glucose monomers • Plants store starch as granules within chloroplasts and other plastids • Amylose: unbranched • Amylopectin: branched

• α 1-6 bonds give rise to branches – Glycogen: storage polysaccharide in animals

• Branched • Stored within liver and muscle • Glucose homeostasis in human:

Campbell & Reece (2008), Fig.41-21

– Chitin: structural polysaccharide • Found in the exoskeleton of arthropods and cell walls of many fungi • Monomer: glucose + appendage containing N


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Lipids

• Group of molecules that have little or no affinity for water • Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar

covalent bonds • Lipids do not form polymers • Lipids include:

– Fatty acids – Eicosanoids – Fats – Phospholipids – Steroids – Waxes – Sphingolipids – Glycolipids

Fatty acids

• Fatty acid: carboxyl group attached to a long hydrocarbon chain – From 2 to >26 C, usually 16-22


• Found:

– In a free form (free fatty acids) – In fats, oils, phospholipids, waxes

• Saturated: no double bonds in hydrocarbon chain • Unsaturated: 1 (monounsaturated) or more (polyunsaturated) double bonds in hydrocarbon

chain – Double bonds are usually cis (2 H removed from same side) � chain bends

• Trans fatty acids (in trans fats): trans arrangement of H around double bond • Trans fats have adverse health effects: increase cardiovascular diseases, may increase the

risk of Alzheimer's disease, cancer, type II diabetes... – Formed by:

• Frying, esp. when oil is used several times (e.g., French fries) • cis � trans bonds

• Hydrogenation of (vegetable) oil • e.g., processed / baked foods, margarine, oil shortening...

• makes desirable texture – Labeling mandatory – Banned in many cities, states and countries

• Regulated in Canada


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• Essential fatty acids – FA involved in biological processes that can't be synthesized in an organism (e.g.,

human) • Must be obtained from diet

– ω-3 fatty acids, e.g., • α-linolenic acid (18:3ω3) • eicosapentaenoic acid or EPA (20:5ω3) • docosahexaenoic acid or DHA (22:6ω3)

– ω-6 fatty acids, e.g., • linoleic acid or LA (18:2ω6) • arachidonic acid or AA (20:4ω6)

– Obtained primarily as fats and phospholipids from diet

– Play important roles in human health – e.g., eicosapentaenoic acid or EPA (20:5ω3)

• Essential for proper development of nervous system • Lowers inflammation • Low levels associated with depression, schizophrenia, heart disease, cancer, ...

Eicosanoids

• Eicosanoids: molecules made by oxygenation of 20C EFA (ω-3 or ω-6) – Signaling molecules involved primarily in inflammation (part of immunity) and as

messengers in nervous system – ω-6 eicosanoids are usually pro-inflammatory – ω-3 eicosanoids are less inflammatory or even anti-inflammatory

• Balance between ω-3 and ω-6 eicosanoids in diet affects a variety of functions, with several

consequences – Triglyceride level – Blood pressure – Cardiovascular disease – Inflammatory disorders (e.g., arthritis)

• Synthesis is extremely complex

– Eicosanoids produced from EFA when needed • Involved in inflammation, e.g., after injury

– Redness, swelling, pain, heat

• Aspirin, ibuprofen and other non-steroidal anti-inflammatory drugs stop the synthesis of eicosanoids involved in inflammation and fever


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Fats

• Fats = triacylglycerol = triglyceride: glycerol + 3 fatty acids (same or different) – Glycerol: three-carbon alcohol with hydroxyl group attached to each C – Produced by dehydration reaction – Ester linkage formed between hydroxyl and carboxyl groups – Broken down by hydrolysis (lipase)

• � glycerol + 3 FA


• Saturated fats (contain saturated fatty acids) tend to be solid at room temperature • e.g., animal fat, butter • Most common in terrestrial animals • Produced by hydrogenation of unsaturated fats • Excess consumption related to cardiovascular disease (plaque deposits)

• Unsaturated fats tend to be liquid at room temperature • = oil • Most common in plants, fish

• Fats are neutral (uncharged, no acidic or basic group) and non-polar

– � hydrophobic – Fats separate from water because water molecules form H-bonds and exclude the fats

• Main functions of fats:

– Energy storage (9.3 kcal/g, vs 4.1 kcal/g for carbohydrates and proteins) • Humans and other mammals store their fat in adipose cells

– Adipose tissue also cushions vital organs and insulates the body


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Phospholipids

• Phospholipid: two fatty acids + phosphate group are attached to glycerol + variable hydrophilic group

– AKA phosphoglycerides, glycerophospholipids


• Amphipathic (amphiphilic) molecule:

– Fatty acid tails are hydrophobic – Phosphate group and its attachments form a hydrophilic head

• When phospholipids are added to water, they assemble into a bilayer, with the hydrophobic

tails pointing toward the interior • Phospholipids are the major component of all cell membranes

• Phospholipids with unsaturated FA have a lower freezing point

– Organisms able to tolerate cold temperatures (marine organisms, some plants...) have unsaturated phospholipids

Steroids

• Steroids: lipids characterized by a carbon skeleton consisting of four fused rings – e.g., cholesterol, a component in animal cell membranes

• Functions? • Cholesterol is essential in animals, but high levels in the blood may contribute to

cardiovascular disease


– e.g., bile acids

• Produced by liver of mammals • Found in bile • Involved in fat digestion


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– e.g., vitamin D

• Produced in skin exposed to sunlight • Found in diet (as supplement) • Promotes absorption and metabolism of Ca and P • Involved in cancer (colorectal, breast, prostate) prevention!

– Canadian Cancer Society recommends supplements of 1 000 IU of vitamin D per day in fall and winter in adults

– e.g., hormones

Waxes

• Wax: substance similar in composition and physical properties to beeswax – Usually distinguished from fats by the lack of triglyceride esters of glycerol and three

fatty acids

• Biological importance: – Insect waxes (cover cuticle)

• Beeswax used to construct honeycomb – Plant cuticle – Found on skin surface – Earwax (cerumen) – In some marine organisms: energy source, insulation, buoyancy control, echolocation – Bird waxes: waterproofing of feathers

Sphingolipids

• Contain sphingosine • Functions:

– Protect cell surface by forming mechanically and chemically stable structure part of the outer leaflet of phospholipid bilayer

– Play a role in signal transmission (form "lipid rafts") – Involved in cell recognition

wikipedia.org

Glycolipids

• Lipids attached to carbohydrates • Functions:

– Recognition sites – Contribute to cell attachment (to form tissues)


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Proteins

• Proteins are the most structurally complex and functionally diverse molecules – Proteins are involved in almost everything organisms do – Proteins are very abundant (>50% of dry mass of most cells)

Campbell & Reece (2008), Table 5.1

• The basic structure or proteins is simple • Proteins are polymers built from the same set of 20 amino acids

• Amino acids are organic molecules with carboxyl and amino groups • Amino acids differ in their properties due to differing side chains (R groups)

Campbell & Reece (2008)

• At a certain pH, amino acids carry both + and – charges = zwitterions

– Net charge = 0 – Polar, hydrophilic

Internal transfer of H from –COOH to –NH2Internal transfer of H from –COOH to –NH2

Modified from: chemguide.co.uk


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• Increasing pH (adding OH-): H removed from –NH3+ � amino acid becomes negative

• Decreasing pH (adding H+): H added to –COO- � amino acid becomes positive

• Isoelectric point (pI) : pH at which the amino acid (or protein) has no net electrical charge • pH < pI: + charge • pH > pI: - charge • For a protein:

– At pH > or < pI: protein molecules in water are charged (have same charge) � repel each other and stay in suspension

– At pH = pI: protein has no net electrical charge • � Protein molecules in suspension will aggregate • (Proteins are usually least soluble at their pI) • e.g., casein precipitates when acid is added to milk (milk coagulates � curd) • Milk + lemon juice, vinegar, lactic acid (produced by bacteria)

– � cottage cheese, quark, paneer, ...

• Amino acids differ in their properties due to differing side chains (R groups) • Non-polar: • Polar: • Electrically charged

• Acidic: • Basic:

• L-amino acids predominate – D-amino acids found in cell wall of bacteria, brain, some marine animals

• Proteins are polymers of amino acids • Amino acids are linked by peptide bonds �� polypeptide

– A proteins is made of 1 or more polypeptides

• Polypeptides range in length from a few to >1 000 monomers • Each polypeptide has a unique linear sequence of amino acids


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• A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape

– The sequence of amino acids determines a protein’s three-dimensional structure – Structure determines function

• e.g., antibody protein recognizing flu virus protein (X-ray crystallography)

• A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape

– The sequence of amino acids determines a protein’s three-dimensional structure – Structure determines function

• e.g., hemoglobin There are four levels of protein structure

• Primary structure: protein's unique sequence of amino acids • Secondary structure: coils and folds in the polypeptide chain • Tertiary structure: determined by interactions among various side chains (R groups) • Quaternary structure: when a protein consists of multiple polypeptide chains

• Primary structure: protein's unique sequence of amino acids

– Determined by inherited information

• Secondary structure: coils (αααα helix) and folds (ββββ pleated sheet) – Result from H-bonds between non-adjacent amino acids

• Tertiary structure: determined by interactions between R groups

– H-bonds – Ionic bonds – Hydrophobic interactions – van der Waals interactions – Disulfide bridges (strong covalent bonds) may reinforce the protein’s structure

• Quaternary structure results when two or more polypeptide chains form one macromolecule – e.g., hemoglobin: globular protein made of four polypeptides – e.g., collagen: fibrous protein

• A slight change in primary structure can affect a protein’s structure and function – Remember: structure determines function – What could change protein's primary structure?

• In addition to primary structure, physical and chemical conditions can affect structure (and function!)

– e.g. changes in temperature, pH, salt concentration can cause a protein to unravel (loses secondary and tertiary structures) = protein denaturation

– Denatured protein is biologically inactive


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• Protein denaturation has several applications • Heat denatures proteins

– Cooking – Sterilizing

• Alcohol

– 70% alcohol solution penetrates bacterial cell wall and breaks H-bonds of proteins inside cell � denatures proteins

• Mercurochrome (merbromin) disrupts S bridges – Contains Hg – no longer sold in many countries

• Many proteins are made exclusively of amino acids • Some kinds of proteins are conjugated, i.e. attached to non-amino group (prosthetic group)

– e.g., lipoproteins • e.g., High-density lipoprotein (HDL, 'good' cholesterol) and low-density

lipoprotein (LDL, 'bad' cholesterol) contain protein, cholesterol, PL and fat – e.g., hemoglobin (contains heme group) – e.g., cytochromes (contains heme group)

Proteins in nutrition

• Proteins are involved in almost everything organisms do • Proteins are very abundant (>50% of dry mass of most cells) • At least 0.8 g protein per kg lean body weight in adults • Dietary proteins serve as:

– Source of amino acids (for protein synthesis and amino acid storage) – Source of energy (4 kcal / g) – Excess is converted to sugars and fatty acids

• Protein deficiency is a common cause of health problems and mortality in developing countries – e.g., kwashiorkor: condition (probably) resulting from protein deficiency

• Symptoms include weight loss and swollen abdomen • Dietary proteins must supply essential amino acids

– Cannot be synthesized de novo by the organism – Must be supplied in diet – e.g., phenylalanine, valine...

• Complete proteins have sufficient amounts of EAA for humans – Most animal sources, as well as quinoa, hempseed, amaranth

• Fish is the most important source of animal protein for human nutrition

• Overfishing threatens fish stocks • Most fish stocks are harvested unsustainably or depleted

• Some proteins trigger allergic reactions to certain foods

– e.g., casein (milk), gluten (wheat and other grains), proteins found un nut and peanuts, fish, shellfish,...


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Nucleic acids Functions

• Proteins are involved in almost everything organisms do • The amino acid sequence of a protein is determined by genes • Genes are sequences of DNA (deoxyribonucleic acid) • RNA (ribonucleic acid) is also involved in protein synthesis

Structure

• Nucleic acids are polymers of nucleotides (i.e., they are polynucleotides) • Nucleotide (monomer) is made of:

– pentose sugar – nitrogenous base – phosphate group


• The portion of a nucleotide without the phosphate group is called a nucleoside = Nitrogenous base + sugar

• Nucleotide polymers are linked together �polynucleotide

• Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3′

carbon of one nucleotide and the phosphate on the 5′ carbon of the next nucleotide – Phosphodiester bond – These links create a backbone of sugar-phosphate units with nitrogenous bases as

appendages • RNA is single-stranded • DNA is double-stranded

– 2 polynucleotides in antiparallel configuration

• Backbones run in opposite 5′ → 3′ directions • Nitrogenous bases of opposite strands pair up and form H-bonds: A-T, C-G • Double strand forms a double helix

• The double-stranded nature of DNA (and complementary base pairing) is key to allow DNA

replication – DNA replication is semi-conservative


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• How did we come to understand the structure of DNA? – Early studies showed that DNA was a polymer of nucleotides – Erwin Chargaff (1950):

• DNA composition is species-specific • In any species %A = %T, and %G = %C (Chargaff's rule)

– 1:1 ratio of pyrimidine and purine – Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study molecular

structure of DNA • Franklin produced a picture of DNA

– Franklin concluded that there were two antiparallel sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior

– Franklin’s X-ray crystallographic images of DNA enabled Watson to deduce the spacing of the nitrogenous bases

– The Watson-Crick model explains Chargaff’s rules – Franklin’s X-ray crystallographic images of DNA enabled Watson to deduce that DNA

was made of a double helix – Watson and Crick built models of a double helix to conform to the X-rays and chemistry

of DNA

III. Membrane structure and function Some important functions of membranes:

• The plasma membrane is the boundary that separates the living cell from its surroundings • Plasma membrane is involved in cell recognition and messaging • Plasma membrane controls internal environment

– Exhibits selective permeability (allows some substances to cross it more easily than others)

– Involved in transport – Essential in maintenance of homeostasis

• Membranes define compartments (organelles) inside the cell • Membranes are involved in metabolic processes

Membrane structure: scientific inquiry

• Langmuir discovered the structure of oil-water films � fatty acids in PL oriented vertically with polar group in water

• Gorter & Grendel (1925): red blood cells covered by bilayer of phospholipids • Davson and Danielli (1935) proposed a sandwich model: phospholipid bilayer lies between two

layers of globular proteins – Later studies found problems with this model (placement of membrane proteins, which

have hydrophilic and hydrophobic regions) • Singer and Nicolson (1972) proposed the fluid mosaic model:

– Membrane is a mosaic of proteins dispersed within the bilayer, with only the hydrophilic regions exposed to water

– Membrane is a mosaic of proteins dispersed within the bilayer, with only the hydrophilic regions exposed to water

– Freeze-fracture studies of the plasma membrane (splitting membrane along phospholipid bilayer) supported the fluid mosaic model

– Phospholipids in the plasma membrane move laterally within the bilayer – Flip-flops are rare – Proteins also drift in membrane; e.g., Frye & Edidin (1970)


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Membrane structure


• Membranes must be fluid to work properly • Membrane fluidity is influenced by:

– Saturation of FA: membranes rich in unsaturated fatty acids are more fluid that those rich in saturated fatty acids

– Presence of cholesterol • Reduces PL movement & membrane fluidity at moderate Tº • Maintains membrane fluidity at low Tº by preventing tight packing

• Biological membranes are a collage of different proteins embedded in the fluid matrix of the lipid bilayer

• Proteins determine most of the membrane’s specific functions:

• Carbohydrates on the plasma membrane are involved in cellular recognition – Membrane carbohydrates may be covalently bonded to proteins (glycoproteins) or

lipids (glycolipids) • Carbohydrates on the external side of the plasma membrane vary among species, individuals,

and even cell types in an individual


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Membrane structure results in selective permeability • A cell must exchange materials with its surroundings, a process controlled by the plasma

membrane • Plasma membranes are selectively permeable, regulating the cell’s molecular traffic

– Hydrophobic (nonpolar) molecules, such as hydrocarbons, can dissolve in the lipid bilayer and pass through the membrane rapidly

– Polar molecules, such as sugars, do not cross the lipid bilayer easily • Exception?

• A cell must exchange materials with its surroundings, a process controlled by the plasma

membrane • Transport mechanisms allow to control molecular traffic

– Passive transport (no energy required from the cell) • Simple diffusion • Facilitated diffusion

– Active transport Passive transport: diffusion

• Diffusion: tendency for molecules to spread out evenly into the available space

– Substances diffuse down their concentration gradient, the difference in concentration of a substance from one area to another

• Osmosis is the diffusion of water across a selectively permeable membrane

– Water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration

• Tonicity is the ability of a solution to cause a cell to gain or lose water – Isotonic solution: Solute concentration is the same as that inside the cell; no net water

movement across the plasma membrane – Hypertonic solution: Solute concentration is greater than that inside the cell; cell loses

water – Hypotonic solution: Solute concentration is less than that inside the cell; cell gains

water

• Hypertonic or hypotonic environments create osmotic problems for organisms – Osmoregulation, the control of water balance, is a necessary adaptation for life in such

environments – The protist Paramecium, which is hypertonic to its pond water environment, has a

contractile vacuole that acts as a pump – In plants, cell walls help maintain water balance

• In hypotonic solution, cell swells until the wall opposes uptake; the cell is now turgid (firm)

• Isotonic: no net movement of water into the cell; the cell becomes flaccid (limp), and the plant may wilt

• Hypertonic environment: plant cells lose water; membrane pulls away from the wall (plasmolysis)


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Passive transport: facilitated diffusion

• Facilitated diffusion: transport proteins speed the passive movement of molecules across the plasma membrane

– Channel proteins provide corridors that allow a specific molecule or ion to cross the membrane

• e.g., Aquaporins, for facilitated diffusion of water • e.g., Ion channels that open or close in response to a stimulus (gated channels)

– Carrier proteins (permeases) undergo a subtle change in shape that translocates the solute-binding site across the membrane

• Facilitated diffusion is passive because the solute moves down its concentration gradient Active transport

• Active transport moves substances against their concentration gradient – Performed by specific integral membrane proteins – Requires energy, usually in the form of ATP – e.g., sodium-potassium pump

Ion pumps create a membrane potential

• Ions pumps (e.g., Na-K pump) create a membrane potential = voltage difference across a membrane

– Voltage is created by differences in the distribution of positive and negative ions – Ion pumps are electrogenic pumps (transport proteins that generate voltage across a

membrane) – The Na-K pump is the main electrogenic pump of animal cells – The main electrogenic pump of plants, fungi, and bacteria is a proton pump

• Ions pumps create an electrical force

– i.e., the membrane potential has an effect on the ion’s movement just like the ion's concentration gradient

How can this be used?

• Electrogenic pumps create membrane potential (voltage across membrane) – This energy can be tapped for cellular work

• e.g., ATP synthesis • e.g., cotransport

• Cotransport occurs when active transport of a solute indirectly drives transport of another

solute • Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive active

transport of nutrients into the cell Bulk transport

• Small molecules enter or leave the cell through the lipid bilayer or by transport proteins • Large molecules, such as polysaccharides and proteins, cross the membrane in bulk via

vesicles – Endocytosis – Exocytosis

• Bulk transport requires energy


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• Endocytosis: cell takes in macromolecules by forming vesicles from the plasma membrane • There are three types of endocytosis:

– Phagocytosis (“cellular eating”): cell engulfs particle by forming vacuole – Pinocytosis (“cellular drinking”): cell takes in extracellular fluid in vesicle – Receptor-mediated endocytosis: cell acquires bulk quantities of specific substance

(ligands) that may not be highly concentration in extracellular fluid

• Exocytosis: transport vesicles migrate to the membrane, fuse with it, and release their contents – Many secretory cells use exocytosis to export their products

IV: Enzymes and metabolism

• The cell is the structural and functional unit of life • The living cell is a miniature chemical factory where thousands of reactions occur

– The cell transforms energy and matter • Extracts energy and applies energy to perform work, to build molecules, to

generate heat, and even light Metabolism

• Metabolism is the totality of an organism’s chemical reactions – Emergent property of life that arises from interactions between molecules within the cell – Metabolism is almost completely dependent on enzymes

• Enzymes catalyze specific reactions – Several enzymes working in sequence form a metabolic pathway

• Begins with a specific molecule and ends with a product • Two main types of metabolic pathways

• Catabolic pathways release energy by breaking down complex molecules into simpler compounds

– e.g., Cellular respiration, the breakdown of glucose in the presence of oxygen • Anabolic pathways consume energy to build complex molecules from simpler ones

– e.g., Synthesis of protein from amino acids • Catabolic and anabolic pathways are related in organisms

Release E

and small

molecules

Consume E

and small

molecules

Release E

and small

molecules

Consume E

and small

molecules

Modified from accessexcellence.org


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Metabolism and the laws of energy transformation • Metabolism is subject to the laws of thermodynamics

– 1st law of thermodynamics: the energy of the universe is constant (principle of conservation of energy)

• Energy can be transferred and transformed, but it cannot be created or destroyed

– 2nd law of thermodynamics: during every energy transfer or transformation, some energy is unusable, and is often lost as heat

• Every energy transfer or transformation increases the entropy (disorder) of the universe

– Chemical reactions occur spontaneously (without energy input) only if they increase the

entropy of the universe – Many chemical reactions (that require an energy input) decrease the entropy in an

organism, i.e., they create more complex structures • Entropy (disorder) may decrease in an organism, but the universe’s total

entropy increases • The evolution of more complex organisms does not violate the second law of

thermodynamics • Energy flows into an ecosystem in the form of light and exits in the form of heat • Overall, the entropy of the universe increases

• Energy is the capacity to cause change • Energy exists in various forms, some of which can perform work

– Kinetic energy: energy associated with motion – Heat (thermal energy): kinetic energy associated with random movement of atoms or

molecules – Potential energy: energy that matter possesses because of its location or structure – Chemical energy: potential energy available for release in a chemical reaction

• Energy can be converted from one form to another

• Free-energy change of a reaction determines whether it occurs spontaneously • A living system’s free energy is energy that can do work when temperature and pressure are

uniform, as in a living cell • The change in free energy (∆G) during a process is related to the change in enthalpy, or

change in total energy (∆H), change in entropy (∆S), and temperature in Kelvin (T): ∆G = ∆H – T∆S

• Only processes with a negative ∆G are spontaneous • Free energy decreases during spontaneous reaction

• Spontaneous processes can be harnessed to perform work

• The concept of free energy can be applied to the chemistry of life’s processes – Exergonic reaction: proceeds with a net release of free energy; spontaneous – e.g., cellular respiration

– Endergonic reaction: absorbs free energy from its surroundings; nonspontaneous – e.g., photosynthesis


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• Cells perform work (chemical, mechanical, transport) by energy coupling: the use of an exergonic process to drive an endergonic one

– Exergonic process 'gives' energy to drive endergonic process – Most energy coupling in cells is mediated by ATP

• Cell's energy shuttle – universal energy currency Metabolism and ATP • ATP is a nucleoside triphosphate, i.e., made of:

– Ribose (sugar) – Adenine (nitrogenous base) – 3 phosphate groups

• The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis • Energy is released from ATP when the terminal phosphate bond is broken (exergonic reaction)

– This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

• Cellular work (chemical, mechanical, transport) is powered by the hydrolysis of ATP

– Energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

– Overall, the coupled reactions are exergonic

• ATP drives endergonic reactions by phosphorylation = transferring a phosphate group to some other molecule, such as a reactant

• The recipient molecule is now phosphorylated

• ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)

• The energy to phosphorylate ADP comes from catabolic reactions in the cell • e.g., cellular respiration

• The chemical potential energy temporarily stored in ATP drives most cellular work Metabolism and enzymes

• Metabolism is the totality of an organism’s chemical reactions – Metabolism is almost completely dependent on enzymes

• Enzymes catalyze specific reactions

• Enzymes: proteins (or RNA: ribozymes) acting as catalysts – Speed up a reaction without being consumed by the reaction – e.g., hydrolysis of sucrose

• Exergonic (spontaneous) reaction – but very slow • Happens very quickly with the enzyme sucrase

• Chemical reaction between molecules may be naturally slow because they require an initial

'energy investment', e.g., to break bonds – = free energy of activation, or activation energy (EA) – 'return on investment' is greater than EA when new bonds containing less energy are

formed


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• Enzymes catalyze reactions by lowering the EA barrier • Enzymes do not affect the change in free energy (∆G); instead, they speed up reactions that

would occur eventually How enzymes work

1. The reactant that an enzyme acts on is the substrate(s) – Substrate binds to enzyme at active site – Forms enzyme-substrate complex – Induced fit of a substrate brings chemical groups of the active site into positions that

enhance their ability to catalyze the reaction

2. The active site can lower an EA barrier by – Orienting substrates correctly – Stressing - straining substrate bonds – Providing a favorable microenvironment – Covalently bonding to the substrate

3. Substrate(s) converted to product(s)

4. Product released 5. Active site is available for new substrate(s)

Effect of local conditions on enzyme activity

• An enzyme’s activity can be affected by – Environmental factors, such as temperature and pH

• Each enzyme has an optimal temperature in which it can function • Each enzyme has an optimal pH in which it can function

– Substrate concentration

• Enzyme activity is influenced by substrate concentration • When substrate concentration increases, reaction rate initially increases

rapidly • Reaction rate increases with substrate concentration until Vmax

(maximum velocity) • All active sites are saturated with substrate at Vmax

• The substrate concentration at ½ Vmax = Km (Michaelis-Menten constant) • Each enzyme has a characteristic Km for a given substrate

• Km is inverse measure of affinity between substrate and enzyme • The lower the Km, the greater the affinity

wikipedia.org


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– Chemicals that specifically influence the enzyme • Many enzymes require non-protein molecules to perform their catalytic activity

• = Cofactors • Inorganic (e.g., zinc, iron, copper) • Organic

• Prosthetic groups • Bound to enzyme

• Coenzymes • Not permanently bound to enzyme; e.g., some

vitamins

• Enzyme activity can be decreased by inhibitors – e.g., some toxins, drugs, pesticides, antibiotics – Competitive inhibitors: bind to the active site of an enzyme

• Similar in molecular structure to substrate � competes with substrate

• Higher substrate concentrations required to reach Vmax – Apparent Km increases

– Noncompetitive inhibitors: bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

• Inhibitor can not be driven from the enzyme by higher substrate concentration � Vmax reduced

• Does not reduce affinity of enzyme for substrate Regulation of enzyme activity helps control metabolism

• Controlling metabolic activity in cells is essential to the process of life – Chaos would result if a cell’s metabolic pathways were not tightly regulated

• Because metabolism is almost completely dependent on enzymes, regulation of enzyme activity helps control metabolism

• Two ways to control enzymatic activity: – Switching on or off the genes that encode specific enzymes – Regulating the activity of enzymes found in the cell

• Allosteric regulation occurs when a regulatory molecule binds to an enzyme at one site and

affects the enzyme’s function at another site • Usually in enzymes made from polypeptide subunits • Each enzyme has active and inactive forms

• The binding of an activator stabilizes the active form of the enzyme • The binding of an inhibitor stabilizes the inactive form of the enzyme

• Cooperativity is a form of allosteric regulation that can amplify enzyme activity • Binding by a substrate to one active site stabilizes favorable conformational changes at all

other subunits

• Feedback inhibition: end product of a metabolic pathway shuts down the pathway – Feedback inhibition prevents a cell from wasting chemical resources by synthesizing

more product than is needed – 'Self-control' of metabolic pathways

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