marieb chapter 2 part b: chemistry comes alive student version

Marieb Chapter 2 Part B: Chemistry Comes Alive

Student version

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Biochemistry

• Study of chemical composition and reactions of living matter

• All chemicals are either organic or inorganic

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Classes of Compounds

• Inorganic compounds• • Do not contain carbon (exception is CO2)

• Organic compounds•

• Contain carbon, are usually large, and atoms are covalently bonded

• Both equally essential for life

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Water in Living Organisms

• Most abundant inorganic compound – 60%–80% volume of living cells

• Most important inorganic compound– Due to water’s properties– Let’s discuss this!

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Properties of Water

• High heat capacity– Absorbs and releases heat with little

temperature change– Prevents sudden changes in temperature

• High heat of vaporization– Evaporation requires large amounts of heat– Useful cooling mechanism

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Properties of Water

• Acts as a polar solvent– Dissolves and dissociates ionic substances– Forms layers around large charged

molecules, e.g., proteins (colloid formation)– Body’s major transport medium– Most biological molecules are happy in it

(uhm, dissolve!)

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Water molecule

δ+

δ+

δ–

Ions insolution

Saltcrystal

Figure 2.12 Dissociation of salt in water.

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Properties of Water

• Formed or used in some chemical reactions– Necessary part of hydrolysis and dehydration

synthesis reactions

• Used as cushioning– Protects certain organs from physical trauma,

e.g., cerebrospinal fluid

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What Are Salts?

•

– Ions ( ) conduct electrical currents in solution– Ions play specialized roles in body functions

– Ionic balance vital for homeostasis

• Contain cations other than H+ and anions other than OH–

• Common electrolytes found in the body– sodium, chloride, carbonate, potassium, calcium,

phosphates

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Acids and Bases

• Both form electrolytes–

• Acids are– Release H+ (a bare proton) in solution– HCl H+ + Cl–

• Bases are– Take up H+ from solution or release OH- into solution

• NaOH Na+ + OH–

– OH– accepts an available proton (H+) to form water– OH– + H+ H2O

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Some Important Acids and Bases in Body

• Important acids– HCl, HC2H3O2 (acetic acid), and H2CO3

• Important bases – Bicarbonate ion (HCO3–) and ammonia (NH3)

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pH: Acid-base Concentration

• Relative free [H+] of a solution measured in a special way

• As free [H+] increases, acidity increases• [OH–] decreases as [H+] increases

• pH decreases

• As free [H+] decreases, alkalinity increases• [OH–] increases as [H+] decreases

• pH increases

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pH: Acid-base Concentration

• pH = negative logarithm of [H+] in moles per liter

• pH scale ranges from 0–14

• Because pH scale is logarithmic (like the Richter Scale)– A pH 5 solution is 10 times more acidic than a

pH 6 solution

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pH: Expression Of Acid-base Concentration• Acidic solutions

[H+], pH – Acidic pH:

• Neutral solutions– Equal numbers of H+ and OH–

– All neutral solutions are pH – Pure water is pH neutral

• pH of pure water = pH 7: [H+] = 10–7 m

• Alkaline (basic) solutions [H+], pH– Alkaline pH:

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Concentration(moles/liter)

[OH−] [H+] pH

100

10−1

10−2

10−3

10−4

10−5

10−6

10−7

10−8

10−9

10−10

10−11

10−12

10−13

10−14

10−14

10−13

10−12

10−11

10−10

10−9

10−8

10−7

10−6

10−5

10−4

10−3

10−2

10−1

100

1

2

3

4

5

6

7

8

9

10

11

12

13

14

1M Hydrochloricacid (pH=0)

Lemon juice; gastricjuice (pH=2)

Wine (pH=2.5–3.5)

Black coffee (pH=5)

Milk (pH=6.3–6.6)

Blood (pH=7.4)

Egg white (pH=8)

Household bleach(pH=9.5)

Household ammonia(pH=10.5–11.5)

Oven cleaner, lye(pH=13.5)

1M Sodiumhydroxide (pH=14)

Examples

Incr

easi

ng

ly a

cid

ic

Neutral

Incr

easi

ng

ly b

asi

c

0

Figure 2.13 The pH scale and pH values of representative substances.

pH Paper

Strong and Weak Acids and Bases

strong weak

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Acid-base Homeostasis

• A pH change interferes with cell function and may damage living tissue

• Even a slight change in pH can be fatal

• What are the extremes of pH of the blood?• Lowest = Highest =

• pH is regulated by kidneys, lungs, and chemical buffers (observe in Lab Expt. 2)

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Buffers

• Acidity reflects only free H+ in solution• Buffers resist abrupt and large swings in pH

– Release hydrogen ions if pH rises– Bind hydrogen ions if pH falls

• Carbonic acid-bicarbonate system (important buffer system of blood):

Buffers

• H2CO3 H+ + HCO3-

• All three present in solution.

• What happens if we add H+?

-

• What happens if we add OH-?

-

Where Do We Find Buffers?

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Organic Compounds

• Molecules that contain – Except CO2 and CO, which are considered

inorganic

• Carbon always shares electrons; never gains or loses them

• Carbon forms four covalent bonds with other elements

• Unique to living systems• Carbohydrates, lipids, proteins, and

nucleic acids

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Organic Compounds

• Many are(ex.= glycogen, DNA, proteins)

– Chains of similar units called(I call them the “building blocks”)

• Polymers are synthesized by dehydration synthesis ( )

• Polymers are broken down by hydrolysis reactions ( )

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Dehydration synthesis

Monomers are joined by removal of OH from one monomer and removal of H from the other at the site of bond formation.

Monomer 1

Hydrolysis

Monomers linked by covalent bond

Monomers are released by the addition of a water molecule, adding OH to one monomer and H to the other.

Example reactions

Dehydration synthesis of sucrose and its breakdown by hydrolysis

+

Glucose Fructose

Water isreleased

Water isconsumed

Sucrose

Monomer 2

Monomer 1 Monomer 2

Monomers linked by covalent bond

+

+

Figure 2.14 Dehydration Synthesis and Hydrolysis.

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Carbohydrates

• Sugars and starches

• Come in monomers and polymers

• Contain C, H, and O [formula =(CH20)n]

• Three classes– Monosaccharides – one sugar– Disaccharides – two sugars covalently

bonded– Polysaccharides – many sugars covalently

bonded

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Carbohydrates

• Functions of carbohydrates

– Major source of cellular fuel (e.g., glucose)

– Structural molecules

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Monosaccharides

• Simple sugars • These are the monomers of carbohydrates• Important monosaccharides

– Pentose sugars• Ribose and deoxyribose (in DNA and RNA)

– Hexose sugars• Glucose (blood sugar)

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Monosaccharides

Monomers of carbohydratesExampleHexose sugars (the hexoses shown here are isomers)

ExamplePentose sugars

Glucose Fructose Galactose Deoxyribose Ribose

Figure 2.15a

Simple carbohydrate molecules important to the body.

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Disaccharides

• Double sugars (two covalently linked monomers)

• Also called simple carbohydrates

• Too large to pass through cell membranes

• Important disaccharides– Sucrose, maltose, lactose– We have enzymes to break these down

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Disaccharides

Consist of two linked monosaccharidesExampleSucrose, maltose, and lactose(these disaccharides are isomers)

FructoseGlucose GlucoseGlucose GlucoseGalactose

Sucrose Maltose Lactose

Figure 2.15b

Simple carbohydrate molecules important to the body.

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Polysaccharides

• Polymers of monosaccharides

• Complex sugars

• Important polysaccharides– Plant starch– Animal starch (glycogen) – Cellulose (woody plants)

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PLAYPLAY Animation: Polysaccharides

Polysaccharides

Long chains (polymers) of linked monosaccharidesExampleThis polysaccharide is a simplified representation of glycogen, a polysaccharide formed from glucose units.

Glycogen

Figure 2.15c Carbohydrate molecules important to the body.

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Animation: Fats

Lipids

• Contain C, H, O (less than in carbohydrates), and sometimes P

• Insoluble in water

• Main types:– – – –

PLAYPLAY

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Neutral Fats or Triglycerides

• Called fats when solid (lard, butter)

• Oils when liquid (canola oil)

• Composed of three fatty acids covalently bonded to a glycerol molecule

• Main functions– Energy storage– Insulation– Protection

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Triglyceride formation

Three fatty acid chains are bound to glycerol by dehydration synthesis.

Glycerol 3 fatty acid chainsTriglyceride, or neutral fat

3 watermolecules

+ +

Figure 2.16a Lipids.

Dehydration Synthesis

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Saturation of Fatty Acids

• Saturated fatty acids– Single covalent bonds between C atoms

• Maximum number of H atoms

– Solid animal fats, e.g., butter

and lard

Saturation of Fatty Acids

• Unsaturated fatty acids– One or more double bonds between C atoms

• Reduced number of H atoms

– Plant oils, e.g., olive oil–

Saturation of Fatty Acids

Saturation of Fatty Acids

• Trans fats – modified oils –

• Omega-3 fatty acids –

Saturation of Fatty Acids

Types Of Fat

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Phospholipids

• Modified triglycerides: – Glycerol + two fatty acids and a phosphorus

(P) - containing group

• “Head” and “tail” regions have different properties

• Important in cell membrane structure

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“Typical” structure of a phospholipid molecule

Two fatty acid chains and a phosphorus-containing group are attached to the glycerol backbone.

ExamplePhosphatidylcholine

Nonpolar “tails”(schematic

phospholipid)

Polar “head”

Phosphorus-containinggroup

(polar “head”)

Glycerolbackbone 2 fatty acid chains

(nonpolar “tails”)

Figure 2.16b Lipids.

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Steroids

• Steroids—interlocking four-ring structure

• Cholesterol, vitamin D, steroid hormones, and bile salts

• Most important steroid–

• Important in cell membranes, vitamin D synthesis, steroid hormones, and bile salts

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Simplified structure of a steroidFour interlocking hydrocarbon rings

form a steroid.ExampleCholesterol (cholesterol is thebasis for all steroids formed in the body)

Figure 2.16c Lipids.

Anabolic Steroids

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Eicosanoids

• Many different ones

• Derived from a fatty acid (arachidonic acid) in cell membranes

• Most important eicosanoid– Prostaglandins

• Role in blood clotting, control of blood pressure, inflammation, and labor contractions

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Other Lipids in the Body

• Fat-soluble vitamins– Vitamins A, D, E, and K

• Lipoproteins– Transport fats in the blood (LDL, HDL)

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Proteins

• Contain C, H, O, N, and sometimes S and P• Proteins are polymers • Amino acids (20 types) are the monomers in

proteins– Joined by covalent bonds called peptide bonds– Contain amine group and acid group– Can act as either acid or base– All identical except for “R group” (in green on figure)

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Generalizedstructure of allamino acids.

Glycineis the simplestamino acid.

Aspartic acid(an acidic aminoacid) has an acidgroup (—COOH)in the R group.

Lysine(a basic aminoacid) has an aminegroup (—NH2) inthe R group.

Cysteine(a basic amino acid)has a sulfhydryl (—SH)group in the R group,which suggests thatthis amino acid is likelyto participate in intramolecular bonding.

Aminegroup

Acid group

Figure 2.17 Amino acid structures.

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Amino acid

Dehydration synthesis:The acid group of one aminoacid is bonded to the aminegroup of the next, with lossof a water molecule.

Hydrolysis: Peptide bondslinking amino acids togetherare broken when water isadded to the bond.

Dipeptide

Peptidebond

Amino acid

+

Figure 2.18 Amino acids are linked together by peptide bonds.

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Primary structure:The sequence of amino acids formsthe polypeptide chain.

Amino acid Amino acid Amino acid Amino acid Amino acid

Figure 2.19a Levels of protein structure.

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Secondarystructure:The primary chainforms spirals(α-helices) andsheets (β-sheets).

α-Helix: The primary chain is coiledto form a spiral structure, which isstabilized by hydrogen bonds.

β-Sheet: The primary chain “zig-zags”back and forth forming a “pleated”sheet. Adjacent strands are heldtogether by hydrogen bonds.

Figure 2.19b Levels of protein structure.

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Tertiary structure:Superimposed on secondary structure.α-Helices and/or β-sheets are folded upto form a compact globular moleculeheld together by intramolecular bonds.

Tertiary structure ofprealbumin (transthyretin),a protein that transportsthe thyroid hormonethyroxine in blood andcerebrospinal fluid.

Figure 2.19c Levels of protein structure.

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Quaternary structure:Two or more polypeptide chains,each with its own tertiary structure,combine to form a functionalprotein.

Quaternary structure of a functional prealbuminmolecule. Two identicalprealbumin subunits joinhead to tail to form thedimer.

Figure 2.19d Levels of protein structure.

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Fibrous and Globular Proteins

• (structural) proteins– – Most have tertiary or quaternary structure (3-D)– Provide mechanical support and strength– Examples:

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Fibrous and Globular Proteins

• (functional) proteins – Compact, spherical, water-soluble and

sensitive to environmental changes– Tertiary or quaternary structure (3-D)– Specific functional regions (active sites) – Examples:

Fibrous and Globular Proteins

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Protein Denaturation

• Denaturation– Globular proteins unfold and lose functional,

3-D shape• activity destroyed

– Can be cause by decreased pH, increased ions, or increased temperature

• Usually reversible if normal conditions restored

• Irreversible if changes are extreme– e.g., cooking meat

Protein Denaturation

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Enzymes

– Globular proteins that act as biological catalysts

• Regulate and increase speed of chemical reactions

– Lower the activation energy, increase the speed of a reaction (millions of reactions per minute!)

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WITHOUT ENZYME WITH ENZYME

Activationenergy required

Less activationenergy required

ReactantsReactants

En

erg

y

En

erg

yProgress of reactionProgress of reaction

Product Product

Figure 2.20 Enzymes lower the activation energy

required for a reaction.

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Characteristics of Enzymes

• Some functional enzymes consist of two parts – Protein portion

– Cofactor (metal ion) or coenzyme (organic molecule often a vitamin)

• Enzymes are specific– Act on specific substrate

• Usually end in the suffix “- ”

• Often named for the reaction they catalyze– Hydrolases, oxidases

–

Enzyme Action

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Figure 2.21 Mechanism of enzyme action.

Substrates (S)e.g., amino acids

Active site

Energy isabsorbed;bond is formed.

Water isreleased.

Product (P)e.g., dipeptide

Peptidebond

Enzyme-substratecomplex (E-S)

Enzyme (E)

The enzyme releasesthe product of thereaction.

Substrates bind at active site, temporarily forming an enzyme-substrate complex.

The E-S complex undergoes internal rearrangements that form the product.

+

1 2

3

Slide 1

Enzyme (E)

Enzyme Action

Enzyme Action

Enzyme Action

Enzyme Reactants

Reactantsapproach enzyme

Reactantsbind to enzyme

Enzymechanges shape

Productsare released

Product

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Nucleic Acids

• Deoxyribonucleic acid ( ) and ribonucleic acid ( )– Largest molecules in the body

• Contain C, O, H, N, and P

• Polymers– Monomer = nucleotide

• a• a• a

Figure 2.23

Adenine (A)

Phosphate

Deoxyribose

Thymine (T) Cytosine (C) Guanine (G)

Nucleotides - The Building Blocks of DNA and RNA

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Deoxyribonucleic Acid (DNA)

• Utilizes four nitrogen bases: – Purines: Adenine (A), Guanine (G) – Pyrimidines: Cytosine (C), and Thymine (T)– Base-pair rule – each base pairs with its

complementary base • A always pairs with T; G always pairs with C

• Double-stranded helical molecule (double helix) in the cell nucleus

• Pentose sugar is deoxyribose• Provides instructions for protein synthesis• Replicates before cell division ensuring genetic

continuity

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PhosphateSugar:

DeoxyriboseBase:

Adenine (A) Thymine (T) Sugar Phosphate

Adenine nucleotide Thymine nucleotide

Hydrogenbond

Deoxyribosesugar

PhosphateSugar-phosphatebackbone

Adenine (A)

Thymine (T)

Cytosine (C)

Guanine (G)

Figure 2.22 Structure of DNA.

Base pair

Phosphate

Sugar

Nucleotide

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Ribonucleic Acid (RNA)

• Four bases: – Adenine (A), Guanine (G), Cytosine (C), and

Uracil (U)

• Pentose sugar is ribose• Single-stranded molecule mostly active

outside the nucleus• Three varieties of RNA carry out the DNA

orders for protein synthesis– Messenger RNA (mRNA), transfer RNA

(tRNA), and ribosomal RNA (rRNA)

Phosphate

Ribose

Uracil

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ATP Carries Energy

Structure and function of adenosine triphosphate (ATP)Nucleotide – adenosine triphosphate

Universal energy source

Bonds between phosphate groups contain potential energy

Breaking the bonds releases energyATP → ADP + P + energy

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High-energy phosphatebonds can be hydrolyzedto release energy.

Adenine

Ribose

Phosphate groups

Adenosine

Adenosine monophosphate (AMP)

Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP)

Figure 2.23 Structure of ATP (adenosine triphosphate).

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Function of ATP

• Phosphorylation – Phosphates are enzymatically transferred to

and energize other molecules – Such “primed” molecules perform cellular

work (life processes) using the phosphate bond energy

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Solute

Membraneprotein

+

Transport work: ATP phosphorylates transport proteins, activating them to transport solutes (ions, for example) across cell membranes.

Relaxed smoothmuscle cell

Contracted smoothmuscle cell

+

Mechanical work: ATP phosphorylates contractile pro-teins in muscle cells so the cells can shorten.

+

Chemical work: ATP phosphorylates key reactants, providing energy to drive energy-absorbing chemical reactions.

Figure 2.24 Three examples of cellular work driven by energy from ATP.