chemistry comes alive

2

Chemistry Comes Alive

P A R T A

Human Anatomy and Physiology, 7eby Elaine Marieb & Katja Hoehn

Copyright © 2007 Pearson Education, Inc.,publishing as Benjamin Cummings.

Figure 2.11: Patterns of chemical reactions, p. 38.

Amino acids Protein molecule

Glucose moleculesGlycogen

+

+

Glucose Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP)Glucosephosphate

(a) Example of a synthesis reaction: amino acids are joined to form a protein molecule

(b) Example of a decomposition reaction: breakdown of glycogen to release glucose units

(c) Example of an exchange reaction: ATP transfers its terminal phosphate group to glucose to form glucose-phosphate

P

P P PO

O P P

O

O

Factors Influencing Rate of Chemical Reactions• Chemicals react when they collide with enough force to

overcome the repulsion by their electrons

• Temperature – chemical reactions proceed quicker at higher temperatures

• Particle size – the smaller the particle the faster the chemical reaction

• Concentration – higher reacting particle concentrations produce faster reactions

• Catalysts – increase the rate of a reaction without being chemically changed

• Enzymes – biological catalysts

Energy Flow in Chemical Reactions

• Exergonic reactions – reactions that release energy

• Endergonic reactions – reactions whose products contain more potential energy than did its reactants

Biochemistry - study of the chemistry of living things

• Organic compounds– Contain carbon, are covalently bonded, and are often

large

• Inorganic compounds– Do not contain carbon– Water, salts, and many acids and bases

Properties of Water• Water is the most important inorganic molecule, and makes up 60–80% of the

volume of most living cells

• High heat capacity – absorbs and releases large amounts of heat before changing temperature

• High heat of vaporization – changing from a liquid to a gas requires large amounts of heat

• Polar solvent properties – dissolves ionic substances, forms hydration layers around large charged molecules, and serves as the body’s major transport medium

• Reactivity – is an important part of hydrolysis and dehydration synthesis reactions

• Cushioning – resilient cushion around certain body organs

Salts

• Inorganic compounds

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

• When salts are dissolved in water they dissociate into their component ions

• Are electrolytes; they conduct electrical currents



Figure 2.12: Dissociation of a salt in water, p. 40.

Watermolecule

Saltcrystal

Ions insolution

H

HO

Na+

Cl–

Na+

Cl–

– +

+

Acids and Bases• Acid – molecule that can release protons (H+) into a solution;

proton donor; pH= less than 7

HCl H+ + Cl –

• Base - molecule that can release OH- (hydroxyl ions) into a solution which may combine with H+ to form water; lowers H+ concentration; proton acceptor; pH = greater than 7

NaOH Na+ + OH–

Acid-Base Concentration (pH)• Acidic solutions have higher H+ concentration and therefore a lower pH

• Alkaline solutions have lower H+ concentration and therefore a higher pH

• Neutral solutions have equal H+ and OH– concentrations

– Water molecules will occasionally break apart (ionize) leaving the hydrogen electron attached to the oxygen atom

– Ionization of water produces equal amounts of H+ and OH-

• Neutralization occurs when an acid and a base are mixed together. They react with each other in displacement reactions to form a salt and water.

pH scale

• Based on the number of hydrogen ions (H+) in solution

• pH scale runs from 0 to 14; each successive change of 1 pH unit represents a 10-fold change in hydrogen ion concentration

• pH = -log10[H+] , where [H+] = molar conc.

• Pure water = [H+] = 10-7M; therefore it has a pH of 7; neutral; [H+] = [OH-]

• If [H+] is greater than [OH-], solution is acid

• If [OH-] is greater that [H+], solution is base

Acid-Base Concentration (pH)

• Acidic: pH 0–6.99

• Basic: pH 7.01–14

• Neutral: pH 7.00

Figure 2.13

Buffers• system of molecules and ions that acts to prevent drastic changes in H+ concentration; stabilizes pH of solution

• Living cells are extremely sensitive to light changes in pH – must remain between 7.35 and 7.45

• Acid-base balance is regulated by the kidneys, lungs, and buffers found in body fluids

• Carbonic acid-bicarbonate system– Carbonic acid dissociates, reversibly releasing bicarbonate ions

and protons– The chemical equilibrium between carbonic acid and bicarbonate

resists pH changes in the blood

• Acidosis – blood pH falls below 7.35; hemoglobin in blood cells cannot carry enough oxygen, hydrogen bonds begin to break in proteins; person may become comatose & die

• Alkalosis – increase in blood pH above 7.45; may be life threatening if pH rises above 7.8 for more than a few hours

Metabolic Acidosis – excess of any acid except H2CO3

Causes:Excess Acid OR Loss of BaseDiabetic ketoacidosis vomitingStarvation ketosis diarrheaLactic acidosisHigh K+ (Hyperkalemia)

Metabolic Alkalosis

Causes:

Too Little Acid OR Too Much Base

Vomiting Ingesting too much HCO3

Hypokalemia (K+ )

Respiratory Acidosis – excess CO2

Causes:

• Impaired gas exchange

• Impaired activity of diaphragm muscle

• Impaired respiratory control in brain stem

• emphysema

Respiratory Alkalosis – deficit of CO2 Causes – Hyperventilation

1. low levels of O2 in plasma

2. Meningitis – stimulation of brain stem3. Head injury4. severe anxiety

Symptoms:• Sweating, numbness, tingling, dizziness, confusion,

• Cerebral vasal constriction – seizures, coma

Controlling Body pH• Chemical Buffers

– Acts within seconds but with limited capacity

• Respiratory Control– Acts within minutes – Compensates for metabolic acidosis & alkalosis

• Renal Mechanisms– Acts in hours or days– Compensates for respiratory acidosis & alkalosis

Compensation Equation

CO2 + H2O H2CO3 HCO3 + H

(carbonic acid) (carbonate)

Organic Compounds

• Molecules unique to living systems contain carbon and hence are organic compounds

• They include:– Carbohydrates

– Lipids

– Proteins

– Nucleic Acids

Carbohydrates - class of molecules ranging from small sugar molecules to large polysaccharides

• Organic molecules unique to living systems that contain carbon, hydrogen, and oxygen in the ratio described by their name - carbo (carbon) and hydrate (H2O) = CH2O

• Their major function is to supply a source of cellular food

May be divided into three groups by size

1) monosaccharides - simplest; monomer, contains one sugar molecule; many form ring-shaped molecules in solution

• Many are structural isomers of each other – glucose, galactose, and fructose have the same molecular formula, but different structural arrangements.

• Glucose = blood sugar, universal cellular fuel

• Ribose & deoxyribose – part of RNA and DNA

Pharmaceutical companies must understand and appropriately deal with isomers

• Isomers – same chemical formula but different structural arrangements of the atoms

• Enantiomers – isomers which are mirror images of each other; L (levo-) and D (dextro)

- cells and tissues will typically respond to only one structural form – L or D - but not both

- our cells can only metabolize L-glucose as an energy source although both forms are present

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• Chloramphenicol – antibiotic which contains both L- and D- isomers; only L- form is effective in killing bacterial pathogens

• Ephedrine – bronchiolar dilator used for asthma patients; L- form is active, D- form is inactive

• Thalidomide – both L- and D- forms are biologically active but in different ways

- drug given to expectant women for severe nausea

- medication contained both forms; one stopped nausea, one caused abnormalities in fetal limb development

2) disaccharides - composed of two monosaccharides by dehydration synthesis in the cells; ex: glucose + fructose = sucrose

- sucrose = glucose-fructose = cane sugar- lactose = glucose-galactose = milk sugar- maltose – glucose-glucose = malt sugar

• Double sugar are too large to pass through cell membranes, they must be digested (broken down by hydrolysis) to monosaccharides to be absorbed from the digestive tract into the blood

• Disaccharides or double sugars

Figure 2.14b

Disaccharides

dehydration synthesis - molecules synthesized by loss of a water molecule between reacting monomers; most

common way to synthesize organic polymers

• Hydrolysis - “breaking apart with water”; the way most organic polymers are degraded

Carbohydrates

3) polysaccharides - long chains of sugar units; glucose is the monomer for many polysacchaarides- considered to be ideal storage molecules because they are not soluble in water

• Starch and glycogen are the two polysaccharides of importance in the body- starch - found in plants for long-term energy storage; long, unbranched, helical polymer of covalently bonded glucose monomers; may be ingested as “starchy” foods such as grain products and root vegetables

Figure 2.14c

- glycogen - similar to starch but is slightly smaller and has more side branches; used for long-term storage in the muscles and liver of animals

- liver and muscles store excess glucose from the blood in the form of glycogen; during fasting or prolonged exercise, the liver adds glucose to the blood through hydrolysis of stored glycogen

Highly branched glycogen

Lipids - diverse nonpolar compounds consisting mainly of carbon and hydrogen (few oxygen); hydrophobic

• Lipids are insoluble in water but dissolve readily in nonpolar solvents

• Most abundant and concentrated source of usable energy• Enter the body in the form of fat-marbled meats, egg yolks, milk

products, and oils• Stored in fat deposits beneath the skin and around body organs;

may help to insulate the body and protect deeper body tissues from heat loss and bumps

Lipids• Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates

• Examples:– Neutral fats or triglycerides - known as fats when solid and

oils when liquid

– Phospholipids - diglycerides with a phosphorus-containing group and two fatty acid chains Steroids

– Steroids - flat molecules made up of four interlocking hydrocarbon rings

– Eicosanoids - group of diverse lipids derived from arachidonic acid

The three most abundant lipids in the body are triglycerides, phospholipids, and steroids

1. Neutral Fats (Triglycerides) - energy storage molecules; most are hydrophobic; contain 3 fatty acids and 1 glycerol

– found in subcutaneous tissue and around organs

Figure 2.15a

- saturated fats - no double bonds between carbons (carbons are “saturated” with hydrogen atoms); backbones are flexible and tend to ball up into tight globules; solid at room temperature; lead to atherosclerotic plaques

- unsaturated fats - many double bonds between carbons; causes molecules to be less flexible; do not pack into solid globules; most are liquid at room temperature

-Trans-fatty acids have straightened double bonds and thus act like saturated fat.

Saturated and Unsaturated triglycerides

health authorities recommend that total fat intake not exceed 30% of the total energy intake per day and that saturated fat contribute less than 10% of that total

2) phospholipids - major component of cell membranes; 1 glycerol + 2 fatty acids + 1 phosphate group; hydrophobic “tail” and hydrophilic “head”

Figure 2.15b

- important physiological functions include their role as the major

component of the cell membrane which allows the cell to be selective about what may enter or leave, and their ability to decrease surface tension of water (surfactant – surface –active agent) – important in preventing the collapse of the lungs

3) steroids – flat lipids with backbones bent into rings

- cholesterol is a steroid formed by animals & functions in the digestion of fats and in the synthesis of hormones produced by the testes, ovaries, and adrenal cortex

- testes and ovaries (gonads) secrete sex steroids

- ovaries produce progesterone and estradiol

- testes produce testosterone - adrenal cortex produces corticosteroids

– Other Steroids include – bile salts, vitamin D

anabolic steroids - synthetic steroids which resemble & mimic the male hormone testosterone; causes buildup of muscle and bone mass, bloating of face, violent mood swings, deep depressions, liver damage leading to cancer, reduced sex drive, cardiovascular problems, infertility due to reduced output of natural sex hormones, etc.

Example of Anabolic Steroid UseTetrahydrogestrinone (THG)

For a time, THG was considered the drug of choice for safe and "invisible" world record breaking in athletics, being used by several high profile gold medal winners such as the sprinter Marion Jones, who resigned from her athletic career in 2007 after admitting to using THG prior to the 2000 Sydney Olympics, where she had won three gold medals

Marion Jones

Comparison of Cholesterol to Hormones

Table 2.2.2

Other Lipids

Proteins – very large biological polymer constructed from amino acid monomers

• Account for over 50% of the organic matter in the body, and have the most varied functions

- structural (cytoskeleton, hair, collagen) - contractile (muscle)- storage (egg whites store AA)- defense (antibodies, membranes)- signaling (hormones)- catalyst (enzymes)- receptors (for hormones)- carriers (transport across membranes)

Proteins - made from 20 kinds of amino acids

• The 20 different amino acids each have their own particular properties

• amino acids are characterized by each having an alpha (central) carbon atom covalently bonded to one hydrogen, one amino group, one carboxyl group, and one other chemical group (R group)

• Differences in the Rgroup makes eachamino acid unique

Amino Acids

Figure 2.16a–c

Amino Acids

Figure 2.16d, e

Amino acids are linked together by peptide bonds

• Using amino acids as monomers, organisms build polymers by dehydration synthesis, forming peptide bonds between each monomer

- peptide bond = covalent bond in proteins- polypeptide = protein

• protein peptide bonds can be broken down by hydrolysis to release free amino acids

Construction of Proteins

Figure 2.17

Amino acid Amino acid

Dehydrationsynthesis

Hydrolysis

Dipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH


Figure 2.17


+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O

OH OH


Figure 2.17



+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

OH OH


Figure 2.17



Dipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH

Decomposition of Proteins

Figure 2.17

Dipeptide

Peptide bond

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH


Figure 2.17

Hydrolysis

Dipeptide

Peptide bond

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH


Figure 2.17


Hydrolysis

Dipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH

Reversible Reactions of Proteins

Figure 2.17



Hydrolysis

Dipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH

Protein’s specific shape determines its function

• Long polypeptide chains (may contain thousands of amino acids) are composed of only 20 different amino acids

• the final structure of a protein depends on the way these long, linear molecules fold up

- each collection of amino acids folds in a different way under natural conditions

- unnatural conditions cause proteins to unravel (denature) and become ineffective; (changes in heat, pH, saltiness, etc.)

Four levels of protein structure - determine the shape of protein; determines role of protein

1) primary structure - the amino acid sequence; three-letter abbreviations represent amino acids; each amino acid is in a precise order in the protein chain

PLAY Chemistry of Life: Proteins: Primary Structure

2) secondary structure - polypeptide coiling or folding produced by hydrogen bonding

- hydrogen bonds occur between -NH and -C=O groups of amino acids- secondary structure takes shape of a coil (alpha helix) or pleated sheet

PLAYChemistry of Life: Proteins: Secondary Structure

Structural Levels of Proteins

Figure 2.18a–c

3) tertiary structure - the overall shape of a polypeptide resulting

from the bonding (hydrogen and ionic) between certain R groups along the coils and pleats

Chemistry of Life: Proteins: Tertiary Structure

4) quaternary structure - relationship among multiple polypeptides of a protein; several tertiary proteins (usually identical) bonded together in a precise pattern by hydrogen bonding

Structural Levels of Proteins

Figure 2.18b,d,e

Fibrous and Globular Proteins• Fibrous proteins

– Extended and strand-like proteins – known as structural proteins and most have only secondary

structure – Examples: keratin, elastin, collagen, and certain contractile fibers

• Globular proteins – Compact, spherical proteins with tertiary and quaternary

structures– water soluble, chemically active molecules, and play an important

role in vital body functions – Examples: antibodies, hormones, and enzymes

• Fibrous proteins are stable but globular proteins are susceptible to denaturing, losing their shape due to breaking of their hydrogen bonds

Protein Denaturation

• Reversible unfolding of proteins due to drops in pH and/or increased temperature

Figure 2.19a

Protein Denaturation

• Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes

Figure 2.19b

Molecular Chaperones (Chaperonins)

• Help other proteins to achieve their functional three-dimensional shape

• Maintain folding integrity• Assist in translocation of proteins across membranes• Promote the breakdown of damaged or denatured

proteins

Enzymes – functional proteins that act as biological catalysts

• Catalyst – chemical that increases the rate of a chemical reaction without becoming part of the product or being changed itself; speed up chemical reactions up to 100,000x

• Without enzymes, biochemical reactions would occur too slowly to sustain life

• Very specific in their activities – most only control one (or a small group of) chemical reaction

• Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion)

Characteristics of Enzymes• Frequently named for the type of reaction they catalyze• Enzyme names usually end in -ase• Lower activation energy

Mechanism of Enzyme Action• Enzyme binds with substrate

• Product is formed at a lower activation energy

• Product is released

Figure 2.21

Active siteAmino acids

Enzyme (E)Enzyme-substratecomplex (E-S)

Internal rearrangementsleading to catalysis

Dipeptide product (P)

Free enzyme (E)

Substrates (S)

Peptide bond

H2O

+

Figure 2.21



Substrates (S)

H2O

+

Figure 2.21




Substrates (S)

H2O

+

Figure 2.21




Dipeptide product (P)

Free enzyme (E)

Substrates (S)

Peptide bond

H2O

+

CPK – creatine phosphokinase

• Enzyme which is released into the blood by damaged cells

• Blood tests used to detect the presence of CPK are used to identify individuals with damaged heart, skeletal, or brain tissue

Nucleic Acids• Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus and are the largest molecules in the

body • Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate

group• Five nitrogen bases contribute to nucleotide structure – adenine (A), guanine (G), cytosine (C), thymine

(T), and uracil (U)• Two major classes – DNA and RNA

Deoxyribonucleic Acid (DNA)

• Genetic material of the cell

• Double-stranded helical molecule found in the nucleus of the cell

• Replicates itself before the cell divides, ensuring genetic continuity

• Provides instructions for protein synthesis



Figure 2.22b-c: Structure of DNA, p. 56.

(b)

A

A

G

A

T

T

T

C

G C

G C

A

A

G

G

A

(c)

Thymine (T)

Adenine (A)

Cytosine (C)

Guanine (G)

Deoxyribosesugar

Phosphate

Hydrogen bond

Key:

Sugar-phosphatebackbone

Ribonucleic Acid (RNA)

• Single-stranded molecule found in both the nucleus and the cytoplasm of a cell

• Used to make proteins using the instructions provided by the DNA

• Uses the nitrogenous base uracil instead of thymine• Three varieties of RNA: messenger RNA, transfer RNA,

and ribosomal RNA

ATP – adenosine triphosphate – universal energy carrier

• Provides a form of chemical energy that is usable by all body cells

• “fuel” for body cells comes from lipids, carbohydrates, and proteins, but energy from these cannot be directly used by the cells

• Energy released as these molecules are catabolized is captured and stored in the bonds of ATP molecules as small “packets” of energy

Adenosine Triphosphate (ATP)

Figure 2.23

• Phosphate groups are connected by high energy bonds• Energy released from the hydrolysis of high-energy phosphate

bonds may be used to power cell processes

Figure 2.24

Solute Solute transported

Contracted smoothmuscle cell

Product made

Relaxed smoothmuscle cell

Reactants

Membraneprotein

P Pi

ATP

PX X

Y

Y

+

(a) Transport work

(b) Mechanical work

(c) Chemical work

Pi

Pi

+ADP

Figure 2.24

Solute

Membraneprotein

P

ATP

(a) Transport work

Figure 2.24


Membraneprotein

P Pi

ATP

(a) Transport work

Pi

+ADP

Figure 2.24


ATP

(b) Mechanical work

Figure 2.24



ATP

(b) Mechanical work

Pi

+ADP

Figure 2.24

Reactants

ATP

PX

Y+

(c) Chemical work

Figure 2.24

Product madeReactants

ATP

PX X

Y

Y

+

(c) Chemical work

Pi

Pi

+ADP

Figure 2.24



Product made


Reactants

Membraneprotein

P Pi

ATP

PX X

Y

Y

+

(a) Transport work

(b) Mechanical work

(c) Chemical work

Pi

Pi

+ADP

chemistry comes alive

Documents

higher h concentration

lower h concentration

patterns of chemical

equal h

protons h

faster reactions catalysts

higher ph neutral solutions

exchange reaction