1

Chapter 2:

The Chemical Level of Organization

2

Introduction to Chemistry

• Matter is made up of atoms• Atoms join together to form

chemicals with different characteristics

• Chemical characteristics determine physiology at the molecular and cellular level

3

Atomic Particles

• Proton: – positive, 1 mass unit

• Neutron: – neutral, 1 mass unit

• Electron: – negative, low mass

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Particles and Mass

• Atomic number: – number of protons

• Mass number: – number of protons plus neutrons

• Atomic weight: – exact mass of all particles (daltons)

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Isotopes

• 2 or more elements with equal numbers of protons but different numbers of neutrons

Electron shell

p+ p+

p+n

n

n

e e e

(a) Hydrogen-1(electron-shell model)

(b) Hydrogen-2 deuterium

(c) Hydrogen-3, tritium

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Elements in the Human Body

Table 2–1

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How do atoms form molecules and compounds?

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Molecules and Compounds

• Molecules: – atoms joined by strong bonds

• Compounds: – atoms joined by strong or weak bonds

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Chemical Bonds

• Ionic bonds: – attraction between cations (+) and anions

(-)• Covalent bonds:

– strong electron bonds– Non polar covalent bonds: equal sharing of

electrons– Polar covalent bonds: unequal sharing of

electrons• Hydrogen bonds:

– weak polar bonds

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Ionic Bonds

Figure 2–3a

Are atoms with positive or negative charge

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Covalent Bond

• Formed between atoms that share electrons

Hydrogen(H2)

Oxygen(O2)

CarbonDioxide

(CO2)

NitricOxide(NO)

MoleculeElectron-Shell Model and

Structural Formula

H–H

O=O

N=O

O=C=O

Free Radicals:Ion or molecule that contain unpaired electrons in the outermost shell. - Extremely Reactive -Typically enter into destructive reactions -Damage/destroy vital compounds

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Hydrogen Bonds

• Attractive force between polar covalent molecules

• Weak force that holds molecules together

• Hydrogen bonds between H2O molecules cause surface tension

Figure 2–6

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How is it possible for two samples of hydrogen to contain the same

number of atoms, yet have different weights?

A. One sample has more bonds.

B. One sample contains fewer electrons, decreasing weight.

C. One sample contains more of hydrogen’s heavier isotope(s).

D. One sample includes more protons, increasing weight.

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Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does

not. Why?

A. Neon has 8 electrons in its valence shell, oxygen has only 6.

B. Neon cannot undergo bonding due to its polarity.

C. Neon is exergonic.D. Neon’s molecular

weight is too low to allow bonding.

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Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does

not. Why?

A. Neon has 8 electrons in its valence shell, oxygen has only 6.

B. Neon cannot undergo bonding due to its polarity.

C. Neon is exergonic.D. Neon’s molecular

weight is too low to allow bonding.

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Which kind of bond holds atoms in a water molecule together?

What attracts water molecules to one another?

A. polar covalent bonds; hydrogen bonds

B. ionic bonds; charge interactions

C. hydrogen bonds; charge interactions

D. covalent bonds; hydrogen bonds

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Why are chemical reactions important to

physiology?

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Energy

• Energy: – the capacity to do work

• Work: – a change in mass or distance

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Forms of Energy

• Kinetic energy: – energy of motion

• Potential energy: – stored energy

• Chemical energy: – potential energy stored in chemical bonds

When energy is exchanged, heat is produced - cells cannot capture it or use it for work

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Break Down, Build Up

• Decomposition reaction (catabolism): AB A + B• Synthesis reaction (anabolism): A + B AB• Exchange reaction (reversible): AB + CD AD + CBIf Water is Involved:• Hydrolysis:

A—B—C—D—E + H2O A—B—C—H + HO—D—E

• Dehydration synthesis (condensation):A—B—C—H + HO—D—E A—B—C—D—E

+ H2O

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KEY CONCEPT

• Reversible reactions seek equilibrium, balancing opposing reaction rates

• Add or remove reactants:– reaction rates adjust to reach a new

equilibrium

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How do enzymes control metabolism?

23Figure 2–7

Activation Energy

• Chemical reactions in cells cannot start without help

• Activation energy gets a reaction started

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Materials in Reactions

• Reactants: – materials going into a reaction

• Products: – materials coming out of a reaction

• Enzymes: – proteins that lower the activation

energy of a reaction

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Energy In, Energy Out

• Exergonic reactions: – produce more energy than they use– Heat will be the by-product

• Endergonic reactions: – use more energy than they produce

• Most chemical reactions that sustain life cannot occur unless the right enzymes are present

26

In cells, glucose, a six-carbon molecule, is converted into two three-carbon molecules by a reaction that

releases energy. How would you classify this reaction?

A. endergonicB. exergonicC. decompositionD. B and C

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In cells, glucose, a six-carbon molecule, is converted into two three-carbon molecules by a reaction that

releases energy. How would you classify this reaction?

A. endergonicB. exergonicC. decompositionD. B and C

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Why are enzymes needed in our cells?

A. to promote chemical reactionsB. for chemical reactions to proceed under conditions compatible with lifeC. to lower activation energy requirementsD. all of the above

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What is the difference between organic and inorganic compounds?

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Organic and Inorganic Molecules

• Organic: – molecules based on carbon and

hydrogen

• Inorganic: – molecules not based on carbon and

hydrogen

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Essential Molecules

• Nutrients: – essential molecules obtained from

food

• Metabolites: – molecules made or broken down in

the body

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Why is water so important to life?

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Properties of Water• Solubility:

– water’s ability to dissolve a solute in a solvent to make a solution

• Reactivity: – most body chemistry uses or occurs in water

• High heat capacity: – water’s ability to absorb and retain heat

• Lubrication: – to moisten and reduce friction

Water is the key structural and functional component of cells and their control mechanisms, the nucleic acids

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Aqueous Solutions

Figure 2–8

Polar water molecules form hydrationspheres around ions and small polar molecules to keep them in solution

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Electrolytes

• Inorganic ions: conduct electricity in solution

• Electrolyte imbalance seriously disturbs vital body functions

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Molecules and Water

• Hydrophilic: – hydro = water, philos = loving– reacts with water

• Hydrophobic:– phobos = fear– does not react with water

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Solutions

• Suspension: – a solution in which particles settle

(sediment)

• Concentration: – the amount of solute in a solvent

(mol/L, mg/mL)

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What is pH and why do we need buffers?

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pH: Neutral, Acid, or Base?

• pH: – the concentration of hydrogen ions (H+) in a

solution• Neutral pH:

– a balance of H+ and OH— – pure water = 7.0

• Acid (acidic): pH lower than 7.0 – high H+ concentration,

low OH— concentration• Base (basic): pH higher than 7.0

– low H+ concentration, high OH— concentration

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pH Scale

Figure 2–9

• Has an inverse relationship with H+ concentration: – more H+ ions mean lower pH, less H+

ions mean higher pH

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KEY CONCEPT

• pH of body fluids measures free H+ ions in solution

• Excess H+ ions (low pH): Acidosis– damages cells and tissues– alters proteins– interferes with normal physiological functions

• Excess OH— ions (high pH): Alkalosis – Uncontrollable and sustained skeletal muscle

contractions

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Controlling pH

• Salts: – positive or negative ions in solution– contain no H+ or OH— (NaCl)

• Buffers: – weak acid/salt compounds– neutralizes either strong acid or

strong base

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Why does a solution of table salt conduct electricity, but a sugar

solution does not?

A. Electrical conductivity requires ions.

B. Sugar forms a colloid, salt forms a suspension.

C. Electricity is absorbed by glucose molecules.

D. Table salt is hydrophobic, sugar is hydrophilic.

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How does an antacid help decrease stomach discomfort?

A. by reducing buffering capacity of the stomach

B. by decreasing pH of stomach contents

C. by reacting a weak acid with a stronger one

D. by neutralizing acid using a weak base

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What kinds of organic compounds are there, and how do they work?

Organic Compounds

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Functional Groups of Organic Compounds

Table 2–4

• Molecular groups which allow molecules to interact with other molecules

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Carbohydrates

• Consist of C:H:O in 1:2:1 ratio1. Monosaccharides:

– simple sugars with 3 to 7 carbon atoms (glucose)• Glucose: important metabolic fuel

2. Disaccharides: – 2 simple sugars condensed by

dehydration synthesis (sucrose)

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Simple Sugars

Figure 2–10

Structural Formula:• Straight-chain form• Ring from• 3-D

Isomers: Glucose vs. Fructose: - Same chemical formula but different shape

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Polysaccharides

• Chains of many simple sugars (glycogen)

• Formation:– Dehydration

synthesis

• Breakdown:– Hydrolysis synthesis

Figure 2–12Glycogen: made and stored in muscle cells

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Carbohydrate Functions

Table 2–5

PolysaccharidesGlycogen: made and stored in muscle cellsCellulose: structural component of plants -Ruminant Animals: Cattle, sheep, and deerCattle, sheep, and deer

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The Ruminant StomachRuminant stomach is polygastric: four compartments

-Rumen -Reticulum

-Abomasum -Omasum

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RumenOccupies 80% of the stomach

Muscular PillarContract to mix feed

Digest starch and fibersMicrobes produce VFA’s

Lined with Papillae

pH of 5.8-7.0Provide a suitable environment for bacteria and protozoa

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KEY CONCEPT

• Carbohydrates are quick energy sources and components of membranes

• Lipids have many functions, including membrane structure and energy storage– Provides 2x more energy then

carbohydrates

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Lipids

• Mainly hydrophobic molecules such as fats, oils, and waxes

• Made mostly of carbon and hydrogen atoms (1:2), and some oxygen– Less oxygen then carbon

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Classes of Lipids

• Fatty acids• Eicosanoids• Glycerides• Steroids• Phospholipids and glycolipids

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Fatty Acids

• Carboxyl group -COOH– Hydrophilic

• Hydrocarbon tail:– Hydrophobic– Longer tail = lower solubility

• Saturated vs. Unsaturated– Saturated: solid at room temp.

• Cause solid plaques in arteries

– Unsaturated: liquid at room temp.

• Healthier

Figure 2–13

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Eicosanoids

• Used for cellular communication • Never burned for energy1. Leukotrienes:

– active in immune system– Used by cells to signal injury

2. Prostaglandins: local hormones– Used for cell-to-cell signaling to

coordinate events

58Figure 2–16

Steroids

• 4 carbon ring with attached carbon chains

• Not burned for energy

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Types of Steroids

• Cholesterol: – cell membrane formation and maintenance,

cell division, and osmotic stability

• Estrogens and testosterone: – Regulation of sexual function

• Corticosteroids and calcitrol: – Tissue metabolism and mineral balance

• Bile salts: – Processing of dietary fats

60Figure 2–15

Glycerides

• Glycerides: are the fatty acids attached to a glycerol molecule

• Triglyceride: are the 3 fatty-acid tails, fat storage molecule

Fat Deposits are Important1. Energy Storage2. Insulation3. Mechanical Protection

-Knees and Eye Sockets

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Phospholipids Vs. GlycolipidsCombination Lipids

Figure 2–17a, b

Diglyceride

Cell Membranes are Composed of these lipids

Hydrophilic

Hydrophobic

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Phospholipids Vs. GlycolipidsCombination Lipids

Figure 2–17c

Spontaneous formation of Micelle

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5 Lipid Types

Table 2–6

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A food contains organic molecules with the elements C, H, and O in a

ratio of 1:2:1. What class of compounds do these molecules

belong to, and what are their major functions in the body?

A. lipids; energy sourceB. proteins; support and

movementC. nucleic acids; determining

inherited characteristicsD. carbohydrates; energy

source

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When two monosaccharides undergo a dehydration synthesis

reaction, which type of molecule is formed?

A. polypeptideB. disaccharideC. eichosanoidD. polysaccharide

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Which kind of lipid would be found in a sample of fatty

tissue taken from beneath the skin?

A. eichosanoidB. steroidC. triglycerideD. phospholipid

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Which lipids would you find in human cell membranes?

A. cholesterolB. glycolipidsC. phospholipidsD. all of the above

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Protein Structure

• Proteins are the most abundant and important organic molecules

• Basic elements: – carbon (C), hydrogen (H), oxygen (O),

and nitrogen (N) • Basic building blocks:

– 20 amino acids

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Protein Functions

• 7 major protein functions:– support: structural proteins– movement: contractile proteins– transport: transport proteins– buffering: regulation of pH– metabolic regulation: enzymes– coordination and control: hormones– defense: antibodies

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Proteins

• Proteins: – control anatomical structure and

physiological function– determine cell shape and tissue

properties– perform almost all cell functions

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Amino Acid Structure

1. central carbon2. hydrogen3. amino group (—

NH2)

4. carboxylic acid group (—COOH)

5. variable side chain or R group

Figure 2-18

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Peptide Bond

• A dehydration synthesis between:– amino group of 1 amino acid– and the carboxylic

acid group of another amino acid

– producing a peptide

73Figure 2–20a

Primary Structure

• Polypeptide:– Linear sequence of amino acids

• How many amino acids were bound together

• What order they are bound

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Secondary Structure

Figure 2–20b

• Hydrogen bonds form spirals or pleats

75Figure 2–20c

Tertiary Structure

• Secondary structure folds into a unique shape

• Global coiling or folding due to R group interaction

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Quaternary Structure

Figure 2–20d

• Final protein shape: – several tertiary structures together

Fibrous proteins: - structural sheets

Globular proteins: - soluble spheres with active functions

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Shape and Function

• Protein function is based on shape• Shape is based on sequence of

amino acids• Denaturation:

– loss of shape and function due to heat or pH

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Enzymes

• Enzymes are catalysts: – proteins that lower the activation

energy of a chemical reaction – are not changed or used up in the

reaction

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How Enzymes Work

Figure 2–21

Substrates: reactants in enzymatic reactionsActive site: location on an enzyme that fits a particular substrate

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Enzyme Helpers

• Cofactor: – an ion or molecule that binds to an

enzyme before substrates can bind• Coenzyme:

– nonprotein organic cofactors (vitamins)

• Isozymes: – 2 enzymes that can catalyze the

same reaction

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Enzyme Characteristics

• Specificity: – one enzyme catalyzes one reaction

• Saturation limits: – an enzyme’s maximum work rate

• Regulation: – the ability to turn off and on

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Conjugated Protein

• Glycoproteins: – large protein + small carbohydrate

• includes enzymes, antibodies, hormones, and mucus production

• Proteoglycans: – large polysaccharides + polypeptides

• promote viscosity

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Proteins are chains of which small organic molecules?

A. saccharidesB. fatty acidsC. amino acidsD. nucleic acids

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Which level of protein structure would be affected by an agent that breaks hydrogen bonds?

A. the primary level of protein structure

B. the secondary level of protein structure

C. the tertiary level of protein structure

D. the protein structure would NOT be affected by this agent

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Why does boiling a protein affect its structural and functional

properties?

A. Heat denatures the protein, causing unfolding.

B. Heat causes the formation of additional quaternary structure.

C. Heating rearranges the primary structure of the protein.

D. Heat alters the radical groups on the amino acids.

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Why does boiling a protein affect its structural and functional

properties?

A. Heat denatures the protein, causing unfolding.

B. Heat causes the formation of additional quaternary structure.

C. Heating rearranges the primary structure of the protein.

D. Heat alters the radical groups on the amino acids.

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How might a change in an enzyme’s active site affect its

functions?

A. increased activity due to a better fit with the substrate

B. decreased activity due to a poor substrate fit

C. inhibited activity due to no substrate fit

D. all of the above

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Nucleic Acids

• C, H, O, N, and P• Large organic molecules, found in the

nucleus, which store and process information at the molecular level

• DNA – deoxyribonucleic acid• RNA – ribonucleic acid

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DNA and RNA

DNA• Determines inherited characteristics• Directs protein synthesis• Controls enzyme production• Controls metabolismRNA• Codes intermediate steps in protein

synthesis

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KEY CONCEPT

• DNA in the cell nucleus contains the information needed to construct all of the proteins in the body

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Nucleotides

• Are the building blocks of DNA• Have 3 molecular parts:

– sugar (deoxyribose)– phosphate group– nitrogenous base (A, G, T, C)

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The Bases

Figure 2–22b, c

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Complementary Bases• Purines pair with pyrimidines:

• DNA: – adenine (A) and thymine (T) – cytosine (C) and guanine (G)

• RNA: – uracil (U) replaces thymine (T)

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RNA and DNA

• RNA: – a single strand

• DNA: – a double helix joined at bases by

hydrogen bonds

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Protein Synthesis:Three forms of RNA

• messenger RNA (mRNA)– Protein blueprint or instructions

• transfer RNA (tRNA)– Carry amino acids to the place where

proteins are being synthesized

• ribosomal RNA (rRNA)– Forms the site of protein synthesis in the

cell• Factory = ribosomes

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High-Energy Compounds:ADP and ATP

- Assembled using RNA Nucleotides- Bonds are broken easily by cells to

release energy as needed- During digestion and cellular

respiration: - energy from food is transferred to high

energy compounds for quick and easy access.

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ADP to ATP:Phosphorylation

ADP vs. ATP:• adenosine diphosphate (ADP):

– 2 phosphate groups (di = 2)• adenosine triphosphate (ATP):

– 3 phosphate groups (tri = 3)Adding a phosphate group to ADP with a

high-energy bound to form the high-energy compound ATP

• ATPase: – the enzyme that catalyzes phophorylation

98Figure 2–24

The Energy Molecule

• Chemical energy stored in phosphate bonds

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A large organic molecule composed of the sugar ribose,

nitrogenous bases, and phosphate groups is which kind

of nucleic acid?

A. DNAB. ATPC. tRNAD. RNA

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What molecule is produced by the phosphorylation of ADP?

A. ATPaseB. ATPC. Adenosine DiphosphateD. Uridine Triphosphate

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Compounds Important to Physiology

Table 2–8

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SUMMARY

• Atoms, molecules, and chemical bonds control cellular physiology

• Metabolism and energy work within the cell

• Importance of organic and inorganic nutrients and metabolites

103

SUMMARY

• Role of water and solubility in metabolism and cell structure

• Chemistry of acids and bases, pH and buffers

• Structure and function of carbohydrates, lipids, proteins, and nucleic acids