Chapter 2Chapter 2

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Dee Unglaub Silverthorn, Ph.D.

H ^UMAN P ^HYSIOLOGY H ^UMAN P ^HYSIOLOGY

PowerPoint^® Lecture Slide Presentation by

Dr. Howard D. Booth, Professor of Biology, Eastern Michigan University

AN INTEGRATED APPROACH

T H I R D E D I T I O N

Chapter 2 Chapter 2

Atoms, Ions, and Molecules

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About this Chapter About this Chapter

• Make up of atoms, ions, & molecules

• Bonds combine atoms, form molecules

• Concentrations

• Biomolecules

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• Structure of an atom

• Protons

• Electrons

• Neutrons

• Mass

• Charge

• Nucleus

• Electron orbitals

• Elements

• Essential & trace elements

Atoms and Elements Atoms and Elements

Figure 2-1: Atomic structure

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All the Elements

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Elements of the Body

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Elements other than C, H, O and N in Humans Elements other than C, H, O and N in Humans

• Primary Elements (3% of all body weight)

• Calcium Ca Bones, teeth, muscle and nerve action, blood clotting

• Phosphorus P Bones and Teeth, DNA, RNA, ATP. Important in

• energy transfer

•

• Trace Elements (Less than 1 % of body weight altogether)

• Potassium K Osmotic balance; cell voltage, muscle and nerve

• action

• Sulfur S Component of proteins (cysteine) and other organic

• molecules

• Sodium Na Osmotic balance; cell voltage, muscle and nerve

• action

• Chlorine Cl Osmotic balance; cell voltage, muscle and nerve

• action

• Magnesium Mg Co-factor for many enzymes

• Iron Fe Hemoglobin and many enzymes

• Copper Cu Co-factor of many enzymes

• Zinc Zn Co-factor of many enzymes

• Manganese Mn Co-factor of many enzymes

• Cobalt Co Co-factor of many enzymes and vitamin B12

• Chromium Cr Co-factor of many enzymes and potentiates Insulin

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• Ions have charge

• Cations +

• Anions -

• Isotopes vary mass

• Neutrons

• Radioisotopes

• Unstable nuclei

• Emit energy -radiation

• Medical uses as tracers Ions and Isotopes

Ions and Isotopes

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Ions and Isotopes

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• Common in biosystems

• Carbon (C)

• Oxygen (O)

• Hydrogen (H)

Molecules and Compounds Molecules and Compounds

Figure 2-6: Electron configuration of the three most common elements in the body

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Oxygen Oxygen

• Oxygen is a highly reactive nonmetallic element. As such, it readily forms

compounds (notably oxides) with almost all other elements.

• Oxygen is a strong oxidizing agent and has the second-highest electronegativity of all reactive elements, second only to fluorine.

• Oxygen can be toxic, especially at high partial pressures. The biochemical basis for the toxicity of oxygen is the partial

reduction of oxygen by one or two

electrons to form reactive oxygen species

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Bonds and Energy Changes Bonds and Energy Changes

During a chemical reaction:

•Bonds in the reactants are broken

•New bonds are made in the products

•Energy is absorbed to break bonds. Bond-breaking is an endothermic process.

•Energy is released when new bonds form. Bond-making is an exothermic process.

•Whether a reaction is endothermic or exothermic depends on the difference between the energy needed to break bonds and the energy released when new bonds form. If more heat energy is released when making the bonds than was taken in when they broke, the reaction is exothermic.

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• Catabolic reactions give out energy. They are exergonic. In a catabolic reaction large molecules are broken down into smaller

ones. For example, hydrolysis reactions, are

catabolic.

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Metabolism of Glucose Metabolism of Glucose

• Along metabolic pathways the energy content of the initial substrate (glucose) differs significantly from the energy content of the product (carbon dioxide and water). In thermodynamic terms the change in Gibbs free energy, deltaG, is quite large (negative value). If such a reaction would occur at once, the chemical energy contained in sugar would be converted to heat. Enzymes of metabolic pathways are able to capture this energy in small portions and store it in the form of internal high energy compounds drastically reducing the amount of energy lost as heat. Compare the caloric content of an ounce of bread to burning a small stick of wood (wood and starch contain the same energy-rich stuff - glucose). The heat of the flame represents the released energy.

• Converting glucose to carbon dioxide and water in one step has also one other important consequence; the reaction is irreversible due to a prohibitively large activation energy of converting carbon dioxide and water into sugar. Living organisms have evolved metabolic

pathways that allow at least partial reversibility of the conversion of such processes by providing many intermediate steps with

small Delta G values close to zero, i.e., near their chemical equilibrium.

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• Bonds capture energy

• Bonds link atoms

• Molecules

• Molecular weight

• Chemical formula

Molecules and Compounds Molecules and Compounds

Figure 2-7b: Chemical structures and formulas of some biological molecules

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• Covalent bonds

• Common in biosystems

• Share a pair of electrons

• Ionic Bonds

• Transfer an electron

• Opposite charges attract

Types of Chemical Bonds

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Ionic Bonds and Ions Ionic Bonds and Ions

• Ionic Bonds and Ions

• Gain 1 positive charge for each electron lost

• Gain 1 negative charge for each electron gained

• Dissolve and

disassociate in polar solutions

• Important ions of

the body

Figure 2-9a : Ions and ionic bonds

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• Polarity of Molecules

• Partial charges on regions of molecule

• Soluble in polar solvents ( i. e.

H

2

O)

• Non polar molecules

• No regional

partial charges

• Do not dissolve easily in water

Figure 2-8: Water is a polar molecule

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Hydrogen Bonds (H-bonds) Hydrogen Bonds (H-bonds)

• Strong polarity

• Attracts to self

• Surface tension

• Form droplets

• Thin films

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• Hydrogen bonds

• Weak partial bonds

• Water surface tension

• Van der Waals forces - weak

Types of Chemical Bonds

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Hydrogen Bonds (H-bonds) Hydrogen Bonds (H-bonds)

Figure 2-10: Hydrogen bonds of water

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Solutions: Water is the main Solvent in Biosystems Solutions: Water is the main Solvent in Biosystems

• Solutes dissolve in liquids

• Solvents dissolve solutes

• Solution: solute dissolves in

solvent

• Solubility , ease of dissolving

• Hydrophobic

• Hydrophilic

Figure 2-11: Sodium chloride dissolves in water

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Ionic Bonds and Ions

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• Direct reactivity of a molecule

• Common

examples in biosystems

Functional Groups

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• Mole defined- 6.02 × 10

²³

atoms, ions or molecules of a substance

• Molarity–# of moles solute dissolved per liter of solution 1M NaCl = 58g NaCl + H2O up to 1 liter

• Molality–# of moles of solute dissolved in 1 Kg of solvent 1m NaCl = 58g NaCl + 1 Kg of H20

• Equivalents of an ion– equal to the molarity of ion times the number of charge of the ion

• Concentrations: Amount of Solute in a Solution

• Weight/volume- Milligrams or Grams solute/(ml, dL or Liter) solution , i.e. (mg/ml, mg/dL or grams/Liter)

• Volume/volume- 0.1% HCl= Add 0.1 ml of conc. Acid to water to give final volume of 100 ml.

• Percent solution- 5% glucose = 5 parts of solute (glucose) per 100 parts of total solution

Concentrations

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Hydrogen Ion Concentration (pH) in Biosystems Hydrogen Ion Concentration (pH) in Biosystems

• Acid - contributes H

+

to solution

(CO

2

+ H

2

O <=> H

2

CO

3

<=> H

⁺

+ HCO

_3-

)

• Base - decreases H

⁺

in solution ( NH

3

+ H

2

O <=> NH

4+

OH

^-

)

• Buffer minimizes changes of pH

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Hydrogen Ion Concentration (pH) in Biosystems Hydrogen Ion Concentration (pH) in Biosystems

Figure 2-12: pH scale

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• Complex carbohydrates: polymers (polysaccharides)

• "Simple sugars" monosaccharides (glucose, ribose)

Carbohydrate Biomolecules:

Carbon, Hydrogen & Oxygen Carbohydrate Biomolecules:

Carbon, Hydrogen & Oxygen

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Carbohydrate Biomolecules:

Carbon, Hydrogen & Oxygen Carbohydrate Biomolecules:

Carbon, Hydrogen & Oxygen

Figure 2-13-1: Carbohydrates

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Carbohydrate Biomolecules:

Carbon, Hydrogen & Oxygen Carbohydrate Biomolecules:

Carbon, Hydrogen & Oxygen

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Glycogen and Water weight Glycogen and Water weight

• A 70Kg person has about 1200 g of glycogen stored in their liver and muscle. Whenever a gram of glycogen is socked away in a muscle fiber or liver cell, three to four grams of water are

tucked in with it. This means, in effect, that if you’ve lost a pound of carbs from your body, a simple meal of a glass of water and just 100 grams of carbohydrate (just slightly more than one-fifth of a pound and a paltry 400 calories) could put that pound of weight right back. After all, 100 grams of

carbohydrate plus 350 grams (12 ounces) of H2O stored with the carbos adds up to 450 grams, or one pound. If this happens repeatedly to the poor soul who is trying to lose weight (and who may have initially rejoiced at the loss of a pound or two), he or she may deduce that PERMANENT weight loss is

impossible and give up the struggle.

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• Triglycerides: Glycerol,Fatty acid chains

• Eicosanoids, Steroids & Phospholipids

Lipids: Mostly Carbon and Hydrogen; little Oxygen

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Lipids: Mostly Carbon and Hydrogen; little Oxygen Lipids: Mostly Carbon and Hydrogen; little Oxygen

Figure 2-14: Lipids and lipid-related molecules

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The importance of selectively permeable membranes

•Membranes are physical barriers of cells and subcellular compartments controlling material exchange

between the internal environment and the extracellular environment

•A membrane is essentially a

hydrophobic permeability barrier consisting of phospholipids,

glycolipids, and membrane proteins

•Membranes contain amphipathic molecules such as phosphatidyl ethanolamine, an example of

phosphoglycerides, the major class of membrane phospholipids in most cells.

Polar

head Nonpolar

tail

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Omega 3 Fatty Acids Omega 3 Fatty Acids

Omega-3 fatty acids that are important in human physiology are α-linolenic acid (18:3, n-3; ALA), eicosapentaenoic acid (20:5, n-3; EPA), and

docosahexaenoic acid (22:6, n-3; DHA). These

three polyunsaturates have either 3, 5, or 6 double bonds in a carbon chain of 18, 20, or 22 carbon atoms, respectively. As with most naturally-

produced fatty acids, all double bonds are in the

cis-configuration ,

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Pathways in biosynthesis of eicosanoids from arachidonic acid:

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• Amino Acids:

essential, amino group, acid

group

• Protein

structure:

polypeptides, primary

-quaternary

Proteins: Amino acid polymers Proteins: Amino acid polymers

Figure 2-15: Amino acid structure

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• Lipoproteins (blood transport molecules)

• Glycoproteins (membrane structure)

• Glycolipids (membrane receptors) Combination Biomolecules

Combination Biomolecules

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• Composition

• Base

• Sugar

• Phosphate

• Transmit and store

• Information (genetic code)

• Energy transfer molecules

• ATP

• Cyclic AMP

• NAD & FAD

Nucleotides, DNA and RNA

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Nucleotides, DNA, and RNA Nucleotides, DNA, and RNA

Figure 2-18: RNA and DNA

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Visualization of DNA Double Helix

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Summary

• Epigenetics is the regulation of gene expression through alterations in DNA or associated factors (other than the DNA sequence).

• These factors control the diverse manifestations of diseases.

• Insights into epigenetic modification may lead to new therapies for common diseases.

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Chapter 2Chapter 2

H UMAN P HYSIOLOGY H UMAN P HYSIOLOGY

Chapter 2 Chapter 2

Atoms, Ions, and Molecules

About this Chapter About this Chapter

• Make up of atoms, ions, & molecules

• Bonds combine atoms, form molecules

• Concentrations

• Biomolecules

• Structure of an atom

• Protons

• Electrons

• Neutrons

• Mass

• Charge

• Nucleus

• Electron orbitals

• Elements

• Essential & trace elements

Atoms and Elements Atoms and Elements

All the Elements

All the Elements

Elements of the Body

Elements of the Body

Elements other than C, H, O and N in Humans Elements other than C, H, O and N in Humans

• Ions have charge

• Cations +

• Anions -

• Isotopes vary mass

• Neutrons

• Radioisotopes

• Unstable nuclei

• Emit energy -radiation

• Medical uses as tracers Ions and Isotopes

Ions and Isotopes

Ions and Isotopes

Ions and Isotopes

• Common in biosystems

• Carbon (C)

• Oxygen (O)

• Hydrogen (H)

Molecules and Compounds Molecules and Compounds

Oxygen Oxygen

• Oxygen is a highly reactive nonmetallic element. As such, it readily forms

compounds (notably oxides) with almost all other elements.

• Oxygen is a strong oxidizing agent and has the second-highest electronegativity of all reactive elements, second only to fluorine.

• Oxygen can be toxic, especially at high partial pressures. The biochemical basis for the toxicity of oxygen is the partial

reduction of oxygen by one or two

electrons to form reactive oxygen species

Bonds and Energy Changes Bonds and Energy Changes

During a chemical reaction:

• Catabolic reactions give out energy. They are exergonic. In a catabolic reaction large molecules are broken down into smaller

ones. For example, hydrolysis reactions, are

catabolic.

Metabolism of Glucose Metabolism of Glucose

• Bonds capture energy

• Bonds link atoms

• Molecules

• Molecular weight

• Chemical formula

Molecules and Compounds Molecules and Compounds

• Covalent bonds

• Common in biosystems

• Share a pair of electrons

• Ionic Bonds

• Transfer an electron

• Opposite charges attract

Types of Chemical Bonds

Types of Chemical Bonds

Ionic Bonds and Ions Ionic Bonds and Ions

• Ionic Bonds and Ions

• Gain 1 positive charge for each electron lost

• Gain 1 negative charge for each electron gained

• Dissolve and

disassociate in polar solutions

• Important ions of

the body

• Polarity of Molecules

• Partial charges on regions of molecule

• Soluble in polar solvents ( i. e.

H ^UMAN P ^HYSIOLOGY H ^UMAN P ^HYSIOLOGY