Human Anatomy & Physiology (Marieb, Hoehn): CHAPTER 2 - CHEMISTRY COMES ALIVE

Matter

Anything that has mass and occupies space (with some exceptions can be seen, smelled, felt)

States of matter:

1) Solid—definite shape and volume (i.e, bones, teeth)
2) Liquid—definite volume, changeable shape (i.e., blood plasma)
3) Gas—changeable shape and volume (i.e., air)

Solid (describe)

definite shape and volume

Liquid (describe)

definite volume, changeable shape

Gas (describe)

changeable shape and volume

Energy

Capacity to do work or put matter into motion (Energy may be converted from one form to another.
Conversion is inefficient because some energy is "lost" as heat.)

Types of energy:

1) Kinetic—energy in action
2) Potential—stored (inactive) energy

Kinetic energy is:

energy in action; works by moving objects which in turn can do work by moving or pushing on other objects (i.e., constant movement of atoms, a bouncing ball, swinging door)

Potential energy is:

stored (inactive) energy; has the potential to do work but is not currently doing so (i.e., batteries in an unused toy, your leg muscles when sitting still). WHEN POTENTIAL ENERGY IS RELEASED, IT BECOMES KINETIC ENERGY.

Chemical reactions underlie ALL physiological processes, including:

movement, digestion, the pumping of your heart, and even your thoughts.

Forms of energy (list)

1) Chemical energy—stored in bonds of chemical substances
2) Electrical energy—results from movement of charged particles
3) Mechanical energy—directly involved in moving matter
4) Radiant or electromagnetic energy—exhibits wavelike properties (i.e., visible light, ultraviolet light, and X-rays)

Chemical energy is:

the form stored in bonds of chemical substances

When chemical reactions occur that rearrange the atoms of chemicals in a certain way, the potential energy is unleased and becomes kinetic energy.

Electrical energy:

results from movement of charged particles

In your body, electrical currents are generated when charged particles called ions move along or across cell membranes. The nervous system uses electrical currents, called nerve impulses, to transmit messages from one part of the body to another.

Mechanical energy is:

energy directly involved in moving matter

When you ride a bike, your legs provide mechanical energy that moves the pedals.

Radiant or electromagnetic energy:

exhibits wavelike properties (i.e., visible light, ultraviolet light, and X-rays); collectively called the electromagnetic spectrum

Elements

unique substances that cannot be broken down into simpler substances by ordinary chemical methods (i.e., oxygen, carbon, gold, silver, copper, iron).

118 elements are recognized, 92 occur in nature

These FOUR elements make up about 96% of body weight:

1) Carbon
2) Oxygen
3) Hydrogen
4) Nitrogen

About 3.9% of body mass:
Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe)

< 0.01% of body mass:
Part of enzymes, e.g., chromium (Cr), manganese (Mn), and zinc (Zn)

Adenosine triphosphate / ATP

Organic molecule that stores and releases chemical energy for use in body cells.

Adenine-containing RNA nucleotide with two additional phosphate groups.

Food fuels cannot be used to energize body activities directly. Some of the food energy is captured temporarily in ATP. Later, ATP's bonds are broken and stored energy is released. Chemical energy in the form of ATP is used to run almost all functional processes.

Atoms

Unique building blocks for each element

ALL ATOMS ARE ELECTRICALLY NEUTRAL.
NUMBER OF PROTONS AND ELECTRONS IS ALWAYS EQUAL.

Hydrogen is the simplest atom.

Atoms are clusters of event smaller particles called protons, neutrons, and electrons.

An atom has a central nucleus containing protons and neutrons tightly bound together. The nucleus, in turn, is surrounded by orbiting electrons.

Atomic symbol

one- or two-letter chemical shorthand for each element

Atomic Structure

Determined by numbers of subatomic particles; Nucleus consists of neutrons and protons

Neutrons

No charge/neutral
Mass = 1 atomic mass unit (amu)

Protons

(p+)
Positive charge

Mass = 1 amu

Electrons

(e-)
Negative charge

Orbit nucleus
Equal in number to protons in atom
1/2000 the mass of a proton (0 amu)

Orbital model

current model used by chemists; depicts probable regions of greatest electron density (an electron cloud); useful for predicting chemical behavior of atoms

Planetary model

oversimplified, outdated model; incorrectly depicts fixed circular electron paths; useful for illustrations (as in the book)

Atomic number

number of protons in nucleus (written as subscript to the left of the symbol)

Mass number

mass/sum of the protons and neutrons (written as superscript to the left of the symbol)

Mass numbers of atoms of an element are not all identical.
Isotopes are structural variations of elements that differ in the number of neutrons they contain.

Atomic weight

average of mass numbers of all isotopes

Radioisotopes

isotope that exhibits radioactive behavior

Spontaneous decay (radioactivity)
Similar chemistry to stable isotopes
Can be detected with scanners
Valuable tools for biological research and medicine
Cause damage to living tissue
Useful against localized cancers
Radon from uranium decay causes lung cancer

Molecule

two or more atoms bonded together (e.g., H2)

Compound

two or more different kinds of atoms bonded together (e.g., C6H12O6)

Mixtures

Two or more components physically intermixed

Most matter exists as mixtures

Three types of mixtures:
1) Solutions
2) Colloids
3) Suspensions

Three types of mixtures:

1) Solutions
2) Colloids
3) Suspensions

Solutions

Homogeneous mixtures; usually transparent, e.g., atmospheric air or seawater

Colloids (emulsions)

Heterogeneous translucent mixtures, e.g., cytosol

Large solute particles that do not settle out
Undergo sol-gel transformations

Suspensions

Heterogeneous mixtures, e.g., blood

Large visible solutes tend to settle out

Mixtures v. Compounds

Mixtures:
No chemical bonding between components
Can be separated physically, such as by straining or filtering
Heterogeneous or homogeneous

Compounds:
Can be separated only by breaking bonds
All are homogeneous

Octet rule (re: chemical bonds)

Electrons occupy up to seven electron shells (energy levels) around nucleus

Octet rule: Except for the first shell which is full with two electrons, atoms interact in a manner to have eight electrons in their outermost energy level (valence shell)

Chemically Inert Elements

-Stable and unreactive
-Outermost energy level fully occupied or contains eight electrons

Chemically Reactive Elements

-Outermost energy level not fully occupied by electrons
-Tend to gain, lose, or share electrons (form bonds) with other atoms to achieve stability

Types of Chemical Bonds

1) Ionic: chemical bond formed by electron transfer between atoms
2) Covalent: chemical bond created by electron sharing between atoms
3) Hydrogen: weak bond in which hydrogen atom forms a bridge between two electron-hungry atoms

Ionic bonds

Ions are formed by transfer of valence shell electrons between atoms; attraction of opposite charges results in an ionic bond

Anions

(- charge) have gained one or more electrons

Cations

(+ charge) have lost one or more electrons

Covalent bonds

Formed by sharing of two or more valence shell electrons; allows each atom to fill its valence shell at least part of the time; sharing of electrons may be equal or unequal

Hydrogen bonds

-Attractive force between electropositive hydrogen of one molecule and an electronegative atom of another molecule
-Common between dipoles such as water
-Also act as intramolecular bonds, holding a large molecule in a three-dimensional shape

Chemical reactions

Occur when chemical bonds are formed, rearranged, or broken; represented as chemical equations

All chemical reactions are either exergonic or endergonic.

Patterns of chemical reactions

1) Synthesis (combination) reactions
2) Decomposition reactions
3) Exchange reactions

Synthesis (combination) reactions

Always involve bond formation

Decomposition reactions

-Reverse synthesis reactions
-Involve breaking of bonds

Exchange reactions

-Also called displacement reactions
-Bonds are both made and broken

Exergonic reactions

release energy

Endergonic reactions

products contain more potential energy than did reactants

Inorganic compounds

Water, salts, and many acids and bases

Do not contain carbon

Organic compounds

Include carbohydrates, lipids, proteins, and nucleic acids

Contain carbon, usually large, and are covalently bonded

Contain carbon (except CO2 and CO, which are inorganic)

Unique to living systems

Water

60%-80% of the volume of living cells

Most important inorganic compound in living organisms because of its properties

-High heat capacity
-Absorbs and releases heat with little temperature change
-Prevents sudden changes in temperature
-Evaporation requires large amounts of heat
-Useful cooling mechanism
-Dissolves and dissociates ionic substances
-Forms hydration layers around large charged molecules, e.g., proteins (colloid formation)
-Body's major transport medium
-Protects certain organs from physical trauma, e.g., cerebrospinal fluid

Salts

Ionic compounds that dissociate in water

Contain cations other than H+ and anions other than OH-

Ions (electrolytes) conduct electrical currents in solution

Ions play specialized roles in body functions (e.g., sodium, potassium, calcium, and iron)

Acid

a substance that releases hydrogen ions when in solution (compare with Base); a proton donor

Base

a substance capable of binding with hydrogen ions, a proton acceptor

pH unit

the measure of the relative acidity or alkalinity of a solution

Pure water is pH neutral (contains equal numbers of H+ and OH-)

pH change:

interferes with cell function and may damage living tissue

Slight change in pH can be fatal

pH is regulated by kidneys, lungs, and buffers

Buffers

Mixture of compounds that resist pH changes

Carbohydrates

Organic compound composed of carbon, hydrogen, and oxygen; includes sugars and starches

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

Three classes:
Monosaccharides
Disaccharides
Polysaccharides

THREE classes of carbohydrates:

1) Monosaccharides
2) Disaccharides
3) Polysaccharides

Monosaccharides

Simple sugars containing three to seven C atoms

Disaccharides

Double sugars

Too large to pass through cell membranes

Polysaccharides

Polymers of simple sugars, e.g., starch and glycogen

Not very soluble

Lipids

Organic compound formed of carbon, hydrogen, and oxygen (examples: fats, cholesterol)

Insoluble in water

Main types:
1) Neutral fats or triglycerides
2) Phospholipids
3) Steroids
4) Eicosanoids

Main types of lipids:

1) Neutral fats or triglycerides
2) Phospholipids
3) Steroids
4) Eicosanoids

Triglycerides A.K.A. neutral fats

Fats and oils composed of fatty acids and glycerol

THE BODY'S MOST CONCENTRATED SOURCE OF ENERGY FUEL

Main functions:
Energy storage
Insulation
Protection

Main functions of triglycerides:

1) Energy storage
2) Insulation
3) Protection

Saturated v. unsaturated fatty acids

Saturated fatty acids:
-Single bonds between C atoms; maximum number of H
-Solid animal fats, e.g., butter

Unsaturated fatty acids:
-One or more double bonds between C atoms
-Reduced number of H atoms
-Plant oils, e.g., olive oil

Phospholipids

Modified lipid; contains phosphorus

"Head" and "tail" regions have different properties
Important in cell membrane structure

Steroids

Group of chemical substances including certain hormones and cholesterol; fat soluble and contain little oxygen

Cholesterol, vitamin D, steroid hormones, and bile salts

Eicosanoids

-Many different ones
-Derived from a fatty acid (arachidonic acid) in cell membranes
-Prostaglandins

Proteins

Organic compound composed of carbon, oxygen, hydrogen, and nitrogen; types include enzymes, structural components

10-30% of cell mass

Polymers of amino acids (20 types)
Joined by peptide bonds
Contain C, H, O, N, and sometimes S and P

Hydrolysis

Process in which water is used to split a substance into smaller particles.

Peptide bonds linking amino acids together are broken when water is added to the bond.

Dehydration synthesis

Process by which a large molecule is synthesized by removing water and covalently bonding smaller molecules together.

The acid group of one amino acid is bonded to the amine group of the next, with loss of a water molecule.

Fibrous proteins

Fibrous (structural) proteins

Strandlike, water insoluble, and stable

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

Globular proteins

Globular (functional) proteins

Compact, spherical, water-soluble and sensitive to environmental changes

Specific functional regions (active sites)

Examples: antibodies, hormones, molecular chaperones, and enzymes

Protein denaturation

Shape change and disruption of active sites due to environmental changes (e.g., decreased pH or increased temperature)

Reversible in most cases, if normal conditions are restored

Irreversible if extreme changes damage the structure beyond repair (e.g., cooking an egg)

Molecular Chaperones (Chaperonins)

Ensure quick and accurate folding and association of proteins

Assist translocation of proteins and ions across membranes

Promote breakdown of damaged or denatured proteins

Help trigger the immune response

Produced in response to stressful stimuli, e.g., O2 deprivation

Enzymes

A protein that acts as a biological catalyst to speed up a chemical reaction

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

Characteristics of enzymes

Often named for the reaction they catalyze; usually end in -ase (e.g., hydrolases, oxidases)

Some functional enzymes (holoenzymes) consist of:
Apoenzyme (protein)
Cofactor (metal ion) or coenzyme (a vitamin)

Nucleic acid

Class of organic molecules that includes DNA and RNA

Largest molecules in the body

Contain C, O, H, N, and P

Building block = nucleotide, composed of N-containing base, a pentose sugar, and a phosphate group

Deoxyribonucleic Acid (DNA)

A nucleic acid found in all living cells. CARRIES THE ORGANISM'S HEREDITARY INFORMATION.

Four bases:
adenine (A), guanine (G), cytosine (C), and thymine (T)

Double-stranded helical molecule in the cell nucleus

Provides instructions for protein synthesis

Replicates before cell division, ensuring genetic continuity

What are the FOUR bases of DNA?

adenine (A)
guanine (G)
cytosine (C)
thymine (T)

Ribonucleic Acid (RNA)

Nucleic acid that contains ribose and the bases A, G, C, and U. CARRIES OUT DNA'S INSTRUCTIONS FOR PROTEIN SYNTHESIS.

Four bases:
adenine (A), guanine (G), cytosine (C), and uracil (U)

Single-stranded molecule mostly active outside the nucleus

Three varieties of RNA carry out the DNA orders for protein synthesis:
messenger RNA, transfer RNA, and ribosomal RNA

What are the FOUR bases of RNA?

adenine (A)
guanine (G)
cytosine (C)
uracil (U)

What is the function of ATP?

Phosphorylation:
Terminal phosphates are enzymatically transferred to and energize other molecules. Such "primed" molecules perform cellular work (life processes) using the phosphate bond energy.

Physical properties

those we can detect with our senses (i.e., color and texture) or measure (i.e., boiling point and freezing point)

Chemical properties

pertain to the way atoms interact with other atoms (bonding behavior)

How do you identify an element?

By its atomic number, mass number, and atomic weight.

Isotopes

structural variations in elements

Different atomic forms of the same element, which vary only in the number of neutrons they contain.

THE HEAVIER SPECIES TEND TO BE RADIOACTIVE.