Matter
anything that takes up space and has mass, made up of atoms
atoms
the smallest stable units of matter, join together to form chemicals with different characteristics
chemical characteristics
determine physiology on the molecular and cellular level
Subatomic Particles
Proton - Positive charge, 1 mass unit
Neutron - Neutral, 1 mass unit
Electron - Negative charge, low mass
Atomic Structure
Nucleus - Contains protons and neutrons
Electron cloud - contains electrons
Atomic number
number of protons
Mass number
number of protons plus neutrons
Atomic weight
exact mass of all particles (daltons)
1 Dalton (Da) = 1.66 x 10-24grams (g) = the mass of
one proton or neutron
Isotopes
2 or more elements with equal numbers of protons but different numbers of neutrons
Chemical Bonds
Involve the sharing, gaining, and losing of electrons in the valence shell
Three major types of chemical bonds
1. Ionic bonds 2. Covalent bonds 3. Hydrogen bonds
Ionic bonds
Attraction between cations (electron donor) and
anions (electron acceptor) are atoms with positive or negative charge
Covalent bonds
Formed between atoms that share electrons
Strong electron bonds involving shared electrons
Non polar covalent bonds: equal sharing of electrons
Polar covalent bonds: unequal sharing of electrons
Hydrogen bonds
Weak polar bonds based on partial electrical attractions
Free Radicals
Ion or molecule that contain unpaired electrons in the outermost shell.
Extremely Reactive
typically enter into destructive reactions
Damage/destroy vital compounds
Hydrogen Bonds
Attractive force between polar covalent molecules
•Weak force that holds molecules together
•Hydrogen bonds between H2O molecules cause surface tension
Molecules
Two or more atoms joined by strong bonds
Compounds
Two or more atoms OF DIFFERENT ELEMENTS joined by strong or weak bonds Compounds are all molecules, but not all molecules are compounds
Energy
the capacity to do work
Work
a change in mass or distance
Forms of Energy
1. Kinetic energy 2. Potential energy 3. Chemical 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
Chemical Reactions
•Decomposition Reaction (Catabolism)
– Breaks chemical bonds
– AB -> A + B
– Hydrolysis A-B+H2O -> A-H + HO-B
•Synthesis Reaction (Anabolism)
–Forms chemical bonds
–A + B->AB
–Dehydration synthesis (condensation reaction)
•Exchange Reaction
-AB + CD->AD + CB
-Involves decomposition first, then synthesis
•Reversible reaction
-AB + CD-><-AD + CB
-At equilibrium the amounts of chemicals do not
change even though the reactions are still occurring
Reaction’s Components
Reactants:
–
materials going
into
a reaction
•
Products:
–
materials coming
out
of a reaction
•
Enzymes:
–
proteins that lower the activation energy of a
reaction
Reactants
materials going into a reaction
Products
materials coming out of a reaction
Enzymes
proteins that lower the activation energy of a
reaction are protein catalysts that lower the activation energy of reactions most chemical reactions that sustain life cannot occur unless the right enzymes are present
Activation energy
the amount of energy needed to get a reaction started
Exergonic (Exothermic)reactions
produce more energy than they use heat will be the by product
Endergonic (Endothermic)reactions
use more energy than they produce
Organic molecules
molecules based mostly on carbon and hydrogen (Carbohydrates, proteins, lipids, and nucleic acids)
Inorganic molecules
molecules not based mostly on carbon and
hydrogen (Carbon dioxide, oxygen, water, and inorganic acids,bases, and salts)
Essential Molecules
1.nutrients 2. metabolites
Nutrients
essential molecules obtained from food
Metabolites
molecules made or broken down in the body
Why is water so important to life?
Water accounts for up to two-thirds of your total body weight
Properties of Water
1. Solubility 2. Reactivity 3. high heat capacity 4. Lubrication
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
Aqueous Solutions
Polar water molecules form hydration spheres
around ions and small polar molecules to keep them in solution
The Properties of Aqueous Solutions
Hydrophilic and hydrophobic compounds
Hydrophilic
hydro = water,
philos = loving
Interacts with water Includes ions and polar molecules
Hydrophobic
phobos = fear
Does NOT interact with water
Includes non polar molecules, fats, and oils
Electrolytes and body fluids
Electrolytes
are inorganic ions that conduct electricity in solution Electrolyte imbalance seriously disturbs vital body functions
Colloid
A solution of very large organic molecules
For example, blood plasma
Suspension
A solution in which particles settle (sediment)
For example, whole blood
Concentration
The amount of solute in a solvent (mol/L, g/L)
pH
The concentration of hydrogen ions (H+) in a
solution
Hydrogen Ions: H+
Unbound protons
•Have important biological effects
•Form when water ionizes:
H2O -> H+ + OH-
Hydrogen Ion (or Proton) Water Hydroxide Ion
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
pH Scale

Has an inverse relationship with H+ concentration:
–more H+ ions mean lower pH, less H+ ions mean
higher pH
Acidosis
Excess H+ ions (low pH
–damages cells and tissues
–alters proteins
–interferes with normal physiological functions
Alkalosis
Excess OH— ions (high pH)
–Uncontrollable and sustained skeletal muscle contraction
Controlling pH
salts and buffers
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
Minimizes extreme shifts in pH
•Partnership between weak acids and bases, which work as pair to counter shifts in pH
•Example: Carbonic Acid
-Bicarbonate Buffer System
–When blood pH rises, carbonic acid dissociates to form bicarbonate and H+H2C03----> HC03-+ H+–
When blood pH drops, bicarbonate binds H+ to form carbonic acid HC03-+ H+-----> H2C03
Organic Molecules
-Contain H, C, and usually O
-Are covalently bonded
-Contain functional groups that determine chemistry: Carbohydrates Lipids Proteins (or amino acids) Nucleic acids
Carbohydrates
Contain carbon, hydrogen, and oxygen in a 1:2:1
ratio
Monosaccharides
Simple sugars with 3 to 7 carbon atoms
Glucose, fructose, galactose
Disaccharides
Two simple sugars condensed by dehydration synthesis Sucrose, maltose
Polysaccharides
Many monosaccharides condensed by dehydration synthesis Glycogen, starch, cellulose
Simple Sugars
Structural Formula:
•Straight
-chain form
•Ring from
•3-D
Isomers: Glucose vs. Fructose:
-Same chemical formula but different shape
Glycogen
made and stored in muscle cells
Lipids
-Mainly hydrophobic molecules such as fats, oils,
and waxes
-Made mostly of carbon and hydrogen atoms (1:2),
and some oxygen
Type of lipids
Fatty acids
Eicosanoids
Glycerides
Steroids
Phospholipids and glycolipids
Fatty Acids
-Long chains of carbon and hydrogen with a
carboxyl group (COOH) at one end
-Are relatively nonpolar, except the carboxyl group
-Fatty acids may be:
Saturated with hydrogen (single covalent bonds)
Unsaturated (one or more double bonds)
Lauric acid demonstrates two structural characteristics common to all fatty acids:
a long chain of carbon atoms and a carboxyl
group (—COOH) at one end
Monounsaturated
one double bond
Polyunsaturated
two or more double bonds
Eicosanoids
derived from the fatty acid called arachidonic acid
Used for cellular communication Never burned for energy
Leukotrienes
Active in immune system Used by cells to signal injury
Prostaglandins
Local hormones, short
-chain fatty acids Used for cell-to-cell signaling to coordinate events
Glycerides
Fatty acids attached to a glycerol molecule Triglycerides are the three fatty
-acid tails Also called triacylglycerols or neutral fats
Glycerides have three important functions
1.Energy source 2.Insulation 3.Protection
Steroids
Four rings of carbon and hydrogen with an assortment of functional groups
Types of steroids
1.Cholesterol 2.Estrogens and testosterone
3.Corticosteroids and calcitriol 4.Bile salts
Cholesterol
Component of plasma (cell) membranes
Estrogens and testosterone
Sex hormones
Corticosteroids and calcitriol
Tissue metabolism and mineral balance
Bile salts
Derived from steroids Processing of dietary fats
Diglycerides
attached to either a phosphate group (phospholipid) or a sugar (glycolipid)
Generally, both have hydrophilic heads and
hydrophobic tails and are structural lipids,
components of plasma (cell) membranes
Proteins
Are the most abundant and important organic molecules Contain basic elements
-Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)
-Basic building blocks
-20 amino acids
Seven Major Protein Functions
1.Support •Structural proteins
2.Movement •Contractile proteins
3.Transport •Transport (carrier) proteins
4.Buffering •Regulation of pH
5.Metabolic Regulation •Enzymes
6.Coordination and Control •Hormones
7.Defense •Antibodies
Protein Structure
Long chains of amino acids
structure of an Amino Acid
Five components of amino acid structure
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
Protein Shape
1.Primary structure 2.Secondary structure 3.Tertiary structure 4.Quaternary structure
Primary structure
The sequence of amino acids along a
polypeptide
Secondary structure
Hydrogen bonds form spirals or pleats
Tertiary structure
Secondary structure folds into a unique shape
Quaternary structure
Final protein shape — several tertiary
structures together
Enzymes
-Catalysts
-Proteins that lower the activation energy of a chemical reaction
-Not changed or used up in the reaction
Enzymes also exhibit
1.Specificity—will only work on limited types of
substrates
2.Saturation Limits—by their concentration
3.Regulation—by other cellular chemicals
Enzyme Function
Cofactor, Coenzyme, Isozymes
Cofactor
An ion or molecule that binds to an enzyme before
substrates can bind
Coenzyme
Nonprotein organic cofactors (vitamins)
Isozymes
Two enzymes that can catalyze the same reaction
Glycoproteins
Large protein + small carbohydrate Includes enzymes, antibodies, hormones, and mucus
production
Proteoglycans
Large polysaccharides + polypeptides Promote viscosity
Nucleic Acids
Nucleic Acids (C, H, O, N, and P) Are large organic molecules, found in the nucleus, which
store and process information at the molecular
level
Deoxyribonucleic acid (DNA)
Determines inherited characteristics Directs protein synthesis Controls enzyme production
Controls metabolism
Ribonucleic acid (RNA)
Controls intermediate steps in protein synthesis
DNA Polymerase
Enzyme that catalyzes the covalent bond between the phosphate of one nucleotide and the deoxyribose (sugar) of the next nucleotide
DNA Replication
3’ end has a free deoxyribose
5’ end has a free phosphate
DNA polymerase:
•can only build the new strand in the 5’ to 3’ direction
•Thus scans the template strand in 3’ to 5’ direction
Types of RNA
-Messenger RNA (mRNA)
-Transfer RNA (tRNA)
-Ribosomal RNA (rRNA)
Nucleotides Can Be Used to Store Energy
Adenosine diphosphate (ADP)
Two phosphate groups; di-= 2
Adenosine triphosphate (ATP)
Three phosphate groups; tri-= 3
Phosphorylation
Adding a phosphate group to ADP with a high
-energy bond to form the high
-energy compound ATP
Adenosine triphosphatase (ATPase)
The enzyme that catalyzes the conversion of ATP to
ADP
High-Energy Compounds:
ADP and ATP
-Assembled using Nucleotides
-Bonds are broken 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.