The Chemical & Physical Basis of Life
Chapter 2
Life is a series of complex chemical reactions.
Chemical reactions are the basis of physiology.Chemistry follows the laws of Physics.Physics is, fundamentally, the study of matter & energy.
Matter•Matter is “stuff”. •It occupies space and has mass.•Mass is measured in grams.•Mass and “weight” are often used interchangeably but are really two different things
•Weight is a measure of the effect of force on an object. It changes. •Mass does not change.
Example: The Moon’s gravitational force is 1/6th that of Earth’s. If you weigh 155 pounds on Earth (70 kg), you will only weigh 26 pounds on the Moon. But you will still have 70 kilograms of mass!(The BE or British Engineering unit of mass is the “slug”.)
Energy
Potential = stored energy. The amount energy contained in an object of a given mass that can be used to do work.
Kinetic Energy = energy of work. This is energy that is actually being released and doing work.
Other Forms of Energy
1. Electrical2. Mechanical3. Chemical4. Radiant5. Nuclear
Energy is governed by the Laws of
Thermodynamics
The 1st Law of Thermodynamics:
Energy cannot be created nor can it be destroyed.
Also known as “the Conservation Statement”
The 2nd law of Thermodynamics:
Energy flows from an area of high density to an area of low density.
This is also referred to as “the Entropy Statement”.The 2nd LTD is perhaps the most relevant concept
to us for our understanding biological systems, chemistry and physiology.
Another way to look at the 2nd LTD:
Since energy is what holds matter together, or maintains “order”, then
the 2nd LTD dictates that systems go from order to disorder.
Example of Entropy
The 3rd Law of Thermodynamics:
You cannot reach absolute zero in a finite number of steps.
This is implied from the first two LTDs.
Absolute zero
That’s really cold!
The Zeroth Law:
There is no net flow of energy between to systems that are in equilibrium.
(The “well duh!” statement.)
Atoms:The Building Blocks of Matter
There are 26 elements essential to most living systems. Humans are composed of the the following:
1. Oxygen - 65%2. Carbon -
18.5%3. Hydrogen - 9.5%4. Nitrogen - 3.3%5. Calcium - 1.5%6. Phosphorus-
1.0%7. Potassium -
0.4%8. Sulfur -
0.3%9. Sodium -
0.2%10.Chlorine - 0.2%11.Magnesium -
0.1%12.Iron - 0.005%
Trace elements (in alphabetical order)AluminumBoronChromiumCobaltCopperFluorineIodineManganeseMolybdenumSeleniumSiliconTinVanadiumZinc
Composition of the Human body
Atomic structure
Atomic number = the number of protonsMass number = protons + neutronsAtomic mass = mass of protons (1.008 amu) + mass of neutrons (1.007 amu) + mass of electrons (0.0005 amu)
More elements
IsotopesThe number of protons defines the element. The number of neutrons and electrons can vary.Isotopes are different forms of elements with different numbers of neutrons. Some are stable, some decay and release energy. This energy is nuclear radiation!
There are 3 basic types of atomic radiation
particles = a He nucleus (2 protons + 2 neutrons) Easily stopped. Dangerous if ingested or inhaled. Produced by
the decay of Polonium, Radon, Radium and Uranium
particles = are electrons and are negatively charged More energetic and therefore, more dangerous. Given off in the
opposite direction of particle. Produced by Krypton, Strontium, Carbon and Indium.
rays = high energy electromagnetic radiation Most deadly, mutagenic and toxic. Produced by Polonium,
Krypton, Radon, Radium, and Uranium
Chemical reactivity:It’s all about electrons
Unfilled valence shells lead to reactivity
The Octet Rule
• Atoms with eight electrons in their valance shell are most stable.
• When a reaction between two atoms leads to full valance shells then the two are more likely to interact.
• Atoms or molecules with partially filled valance shells are more reactive.
Free Radicals
Superoxide free radical is highly reactive
Chemical bonds and the combining of matter
•Atoms can combine by chemical reactions to form molecules.•Two or more atoms of the same element bound together form a molecule.•Two or more atoms of different elements bound together form a compound.
This is different than a mixture, which is when substances are physically combined but are not chemically bonded. Mixtures include: Solutions, Colloids, and Suspensions.
Ionic compounds
An important Ionic
compound: NaCl
Or “table salt”!
Covalent bonds:the sharing of electrons
Covalent molecules
Two covalent
compounds
Important characteristics & relative strength
of chemical bonds
Weakstrong
Water:its structure gives it special properties
Hydrogen Bonds
Hydrogen bonds are too weak to form compounds but are an important influence on chemical structure.
The electrical attraction between the partial charge on the hydrogen of one water molecule and the oxygen of another gives water its special properties.
Important properties of H2O
It is polar, which gives rise to the following: Cohesion - it clings to itself Adhesion I it clings to other things
These properties account of its high surface tension and capillary action.
It is the “universal solvent”. It has high heat capacity, latent heat of vaporization
and specific heat.
How water works to dissolve an ionic compound
(this is actually a chemical reaction)
Solutions
• Colloid: – a solution of very large organic
molecules• Suspension:
– a solution in which particles settle (sediment)
• Concentration: – the amount of solute in a solvent
(mol/L, mg/mL)
ElectrolytesTable 2–3
Chemical Reactions:Water is formed by a chemical
reaction
Reactions & energy
• Reactions that absorb more energy than they release are endergonic
• Reactions that release more energy than they absorb are exergonic
• Life is a series of these reactions that are coupled together
• Reactions require energy to initiate them – Activation energy
Activation Energy
Catalyst activity
Enzymes are organic catalysts that speed up chemical reactions by
lower the energy needed to activate
them.
They are not changed by the reaction, nor are they a product or a reactant.
Chemical Reactions:Synthesis
Synthesis reactions build more complex molecules from individual building blocks. Biological molecules are synthesized by removing producing water molecules.
DecompositionDecomposition reactions break large molecules into their constituent components. Biological molecules are generally broken down by addition of water molecules. This type of reaction is called hydrolysis.
Oxidation-reduction reactionsor “redox”
When something is reduced, something else is always oxidized
1. Electrons are exchanged between reactants.2. The electron donor is oxidized. (It is the reducing
agent).3. The electron acceptor is reduced. (It is the oxidizing
agent).4. Also defined as the loss of hydrogens (and
electrons) or the addition of oxygen.
Example of a simple redox reaction
Exchange reactions
Aerobic respiration:A very important redox reaction!
ADP + Pi
C6H12O6 + 6 O2 6 CO2 + 6 H2O
ATP
Stored energy
Some other
important redox
reactions
Influences on reaction rates
• Concentration• Temperature• pH• Catalysts
Acids, Bases & Salts
One version of the pH scale
Acid and Alkaline
• Acidosis: – excess H+ in body fluid (low pH)
• Alkalosis: – excess OH— in body fluid (high
pH)
Organic Compounds
• Carbohydrates• Lipids• Proteins• Nucleic acids
Functional Groups
Table 2–4
• Molecular groups which allow molecules to interact with other molecules
CarbohydratesSimple sugars
Disaccharides
Simple Sugars
Figure 2–10
Formation of Sucrose from glucose & fructose
Polysaccharides
• Chains of many simple sugars (glycogen)
Figure 2–12
Carbohydrate Functions
Table 2–5
Classes of Lipids
• Fatty acids• Eicosanoids• Glycerides• Steroids• Phospholipids and glycolipids
Lipids
Triglycerides = glycerol + 3 free fatty
acidsAlso known as “neutral fats”
Figure 2–15
• Glycerides: are the fatty acids attached to a glycerol molecule
• Triglyceride: are the 3 fatty-acid tails, fat storage molecule
Combination Lipids Figure 2–17a, b
Combination Lipids
Figure 2–17c
Cholesterol is another lipid.
It is a component of plasma membranes and is the basis for steroid hormones.
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
Protein Functions (1 of 2)
• 7 major protein functions:– support:
• structural proteins
– movement: • contractile proteins
– transport:• transport proteins
Protein Functions (2 of 2)
– buffering: regulation of pH– metabolic regulation:
• enzymes
– coordination and control: • hormones
– defense:• antibodies
Amino AcidsFigure 2-18
Amino Acid Structure
1. central carbon2. hydrogen3. amino group (—NH2)
4. carboxylic acid group (—COOH)5. variable side chain or R group
Peptides
Figure 2–19
Peptide Bond
• A dehydration synthesis between:– the amino group of 1 amino acid– and the carboxylic acid group of
another amino acid– producing a peptide
Figure 2–20a
Primary Structure
• Polypeptide:– a long chain of amino acids
Secondary Structure
Figure 2–20b
• Hydrogen bonds form spirals or pleats
Figure 2–20c
Tertiary Structure
• Secondary structure folds into a unique shape
Quaternary Structure Figure 2–20d
• Final protein shape: – several tertiary structures together
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 Shapes
• Fibrous proteins: – structural sheets or strands
• Globular proteins: – soluble spheres with active functions
Enzymes
• Enzymes are catalysts: – proteins that lower the activation
energy of a chemical reaction – are not changed or used up in
the reaction
How Enzymes Work
Figure 2–21
How Enzymes Work
• Substrates: –reactants in enzymatic reactions
• Active site: –a location on an enzyme that fits a particular substrate
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
Enzyme Characteristics
• Specificity: – one enzyme catalyzes one
reaction• Saturation limits:
– an enzyme’s maximum work rate• Regulation:
– the ability to turn off and on
Protein Combinations• Glycoproteins:
– large protein + small carbohydrate•includes enzymes, antibodies, hormones, and mucus production
• Proteoglycans: – large polysaccharides +
polypeptides•promote viscosity
Nucleic Acids
• Large organic molecules, found in the nucleus, which store and process information at the molecular level
• DNA and RNA
Deoxyribonucleic Acid (DNA)
• Determines inherited characteristics
• Directs protein synthesis• Controls enzyme production• Controls metabolism
Ribonucleic Acid (RNA)
• Codes intermediate steps in protein synthesis
Nucleotides
• Are the building blocks of DNA• Have 3 molecular parts:
– sugar (deoxyribose)– phosphate group– nitrogenous base (A, G, T, C)
The Bases
Complementary Bases
• Complementary base pairs:– purines pair with pyrimidines:
•DNA: –adenine (A) and thymine (T) –cytosine (C) and guanine (G)
•RNA: –uracil (U) replaces thymine (T)
Nucleic Acids
• Long chains of nucleotides form RNA and DNA
Figure 2–23
RNA and DNA
• RNA: – a single strand
• DNA: – a double helix joined at bases by
hydrogen bonds
Forms of RNA
• messenger RNA (mRNA)• transfer RNA (tRNA)• ribosomal RNA (rRNA)
ADP and ATP
• adenosine diphosphate (ADP): – 2 phosphate groups
• di = 2
• adenosine triphosphate (ATP): – 3 phosphate groups
• tri = 3
Phosphorylation
• Adding a phosphate group to ADP with a high-energy bond to form the high-energy compound ATP
• ATPase: – the enzyme that catalyzes
phophorylation
Figure 2–24
The Energy Molecule
• Chemical energy stored in phosphate bonds
ATP supplies energy for the work required
to maintain homeostasis
ATP is formed by cellular respiration
Compounds Important to Physiology
Recycling Old Molecules
Table 2–9
Next - Cells