The Chemical & Physical Basis of Life

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”.)

EnergyPotential = 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)

Electrolytes

Table 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 + PiC6H12O6 + 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 Structure1. 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