Chapter 2

The chemical Basis of Life

Introduction

Why study chemistry in an Anatomy and Physiology class?

• body functions depend on cellular functions

• cellular functions result from chemical changes

• biochemistry helps to explain physiological processes, and develop new drugs and methods for treating diseases

Introduction cont.

• Chemistry = the study of matter

• Biochemistry= the study of the chemistry of life

• Matter = anything that occupies space and has mass– composed of elements– (i.e. solids, liquids, gases)

Structure of Matter

Structure of Matter

• Elements – composed of chemically identical atoms– bulk elements – required by the body in large

amounts– trace elements – required by the body in small

amounts

• Atoms – smallest particle of an element– the least complex level of organization

Subatomic Particles

• Proton = a positively charged particle in the nucleus of an atom – Mass=1

• Neutron = an electrically neutral particle in the nucleus of an atom – Mass=1

• Electron = an electrically negative particle that revolves around the nucleus – Mass = 0

Elements

• Element = a basic chemical substance composed of atoms

• Elements are represented by a 1 or 2 letter symbol

• 120 elements exist in nature• Approximately 26 are naturally occurring in

humans.– most abundant=carbon (C), Hydrogen (H),

Oxygen (O) Nitrogen (N), Phosphorus (P) = CHONP

– Referred to a bulk elements (Know Table 2.2 and 2.3 for the test)

Elements You need to KnowKnow this table

Elements cont.• Atoms are neutral in charge

- The number of protons is equal to the number of electrons.

• The Atomic Number (A#) of an atom represents the number of protons in its nucleus.

• The Atomic Mass (AM) of an atom is equal to the number of protons plus the number of neutrons in its nucleus – Average weight of common

isotopes

Isotopes

• Isotopes = atoms of an element that have the same A#'s but different AW's (i.e. same # of protons, different # of neutrons) – Any sample of an element is likely to contain

multiple isotopes– The nuclei of some isotopes are stable – The nuclei of other isotopes are unstable and

break apart to become more stable • When the nucleus of an atom breaks apart, it releases

radioactive energy • Radioactive isotopes have many biological uses (i.e.

Carbon Dating)

Molecules and Compounds

• Molecule – particle formed when two or more atoms chemically combine

• Compound – particle formed when two or more atoms of different elements chemically combine

• Molecular formulas – depict the elements present and the number of each atom present in the molecule– water (H2O), glucose (C6H12O6)

Bonding of Atoms

• The electrons of an atom are arranged in orbits, shells, or energy levels around the central nucleus

• A characteristic number of electrons fill each shell – 2 electrons fill the first shell (closest to nucleus) – 8 electrons fill the second shell – 8 electrons fill the third shell

Bonding of Atoms cont.

• The way in which atoms react with one another (i.e. their chemical properties) is based on the electrons in their outermost shell = Valence Electrons

• The outermost shell of an atom is called its valence shell

Electron Shells (valence)

Bonding of Atoms cont.

• Atoms form bonds with other atoms to fill their outermost or valence electron shell (energy level) – "Rule of Octets" = except for the first energy

level (which contain 2 electrons), atoms react with other atoms so they will have 8 electrons in their valence shell

– All 8 slots filled=inert, non reactive– Less that 8 slots filled= atom seeks a stable

energy level with a full shell

Example Problem #1

Fluorine has an Atomic Number of 9. Draw an atom of fluorine. How and why will fluorine react?

Example Problem #1

Fluorine has an Atomic Number of 9. Draw an atom of fluorine. How and why will fluorine react?

9p+

9n0

-

--

-

-

-

- -

-

Since atoms are stable with 8 electrons in their valence shell, fluorine will tend to bind with atoms that have one electron to donate

Example Problem #2

Argon has an Atomic Number of 18. Draw an atom of argon. How and why will argon react?

Example Problem #2

Argon has an Atomic Number of 18. Draw an atom of argon. How and why will argon react?

18p+

18n0

-

--

-

-

- -

-

Since Argon has a full valence shell, it will not tend to bond to other atoms and be relatively inert

--

-

-

-

-

-

-

-

-

Ions

• Ions = atoms that have lost or gained electrons to fill their valence shell– anion = a negatively charged ion (Cl-) – cation = a positively charged ion (Na+) – An attraction exists between oppositely charged

ions and an ionic bond results (i.e. Na+Cl-)

• Formed when electrons are transferred from one atom to another

Ionic Bond

• An ionic bond results due to the attraction that exists between oppositely charged ions and (i.e. Na+Cl-)– They are formed when electrons are transferred

from one atom to another

Ionic Bond

Covalent Bond• A covalent bond is formed by the equal

sharing of electrons between atoms – very strong bond

– i.e. H2 and O2

• Atoms tend to make the same number of covalent bonds– Same number of slots on the valence shell– Structural formula – More than one elector can be bound

• Double, triple bonds

Covalent Bond• Hydrogen atoms form single bonds

• Oxygen atoms form two bonds

• Nitrogen atoms form three bonds

• Carbon atoms form four bonds

H ― HO = ON ≡ NO = C = O

Covalent Bond

Structural FormulaStructural formulas show how atoms bond and

are arranged in various molecules

• Polar Bond=A polar covalent bond is formed by the unequal sharing of electrons between atoms– strong bond– results in molecules that are polar

• one end of the molecule is slightly positive, one end of the molecule is slightly negative

– i.e. water (H2O)

Polar Bond

Hydrogen Bond

• Hydrogen Bonds= a weak attraction between the positive end of one polar molecule and the negative end of another polar molecule– formed between water molecules– important for protein and nucleic acid structure– Examples include interaction between water

molecules and DNA chains– These bonds are easily broken and put back

together (very weak)

Types of Chemical Reactions

• Synthesis Reaction – more complex chemical structure is formed

A + B AB

• Decomposition Reaction – chemical bonds are broken to forma simpler chemical structure

AB A + B

Types of Chemical Reactions cont.

• Exchange Reaction – chemical bonds are broken and new bonds are formed

AB + CD AD + CB

• Reversible Reaction – the products can change back to the reactants

A + B ↔ AB

Acids, Bases, and Salts

• Electrolytes – substances that release ions in water

• Acids – electrolytes that dissociate to release hydrogen ions in water

• Bases – substances that release ions that can combine with hydrogen ions

• Salts – electrolytes formed by the reaction between an acid and a base

NaCl Na+ + Cl-

HCl H+ + Cl-

NaOH Na+ + OH-

HCl + NaOH H2O + NaCl

Acid and Base Concentrations

• pH scale - indicates the - concentration of hydrogen ions in

- solution • Neutral – pH 7

- indicates equal concentrations of H+ and OH-

• Acidic – pH less than 7- indicates a greater concentration of H+

• Basic or alkaline – pH greater than 7- indicates a greater concentration of OH-

Chemical Constituents of Cells

Inorganic Substances

• Inorganic Substances are small compounds that do not contain both the atoms C and H– Examples include oxygen, carbon dioxide (CO2)

water, salts, acids & bases

Water

• Water is a polar molecule that demonstrates hydrogen bonding and therefore it possesses very unique characteristics – Water is an excellent solvent (universal?) – Many solutes are dissolved in our body's water

(i.e. polar substances dissolve in polar water) – Many ionic compounds (i.e. NaCl) dissociate or

break apart in water

Water cont.

• Water participates in many chemical reactions (in our cells and fluids) – Dehydration (synthesis) is when water is

removed from adjacent atoms (of molecules) to form a bond between them

– Hydrolysis (degradation) is when water is used to break bonds between molecules

• Water is an excellent temperature buffer – absorbs and releases heat very slowly

• Water is the most abundant component in cells (about 70%)

Water cont.

• Water provides an excellent cooling mechanism – It requires a lot of heat to change water from a

liquid to a gas (i.e. high heat of vaporization). If water does change forms and evaporate, it leaves a cool surface behind

• Water serves as a lubricant – mucus – internal organs – joints

Inorganic Substances cont.

• Oxygen (O2)

– gas that is transported in the blood – used to release energy from nutrient molecules

• Carbon Dioxide (CO2)

– a by-product of cellular respiration

• Inorganic salts – Abundant in body fluids– Source of necessary ions (Na+, Cl-, K+, Ca2+,

etc…) – Play important roles in metabolism

Organic Substances

• Organic Substances= contains the atoms carbon (and hydrogen)

• Small molecules (monomers or building blocks) are covalently bonded together to form large polymers or macromolecules

• Water is usually involved in the formation and breakage of bonds between monomers – Dehydration Synthesis = removal of water to

form a covalent bond between monomers – Hydrolysis = using water to break bonds

between monomers

Organic Substances cont.

• The four major classes found in cells include: – carbohydrates – lipids – proteins – nucleic acids

Carbohydrates

• Provide Energy to cells

• Supply materials to build cell structures

• Water-soluble

• Contain C, H, O

• Carbohydrates (sugars)= contains C, H, and O in a 1:2:1 ratio (usually) – glucose = C6H12O6

Carbohydrates

• Monomers (building blocks) are monosaccharides– glucose, fructose

• Hexoses = simple 6-C sugars – glucose – fructose – galactose

• Polymers are formed by dehydration synthesis

Monosaccharide

Monosaccharide cont.

Carbohydrates cont.Disaccharides: 2

monosaccharides covalently bonded together – maltose = glucose +

glucose – lactose = glucose +

galactose – sucrose = glucose +

fructose

Carbohydrates cont.

• Polysaccharides: many glucose molecules covalently bonded together – starch = plant storage

carbohydrate – glycogen = animal

storage carbohydrate; stored in liver and skeletal muscle

– cellulose=plant starch

Carbohydrates cont.

• Polymers are broken down by hydrolysis resulting in monosaccharides

• Function = energy source / energy storage!

CELLULAR RESPIRATION OVERVIEW

glucose + oxygen energy + H2O + CO2

(ATP)

Lipids

• Lipids= contain C, H, and O, but much less O than in carbohydrates

• Soluble in organic solvents

• Insoluble in water

• Types of lipids – Fats– Phospholipids– Steroids

Fats

• Monomers (building blocks) = triglycerides (glycerol + 3 fatty acids)

• Function = energy store/ energy source

• Saturated fats=have only single bonds between the carbons in their fatty acid chains – are solid at room temperature – are animal fats – are nutritionally "BAD" fat – include bacon grease, lard, butter

Fats

• Unsaturated fats= have one or more double bond between the carbons in their fatty acid chains – are liquid at RT (oils) – are plant fats – are nutritionally "GOOD" fat – include corn and olive oil

Fatty Acids

Triglycerides

Phospholipids• Phospholipids=

triglyceride with the substitution of a polar phosphate group (PO4-) for one fatty acid chain

• One glycerol, 2 fatty-acids, 1 phosphate

• Function = major cell membrane component

Steroids

• Steroids= four interconnected carbon rings – Example is cholesterol

• Function = compose cell membranes; chemical messengers (hormones)

Proteins• Monomers = amino acids

– Structure=amino group, carboxyl group, side chain (R group)

– 20 different types of Amino Acids (R groups differ)

Proteins cont.

• Polymers are formed by dehydration synthesis between the amino group of one amino acid and the carboxyl group of a 2nd amino acid

• Bond formed = a peptide bond

Peptide Bond

Proteins cont.

• Length of amino acid chains may vary – peptide = 2-100 aa's – polypeptide = 100-thousands aa's without a

function – protein = 100-thousands of aa's with a specific

function

Functions of Proteins• Structure

– keratin in hair, nails and skin

• Transport– hemoglobin

• Movement– actin and myosin in

muscles

• Chemical messengers– hormones– neurotransmitters

• Defense– antibodies

• Catalysts – enzymes=Biological

catalysts, that increase the rate of chemical reactions without being consumed by the reaction

Denaturation of Proteins

• Denaturation of Proteins= the loss of 3-dimensional conformation (shape) of a protein. This results in loss of function

• Reasons for denaturation – extreme pH values – extreme temperature values – harsh chemicals (disrupt bonding) – high salt concentrations

Protein Structure

• Primary (1o) = sequence of amino acids

• Secondary (2o) = twisting of amino acid chain; due to hydrogen bonding;

• Tertiary (3o) = folding of the amino acid chain; due to ionic bonds, disulfide bridges, and hydrophobic interactions;

• Quaternary (4o) = interactions between different amino acid chains (See the four amino acids chains that compose hemoglobin on page 518).

Primary Structure

Secondary Structure

Tertiary Structure

Quaternary Structure

Nucleic Acids

• Monomers = nucleotides

• Nucleotide structure = 3 parts – pentose sugar (5-C) – phosphate group – nitrogenous base

• purine (double ring) • pyrimidine (single ring)

• Polymers are formed by bonding between the sugar of one nucleotide and the phosphate group of a second nucleotide = sugar/phosphate backbone

Nucleic Acids

Deoxyribonucleic Acid = DNA • Structure

– Sugar = deoxyribose – Bases = adenine (A), thymine (T), cytosine (C),

guanine (G) – double stranded (resembles ladder); strands

held together by H-bonds between bases on opposite strands

• A complements T (2 hydrogen bonds) • C complements G (3 hydrogen bonds)

Nucleotides

DNA cont.

• double helix (ladder is twisted)

• Function = genetic material (i.e. genes, chromosomes)

• DNA contains all necessary information needed to sustain and reproduce life!

DNA Structure: One Strand

DNA Structure: Two Strands

DNA Structure cont.

Ribonucleic Acid = RNA

• Structure – Sugar = ribose– Bases = A,G,C, and uracil (replaces thymine)– single stranded.

• Function = transport DNA code during protein synthesis

RNA vs. DNA