Chemistry of life

Introduction

Biochemistry - is the set of chemical reactions that happen in the cells of living organisms to sustain life.

Chemical Elements in Living things: C, H, O, N, S

Processes:

Metabolism – the sum total of all biochemical processes

Catabolism – breaking down of large molecules

Ex. Cellular respiration, Digestion

Anabolism – building up of molecules

Ex. Photosynthesis, carbon fixation, Synthesis of biomolecules

Terms to knowElement - matter composed of atoms that all have the same atomic

number (protons).Atom - the smallest component of an element that still has properties of

the element, consisting of a positively charged nucleus surrounded by a charged cloud of electrons."+" and "-" charges strongly attract.

Proton - particle in the nucleus with a positive charge of +1 and an atomic mass number of 1 Dalton.

Neutron - a non-charged nuclear particle with the same mass as the proton.

Electron - negatively charged particle (-1) with a mass 1/1837 of that of a proton.

Isotope - atoms with the same number of protons and electrons, but different numbers of neutrons.

Electrons determine chemical properties of elements Chemical reactions involve sharing

(COVALENT) or exchanging electrons (IONIC).

Absorption of energy can cause an electron to move up to a higher energy level.

The atom is stable when the outermost energy level of most atoms has eight electrons (Octet Rule). The H atom can carry electrons for

transferring energy. Oxygen has a strong affinity for electrons. Redox reaction transfer of electrons from

one molecule (oxidized) to another (reduced).

Stability can be achieved by adding, losing, or sharing electrons.

element

number of

covalent

bonds

H 1

O 2

N 3

C 4

S 5

Chemical bonds and Attractive forces Covalent bonds – electrons are shared

Ionic bonds – electrons are transferred

Electronegativity - tendency for atoms to bind electrons.

Oxygen (O) - electronegativity of 3.5 has a strong affinity.

Hydrogen (H)(2.1) and carbon (C)(2.5) each have lower affinities.

A bond between C and H will have nearly equal sharing of electrons.

Oxygen and hydrogen form a highly polar bond because of the much stronger affinity for electrons by O.

Non-covalent bonds and other weak forces Electrostatic bonds(ionic)-result from the electrostatic attraction

between two ionized groups of opposite charge, such as carboxyl (-COO-) and amino (-NH3

+). In water, these bonds are very weak.

Hydrogen bonds-result from electrostatic attraction between an electronegative atom (O or N) and a (partially +) hydrogen atom that is bonded covalently to a second electronegative atom.

Van der Waals force-are short range attractive forces between chemical groups in contact. Caused by slight charge displacements.

Hydrophobic attractions-cause non-polar groups such as hydrocarbon chains to associate with each other in an aqueous environment.

Chemistry of Water It is composed of one oxygen atom and two

hydrogen atoms, forming a covalent bond.

H bond – joins 2 molecules of water

Bond formed between the partially (+) H of one water molecule and the partially (-) O of another water molecule

Water is a "polar" molecule - there is an uneven distribution of electron density.

partial negative charge (-) near O and partial positive charges (+) near H. Oxygen is an "electronegative" or electron "loving" atom compared with hydrogen.

Water as a universal solvent The ability of ions and other molecules to dissolve in

water is due to polarity.

Positively charged ions are attracted with patially (-) O in water and negatively charged ions are attracted with partially (+) H.

Surface tension of water The molecular polarity of water is responsible for its

surface tension property.

Partially positive side of water is attracted to the partially negative side. The resulting polarity of charge causes molecules of water to be attracted to each other forming strong molecular HYDROGEN bonds. – this is surface tension

Water: Surface Tension This phenomenon also causes water to stick to the

sides of vertical structures despite gravity's downward pull. Water's high surface tension allows for the formation of water droplets and waves, allows plants to move water (and dissolved nutrients) from their roots to their leaves, and the movement of blood through tiny vessels in the bodies of some animals.

Water: Cohesion and Adhesion Cohesion – attraction between like particles

Water is attracted to other water. Results to surface tension

Adhesion – attraction between unlike particles Water can also be attracted to other materials. Rationale of capillary action

Factors: Size of capillary tube – indirect proportion Gravity – indirect proportion

Plants take advantage of capillary action to pull water from the soil to the roots. From the roots water is drawn through the plant by another force, transpiration.

Physical states of water

Frozen water molecules arranged in a particular highly organized rigid geometric pattern that causes the mass of water to expand (increase in volume) and to decrease in density. Expansion causes ice to float in liquid water.

Liquid phase - water molecules arranged into small groups of joined particles. The fact that these arrangements are small allows liquid water to move and flow.

Water vapor are highly charged with energy. This high energy state causes the molecules to be always moving reducing the likelihood of bonds between individual molecules from forming.

Thermal Properties of water – due to H bond Has a HIGH specific heat capacity

is the amount of energy needed to raise the temperature of a given mass of a substance. Water's specific heat capa

it can absorb large amounts of heat energy before it begins to get hot. releases heat energy slowly when situations cause it to cool. Water's high specific heat allows for the moderation of the Earth's

climate and helps organisms regulate their body temperature more effectively.

Has a HIGH specific heat of vaporization Heat of vaporization is the amount of energy needed to vaporize a

given amount of mass of a substance.

High Boiling point and High freezing point If water will boil at a lower temperature, water inside the living

organism would boil and the organism would not survive.

Water becomes less dense as it freezes Ice first forms on the surface of water – beneficial to aquatic organisms

as it insulates the water underneath and maintains the habitat.

Water in a pure state has a neutral pH Acids and Bases, Ionization of Water

Acid release H+

Bases accept H+

The pH of a solution is the negative logarithm of the hydrogen ion concentration.

at pH 7.0, a solution is neutral at lower pH (1-6), a solution is acidic at higher pH (8-14), a solution is basic

Water in a pure state has a neutral pH. As a result, pure water is neither acidic nor basic. Water changes its pH when substances are dissolved in it. Rain has a naturally acidic pH of about 5.6 because it contains

natural derived carbon dioxide and sulfur dioxide.

Water and metabolism Water is the medium for various enzymatic & chemical

reactions in the body. It moves nutrients, hormones, antibodies and oxygen through the blood stream and lymphatic system.

The waste products of metabolism and surplus salts get removed from your body through urine.

Water cools body surfaces (sweat) and plant leaves (transpiration).

Other Elements Needed by living organisms Calcium – acts as messenger that binds to calmodulin and a

few other proteins which regulate transcription and other processes in the cell. Stimulates release of neurotransmitters

Sulfur –for the synthesis of methionine and cysteine(amino acids)

Phosphorus – forms part of the nucleic acids and ATP Iron – needed for the synthesis of cytochromes needed in

electron transport during cellular respiration and photosynthesis Forms the hemoglobin in red blood cells

Sodium – major extracellular electrolyte Potassium – major intracellular electrolyte

Introduction to Organic Molecules Organic molecules contain carbon; inorganic

compounds has NO carbon, except oxides of carbon (CO2 and CO) , carbonates, and hydrogen carbonates

Organic compounds are classified according to the functional groups they contain.

Alcohol - "OH“ Aldehyde – carbonyl “HC=O” Acid - carboxyl "COOH” Amine - amine "NH3

+” Phosphate - addition of –PO4 = Amino Acid - with amino "NH3

+” and carboxyl groups "COOH”

Key Biochemicals

Type of moleculeName of

monomer formsName of polymer

formsExamples of

polymer forms

Proteins Amino acids PolypeptidesFibrous and

Globular proteins

Carbohydrate Monosaccharides PolysaccharidesStarch, lycogen,

Cellulose

Nucleic Acid Nucleotides Polunucleotide DNA, RNA

LipidsFatty acid and

glycerolLipids, triglycerides

Steroid, cholesterol, wax

Carbohydrate – alcoholic derivatives of aldehydes or ketones Function:

storage of energy – polysaccharides (starch and glycogen)

structural components (e.g., cellulose in plants and chitin in arthropods).

important component of coenzymes (e.g. ribose in ATP, FAD, and NAD) and the backbone of the genetic molecule known as RNA. The related deoxyribose is a component of DNA.

Saccharides and their derivatives include many other important biomolecules that play key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and development.

Classification of Carbohydrate Monosaccharide – with one saccharide unit

Named according to number of C (triose, tetrose, pentose, hexose….) Triose – ex. Glyceraldehyde Pentose – ex. Ribose and deoxyribose Hexose – glucose, fructose, galactose

Disaccharide – with two monosaccharides joined by covalent glycosidiclinkage Lactose glucose + galactose Maltose glucose + glucose Sucrose fructose + glucose

Polysaccharide – long chain of saccharide units Starch Glycogen Cellulose

Functions of some Carbohydrates Energy source

Glucose – from hydrolysis of polysaccharides

Fructose – found in fruits

Lactose – found in milk

Structural component

Cellulose – in cell walls

Condensation of Carbohydrates

Lipids

The spectrum of lipid functions can be condensed into the three broad areas of:1. Storage of energy2. Structure of cell membranes3. Signal of chemical biological activities

Esterification of lipids

Energy: Carbohydrate vs LipidsCarbohydrate Lipid

Terms of storage Short term Long tern

Water solubility Water solubility allows easy transport

Insoluble

Digestion Immediate, starts from the mouth

Latter in the small intestine

Energy yield 38 ATP per glucose 3-5x more than carbohydrate

Proteins Proteins are probably the most important class of

biochemical molecules

Peptide bonds are formed between the carboxyl group of one amino acid and the amino group of the next amino acid. Peptide bond formation occurs in a condensation reaction involving loss of a molecule of water.

Functions of Proteins Enzymes are biological catalysts.

Pepsin, trypsin chymotrypsin are digestive enzymes, of protein in nature.

Defense proteins include antibodies which are specific protein molecules produced by specialized cells of the immune system in response to foreign antigens.

Transport proteins carry materials from one place to another in the body Transferrin – carry iron form the liver to the bone marrow Hemoglobin and myoglobin – carry oxygen

Regulatory proteins control many aspects of cell function, including metabolism and reproduction. Hormones such as insulin and glucagon, for the regulation of blood glucose

levels, are proteins.

Structural proteins provide mechanical support to large animals and provide them with their outer coverings. Keratin – of the hair, nails and skin Collagen and elastin

Classification of Amino Acids With reference to their side chains, amino acids

can be classified into 2 groups:

Nonpolar amino acids – are hydrophobic. They are generally buried in the interior of proteins, where they can associate with each other and remain isolated from water.

embedded in membranes

Polar amino acids – are hydrophilic found on the surfaces of proteins. Protrude out on the surface of membrane

Proteins and the Cell membrane Functions:

Hormone binding site

Electron carriers

Pumps for active transport

Channels for passive transport – hydrophillicmolecules pass

Enzymes

Cell to cell communication

Cell adhesion

Protein Structure Primary structure: the linear arrangement of amino acids in a protein and the

location of covalent peptide linkages between amino acids. Ex. mRNA

Secondary structure: areas of folding or coiling within a polypeptide chain; examples include alpha helices and pleated sheets, which are stabilized by hydrogen bonding.

Tertiary structure: the final three-dimensional structure of a protein; alpha helix and beta pleated sheets are folded into a compact globule which results from a large number of non-covalent hydrophobic interactions between amino acids, such as salt bridges, H-bond, tight packing of side chains and disulfide bonds.

Quaternary structure: non-covalent interactions that bind multiple tertiary proteins into a single, larger protein. Ex. Hemoglobin has quaternary structure due to association of two alpha globin

and two beta globin polyproteins.

Sickle Cell Anemia A variant of HBB (hemoglobin) gene. Amino acid Valine substitutes Glutamine at the 6th amino

acid position of the polypeptide. This substitution creates a hydrophobic spot on the outside

of the protein that binds with the hydrophobic region of another beta chain of a Hgb molecule causing clumping together (polymerization) of Hb molecules into rigid fibers – sickle cell.

Polymerization happens after the O2 is detached from the HBS molecule.

Oxygenation in the lungs depolymerizes the HBS. Polymerization and depolymerization patterns cause the rigidity of the cell resulting to sickled red blood cell

Denaturation of Proteins Denaturation of proteins involves the disruption and

possible destruction of both the secondary and tertiary structures, but not strong enough to break the peptide bonds, the primary structure (sequence of amino acids) remains the same after a denaturation process. Denaturation disrupts the normal alpha-helix and beta sheets in a protein and uncoils it into a random shape.