Biochemistry

The Chemistry of Life

Basic Chemistry

• Atom– Simplest unit of matter– Made up of three different “subatomic”

particles

Subatomic Particles

• Protons– Have a positive charge (+)– Have mass– Located in nucleus

• Neutrons– Are neutral, have no charge (0)– Have mass– Located in nucleus

• Electrons– Have a negative charge (-)– Almost no mass– Located in “energy levels” outside of nucleus

• Atomic Number: – Tells you the number of protons an atom has,

and also the # of electrons

Atoms are neutral

# Protons (+) = # Electrons (-)

• Atomic Mass:– Add together the number of protons and

neutrons in nucleus of atom– Electrons hardly contribute any mass

• Isotopes:– Atoms of one type of element with different

atomic masses

– Same # of protons– Different # neutrons

– Changes the mass only, the properties are the same

• Radioactive Isotopes:– The nucleus of some isotopes is unstable– The atom with emit radiation – Radiation can be measured with tools

• ex. Geiger counter

– These isotopes can be used as useful tools in science

– Ex: • Carbon-14 dating• Radiation treatment for cancer

• Elements– Substance made of only one type of atom– Each element has a unique atomic #

– Elements most commonly found in living things

• Carbon (C) • Hydrogen (H)• Oxygen (O)• Nitrogen (N)

• Compounds– Two or more elements chemically combined – Atoms held together by bonds.– Once bonds form, compounds will have new,

and different properties

– Organic Compounds• Contains carbon and hydrogen (and often O, N)

• Ex: Glucose (C6H12O6), carbohydrate, lipids, proteins

– Inorganic Compounds• Doesn’t contain carbon and hydrogen together

• Ex: H2O, CO2, NH3, NaCl

• Why do atoms form compounds?

– Bonds that form between atoms give atoms a stable outer electron level.

– Called a “stable octet” of valence electrons (8)

Types of Chemical Bonds

• Ionic Bonds:– One or more electrons are transferred from

one atom to another.– Neutral atoms become positive & negative ions– Forms salts

• (Ex: NaCl)

Ionic bond = attraction between (+) and (-) ions

• Covalent Bonds:– Electrons are shared between atoms– Each bond represents a shared pair of electrons– Can form single, double or even triple bonds

Covalent bonds form molecules– Subscripts in the formula tell # of each atom

• Ex: H2O, NH3, CO2, CH4

Ionic Bonds:

Transfer electrons

Covalent Bonds:

Share Electrons

Properties of Water

• Water is necessary for life

• Contains covalent bonds

Water Molecules: H2O

(look like Mickey Mouse)

• Water is a “Polar” molecule (like a magnet)

• The bonds are “polar”– Oxygen attracts the electrons

more than Hydrogen

• Hydrogen Bonding: bonding between the (+) H of one molecule and the (-) end of another molecule.

–Makes water good at sticking to itself and other substances–Makes water good dissolver

• Cohesion: water sticks to itself– Ex:

• Water forms “beads” on smooth surface• Surface Tension allows insect to “skate”

• Adhesion: water sticks to other substances

– Ex: Capillary action: water molecules rise up small tubes

• Heat Capacity:– Water has a relatively high heat capacity– Ex:

• Lakes and oceans can absorb a lot of heat from sun without a drastic temperature change

• Water as a Solvent:– Dissolves most ionic and covalent substances– “Universal Solvent” = many things can

dissolve in it.

– Solute: substance being dissolved– Solvent: substance in which solute dissolves– Solution: evenly disbursed mixture

– Suspensions: material in the water but just suspended not dissolved (ex: blood cells in blood)

pH of Solutions• pH Scale: way to measure concentration

of H+ ions in solution– Ranges from 0 to 14– Pure water is neutral pH = 7

• Litmus Paper:– Used to test pH of a solution

• Red = acidic• Blue = basic

• Acids: Form H+ ions

–pH is <7

–Ex: HCl (stomach acid), lemon juice

• Bases: Produces OH- (hydroxide ions)– Also called “alkaline”

– pH >7

– Ex: Lye (NaOH) used as drain cleaner

• Buffers:– Maintain pH at a certain level – Usually between 6.5 – 7.5 (close to neutral)– Helps to maintain homeostasis in organism

Major Types of Chemical Reactions

• Dehydration Synthesis: (Condensation)

– Chemically combine two smaller molecules– Water is removed

– “Dehydrate” = remove water– “Synthesis” = to make

• Hydrolysis:

– Break apart large molecule into smaller pieces

– Water is added

– “Hydro” = water “Lysis” = to break

• Polymerization:– Create a large molecule (polymer)– Join up smaller “monomer” units– Often a dehydration synthesis reaction

Ex: Join amino acids (monomer) to make protein (polymer)

Join glucose (monosaccharide) to make starch (polysaccharide)

Organic Compounds

Carbohydrates

• Sugars and starches• FUNCTION:

– Used as an energy source– Energy released during cellular respiration

• Made of carbon, hydrogen and oxygen

Ex:

C6H12O6, C12H22O11

• Ratio of H of O is always 2:1

• Basic Structure:– “Ring” made of 5 carbons and 1 oxygen– Rings can join up by dehydration synthesis

3 Types of Carbohydrates

• Monosaccharide's: 1 sugar ring

• Disaccharides: 2 sugar rings

• Polysaccharides: many sugar rings

• Monosaccharide's: (Simple sugars)– All have formula C6H12O6

– Single ring structure– End in “-ose”– Ex: glucose, fructose, galactose

• Disaccharides: double sugars– All have formula C12H22O11

– End in “-ose”– Ex: sucrose, lactose, maltose

• Polysaccharides: 3 or more sugar units

• Ex: – Starch (energy storage in plants)– Glycogen (how animals store sugar in liver)– Cellulose (plant cell walls)– Chitin (insect exoskeletons)

• Simple sugars form into complex sugars by dehydration synthesis (condensation).

• Combining molecules by removing water

Monosac. + Monosac. Disac. + Water

C6H12O6 + C6H12O6 C12H22O11 + H2O

and H2O

• Complex sugars are broken down into simple sugars by hydrolysis.

• Breaking down molecules by adding water

• Also called chemical digestion

Disac.+ Water Monosac. + Monosac.

C12H22O11 + H2O C6H12O6 + C6H12O6

Dehydration Synthesis and Hydrolysis are

OPPOSITE Reactions

**Chemical reactions are often enzyme mediated.

Lipids

• Fats, oils and waxes• FUNCTION:

– Long term energy storage– Insulation – Protective coating around cells– Cell membranes

• Made of carbon, hydrogen, and oxygen• Ratio of H to O is not 2:1

– Ex: C15H26O6 (fewer oxygens)

• Animals store energy mostly as fats

• Plants store energy mostly as oils

Lipids

• Made up of:– 1 glycerol molecule– 3 long fatty acid chains

– Looks like a giant letter “E”– Also called a “triglyceride”

GLYCEROL

FATTY ACID CHAIN

Note: 3 “OH” groups

Note: CARBOXYL GROUP: “COOH” group at end of molecule

Basic Lipid Structure

• Lipids are:– formed by dehydration synthesis– broken down by hydrolysis

Saturated vs. Unsaturated Fats

– Saturated: • all single bonds between carbon atoms

– Unsaturated:• One or more double bonds between carbon atoms• Makes fatty acid more bent

Proteins

• Protein Structure:– Made of carbon, hydrogen, oxygen and

NITROGEN

– Large complex polymer molecules that can have a large range of sizes, shapes and properties

Proteins• FUNCTIONS:

– Enzymes: speed up chemical reactions

– Hormones: chemical messengers

– Antibodies: defend against disease

– Hemoglobin: binds oxygen to red blood cells

– Cell growth and repair

– Cell Membrane Channels

• Amino Acid: basic building block of proteins

Parts of an Amino Acid

• Carboxylic Acid Group

• Amino Group

• “R”-Group (varies depending on amino acid)

Examples of Different Amino Acids

• There are 20 different amino acids

• All have different “R” groups

Peptide Bond: bond between amino acids

Dipeptide: two amino acids joined.

Polypeptide: many amino acids joined– Proteins are polypeptides

Forming a Peptide Bond

and H2O

+ H2O

• Amino acids join up to form proteins at ribosome• The function of the protein comes from it’s

specific sequence of amino acids and the shape the protein forms

• The “code” for the specific sequence of amino acids comes from DNA

Nucleic Acids

• Large complex macromolecule

• Stores information in “code”

• Composed of carbon, hydrogen, oxygen, nitrogen and phosphorus

Structure of Nucleic Acids:

•Made of chains of nucleotides

Nucleotide: (made of 3 components)– Phosphate Group– Sugar– Nitrogenous Base

Two Types of Nucleic Acids

• DNA: (Deoxyribonucleic Acid)– Contain genetic information– Found in nucleus– Divides when cell divides

• RNA: (Ribonucleic Acid)– Copies code from DNA– Takes code to ribosomes for protein synthesis– Found in nucleus and cytoplasm

Differences Between DNA & RNA

– DNA: • Double strand of nucleotides• Sugar is deoxyribose• Nitrogenous Bases

– Adenine, Thymine, Cytosine, Guanine

– RNA: • Single strand of nucleotides• Sugar is ribose• Nitrogenous bases

– Adenine, Uracil, Cytosine, Guanine

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