Biochemistry

Atoms

• An atom that has either gained or lost an electron is called an Ion

• CONSERVATION OF MASS – – Things can move / change position. But ALL the mass

that is available is ALL the mass that will ever be available.

• Periodic Table – Mass Number – how much it weighs in grams– Atomic Number – location on the periodic table

(number of protons)– Isotopes – variations in elements based on number of

neutrons

Atomic Mass = # Protons + # NeutronsThe atomic mass of carbon = 12The atomic # of carbon = 6 = the # of protons# neutrons = Atomic Mass - # protons# neutrons =12 - 6 = 6

1

2

3

4

5

6

7

2

3

4

5

6

7

3

4

5

6

4

5

s- block

d- block (n-1)

p- block

f- block (n-2)

Label your Periodic Table

Compound-2 or more elements combined chemically

– A compound is made up of different elements– The smallest particle of a compound with

independent existence is: The molecules of that compound Ex: A CO2 Molecule as opposed to millions of CO2 Molecules

• Nobel Gases: always have their outside electron shell full: They never bond with other atoms

Covalent Bonds:

• When Atoms share electrons in their outer energy levels:

• O2 H20

Ionic Bonds: an electric attraction between two or more differently charged atoms or groups

• Atoms that have gained or lost an electron are called ions.

• NaCl HCl

Properties of Matter

• Physical Properties – Properties that do not change the

chemical nature of matter• Examples

– Color, Smell, Freezing Point, Boiling Point, Melting Point, Polarity, and Density

– Physical change – change in its state

Properties of Matter• Chemical Properties

– Properties that DO change the chemical nature of matter

• Examples– PH, Combustion, reactivity with water,

explosions!– Compounds put together that create a new

compound

States of Matter

• Physical Changes– Solid, Liquid, Gas

• Chemical Changes– Changes properties of matter all

together• Ex. Spoiling Milk

Properties of Chemical Change

• Forms or breaks chemical bonds

• Energy is taken (endothermic) or energy is released (exothermic)

• One or more new chemical substances are formed

• The process is usually difficult to reverse

Examples of Chemical Change

• Digestion

• Photosynthesis

• Respiration

• Burning

• Decomposition

Structure of Atoms

• Protons:– A sub atomic particle that is located in the

nucleus and has a positive charge

• Neutron: – A sub atomic particle that is located in the

nucleus and has a neutral charge

• Electron: – The smallest of the subatomic particles that

carry a negative charge and surround the nucleus.

Energy and Chemical Change

• Any energy an object has because of its position is called Potential energy.

• The energy in motion (actual) is called Kinetic energy.

Atoms• Electrons circle the nucleus in the

electron shell

• Noble gases all have there outer most electron full of electrons.

Mixtures

• Solution– Homogenous (same) mixture of

components that stay mixed• Sugar and water

• Suspension– Mixture of two substances that may mix

right away, but do NOT stay mixed up• Starch and water

Mixtures

• Colloid– A suspension of small particles that are

dispersed into another substance• Partial Mix

Types of Bonds

• Cation-– A positivily charged ion (more protons

than electrons)

• Anion – – Negatively charged ion that contains

more electrons in its outer shell compared to the protons.

Bonds

• Ionic Bond– Sending an electron to an atom that is

positively charged (opposing charges attract)

• EX.– Na (+) = Cl (-)

» Salt – H (+) = Cl (-)

» Hydrochloric Acid

Bonds

• Covalent Bonds– Sharing of electrons for the benefit of

both• EX.

– O2

– H20

Bonds

• Hydrogen– Weaker bond

• It is the type of bonds that hold our DNA molecules together.

– Must include a Hydrogen molecule– Also, usually attaches to a electronegative

atom

Properties of Water

• Polarity of water– Water is made up of two polar covalent

bonds, but the molecule has no overall net charge

– Oxygen slightly negative (heavier)– Hydrogen slightly positive (lighter)

• Allows for cohesion of other water molecules

Properties of water

• Temperature stabilizing effects– Water is warm – hydrogen electrons

move about and break leading to evaporation

– Water is cold – Hydrogen molecules get closer together and form a lattice (solid) structure that we know as ICE

Properties of water

• Water Cohesion-– Water molecules binding to other water

molecules• Hydrogen bonds attracted to each other

and stick together!

– Ions and polar molecules easily dissolve in water. The water molecules surround and separate the solute being dissolved.

Acids, Bases, and Buffers

• pH – “Potential Hydrogen ions”..– Measurement of how many

concentrated H+ ions there are.• 1 – very acidic• 14 – very basic• 7 – Neutral

• Acids – donate H+ to a solution increasing the conc. of H+ in the solution

• Bases – Absorb / accept H= and they lower their concentration in the solution

• Buffers – Are compounds that help absorb or donate H+ at the appropriate time as to keep a solution balanced

• Salts – Can be formed by the combination of a strong acid and a strong base

Acids, Bases, and Buffers

Carbon Compounds

• All life organisms are made up of Carbon – Organic Molecules

• Organisms consist mostly of which atoms?– Carbon, Nitrogen, Hydrogen, Oxygen,

Phosphorous, trace elements

Chemistry of Carbon

• Carbon has how many bonds?– How many valence electrons does

carbon have?• Carbon can bond to 4 other molecules• Carbon can form a single, double, or triple

bond

Functional Groups of Carbon

• A chain of carbon and hydrogen is called a hydrocarbon. – EX. Methane, Ocatane

• Just C and H

• There is ENERGY in these bonds!!! Do you recognize the molecules?

Other important carbon based groups:

• Hydroxyl Group:– OH

• Carboxyl Group:– COOH

• Amino Group:– NH2 or NH3

• Phosphate Group:– PO3 or PO4

Hydroxyl

• –OH– organic compounds with OH = alcohols – names typically end in -ol

• ethanol

Carboxyl

• –COOH – C double bonded to O & single bonded

to OH group• compounds with COOH = acids

– fatty acids– amino acids

Amino

• -NH2

– N attached to 2 H• compounds with NH2 = amines

– amnio acids

• NH2 acts as base

– ammonia picks up H+ from solution

Phosphate

• –PO4

– P bound to 4 O • connects to C through an O• PO4 are anions with 2 negative charges• function of PO4 is to transfer energy

between organic molecules (ATP)

How do cells build organic compounds?

• Reactions: the use of raw materials “atoms”, energy, and enzymes to do one of the following

– Functional group transfer – One molecule gives up a functional group which is then attached to another molecule

– Electron transfer – One or more electrons is stripped from one molecule and donated to another molecule

– Rearrangement – A juggling of internal bonds converting one type of organic compound into another

– Condensation (Hydrolysis) – the removal or addition of water to create new bonds and break existing ones

– Cleavage – A molecule splits into two smaller ones.

Important construction terms

• Monomer : a molecule that is building block for something larger

• Dimer : two monomer stuck together• Polymer : more than two monomers stuck

together• Dehydration : Pulling water out of two

molecules so as to bind them together• Hydrolysis : Adding water to a molecule to

break it apart

Carbohydrates

• Contain – Carbon, Hydrogen, and Oxygen in a 1:2:1 ratio

– Example: Glucose (C6H12O6)

• The monomers that make them up are called monosaccharides

What are Carbs used for?

• Uses – Energy, Structure, Signals

• These monomers usually form a ring structure, especially in water.– Examples Glucose and Fructose

Carbohydrates• When do you notice about glucose and

fructose?– They have the same number of atoms but

they are in a different arrangement.• They are called isomers

– The condensation of two monosaccharides is called a disaccharide.

• Example - Sucrose

Carbohydrates

• The largest carbohydrates are starches

Carbohydrates

• The reaction that breaks down complex molecules – reverse condensation is called hydrolysis.

– We have an enzyme in our body to do this process

• Amylase (found in saliva)– New Study in sleep deprivation

Starch VS. Cellulose

• We can break down starches, but our body cannot break down cellulose.

Tests for Carbohydrates

TEST Monosaccharides Disaccharides Polysaccharides

Iodine No Change No Change Turns Black

Benedicts Solution

Color changes with heat

No Change No Change

Lipids

• Lipids contain– Carbon, Hydrogen, and Oxygen

• EX – Fats, Phospholipids, waxes, sterols “Steroids”

Lipids

• They are used in living things for energy storage, structural molecules, and signaling molecules

• Basic Structures – Tail and Head

Triglycerides

• Saturated Fats:• Only form single bonds with Carbon

Atoms: No room for more hydrogen atoms

• Unsaturated Fats: • Form double bonds in Carbon atoms

All lipids are insoluble in water – A good test? Water SolubilityPaper smear test

Phospholipids

• Found in the cell membrane

Cell Membrane

Test for Fats

TEST FAT NOT A FAT

Brown Paper Paper Changes

(transparent)

Dries the same

Water Solution

They separate

They Mix

Proteins

• Proteins are made up of:– Carbon, Hydrogen, Oxygen, & Nitrogen

• Ex. – Eggs, seeds, hair, and meat

– Basic Monomers – Amino Acids (aa)

Amino Acids (aa)

• Each aa is going to contain four distinct groups– Carboxyl Group – COOH– Amino Group – NH3– R Group (20 different R groups)– A Hydrogen atom – H

• If there are twenty different amino acids

Protein Structure

• Through a series of dehydration reactions, aa are joined into a chain to form a protein.

• A special bond is formed– Peptide Bond

• Polypeptide – polymer of aa

Protein Structure

• When you have two aa together – Dipeptide

• Three or more aa– Polypeptide

These are used by living organisms for:

Enzymes, structures, transport, and signaling

3D structure of proteins

• Level 1

• Level 2

• Level 3

• Level 4

Proteins

• DENATURATION

• Is the breaking down of molecules

• Other molecules can be attached to proteins– Glycoproteins and Lipoproteins

Test for Proteins: Xanthopoetic testTEST PROTEIN NOT A

PROTEIN

Nitric Acid Turns Yellow No Color Change

Enzymes

• A chemical that speeds up a reaction is called a – Catalyst

• Proteins that do this process are called – Enzymes

• Ex. – Sucrase, Amylase, Lactase

Nucleic Acids

• All instructions for cellular activity are in the Nucleic Acids– Two kinds of Nucleic Acids

• DNA– Holding genetic information– Where is it found?

» In nucleus on chromosomes

• RNA– Holding info for building proteins– Where are they found?

» Everywhere in a cell

What makes them up?

• Complex monomers – Nucleotides

• Bonds between them are called phosphodiester bond– Formed by a phosphate