Biochemistry

The chemical basis of life

Based on organic (carbon) chemistry

Matter is recycled and rearranged for living organisms

• Living matter is made up of different substances.

• Example of substances: pure CO2, glucose, pure salt, H2O…..

CO2

glucose

Atoms, Molecules and Compounds

Atoms - Smallest unit of an element (with properties of that element)

• Nucleus - dense center containing:– Protons - positively charged

particles– Neutrons - particles with no

charge

• Electrons (e-) - small, negatively charged particles that orbit nucleus in clouds or shells (2, 8, 8)

– Valence e- - found in outermost energy level

How many total e-? How many valence e-? What element?

Lewis Dot Diagrams

• The inner shells are not involved in bonding

• Carbon is in group 14, so that means 4 valence electrons

• We often write the element symbol and only the valence electrons

You try…

What does the Lewis dot diagram look like for Oxygen?

What does the Lewis dot diagram look like for Sodium?

Hydrogen?

How about Lithium?

Why are they all the same?

NaH

Li

Ions = electrically charged matter

• Ions form when electrons are lost or gained.• Ionic bonds form when a positive ion is attracted

to a negative ion.

OIL RIG Oxidation is losing, Reduction is gaining

Covalent bond = two

atoms sharing electrons

• “Strong” • Relatively stable• H, O and N can

readily form covalent bonds with C.

Chemical Equations

2H2O2 → 2H2O + O2

Reactants

Hydrogen peroxide

Products

Water & Oxygen

Yield sign

coefficientSubscripts

coefficient

• How many hydrogen atoms are in the reactants?• How many hydrogen atoms are in the products?• How many water molecules are produced?• How many molecules of hydrogen peroxide are

broken down?

Chemical reactions

6CO2 + 6H2O C6H12O6 + 6O2

• Lead to changes in substance or matter.

• Occurs when electrons are transferred between two atoms (lost, gained or shared)

The 17 essential elements in plants (autotrophs)…

CHOPKINS Ca Fe Mg B Mn Cu Zn Mo Cl

Carbon, Hydrogen, Oxygen, Phosphorous, Potassium, Iodine, Nitrogen, Sulfur, Calcium, Iron, Magnesium, Boron, Manganese, Copper, Zinc, Molybdenum, Chlorine

C HOPKINS Café Managed by my cousin Mo Cline

• 96% of living matter: C, H , O, and N

• 4% of living matter: Ca, K, P, S, Na, Cl, Mg, Fe, and trace elements

Hydrogen Bonding• Weak bonds between

a hydrogen of one molecule to an adjacent negative molecule

• Ex: attraction between water molecules.

Properties of Water

Check for Understanding • What is the name of the

compound in the bottle?• What is the molecular

formula?• What is the structural

formula?• How many molecules of

the substance are in the bottle?

• How would you calculate this?

Water

The universal solvent in living things which makes up over 90% of cells and the

majority of Earth

Why water works well in living things

1. Water is Polar and is really good at dissolving substances

2. Water is needed for all cellular chemistry

3. Water molecules adhere to some things

4. Water molecules stick together

5. Water molecules form surface tension

6. Ice floats

7. Water has a high specific heat

Universal solvent

• Water is a solvent (it dissolves stuff for living things)

• Water can dissociate (break apart) most ionic compounds such as salts.

• Solutes + Solvent = Solutions

The Lewis dot structure for water shows the electron from hydrogen and an electron from oxygen being shared in a covalent bond.The other four valence electrons in oxygen are in pairs at the bottom.The lines are a short-hand version of the two dots representing the covalent bonds.

+

-

+

• Polar or angular molecules have a non-linear shape.

• For example, water (H2O), has an angle of about 105°.

• A water molecule has two pairs of bonded electrons and two unshared lone pairs.

Water is a Polar molecule

Create a Polar Water molecule

• On page 2 (left facing page side) of your learning journal and using construction paper, create a water molecule. Try to mimic the 105° angle using a protractor if possible.

• Show the covalent bonds as solid lines between the Oxygen and the Hydrogens.

• The water molecule is Polar because……

_________________________________________________________________________________________________________

Page 2 ++

-

Hydrogen Bonding

• Hydrogen bonds show the attraction between …. ____________________________________________________________________

Page 3

Polarity

• Water molecules are polar.

• Polarity: one end of the molecule is positively (+) charged and the other end negatively (-) charged

• Polarity causes hydrogen bonding between water molecules

• Water molecules are attracted to each other.

• Water molecules “stick” together.

Cohesion

Hydrogen Bonds

Cohesion causes Surface Tension

• Surface Tension• Water molecules tend

to stick together, forming a sort of “skin”

• Some animals can use this “skin” as surface on which it can walk.

Water strider spider

• What properties of water makes a belly flop hurt so bad?

• http://www.youtube.com/watch?v=N8gavevFX-0&feature=fvsr

Surface Tension

Capillary action in Plants

Adhesion• Water molecules are

attracted to surfaces that have charges (hydrophilic).

• Water molecules are repelled from surfaces that have no charge (hydrophobic).

Density

• Water becomes less dense (more space between molecules) when it freezes.

Properties of water’s density

• Ice floats, creating buffer from cold air, enabling organisms to still survive underneath the frozen surface.

Why is carbon the basis for life?

• It has 4 electrons in its outer (valence) electron shell.

• Octet rule: The most stable

elements have 8 electrons in its outer shell, with few exceptions.

• Carbon forms 4 covalent bonds to fulfill the octet rule.

• Therefore, Carbon is really good at forming rings and chains

Methane Acetylene Butadiene Benzene Isooctane

Section 2-3Some Carbon Compounds

Organic compounds• Always contain carbon (carbon can bond

with many other elements)• Small units called monomers join together

to form polymers

Making polymers

• Think of molecules as “mers”

• When 2 monomers join, they form dimers.

• Adding more monomers form polymers.

1 “mer” = monomer 2 “mers” (mer+mer) = dimer 3 or more “mers” (mer+mer+mer+mer) = polymer

4 Important carbon polymers & complex molecules

1. Carbohydrates

2. Proteins

3. Lipids

4. Nucleic acids

Dehydration synthesis - • Joining monomers

into polymers while taking away water molecules

• A-OH + B-HAB + H2O

• Dehydrate – to take away water

• Synthesis – to make

Carbohydrates – sugars, starch, cellulose, chitin• Function: quick energy

(4 calories per gram)

• Building blocks: Monosaccharides or simple sugars like glucose C6H12O6

• Carbohydrates provide cellular energy• Cell Membrane functions and support• Examples:

– Monosaccharides (glucose, fructose, etc)– Disaccharides (sucrose, lactose, etc)– Polysaccharides (starch, cellulose, glycogen, chitin)

Starch

Glucose

Section 2-3 Starch

Proteins – used for structure and function• Purpose: can be used for energy (4 calories per gram) but

mostly used for cell structure and metabolism (enzymes)

• Building blocks: amino acids (20) held together by peptide bonds

• Sometimes very large, complex molecules

General structure Alanine Serine

Section 2-3

Amino group Carboxyl group

Amino Acids

ATP Synthase

Antibodies

Hormones

Hemoglobin

Enzymes

Muscle fibers

Lipids – fats, oils, waxes, sterols• Function: long term stored energy • (9 calories per gram)

• Provides insulation & cushioning• Does NOT have monomer/polymer

structure• Examples:

– Saturated (animal fats)– Unsaturated (plant oils)– phospholipids are the basic structure of cell

membranes.– Steroids are signal chemicals to initiate a process

in the body

Examples of Sterols

• cholesterol • steroids• estrogen• testosterone

Click on the testosterone molecule

Lipid Structure

http://www.google.com/url?sa=i&source=images&cd=&cad=rja&docid=8qhGvfq4t-T4SM&tbnid=S8FMFSkFwMbvFM:&ved=0CAgQjRwwAA&url=http://www.indiana.edu/~oso/Fat/SolidNLiquid.html&ei=MEozUsHlNOXP2wWeo4H4BA&psig=AFQjCNGlHV5ZWXKIguZyjQad8NDA67DnnQ&ust=1379179440930463

Some examples of lipids

Lipids are a vital component of cell membranes

Nucleic acids• Functions: store &

translate hereditary information.

• Building blocks: Monomers of nucleotides (sugar, phosphate, base)

• Examples:– DNA (stores code)– RNA (translates code to

protein)

Parts of a Nucelotide

• Phosphate• Sugar• Nitrogen containing Base

What does DNA do?

• DNA does NOT govern cell activity directly!!

• “DNA is the code for the making of proteins used for structure and function”.

The 4 Bases found in DNA

The 4 Bases found in DNA as Nucleotides

DNA Structure

Organic macromolecule

Monomer(building block)

Polymer(Types)

Carbohydrates4 calories per gram

Monosaccharide (ex: Glucose)

Polysaccharides(ex: sugars, starch, cellulose, glycogen,

chitin, etc.)

Proteins4 calories per gram

Amino acids Structural proteins and enzymes

Lipids9 calories per gram

Glycerol and fatty acids

Fats, oils, waxes, sterols

Nucleic acidsHeredity information

Nucleotides DNA, RNA