BiochemistryThe chemical basis of life

Based on organic (carbon) chemistry

Carbon Compounds

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. Proteins3. Lipids4. 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 function

• 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

Enzymes -Functional proteins in your body

“Enzymes are proteins that act as catalysts and control chemical reactions”.

• Enzymes are usually named with –ase ending.• Ex: Peptidase in the stomach breaks down peptide

bonds (proteins) • Substrates are the molecules enzymes act upon (Ex:

proteins or disaccharides)• Enzymes are catalysts = speeds up reactions

“ose” for sugars “ase” for enzymes

• What would you call the enzyme that breaks down sucrose?

• What would you call the enzyme that breaks down lactose?

• What would you call the enzyme that breaks down maltose?

How enzymes work on reactants (substrates)

Label the diagram in your notes.

Two laws of thermodynamics

• 1st law of thermodynamics: conservation of energy. Energy is neither lost nor gained but just changes from one form to another.

• 2nd law of thermodynamics: entropy– Tendency to move from order to disorder.

Conservation of energy

• Energy can neither be created nor destroyed.

• Energy can only be changed from one form to another.

Entropy: disorder

• For living beings or just molecules to be organized, there must be a lot of energy.

• Very little energy is needed to create disorder.

A B + C

• Breaking down a reactant (A) into products (B and C)

• Requires little energy to start breaking down substances

• Exergonic reaction – releases energy

A + B C

• Making a product (C) from reactants (A and B)

• Requires much energy to start this reaction – Why?

• Endergonic reaction – absorbs energy

Energy graphs

Activation energy

• Activation energy: how much energy is required to start a reaction

• http://www.youtube.com/watch?v=-vgkvUxxZFg&feature=related

• http://www.britishpathe.com/record.php?id=50144

Activation energy on two types of reactions

Energy-Absorbing Reaction Energy-Releasing Reaction

Products

Products

Activation energy

Activation energy

Reactants

Reactants

Graph of Energy of a reaction

Which graph is Endergonic?

Which graph is Exergonic?

Enzyme action

• Enzymes: special proteins that help to reduce the activation energy (Ea)

• What will enzymes do to the speed (rate) of a reaction?

Effects of Enzymes

Reaction pathwaywithout enzyme Activation energy

without enzyme

Activationenergywith enzymeReaction pathway

with enzyme

Reactants

Products

• How do enzymes help with the activation energy required for metabolic processes?

Enzymes and Metabolism

• Enzymes facilitate the metabolic processes (chemical reactions) to sustain life.

• Enzymes help to maintain homeostasis.

• Enzymes help to build cells.

• Enzymes help in reproduction.

Glucose

Substrates

ATP

Substratesbind toenzyme

Substratesare convertedinto products

Enzyme-substratecomplex

Enzyme(hexokinase)

ADPProducts

Glucose-6-phosphate

Productsare released

Section 2-4

Figure 2-21 Enzyme Action

Active site

Enzyme activity (4)

Proteins can be Denatured

• Denature – “destroying the nature or the shape”– changes the Secondary,

Tertiary or Quaternary structure of a protein.

• Salts, Heat and pH changes affect proteins (polypeptides) and may denature them.

In living cells, biological pathways are NOT a one step process

• What would happen in this process if enzyme 2 was denatured?

A

B

C

D

E

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

• Provides insulation & cushioning• Building blocks: 1 glycerol & 3 fatty acids• 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

Base Pairing in DNA

A ↔ TC ↔ G

How does the decoding work?• The ATC’s & G’s of the DNA are transcribed into an

RNA code then read in groups of 3 letters.• DNA: TAC,GCT,CCC,TCT,AAT,ATC,CTG

• RNA: AUG,CGA,GGG,AGA,UUA,UAG,GAC

• Ribosomes read AUG – CGA – GGG – AGA – UUA – UAG – GAC.

• Each 3 nucleotide “word” is called a codon.

Ribosomes use this decoding scheme to determine how to build the appropriate protein.

DNA

Polypeptide= protein

Amino acids

Organic MacroMolecule Foldable1. Name of macromolecule group

– Water, Vitamins & Minerals, Lipids, – Nucleic Acids, Proteins, Carbohydrates

2. Types of molecules in the group• (ex, sugars, starches, cellulose, chitin)

3. Monomer used as building blocks• (built from monosaccharides)

4. Examples of the polymers• Simple sugars, honey, pasta, potato, rice, grains)

5. Pictures/examples (3) of food sources that provide the building blocks to our bodies.

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