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• Office Hours:– Tues 10am - noon– Wed 1 - 2pm– Thur 5 - 6pm– Friday 1 - 2pm– Additional hours available

Energy matters!

• Energy is the capacity to do work!

– Kinetic energy is found in moving objects, like: • a rock rolling down a hill • wind blowing • water flowing

– Potential Energy is stored energy, for example: • a rock poised on top of a hill• coiled spring• food• fossil fuels• Hydrogen gas

Thermodynamics and Energy….

• 1st law of Thermodynamics:

*Energy is conserved; it cannot be created or destroyed

.…energy can be transferred or transformed, but nothing is perfectand with each transfer, there is less energy available to do work…..

• 2nd law of Thermodynamics:

*All natural systems tend to go from a state of order toa state of increasing disorder (entropy); energy disperses, gets lost as heat and movement…...

Chemical bonds

• Takes energy to form bonds• !Energy released when bonds are broken!• Are different kinds of bonds:

– Ionic bonds (opposites attract - positive and negative)

– Covalent bonds share electrons and are quite strong (e.g., H2O)

– Covalent bonds between Carbon atoms are the main biological building blocks….

Biological Chemistry• Inorganic Molecules• Organic Molecules

– Carbohydrates– Lipids– Proteins– Nucleic Acids

Intro to your biochemicals:What is your dry weight?

• 2% = Inorganic molecules– Low energy– Simple, lacking carbon chains

• 98% = Organic molecules– High Energy (covalent bonds)– Complex molecules held together by

carbon chains– Common pattern: monomers

polymers• Dehydration synthesis and hydrolysis

reactions• 4 major classes of organic molecules

– Carbohydrates– Lipids– Proteins– nucleic acids

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Inorganic Components of the Cell

• <2% of the dry weight of the cell• Ions: K+, Na+, Cl-, Mg++, Ca++ • Trace elements (<.01%): Mn++, Mo++, F,

Fe, I, Cr, Co, Cu• Buffers: HCO3-

• Inorganic carbon: CO, CO2, NO, N2

OH H+ + H2Ocondensation

hydrolysis

• Reactants and products:– A + B ---> C

• Often times water is involved in these reactions:

• What are the possibilities? Energy, structural support, mechanical functions, catalysis, information storage

The Synthesis of BIG Molecules

Linking polymers

• Dehydration synthesis

• Hydrolysis

Common Organic Compounds:•Hydrocarbons (Fats and Oils)

-cell membranes-energy storage

•Carbohydrates (Sugars, Starches Cellulose,)

-energy source

• Proteins (Muscles & Enzymes)-cell structure, function-catalyze reactions (tools)

• Nucleic acids (building blocks of DNA and RNA)

-genetic info-protein synthesis

Carbohydrates: CHO:1:2:1• Monosaccharides: simple sugars (C6H12O6)

– 3-7 carbons in length (3, 5 and 6)– Linear and ring structures

• Disaccharides: dehydration synthesis of covalent bonds

• Polysaccharides: complex sugars– Energy Storage (hydrophilic)– Structural

Examples of Disaccharides

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Polysaccharides: glycogen, starch and cellulose Lipids: CHO

• Neutral Fats– Energy Storage (hydrophobic)

• Phospholipids– Amphipathic character– Micelles and Bilayers– Structural role

• Steroids- cholesterol– Structure and communications

Carbohydrates at work Saturated and Unsaturated Fats

Triglyceride synthesis and structure Phospholipid structure

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Phospholipids in water Steroids: cholesterol derivatives• 4 fused carbon

rings• Hormones• Animal cell

membranes

cholesterol

Other Lipids

• Fat Soluble vitamins-– A, D, E, K

• Waxes

• Rubber

Proteins: CHONS• Molecular tools: diversity and versatility

– Structural proteins– Enzymes– Movement– Defense proteins (antibodies)– Hormones– Cell surface receptors– Transport proteins

• Amino acids and peptide bonds• Functional groups, conformation and denaturation• 4 levels of protein structure

Using dehydration synthesis to form a peptide bond between amino acids…

Building a polypeptide chain

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Amino acids with nonpolar R-groupsAmino acids with polar or charged R groups

4 Levels of Protein Structure• Primary Structure - linear chain

– amino acid sequence• Secondary Structure - regular folding

– Non-R Group Interactions– Internal H-Bonds: a-helix

• Tertiary Structure - irregular folding– R group Interactions– The Hydrophobic Effect

• Quaternary Structure - complex folding– Multiple polypeptide chains

Figure 3.14A–D Protein structure (layer 1)

Levels of Protein Structure

Gly ThrGly Glu

Ser Lys

Cys

ProLeu Met

ValLys

ValLeu Asp Ala Val Arg Gly Ser

Pro

Ala

Ile

Asn ValAla

ValHis Val

Amino acids

PheArg

Figure 3.14A–D Protein structure (layer 2)

Levels of Protein Structure

Gly ThrGly Glu

Ser Lys

Cys

ProLeu Met

ValLys

ValLeu Asp Ala Val Arg Gly Ser

Pro

Ala

Ile

Asn ValAla

ValHis Val

CN

O C

C

N H

O C

C

H

Hydrogenbond

O C

N HC

CO

N H

O C

C

N H

C

N

O C

C

N H

O C

C

N H

CO

C

H

N H

CO

H C R

HN

Alpha helix

Amino acids

C N

H

C C

H HO

N

R C C

ON

H

O

C C NH

C C

O

N

H

O

C C N

H

C

O

C N

H

O

C C N

H

C

O

O

CC

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

C C

O

N

H

CC

O

H

NC

Pleated sheet

PheArg

Figure 3.14A–D Protein structure (layer 3)

Levels of Protein Structure

Gly ThrGly Glu

Ser Lys

Cys

ProLeu Met

ValLys

ValLeu Asp Ala Val Arg Gly Ser

Pro

Ala

Ile

Asn ValAla

ValHis Val

CN

O C

C

N H

O C

C

H

Hydrogenbond

O C

N HC

CO

N H

O C

C

N H

C

N

O C

C

N H

O C

C

N H

CO

C

H

N H

CO

H C R

HN

Alpha helix

Amino acids

C N

H

C C

H HO

N

R C C

ON

H

O

C C NH

C C

O

N

H

O

C C N

H

C

O

C N

H

O

C C N

H

C

O

O

CC

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

C C

O

N

H

CC

O

H

NC

Pleated sheet

Polypeptide(single subunitof transthyretin)

PheArg

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Figure 3.14A–D Protein structure (layer 4)

Levels of Protein Structure

Gly ThrGly Glu

Ser Lys

Cys

ProLeu Met

ValLys

ValLeu Asp Ala Val Arg Gly Ser

Pro

Ala

Ile

Asn ValAla

ValHis Val

CN

O C

C

N H

O C

C

H

Hydrogenbond

O C

N HC

CO

N H

O C

C

N H

C

N

O C

C

N H

O C

C

N H

CO

C

H

N H

CO

H C R

HN

Alpha helix

Amino acids

C N

H

C C

H HO

N

R C C

ON

H

O

C C NH

C C

O

N

H

O

C C N

H

C

O

C N

H

O

C C N

H

C

O

O

CC

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

C C

O

N

H

CC

O

H

NC

Pleated sheet

Polypeptide(single subunitof transthyretin)

Transthyretin, withfour identicalpolypeptide subunits

PheArg

4 levels of protein structure

Nucleic Acids: Storing “information”

• Monomers: Nucleotides, four units of information

• Polymers: DNA and RNA– Single and double stranded molecules

• Adenosine triphosphate: ATP, the energy currency of the cell– The phosphate bond– The ATP/ADP Cycle

DNA and RNA: Polymers of nucleotides

Nucleotide Polymers: DNA and RNA

DNA and RNA: The flow of

information in the cell:

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The ATP Cycle: What’s happening when you eat and run?

ATP: The energy currency of the cell

Metabolism: the sum of all chemical reactions occurring in

the cell.• Catabolism - energy releasing reactions

– Oxidations, hydrolysis rxns.• Anabolism - energy requiring reactions

– Reductions, synthesis rxns– The role ATP