Chemical Reactions in Living Cells• Chemical Reaction

– Involves the making and breaking of chemical bonds

– Represented as a “short statement”:

H2O H2 + O2

How would you balance this?

22 22

Does this happen on its own?

• Activation Energy: The amount of energy needed to initiate a reaction

Biochemistry: Chemical Reactions in Living Cells

δ +

δ +

δ -

Water molecules are polar covalent bonds.

Biochemistry: The unique properties of water

They are attracted to other water molecules through relatively weak Hydrogen bonds.

Can water form ions?Yes, at a very small rate (1 out of 500,000,000!)

H2O H+ OH-+

+ -

How would you quantify (count) this ionic disassociation? The pH scale

The “powerpower of HydrogenHydrogen” scale

pH

Biochemistry: The unique properties of water

Stomach Acid, lemon juiceVinegar, cola

Tomato juice

Black coffee; RainwaterUrine

Pure water; Human blood

Seawater

Milk of magnesia

Household ammonia

Household bleach

Oven cleaner

Incr

easi

ngly

Aci

dic

Inc

reas

ingl

y B

asic

Neutral

<[H+] >[OH-]

[H+] = [OH-]

>[H+] <[OH-]

Besides water, what elements and compounds are essential to life?

Organic compounds1. Mostly contain Carbon, Hydrogen, Oxygen,

Nitrogen, Phosphorus and Sulfur*

*For Homework: Left Side IntNB Assignment: Write an Acrostic Poem for the six elements often found in organic compounds

Carbon

C CC CC C

H

H HH

H HH

OHO H

HHHO O

O

O

Organic Compounds: An Overview

Organic compounds (continued…)2. Four categories of organic compounds:

a. Carbohydrates

b. Lipids

c. Proteins

d. Nucleic Acids

3. All formed and separated in similar waysa. Formation (Polymerization): Dehydration

Synthesis

b. Separation: Hydrolysis

Hey Sugar, I sure am happy that you’re a Carbohydrate

like me.

Awww, how sweet!

Hurry up, Lipids! You should have more energy

stored up than this!

Does this bond structure make

me look fat?

Hi there! My name is Polly

Peptide.

Can you believe that each of your cells contains

about 2 meters of me?

Organic Compounds: Carbohydrates

Polymerization

• Polymerization (definition):– Forming of large organic macromolecules by

the joining of smaller repeating units called monomers

Bonding: Polymerization

Dehydration Synthesis

• Dehydration Synthesis is the removal of a water molecule to form a new bond.

HOH

H2O

HO H

HHO

Short Polymer Monomer

Dehydration removes a water molecule forming a new bond

1 2 3

1 2 3 4

Bonding: Polymerization: Dehydration Synthesis

Hydrolysis

HOH

H2O

HO

H

H

HO

Short Polymer Monomer

Hydrolysis adds a water molecule to break a bond

1 2 3

1 2 3

4

• Polymers are broken by adding water.

• Literally, “Water Splitting”

Bonding: Polymerization: Hydrolysis

C CC CC C

Carbon = The element of life

• Carbon’s Valence has ____ electrons

• Can bond with ____ elements

• Can form chains, rings, branches, & isomers

44

CCHO

OHH

HCC

HO OH

H H

What biological impact do you think isomers have on living systems?

Bonding: Carbon

Thalidomide: an optical isomerBonding: The importance of chemical structure

Bond energy

• When bonds are made, energy (E) is stored.

• When bonds are broken, energy (E) is released for use.

Bonding: Bond Energy

Glucose: A Monosaccharide Fructose: A Monosaccharide

Sucrose: A Disaccharide

Carbohydrates

• Carbohydrates are:– an important energy (E) source– Cellular structures

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

• General Formula (CH2O)n

Organic Compounds: Carbohydrates

CH2O

Water = hydrateCarbon hydrate

Organic Compounds: Carbohydrates: Monomers

Carbohydrates

• Monosaccharides (simple sugars) – Contain 3-7 Carbons each

• Examples: Glucose, Galactose, FructoseGlucose

Organic Compounds: Carbohydrates: Dimers

Carbohydrates

• Disaccharides (two sugars)

• Examples: Sucrose, Maltose, Lactose– Maltose = Glucose + Glucose– Lactose = Glucose + Galactose

Sucrose

Glucose Fructose

Organic Compounds: Carbohydrates: Polymers

Carbohydrates

• Polysaccharides (many sugars)

• Examples: Starch, Glycogen, CelluloseStarch Cellulose

Chloroplast Starch

Glycogen

Liver Cell

Plant Cells

Plant Cells

Cellulose

LipidsOrganic Compounds: Lipids

• Lipids function in:– Energy (E) storage, – forming cell membranes, – and as chemical messengers

(e.g., hormones)

• Nonpolar (hydrophobic)

• Made up mostly of Carbon and Hydrogen (with a few Oxygen)

Lipids1. Fats (Triglycerides)

– Glycerol + 3 Fatty Acids– Saturated = No Double Bonds (solid)– Unsaturated = Double Bonds (liquid)

Organic Compounds: Lipids: Fats

OH

OH

OH

OH

OH

OH

Ester Bonds

Lipids2. Phospholipids

– Glycerol with Phosphate Head + 2 Fatty Acid Chains

– Amphiphilic (“Both” “lover”)• Hydrophilic head• Hydrophobic tail

– Forms 2 layers in water– Makes up cell membranes

Organic Compounds: Lipids: Phospholipids

Phosphate

Glycerol

Fatty Acids

Organic Compounds: Lipids: Sterols

Lipids

OH

O

Testosterone

HO

O

Estrogen

3. Sterols– Lipids whose Carbon Skeleton consists of 4

fused rings– Includes:

• Hormones• Cholesterol• Cortisol

– Makes up cell membranes

HOOH

O

O

OH

Proteins

• Made up of Carbon, Hydrogen, Oxygen and Nitrogen (and some Sulfur)

• Many functions represented through different types of proteins

Organic Compounds: Proteins

Proteins

• Enzymes: Catalysts that speed up the rate of a chemical reaction – Build up or break down substrate

• Fit together like a “lock” and a “key”

– Not used up in the reaction– Work in a very specific biological range– Usually end with “-ase”

Organic Compounds: Proteins: Functions

Hi sweeties, Do you remember

me?

In addition to what you know. I am a substrate.

I am an enzyme. I am going to try to convert you.

I am now a product.

I am a glucose now.

I am a product, too.

I am a fructose now.

I am completely unchanged, and ready for some more sucrose!

I am the active site. The substrate binds

to me.

Proteins

• Structural Proteins– Provides mechanical support to cells and

tissues

• Transport Proteins– Transports small ions or molecules

• Motor Proteins– Enables structures to move

Organic Compounds: Proteins: Functions

Proteins

• Hormones (signaling proteins)– Carries signals from cell-to-cell– e.g., insulin

• Storage– Stores small molecules or ions– e.g., iron is stored in the liver in ferritin

• Other specialized functions– Defense (antibodies), – Receptor proteins (in eyes and muscles to

detect stimulus)

Organic Compounds: Proteins: Functions

Proteins• Monomers: Amino Acids

– Peptide Bond: Bond between 2 Amino Acids: Amino end (NH2) and the Carboxyl end (COOH)

Organic Compounds: Proteins: Monomers

HH22OO

Side Chains

Backbone

R Group =

Amino end Carboxyl end

Proteins

• R Groups (Side chains)– Differ in:

• Size• Charge• Polarity

• There are 20 protein-building Amino Acids– 9 Essential Amino Acids

• Can’t be synthesized by the body, but are necessary for life

Organic Compounds: Proteins: Monomers

Hydrophilic Amino Acid Hydrophobic Amino Acid

Proteins

• Polymers: Polypeptides “Many Peptides”

• Four Levels of Structure– Primary (1°)– Secondary (2°) – H bonds– Tertiary (3°)– Quaternary (4°) – several

polypeptides

• These specific shapes allow proteins to function

Organic Compounds: Proteins: Polymers

Polypeptides

Organic Compounds: Proteins: Denaturation

Proteins

• Denaturation– When the protein loses its

shape, and becomes non-functional due to:

– Changes in • temperature • pH• salinity (salt concentration)• alcohol concentration

Nucleic Acids

• Nucleic Acids– Informational Polymers: Code for all of the

proteins in an organism– Monomers: Nucleotides

• Phosphate Group• 5-Carbon Sugar• Nitrogenous base

Organic Compounds: Nucleic Acids

Nucleic Acids

• DNA (Deoxyribonucleic Acid)– Backbone sugar: Deoxyribose– Four Bases

• Adenine (A)• Guanine (G)• Thymine (T)• Cytosine (C)

• RNA (Ribonucleic Acid)– Messenger RNA: mRNA conveys the

instructions to build proteins from the genetic information in DNA

– Differences from DNA:• Backbone sugar: Ribose• Uracil in place of Thymine

Organic Compounds: Nucleic Acids

Deoxyribo

Adenine Guanine

ThymineCytosine Uracil

Flow of Information

DNA

RNA

Protein

Organic Compounds: Nucleic Acids and Proteins