Raw materials and fuel for our bodies I. Atoms and...

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Chapter 2: Chemistry

Raw materials and fuel for our bodies

Lecture 2 Outline

I. Atoms and Bonds II. Water III. Acids, Bases, and Buffers IV. Chemistry of Carbon V. Carbohydrates VI. Lipids VII. Proteins VIII. Nucleic Acids

Everything is made of atoms.

q  An element is a substance that cannot be broken down chemically into any other substances.

q  An atom is a bit of

matter that cannot be subdivided any further without losing its essential properties.

I. Atoms and Bonds

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Atomic Structure Atomic Numbers

Insert new figure 2.3

25 Elements Found in Your Body and the Big 4

2.2 An atom’s electrons determine how (and whether) the atom will bond with other atoms.

Electron shells

3

Electron Shells

Insert new fig 2-6 Products of bonding!

Molecules

Covalent Bonds

Insert fig 2-9 to right side of slide

Ions and Ionic Bonds

Insert fig 2-10

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Hydrogen Bonds

Insert fig 2-11

Insert fig 2-12

II. Water

• H20 is a polar molecule attracted to itself. This is the critical factor for all of water’s most important properties.

• Most important molecule for life on Earth.

• Life began in water and evolved here for 3 Billion years before spreading to land.

• Our cells are 70-95% water; we can only survive for 1 week without water.

Properties of Water:

• ICE FLOATS: Solid H20 is ~10% less dense than liquid form. This unusual feature results in a crystal-like matrix of H20 molecules in ice. Insulates water underneath.

• COHESION: Water molecules stay close together due to hydrogen bonding.

• HIGH SPECIFIC HEAT: A great deal of energy is required to break H-bonds to release/vaporize individual molecules.

• EVAPORATIVE COOLING: H20 molecules with highest energy leave water reservoir as vapor, lowering the T of remaining liquid.

• EXCELLENT SOLVENT: Dissolves polar, nonpolar substances and salts.

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2.4 Hydrogen bonds make water cohesive.

Insert fig 2-13

Cohesion

Heat Capacity

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Why do coastal areas have milder, less variable climates than inland areas?

Low Density as a Solid

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

A water-soluble protein

This oxygen is attracted to a slight positive charge on the lysozyme molecule.

This hydrogen is attracted to a slight negative charge on the lysozyme molecule.

(a) Lysozyme molecule in a nonaqueous environment

(b) Lysozyme molecule (purple) in an aqueous environment such as tears or saliva

(c) Ionic and polar regions on the protein’s Surface attract water molecules.

δ+ δ–

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2.6 Living systems are highly sensitive to acidic and basic conditions.

III. Acids, Bases, and Buffers


Hydrogen Ions and Hydroxide Ions

Ionized Hydroxide Molecule

OH -

Non-Ionized Water Molecule

H2O O O

H H H


pH Scale

q The amount of H+ in a solution is a measure of its acidity and is called pH.

q Acids

q Bases


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Blood pH

q Buffers

•  can quickly absorb excess H+ ions to keep a solution from becoming too acidic

•  can quickly release H+ ions to counteract any increases in OH- concentration


Four Types of Macromolecules

q Carbohydrates

q Lipids

q Proteins

q Nucleic acids

MACROMOLECULES

IV. Chemistry of Carbon • Whereas H2O is the universal medium for life, C makes up the majority of the cell’s structures. • The C in our bodies ultimately derives from the action of plants. Plants harness the power of sunlight to convert CO2 into Carbon-based macromolecules.

IV. Chemistry of Carbon, ...

Organic Chemistry: The study of carbon compounds Organic compounds range from simple structures to huge macromolecules:

Plant cells 0.5 µm

Cell walls Cellulose

microfibrils in a plant cell wall

∩ Microfibril

CH2OH

CH2OH OH

OH

O O OH O CH2OH O

O OH

O CH2OH OH

OH OH O

O

CH2OH O

O OH

CH2OH O

O OH

O

O

CH2OH OH CH2OH OH

O OH OH OH OH

O

OH OH CH2OH

CH2OH OH O

OH CH2OH O

O

OH CH2OH OH

β  Glucose monomer

O

O

O

O O

O

Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl

groups attached to carbon atoms 3 and 6.

About 80 cellulose molecules associate

to form a microfibril, the main architectural unit of the plant cell wall.

A cellulose molecule is an unbranched β glucose polymer.

OH

OH

O

O OH

Cellulose molecules

Methane

CH4

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IV. Chemistry of Carbon, ...

• With a VALENCE (# of covalent bonds an atom can form) of 4, carbon is able to simultaneously bond to 4 other elements. This is key to the formation of complex macromolecules.

H O N C

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

• This electron configuration gives it covalent compatibility with many different elements.


•  The bonding versatility of carbon

–  Allows it to form many diverse molecules, including carbon skeletons

(a) Methane

(b) Ethane

(c) Ethene (ethylene)

Molecular Formula

Structural Formula

Ball-and-Stick Model

Space-Filling Model

H H

H H

H H

H H

H H

H H H H

C

C C

C C

CH4

C2H6

C2H4

Name and Comments


Molecular Diversity Arising from Carbon Skeleton Variation

•  Carbon chains

–  Form the skeletons of most organic molecules

–  Vary in length and shape

H H H

H H

H H H

H H

H

H H H

H H H H H

H

H

H

H

H

H

H H

H H H H H

H H H H

H H H H

H H

H H

H H H H H

H H

C C C C C

C C C C C C C

C C C C C C C C

C

C C

C C

C

C

C C C

C C

H

H

H

H H H

H

(a) Length

(b) Branching

(c) Double bonds

(d) Rings

Ethane Propane

Butane 2-methylpropane (commonly called isobutane)

1-Butene 2-Butene

Cyclohexane Benzene

H H H H H


Hydrocarbons

• Molecules consisting of Carbon and Hydrogen.

(a) A fat molecule (b) Mammalian adipose cells 100 µm

Fat droplets (stained red)

• Found in many of the cell’s organic molecules. • Store a great deal of potential energy in their many bonds.

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I. Chemistry of Carbon, ...

• The diversity of products that C can form is due to:

1) Endless geometries possible due to its valency

2) Its ability to bond to a wide variety of functional groups.

• Functional groups are the parts of molecules involved in chemical reactions.

MACROMOLECULES,...

Polymers • Four main classes of biological macromolecules:

Monomers: 1)  CARBOHYDRATES (Polysaccharides) SUGARS

2)  (LIPIDS - Make up membranes) Glycerol / FAs

3)  PROTEINS - Enzymes, etc. Amino Acids

4)  Nucleic Acids - DNA, RNA Nucleotides

MACROMOLECULES,...

V. Carbohydrates • Polysaccharides = sugar polymers = (CH2O)n • CH2O = basic formula for Monosaccharides

• Simplest Sugars • Can be used for fuel, converted into other

organic molecules or combined into polymers • Two major purposes of carbohydrates: 1)  Store energy (Glycogen in animals; Starch in plants)

2)  Provide structural support (Cellulose in plants; Chitin in insects, crustaceans)


Carbohydrates

q C, H, and O

q Primary fuel for organisms

q Cell structure

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Glucose

q Most carbohydrates— ultimately converted into glucose

q Blood sugar


Chloroplast Starch

Amylose Amylopectin

1 µm

Starch: a plant polysaccharide

Storage Polysaccharides • STARCH: Comprised entirely of Glucose monomers and is the major form of energy storage in plants


Mitochondria Giycogen granules

0.5 µm

Glycogen: an animal polysaccharide

Glycogen

Storage Polysaccharides,...

• GLYCOGEN: Comprised entirely of Glucose monomers and is the major form of energy storage in animals.

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Cellulose

Plant cells 0.5 µm

Cell walls Cellulose microfibrils

in a plant cell wall

∩ Microfibril

CH2OH

CH2OH OH

OH

O O

OH O CH2OH

O O

OH O

CH2OH OH

OH OH O

O

CH2OH O

O OH

CH2OH

O O

OH

O

O

CH2OH OH

CH2OH OH O OH OH OH OH

O

OH OH

CH2OH

CH2OH OH

O

OH CH2OH

O O

OH CH2OH OH

β  Glucose monomer

O

O

O

O

O

O

Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl

groups attached to carbon atoms 3 and 6.

About 80 cellulose molecules associate

to form a microfibril, the main architectural unit of the plant cell wall.

A cellulose molecule is an unbranched β glucose polymer.

OH

OH

O

O OH

Cellulose molecules

–  Is a major component of the tough walls that enclose plant cells


Cellulose, ...

• Not digestible by humans. Cows and termites possess symbiotic bacteria that break down cellulose into glucose monomers for energy utilization by their hosts.


Structural Polysaccharides

• CELLULOSE: Also made with Glucose monomers BUT uses Glucose enantiomer.

(c) Cellulose: 1– 4 linkage of β glucose monomers

H O

O

CH2OH

H OH H

H

OH OH H

H

HO 4

C

C

C

C

C

C

H

H

H

HO

OH

H

OH

OH

OH

H

O

CH2OH

H H

H

OH

OH H

H

HO 4 OH

CH2OH

O

OH

OH

HO 4 1

O

CH2OH

O

OH

OH

O

CH2OH

O

OH

OH

CH2OH

O

OH

OH

O O

CH2OH

O

OH

OH

HO 4 O 1

OH

O

OH OH O

CH2OH

O

OH

O OH

O

OH

OH

(a) α and β glucose ring structures

(b) Starch: 1– 4 linkage of α glucose monomers

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α glucose β glucose

CH2OH

CH2OH

1 4 4 1 1 • STARCH: all monomers “right-side up”.

• CELLULOSE: every other monomer is upside down.


•  another important structural polysaccharide

–  Is found in the exoskeleton of arthropods

–  Can be used as surgical thread

(a) The structure of the chitin monomer.

O

CH2OH

OH H

H OH

H

NH

C

CH3

O

H

H

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging

in adult form.

(c) Chitin is used to make a strong and flexible surgical

thread that decomposes after the wound or incision heals.

OH

Chitin

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MACROMOLECULES,...






MACROMOLECULES,...

VI. Lipids • Three main types of lipids: 1)  FATS = Glycerol + 3 Fatty Acids

2)  PHOSPHOLIPIDS = Spontaneously form membranes

3)  STEROIDS = Skeleton consists of 4 fused carbon rings

• Macromolecule but NOT a polymer (no covalent bonds) • Share the common trait of being HYDROPHOBIC

VI. Lipids, ... 1)  FATS = Glycerol + 3 Fatty Acids

(b) Fat molecule (triacylglycerol)

H H H H

H H H H H H H H H

H H H O

H O H C

C

C

H

H OH

OH

H

H H

H H

H H H H

H H H H H H

H

H C C C C C C C C C

C C

C C

C C C

Glycerol

Fatty acid (palmitic acid)

H H

H

H

H H H H

H H

H H

H H H H H

H H H

H H H H H H H H H H H H H H H H

H


H H H H H H H H H H H H H H


H H H H H H H H H H H H H H H

HO

O O

O

O C

C

C C C C C C C C C C C C C C C C C

C

C C C C C C C C C C C C C C C C

C C C C C C C C C C C C C C C O

O

(a) Dehydration reaction in the synthesis of a fat Ester linkage


Fatty Acids

•  Saturated:

–  Have the maximum number of hydrogen atoms possible

–  Have no double bonds

(a) Saturated fat and fatty acid

Stearic acid

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•  Unsaturated:

–  Have one or more double bonds

–  Causes kinks in tail resulting in looser packing

(b) Unsaturated fat and fatty acid cis double bond causes bending

Oleic acid

Fatty Acids, ... VI. Lipids, ... 2) PHOSPHOLIPIDS

• Have only TWO Fatty Acids, with a P group replacing third FA

CH2

O P O O O

CH2 CH CH2 O O

C O C O

Phosphate

Glycerol

(a) Structural formula (b) Space-filling model

Fatty acids

(c) Phospholipid symbol

Hyd

roph

obic

tails

Hydrophilic head

Hydrophobic tails

–

Hyd

roph

ilic

head

CH2 Choline +

Figure 5.13

N(CH3)3

• Consist of a Hydrophilic head and two Hydrophobic tails


Phospholipids

Hydrophilic head

WATER

WATER

Hydrophobic tail

• Spontaneously form lipid bilayers due to amphipathic nature of lipid molecules. Found in all cell membranes.

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VI. Lipids, ... 3) STEROIDS

• Lipids characterized by a C skeleton with 4 fused rings

• Cholesterol: A steroid important in cell membranes and acts as a precursor to some sex hormones.

HO

CH3

CH3

H3C CH3 CH3

MACROMOLECULES,...






Proteins are bodybuilding macromolecules.

VII. Proteins

Amino Acids

q Twenty different amino acids

q Strung together to make proteins

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2.16 A protein’s function is influenced by its three-dimensional shape.

q Peptide bonds

Primary Structure

q The sequence of amino acids

Secondary Structure

q Hydrogen bonding between amino acids

q The two most common patterns:

•  twist in a corkscrew-like shape

•  zig-zag folding

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Tertiary Structure

q Folding and bending of the secondary structure

q Due to bonds such as hydrogen bonds or covalent sulfur-sulfur bonds.

Quaternary Structure

q When two or more polypeptide chains are held together by bonds between the amino acids on the different chains.

q Hemoglobin

Take-home message 2.14

q Unique combinations of 20 amino acids give rise to proteins, the chief building blocks of physical structures that make up all organisms.

q Proteins perform myriad functions, from assisting chemical reactions to causing blood clotting to building bones to fighting microorganisms.

Nucleic acids are macromolecules that store information.

VIII. Nucleic Acids

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2.20 DNA holds the genetic information to build an organism.

Insert new fig 2-46

Two Types of Nucleic Acids

q Deoxyribonucleic acid (DNA)

q Ribonucleic acid (RNA)

q  Both play central roles in directing the production of proteins.

Insert fig 2-45 to right

2.21 RNA is a universal translator, reading DNA and directing protein production.

Insert fig 2-47

RNA differs from DNA in three important ways.

q The sugar molecule of the sugar-phosphate backbone

q Single-stranded

q Uracil (U) replaces thymine (T)

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Take-home message 2.21

q RNA acts as a middleman molecule—taking the instructions for protein production from DNA to another part of the cell where, in accordance with the RNA instructions, amino acids are pieced together into proteins.

Building Blocks of Life

Reading: Chapter 2 For Next Week: Chapter 3 (Architecture of the Cell) Problem set #1 will be posted on the website tomorrow PS#1 will form basis of discussion sections next week PS#1 answers posted next Friday

Raw materials and fuel for our bodies I. Atoms and...

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