CH 3: The Molecules of
Cells
Molecules of Life
 The
molecules of life are all organic
compounds….meaning carbon containing




Carbohydrates: C, H, O
Lipids: C, H, O
Proteins: C, H, O, N, S
Nucleic acids: C, H, O, N, P
Carbon (3.1)
 In
compounds, C always forms 4
covalent bonds

C
Diagramming C compounds
to C single bonds can rotate freely
• Allows C compounds to form rings

C to C double bonds are rigid
Hydrocarbons
– compounds
containing only C and H
 Hydrocarbons


Are hydrocarbons polar or nonpolar?
Are they hydrophilic or hydrophobic?
Isomers
– compounds with same formula,
but different arrangement of the atoms
 Isomers

Isomers differ in properties and in biological
activity
Functional Groups
 Molecules
of life are all substituted
hydrocarbons

(Most) functional groups contain atoms
other than C and H
• Many are polar and change properties of the
compound

Substitute functional group(s) for
hydrogens

Six main functional groups are important
in the chemistry of biological molecules:
POLAR Functional groups

Hydroxyl group (OH)

Carbonyl group (C=O)
•



May be an aldehyde or ketone
Carboxyl group (COOH) - Acidic
Amino group (NH2) - basic
Phosphate group (OPO3)
NONPOLAR Functional Group
• Methyl (CH3)
Functional Groups Impact Function
 Differences in position and types of functional groups greatly impact
the function of the molecule
Estradiol
Female lion
Testosterone
Male lion
Classes of Chemical
Reactions (3.3)
1. Rearrangement
Convert one isomer to another
Example
•
•
•
•
Reaction that converts glucose to fructose
Reaction is used to make high fructose corn
syrup
Making Polymers
2. Dehydration* Reaction - links
molecules together
•
A covalent bond forms between
molecules and water is removed
•
Reaction by which monomers are joined to form
larger molecules
•
Examples:
•
*Also called a condensation reaction
Breaking Polymers
3. Hydrolysis reaction – breaks down
larger molecules
•
Water is added to a larger molecule to
split off a smaller molecule.
•
Reaction involves breaking a covalent
bond by adding water
• Reverse of a dehydration reaction
Example from lab this week
Monomers
 Monosaccharides
 Fatty acids
 Amino acids
 Nucleotides
Polymer Formed
Di & Polysaccharides
Triglycerides
Proteins
Nucleic acids
SUMMARY


Monomers are linked by condensation reactions
(also called dehydration reactions)
• A water molecule is produced
• A covalent bond is formed between monomer
units
Polymers are broken down to monomers by the
reverse process, hydrolysis
• A water molecule is broken
• A covalent bond is broken between monomer
units
Carbohydrates (3.4-3.7)
 Class
of molecules with many
hydroxyl groups (OH) and one
carbonyl group (C=O)
 Consider 3 Classes of Carbohydrates


Monosaccharides
Disaccharides
• and other moderate size carbohydrates

Polysaccharides
Monosaccharides
 General
Formula: CnH2nOn
 Typically 3-7 carbons long
• Many –OH groups and one carbon is
attached to an aldehyde or ketone group
• Form rings – see pg 37
Common Monosaccharides
Pentose monosaccharides:


Deoxyribose – sugar in DNA
Ribose – sugar in RNA
Hexose Monosaccharides:
 Glucose
all isomers of
 Fructose
C6H12O6
 Galactose
6 C - Hexose Sugars

All isomers of C6H12O6
 Glucose • Blood sugar
• Primary source of energy for cells

Fructose
• “Fruit” sugar
• Sweetest of all the sugars

Galactose
• Formed when lactose is digested
Glucose is an
aldehyde sugar
Aldose
Fructose is a
________ sugar
_____ose
Disaccharides
 Formed
when 2 monosaccharides are
joined in a ___________ reaction.

3



One sugar gives up a H and the other a -OH
Disaccharides to know
Sucrose = glucose Lactose = glucose Maltose = glucose -
Synthesis of Maltose
Disaccharides
 Sucrose
= glucose covalently
bonded to a fructose


Table sugar
In the small intestines the enzyme
sucrase catalyzes the hydrolysis of the
bond between glucose and fructose
• In the lab this bond can be broken by…..?
Disaccharides
Lactose = glucose-galactose


Milk sugar
The enzyme lactase catalyzes the
hydrolysis of the bond between glucose
and galactose.
• Individuals who do not make the enzyme lactase
are lactose intolerant.
Lactose Intolerance

Populations at greatest risk:
Asian - ~ 90%
 African descent - ~ 75%
 Hispanic, Native Americans - ~ 75%

Last Disaccharides
 Maltose


= glucose-glucose
Found in germinating grains, malt
products
Formed when starch is hydrolyzed
(digested)
Oligosaccharides

~20- 30 monosaccharides long

found on the outside of the plasma
membrane, Often branched, Help cells
recognize each other
Polysaccharides
 All

polymers of glucose
Differ in:
• Function
• Type of bonding between glucose
• Length of the glucose chain
• Frequency of branching
• Incidence of coiling
Major Polysaccharides
Glycogen
Starch
Cellulose
Glycogen
– animal storage form of glucose
 Made and stored in:
 Function

Liver
• Source of glucose for the entire body

Muscle cells
• Source of glucose for muscle cells only
Glycogen
 Structure

~ 1 million glucose joined by covalent bonds
called alpha glycosidic bonds
• We have the enzymes needed to hydrolyze the
alpha bonds in glycogen

Highly branched
• Branch every 5-6 glucose
Starch
Function – plant storage form of glucose


Structure – ~100, 000 glucose joined by
covalent bonds called alpha glycosidic
bonds
• Molecules are either coiled or branched –
depending on type of starch
Cellulose

Function – structural polysaccharide
• Component of cell walls

Structure
• Long chains of glucose joined by covalent bonds
called beta glycosidic bonds
• We do not have the enzymes needed to hydrolyze
beta bonds
Cellulose
 Structure


Hydrogen bonds link chains to each other to
form fibers
The fibers then form bundles
• See page 39

The resulting structure is VERY strong.
Cellulose
Lipids (3.8 – 3.10)
 Water


insoluble components of cells
Primarily hydrocarbon, nonpolar
substances
Classes of Lipids:
• Triglycerides (fats) and fatty acids
• Phospholipids
• Sterols
• Waxes (no coverage)
Triglycerides and Fatty Acids
 Triglycerides
are made by linking 3 fatty
acids to a glycerol molecule

Triglyceride
Fatty Acids
 Fatty

Acids (FA)
Long hydrocarbon chains with a
carboxylic acid head.
• Saturated FA: all carbon to carbon single
bonds
• Unsaturated FA: at least one carbon to
carbon double bond
Fatty Acids
Red = polar head
Black = nonpolar tail
Triglycerides: (TG)


Function: storage form of energy
Structure: 3 fatty acids covalently
bonded to a glycerol backbone
• 3 FA are often different from each other
• FA determine the properties of the TG



Mostly unsaturated FA => liquid (oil), healthier
Mostly saturated FA => solid, heatlh issues
Trans FA => health issues, formed in
hydrogenation reaction
Triglyceride
Phospholipids (3.9)
 Function:
major component of
plasma membrane

Structure: ………….
Steroids
 Steroids


(sterols)
Functions vary
Examples of sterols include:
• Hormones – testosterone, estrogen
• Vitamin D
• Cholesterol

Structure: 4 linked rings……..
Steroids
General steroid structure
Cholesterol
Proteins
 Functions/examples of proteins:
 Enzymes
 Antibodies
 Hemoglobin
 Insulin
 Component of cell membranes
 Hair, nails, cartilage
Proteins
 Structure:



Chain of covalently bonded amino acids
(a.a)
Bond between a.a. called a peptide
bond
20 different amino acids…………..
Amino Acid Structure
Amino
group
Carboxyl (acid)
group

The structure of the R group determines the specific
properties of each amino acid
Leucine (Leu)
Hydrophobic R Group
Serine (Ser)
Aspartic acid (Asp)
Hydrophilic R groups
Proteins
 Synthesis
a.a. +
 What
of proteins:
a.a  dipeptide + H2O
type of reaction is this?
Proteins
 Order
of the a.a. in a protein determines
the:
 3D shape of the protein
 Function of the protein
 Any change in protein structure may
impact the ability of the protein to function.

More to come on this.
Describing Protein Structure
 Primary


structure: 10
Order of amino acids in a protein
Bonding: peptide bonds between amino
acids
• Peptide bonds are _________ bonds
Protein Structure
 Example
of a Primary structure:
Methonine-proline-serine-asparagine-tryptophan-leucinetyrosine-valine-proline-alanine-glycine…….
Secondary Structure: 20

The polypeptide (protein) chain coils or
folds to form:
• Alpha helix or beta pleated sheets

Bonding: H bonds
Alpha helix
Beta-sheet
Tertiary Structure: 30

Folding of the secondary structure to
form domains
• order of aa determines how the protein
folds
• Domain = self-organized, stable, functional
unit
Describing Protein Structure
 Tertiary
Structure Bonding:
• R group interactions
H bonds
 Hydrophilic R groups on the outside and
hydrophobic R groups are on the inside
of the protein
 Disulfide bonds between S containing
a.a.
 Ionic bonds between charged R groups

Tertiary Structure: 30
Tertiary structure descries the overall 3D
shape of single polypeptide
 Most polypeptides can be described as either:
Globular
Fibrous
most enzymes
hair, spider silk

Describing Protein Structure
 Quaternary


Structure: 40
Arrangement of 2 or more protein
chains.
Bonding – same R group interactions as
30 structure
Collagen – fibrous protein
with 40 structure
Simple Diagram of Levels of
Protein Structure
Identify the stabilizing forces at each level
 Protein
denaturation - change in the
3D structure of a protein


Changes occur to 20 -40 structure
Causes a loss of protein function
Functional
protein
Protein is
no longer
functional
Partially denatured proteins
Minor changes to active site(s)
 Can still function but very reduced rate

Fully denatured proteins
Major changes to active site(s)
 Protein cannot function at all

Denaturing Agents
 pH
changes - changes ionic interactions
between charged amino acids
 Salt concentration increased- interferes
with ionic bonds between charged aa
 Higher temperatures – break hydrogen
bonds
 Heavy metals - break S-S bonds between
cysteines
Nucleotides & Nucleic Acids
 Nucleotides



- General composition
5 Carbon sugar
1 or more phosphate groups
Nitrogenous base
Nucleotides
 Examples
of nucleotides:

ATP - major energy carrier in cells

NADH/NAD+ - Coenzyme that transports H+
and electrons
Nucleic Acids
 Nucleic


Acids
Long chain(s) of covalently bonded
nucleotides
2 types of nucleic acids:
• RNA – single stranded, shorter
• DNA – double stranded, very long
DNA  RNA
Nucleic Acids - RNA
 RNA

– ribonucleic acid
1 strand of covalently bonded nucleotides
 Composition



of RNA nucleotides:
Ribose
Phosphate
1 of 4 possible nitrogenous bases
•
•
•
•
Adenine
Guanine
Uracil
Cytosine
Nucleic Acids - DNA
 DNA

2 strands of covalently bonded nucleotides
 DNA



– deoxyribonulceic acid
nucleotides:
Deoxyribose
Phosphate
1 of 4 Nitrogenous bases
• Adenine
• Guanine
• Thymine
• Cytosine
Nucleic Acids
– deoxyribonucleic acid
Double stranded
• Hydrogen bonds between bases join
the two strands
 DNA

DNA