(DONE)Module I_2_Structure and Function of Macromolecules.pdf

Atom- Molecule-Element- Compound Relationship
▪ Everything is made of matter
▪ Matter is made of atoms

Life requires ~25 chemical elements
• About 25 elements are essential for life
– Four elements make up 96%
of living matter:
• carbon (C)
• hydrogen (H)
• oxygen (O)
• nitrogen (N)
– Four elements make up most
of remaining 4%:
• phosphorus (P)
• calcium (Ca)
• sulfur (S)
• potassium (K)

Water = Life
• Three-quarters of the Earth’s surface is submerged in water
• The abundance of water is the main reason the Earth is habitable
Properties of Water Why are we studying water?
All life occurs in water ---- inside outside the cell
Metabolism
– all
chemical
reactions
that occur in
a living
organism
98% Liquid
2% Vapor/ice
on earth

The polarity of water molecules
– Allows them to form hydrogen bonds with each other
– Contributes to the various properties water exhibits
• H2O molecules form H-bonds with each other
• Special properties of water
1. cohesion & adhesion
– surface tension, capillary action
2. good solvent
– many molecules dissolve in H2O
– hydrophilic vs. hydrophobic
3. lower density as a solid
– ice floats!
4. high specific heat
– water stores heat
5. high heat of vaporization
– heats & cools slowly

1. Cohesion & Adhesion
• Cohesion
– H bonding between H2O molecules
– water is “sticky”
• surface tension
• Adhesion
– H bonding between H2O & other substances
• capillary action
• water climbs up paper towel or cloth

HOW DOES H2O GET TO TOP OF TREES?
Transpiration is built on cohesion & adhesion

2. Water is the solvent of life
• Polarity makes H2O a good solvent
– polar H2O molecules surround + & – ions
– solvents dissolve solutes creating solutions

What dissolves in water?
• Hydrophilic
– substances have attraction
to H2O:polar
What doesn’t dissolve in water?
• Hydrophobic
– substances that don’t
have an attraction to
H2O non-polar
fat (triglycerol)

Insulation of Bodies of Water by Floating Ice
• The hydrogen bonds in ice
– Are more “ordered” than in liquid water, making ice less
dense
Liquid water
Hydrogen bonds
constantly break and re-form
Ice
Hydrogen bonds are stable
Hydrogen
bond
Oceans & lakes don’t freeze solid
surface ice insulates water below allowing life to survive the winter

4. Specific heat
• H2O resists changes in temperature
– high specific heat
– takes a lot to heat it up
– takes a lot to cool it down
– Heat is absorbed when hydrogen bonds break
– Heat is released when hydrogen bonds form
➢ Is the amount of heat that must be absorbed or lost for 1
gram of that substance to change its temperature by 1ºC

5. Heat of vaporization
Organisms rely on heat of vaporization
to remove body heat
Evaporative cooling

Ionization of water & pH
• Water ionizes
– H+ splits off from H2O, leaving OH–
• if [H+] = [-OH], water is neutral
• if [H+] > [-OH], water is acidic
• if [H+] < [-OH], water is basic
• pH scale
– how acid or basic solution is
– 1 → 7 → 14
H2O → H+ + OH–
pH Scale
tenfold change
in H+ ions
pH1 → pH2
10-1 → 10-2
10 times less H+
pH8 → pH7
10-8 → 10-7
10 times more H+
pH10 → pH8
10-10 → 10-8
100 times more H+

1
0
0
1
2
3
4
5
6
7
8
9
3
Amount of base added
Buffering
range
4 5
2
pH
Buffers & cellular regulation
• pH of cells must be kept ~7
– pH affects shape of molecules
– shape of molecules affect function
– pH affects cellular function
• Control pH by buffers (Are substances that minimize changes in
the concentrations of hydrogen and hydroxide ions in a solution)
– reservoir of H+
• donate H+ when [H+] falls
• absorb H+ when [H+] rises

Macromolecules
• Macromolecules
– Are large molecules composed of smaller molecules
– Are complex in their structures
•Four of the classes of life’s organic molecules are polymers
– Carbohydrates
– Proteins
– Lipids and Fats
– Nucleic acids

• A polymer
– Is a long molecule consisting of many
similar building blocks called
monomers
• Each class of polymer
– Is formed from a specific set of
monomers
Most macromolecules are polymers, built from monomers
• Monomers form larger molecules by
condensation reactions called dehydration
reactions
(a) Dehydration reaction in the synthesis of a polymer
HO H
1 2 3 HO
HO H
1 2 3 4
H
H2O
Short polymer Unlinked monomer
Longer polymer
Dehydration removes a water
molecule, forming a new bond
• Polymers can disassemble by
– Hydrolysis
(b) Hydrolysis of a polymer
HO 1 2 3 H
HO H
1 2 3 4
H2O
H
HO
Hydrolysis adds a water
molecule, breaking a bond

• Concept: Carbohydrates serve as fuel and building material
• Carbohydrates
– Include both sugars and their polymers
Sugars
• Monosaccharides
– Are the simplest sugars
– Can be used for fuel
– Can be converted into other organic molecules
– Can be combined into polymers
Examples of monosaccharides
Triose sugars
(C3H6O3)
Pentose sugars
(C5H10O5)
Hexose sugars
(C6H12O6)
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
HO C H
H C OH
H C OH
H C OH
H C OH
HO C H
HO C H
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
C O
C O
H C OH
H C OH
H C OH
HO C H
H C OH
C O
H
H
H
H H H
H
H H H H
H
H H
C C C C
O
O
O
O
Aldoses
Glyceraldehyde
Ribose
Glucose Galactose
Dihydroxyacetone
Ribulose
Ketoses
Fructose

• Monosaccharides
– May be linear
– Can form rings
H
H C OH
HO C H
H C OH
H C OH
H C
O
C
H
1
2
3
4
5
6
H
OH
4C
6CH2OH 6CH2OH
5C
H
OH
C
H OH
H
2 C
1C
H
O
H
OH
4C
5C
3 C
H
H
OH
OH
H
2C
1 C
OH
H
CH2OH
H
H
OH
HO
H
OH
OH
H
5
3 2
4
(a) Linear and ring forms. Chemical equilibrium between the linear and ring
structures greatly favors the formation of rings. To form the glucose ring,
carbon 1 bonds to the oxygen attached to carbon 5.
OH
3
O H O
O
6
1

• Examples of disaccharides
Dehydration reaction
in the synthesis of
maltose. The bonding
of two glucose units
forms maltose. The
glycosidic link joins
the number 1 carbon
of one glucose to the
number 4 carbon of
the second glucose.
Joining the glucose
monomers in a
different way would
result in a different
disaccharide.
Dehydration reaction
in the synthesis of
sucrose. Sucrose is
a disaccharide formed
from glucose and fructose.
Notice that fructose,
though a hexose like
glucose, forms a
five-sided ring.
(a)
(b)
H
HO
H
H
OH H
OH
O H
OH
CH2OH
H
HO
H
H
OH H
OH
O H
OH
CH2OH
H
O
H
H
OH H
OH
O
H
OH
CH2OH
H
H2O
H2O
H
H
O
H
HO
H
OH
O
H
CH2OH
CH2OH HO
OH
H
CH2OH
H
OH H
H
HO
OH
H
CH2OH
H
OH H
O
O H
OH
H
CH2OH
H
OH H
O
H
OH
CH2OH
H HO
O
CH2OH
H
H
OH
O
O
1 2
1 4
1–4
glycosidic
linkage
1–2
glycosidic
linkage
Glucose
Glucose Glucose
Fructose
Maltose
Sucrose
OH
H
H
• Disaccharides
– Consist of two monosaccharides
– Are joined by a glycosidic linkage

• Polysaccharides
– Are polymers of
sugars
– Serve many roles in
organisms
Storage
Polysaccharides
• Starch &
Glycogen
– polymer
consisting
entirely of
glucose
monomers
Starch Glycogen
Starch- Is the major storage
form of glucose in plants
Chloroplast Starch
Amylose Amylopectin
1 m
Starch: a plant polysaccharide
Glycogen- Consists of glucose
monomers
Is the major storage form of glucose in
animals
Mitochondria
Giycogen granules
0.5 m
Glycogen: an animal polysaccharide
Glycogen

Each straight chain monomer is connected by the α-1,4-glycosidic
bond, while the branches are connected by α-1,6-glycosidic bond
Starch consists of two types of molecules: the linear and helical
amylose and the branched amylopectin

Structural Polysaccharides
• Cellulose
– Is a polymer of glucose
– Is a major component of the tough walls that enclose plant cells
– a polysaccharide consisting of a linear chain of several hundred to
many thousands of β(1→4) linked D-glucose units
Has different glycosidic linkages than starch
(c) Cellulose: 1– 4 linkage of  glucose monomers
H O
O
CH2O
H
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
CH2O
H
H
H
H
OH
OH
H
H
HO
4
OH
CH2O
H
O
OH
OH
HO
4
1
O
CH2O
H
O
OH
OH
O
CH2O
H
O
OH
OH
CH2O
H
O
OH
OH
O O
CH2O
H
O
OH
OH
HO
4
O
1
OH
O
OH OH
O
CH2O
H
O
OH
O OH
O
OH
OH
(a)  and  glucose ring structures
(b) Starch: 1– 4 linkage of  glucose monomers
1
 glucose  glucose
CH2O
H
CH2O
H
1 4 4
1 1

Cellulose
Cellulose is difficult to digest
Cows have microbes in their
stomachs to facilitate this
process

• Chitin, 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
CH2O
H
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

• Lipids are a diverse group of hydrophobic
molecules
• Lipids
– Are the one class of large biological molecules
that do not consist of polymers
– Share the common trait of being hydrophobic

• Fats
– Are constructed from two types of smaller molecules, a
single glycerol and usually three fatty acids
• Fatty acids
– Vary in the length and number and locations of double
bonds they contain
(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
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

• Saturated fatty acids
– Have the maximum number of hydrogen atoms
possible
– Have no double bonds
Saturated fat and fatty acid
Stearic acid

• Unsaturated fatty acids
– Have one or more double bonds
Unsaturated fat and fatty acid
cis double bond
causes bending
Oleic acid
Oil normally refers to a lipid with short or unsaturated fatty acid
chains that is liquid at room temperature

CH2
O
P
O O
O
CH2
C
H
CH
2
O
O
C O C O
Phosphate
Glycerol
(a) Structural formula (b) Space-filling model
Fatty acids
(c) Phospholipid
symbol
Hydrophilic
head
Hydrophobic
tails
–
CH
2 Choline
+
N(CH3)
3
Phospholipids
– Have only two fatty acids
– Have a phosphate group instead of a third fatty acid
– Consists of a hydrophilic “head” and hydrophobic “tails”

• The structure of phospholipids
– Results in a bilayer arrangement found in cell
membranes
Hydrophilic
head
WATER
WATER
Hydrophobic
tail

Polypeptides
• Polypeptides
– Are polymers of amino acids
• A protein
– Consists of one or more polypeptides
Amino Acid Monomers
• Amino acids
– Are organic molecules possessing both carboxyl and amino
groups
– Differ in their properties due to differing side chains, called
R groups

• 20 different amino acids make up proteins
O
O–
H
H3N+
C C
O
O–
H
CH3
H3N+
C
H
C
O
O–
CH3 CH3
CH3
C C
O
O–
H
H3N+
CH
CH3
CH2
C
H
H3N+
CH3
CH3
CH2
CH
C
H
H3N+ C
CH3
CH2
CH2
C
H3N+
H
C
O
O–
CH2
C
H3N+
H
C
O
O–
CH2
NH
H
C
O
O–
H3N+
C
CH2
H2C
H2N C
CH2
H
C
Nonpolar
Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)
Methionine (Met) Phenylalanine (Phe)
C
O
O–
Tryptophan (Trp) Proline (Pro)
H3C
S
O
O–

O–
OH
CH2
C C
H
H3N+
O
O–
H3N+
OH CH3
CH
C C
H
O–
O
SH
CH2
C
H
H3N+
C
O
O–
H3N+ C C
CH2
OH
H H H
H3N+
NH2
CH2
O
C
C C
O
O–
NH2 O
C
CH2
CH2
C C
H3N+
O
O–
O
Polar
Electrically
charged
–O O
C
CH2
C C
H3N+
H
O
O–
O– O
C
CH2
C C
H3N+
H
O
O–
CH2
CH2
CH2
CH2
NH3
+
CH2
C C
H3N+
H
O
O–
NH2
C NH2
+
CH2
CH2
CH2
C C
H3N+
H
O
O–
CH2
NH+
NH
CH2
C C
H3N+
H
O
O–
Serine (Ser) Threonine (Thr)
Cysteine
(Cys)
Tyrosine
(Tyr)
Asparagine
(Asn)
Glutamine
(Gln)
Acidic Basic
Aspartic acid
(Asp)
Glutamic acid
(Glu)
Lysine (Lys) Arginine (Arg) Histidine (His)

Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
OH
DESMOSOMES
DESMOSOMES
DESMOSOMES
OH
CH2
C
N
H
C
H O
H OH OH
Peptide
bond
OH
OH
OH
H H
H
H
H
H
H
H
H
H H
H
N
N N
N N
SH
Side
chains
SH
O
O
O O O
H2O
CH2 CH2
CH2 CH2 CH2
C C C C C C
C C
C C
Peptide
bond
Amino end
(N-terminus)
Backbone
(a)
(b)
Carboxyl end
(C-terminus)

Determining the Amino Acid Sequence of a Polypeptide
• The amino acid sequences of polypeptides
– Were first determined using chemical means
– Can now be determined by automated
machines

Four Levels of Protein Structure
• Primary structure
– Is the unique sequence of amino acids in a
polypeptide
–
Amino acid
subunits
+H3N
Amino
end
o
Carboxyl end
o
c
GlyProThr Gly
Thr
Gly
Glu
Seu
Lys
Cys
Pro
Leu
Met
Val
Lys
Val
Leu
Asp
AlaVal ArgGly
Ser
Pro
Ala
Gly
lle
Ser
ProPheHisGluHis
Ala
Glu
Val
Val
Phe
Thr
Ala
Asn
Asp
Ser
GlyPro
Arg
Arg
Tyr
Thr
lle
Ala
Ala
Leu
Leu
Ser
Pro
Tyr
Ser
Tyr
Ser
Thr
Thr
Ala
Val
Val
Thr
AsnPro
LysGlu
Thr
Lys
Ser
Tyr
Trp
Lys
Ala
Leu
GluLle Asp

O C  helix
 pleated sheet
Amino acid
subunits N
C
H
C
O
C N
H
C
O H
R
C N
H
C
O H
C
R
N
H
H
R C
O
R
C
H
N
H
C
O H
N
C
O
R
C
H
N
H
H
C
R
C
O
C
O
C
N
H
H
R
C
C
O
N
H
H
C
R
C
O
N
H
R
C
H C
O
N
H
H
C
R
C
O
N
H
R
C
H C
O
N
H
H
C
R
C
O
N H
H C R
N H
O
O C N
C
R
C
H O
C
H
R
N H
O C
R
C
H
N H
O C
H C R
N H
C
C
N
R
H
O C
H C R
N H
O C
R
C
H
H
C
R
N
H
C
O
C
N
H
R
C
H C
O
N
H
C
• Secondary structure
– Is the folding or coiling of the polypeptide into a repeating
configuration
– Includes the  helix and the  pleated sheet
– Gly, Ala – spider silk, Ala-elasticity
H H

• Tertiary structure
– Is the overall three-dimensional shape of a
polypeptide
– Results from interactions between amino acids
and R groups
CH2
CH
O
H
O
C
HO
CH2
CH2 NH3
+ C
-O CH2
O
CH2
S
S
CH2
CH
CH3
CH3
H3C
H3C
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Hyrdogen
bond
Ionic bond
CH2
Disulfide bridge

• Quaternary structure
– proteins consisting of two or more identical or
different polypeptide chains (subunits)
Polypeptide
chain
Collagen
 Chains
 Chains
Hemoglobin
Iron
Heme

The four levels of protein structure
Primary structure Secondary structure
Tertiary structure Quaternary structure

What Determines Protein Conformation?
• Protein conformation
– Depends on the physical and chemical conditions of the
protein’s environment
• Denaturation
• Is when a protein unravels and loses its native
conformation
Denaturation
Renaturation
Denatured
protein
Normal protein

An overview of protein functions

Sickle-Cell Disease: A Simple Change in Primary Structure
❑caused by the substitution of one amino acid (valine) for the normal one
(glutamic acid) at the position of the sixth amino acid in the primary structure
of hemoglobin

• Nucleic acids store and transmit hereditary
information
• Genes
– Are the units of inheritance
– Program the amino acid sequence of
polypeptides
– Are made of nucleic acids

The Roles of Nucleic Acids
• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• DNA
– Stores information for the synthesis of specific
proteins

Nucleic Acids exist as polymers called Nucleotides

Nucleotide Polymers
• Nucleotide polymers
– Are made up of nucleotides linked by the–OH
group on the 3´ carbon of one nucleotide and
the phosphate on the 5´ carbon on the next
• The sequence of bases along a nucleotide
polymer
– Is unique for each gene

The DNA Double Helix
• Cellular DNA molecules
– Have two polynucleotides that spiral around an
imaginary axis
– Form a double helix
• The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary
fashion (A with T only, and C with G only)

• The DNA double helix
– Consists of two antiparallel nucleotide strands
3’ end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
Nucleotide
about to be
added to a
new strand
A
3’ end
3’ end
5’ end
New
strands
3’ end
5’ end
5’ end
Figure 5.27

RNA
• Single stranded
• Uracil instead of Thiamine
• Ribose instead of Deoxy ribose
• Major Types:
– mRNA
– tRNA
– rRNA

DNA vs RNA
• Components of DNA
– Sugar (deoxyribose)
– Base (A,G,C,T)
– Phosphate group
• Structural Characteristics of
DNA
– Double stranded
– Base-pairing rules apply
(A:T & G:C)
• Components of RNA
– Sugar (ribose)
– Base (A,G,C,Uracil)
• RNA does not
contain thymine
– Phosphate group
• Structural Characteristics
of RNA
– Primarily single
stranded
– Limited base-pairing
(G:C & A:U)

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