Advanced Biology

Biochemistry
(the study of biology at the molecular level)
 Four Classes of Biomolecules
 Carbohydrates
• Monosaccharides (sugars), Polysaccharides
(starches and cellulose)
 Proteins
• Enzymatic, structural, transport
 Nucleic Acids
• DNA/RNA/ATP
 Lipids
• Fatty acids, triglycerides, cholesterol
4.1
 Monomers and Polymers
 Monomers are bonded together to form
polymers
 Monomers form polymers by condensation
reactions that remove a water molecule
HO 1 2 3 H HO H

Unlinked
Short polymer
monomer
Dehydration removes a water H2O
molecule, forming a new bond

HO 1 2 3 4 H

Longer polymer 4.2/4.3

 Monomers and Polymers
 Polymers can disassemble by
hydrolysis
HO 1 2 3 4 H

Hydrolysis adds a water H2O

molecule, breaking a bond

HO 1 2 3 H HO H
4.3
 Carbohydrates
 Monosaccharides
• Are the simplest sugars
• Can be used for fuel
• Can be converted into
other organic molecules
• Can be combined into
polymers

4.4
 Carbohydrates
 Disaccharides
• Consist of two
monosaccharides
• Are joined by a
glycosidic linkage

4.4
 Carbohydrates
 Glycosidic Linkage Formation

Be able to complete a partial diagram for examinations

4.5
 Model Building
n Draw glucose on scratch paper.
Build glucose.
n Link your glucose to that of another
group. Show how water is
released. Draw the molecule that
results.
n Draw fructose. Build fructose. How
is it different from glucose?
 Carbohydrates
Chloroplast Starch
 Polysaccharides
• Starch (amylose)
 Consists of
glucose
monomers
 Is the major
storage form of
glucose in plants
1 µm

Amylose
4.4 Amylopectin
 Carbohydrates
Glycogen
Mitochondria granules
 Polysaccharides
• Glycogen
 Consists of glucose
monomers
 Is the major
storage form of
glucose in animals 0.5 µm

Glycogen
4.4
 Carbohydrates
 Polysaccharides
• Cellulose
 Is a polymer of glucose
 Is a structural carbohydrate in plant cell walls
Cellulose About 80 cellulose
microfibrils molecules associate
in a plant cell to form a microfibril,
Microfibril
Cell walls wall the main
architectural unit
of the plant cell wall.

0.5 µm

Plant cells
CH2OH OH CH2OH OH
O O O
OH O OH OH OH
O O
O CH OHO O O
OH CH2OH
2
H
CH2OH OH CH2OH OH
O O O
OH OH OH O OH
O O
Cellulose
O O O
O CH OH
H
2 OH CH2OH
molecules
CH2OH OH CH2OH OH
O O O
OH OH OH O OH
O O O O O
O CH OH
4.4 H
2
βOH CH2OH
Glucose
monome
r
 Carbohydrates
H O
C CH2OH
Cellulose
CH2OH
 H O H H C OH H O OH
H H
4 HO C H 4 1
• Has different HO
OH H
OH HO
OH H
H
H C OH
glycosidic H OH C H OH
H OH
linkages than α glucose H C OH β glucose
starch
(a) α and β glucose ring structures
CH2O CH2OH CH2OH CH2OH
H
O O O O
1 4 1 4 1 4 1
OH OH O OH O OH O
HO O

OH OH OH OH

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

CH2OH OH CH2OH OH
O O
O OH O OH
OH 1 4 O OH
HO OH
O O
CH2O
OH OH CH2OH
H
(c) Cellulose: 1– 4 linkage of β glucose monomers 4.6
 Lipids
• Are the one class of large biological
molecules that do not consist of
polymers
• Share the common trait of being
hydrophobic or nonpolar
• Store more energy than any other
biomolecule
 Lipids
 Fats
• Are constructed from two types of smaller molecules, a
single glycerol and one or more fatty acids
H H H H H H H H
O H H H H H H H H
H C OH C C C C C C C C H
C C C C C C C C
HO
H H H H H H H
H H H H H H H H
H C OH
Fatty acid
H C OH (palmitic acid)
H

Glycerol Dehydration reaction in the synthesis of a fat

Ester linkage

H O H H H H H H H
H H H H H H H H
H C O C C C C C C C C H
C C C C C C C C
H H H H H H H
H H H H H H H H
O H H H H H H H
H H H H H H H H
H C O C C C C C C C C H
C C C C C C C C
H H H H H H H
H H H H H H H H

O H H H H H H H
H H H H H H H H
H C O C C C C C C C C H
C C C C C C C C
H H H H H H H H
4.7
H H H H H H H H
Fat molecule (triacylglycerol)
 Lipids
 Saturated fatty acids
• Have the maximum number of hydrogen atoms
possible
• Have no double bonds

Stearic acid

Saturated fatty acid 4.8

 Lipids
 Unsaturated fatty acids
• Have one or more double bonds

Unsaturated fatty acid

Oleic acid

cis double bond

causes bending
4.8
 Lipids
 Phospholipids
• Have only two fatty acids
• Have a phosphate group instead of a
third fatty acid
 Lipids
 Phospholipid structure
• Consists of a hydrophilic “head” and hydrophobic “tails”
CH2 +N(CH )
Hydrophilic head

3 3 Choline
CH2

O
Phosphate
O P O–
O
CH2 CH CH2
Glycerol
O O

C O C O

Phospholipid
Fatty acids
Hydrophobic tails

symbol

Hydrophilic
head

Hydrophobic
tails
Structural formula Space-filling model
 Lipids
 Phospholipid structure
• Results in a bilayer arrangement found in cell
membranes

WATER

Hydrophilic
Head Groups

Hydrophobic
Tails

Hydrophilic WATER
Head Groups
 Lipids
 Steroids
• Are lipids characterized by a carbon skeleton
consisting of four fused rings

H3C CH3

CH3 CH3

CH3
Cholesterol
•Is found in cell
membranes
HO •Is a precursor for
some hormones
 Lipids - ???
 Name three common food products and
describe how their state of matter (solid or
liquid) relates to their lipid structure.

4.9
 Proteins
 Proteins
 Have many structures and roles
inside the cell
 20 amino acids leads to great
variability
 Types
• Structural - collagen
• Enzymatic – DNA polymerase
• Transport - hemoglobin
• Receptor – insulin receptor
 Proteins
 Amino Acid – Polypeptide – Protein
• Amino acids are the monomers
• Polypeptides are the polymers
• Proteins consist of one or more
polypeptides

4.10
 Proteins
 Amino Acids
• 20 types
• Differ in their “R”
groups

4.12
 Proteins
Peptide
bond
 Peptide OH

CH2 CH2
SH

CH2

bond H H H

formation
C C
N
H C C N C OH H N C OH
H O H O H O

H2O

OH

OH SH Side chains
Peptide
CH2 CH2 bond CH2
H H H
H N C C N C C N C C OH Backbone
H O H O H O

Amino end Carboxyl end

(N-terminus) (C-terminus)
4.11
 Proteins
 Non-polar amino acids

4.13
 Proteins
 Polar amino acids

4.13
 Proteins Beta sheets

Alpha helix
 Determining Groove

conformation
• Primary structure

ribbon model
• Secondary structure

• Tertiary structure

• Quaternary structure
Groove

space-filling model
4.14
 Four Levels of Protein Structure
Gly Pro Thr Gly

Amino acid
Thr
+H3N Gly

subunits
Glu

Amino end
Seu
Pro Cys Lys
Leu
Met
Val

Primary structure
Lys

Val

 Leu
Asp
Ala Val Arg
Gly
Ser
Pro
Ala

• Is the unique
sequence of
amino acids in a
polypeptide Glu Lle
Asp
Thr
Lys

Ser
Lys Trp Tyr
Leu Ala
Gly

lle
Ser
Pro Phe
His Glu
His
Ala

Glu
Val
Ala Thr Phe Val
Asn
lle
Thr
Asp Tyr Ala
Arg
Ser Arg Ala
Gly Pro
Leu

Leu
Ser
Tyr Pro
Ser
Ser Tyr
Thr
Thr

o
Ala

c
Val
Val Lys Glu

o– Thr
Asn Pro

4.14 Carboxyl end

Four Levels of Protein Structure
 Secondary structure
• Is the folding or coiling of the polypeptide into a
repeating configuration
• Includes the α helix and the β pleated sheet
β pleated sheet O H O H H
H O H H O H H
R R R
C C N C C N C C N C C N
N C C N C C N C C N C C
C R R R R
H O H H OH H O H H O

R R R R
Amino acid O C H O C H O C H O C H
H H
subunits C N HC N H C N H C N C NH C N C N HC N
H H C H C H
C O C O O O C
R R R
R H R H
C C
N H O C N H O C
N H N H
O C O C α helix
H C R H C H C R H C R
R
N H O C N H
O C
O C N H O C
C
N H 4.16
C H
R H R
Four Levels of Protein Structure
 Tertiary structure
• Is the overall three-dimensional shape of a
polypeptide
• Results from interactions between amino acids and R
groups
Hydrophobic
and van der Waals
CH2
CH CH interactions
2
H3C CH3
O
Hydrogen H H3C CH3
bond O CH
Polypeptide
HO C backbone
CH2 CH2 S S CH2

O Disulfide bridge
CH2 NH O C CH2
3
+ -

Ionic bond

4.17
Four Levels of Protein Structure

 Quaternary
β Chains
structure
• Is the overall protein
structure that results
from the aggregation
of two or more Iron
polypeptide subunits
• Hemoglobin contains
four subunits – two Heme
alpha and two beta α Chains
chains of amino acids
Hemoglobin
 Protein Folding
 Chaperonins
• Are protein molecules that assist in the proper folding
of other proteins

Chaperonin Primary polypeptide

(fully assembled) Correctly
sequence folded
Cap protein

Hollow
cylinder

1 An unfolded poly- 2 The cap attaches, causing 3 The cap comes

Steps of Chaperonin
peptide enters the the cylinder to change shape in off, and the properly
Action:
cylinder from one end. such a way that it creates a folded protein is
hydrophilic environment for the released.
folding of the polypeptide.
4.18
 4.19
Proteins
 Denaturation
• Is when a protein unravels and loses its native
conformation
• Caused by unfavorable: temperatures, pH, salt
concentration, and other chemicals

Denaturation

Normal protein Denatured protein

Renaturation
 Nucleic Acids
 Nucleic acids (DNA/RNA)
• Store and transmit hereditary
information
 Genes
• Are the units of inheritance
• Code for the amino acid sequence of
polypeptides
• Are made of nucleic acids
 Nucleic Acids (DNA/RNA)
 Consists of Nucleoside
monomers called
nucleotides made of Nitrogenous
base
O
• Phosphate group −
5’
O P O CH2
• Nitrogenous base O
O−
4’ 1’
• Ribose sugar Phosphate
group 3’ 2’
Ribose
sugar

Nucleotide
4.20/4.21
 Nucleic Acids (DNA/RNA)
Nitrogenous bases
Prymidines
Pyrimidines

NH2 O O

C C CH3 C
N CH HN C HN CH
CH

 Nitrogenous O
C
N
CH
O
C
N
CH
O
C
N
CH
CH

Bases H H H

Cytosine Thymine (in DNA) Uracil (in

Uracil (inRNA)
RNA)
C T UU

Purines
NH2 O

N C N C
C N C NH
HC HC
CH C
N C N NH2
N N
H H
Adenine Guanine
A G
 Nucleic Acids (DNA/RNA)
 Pentose Sugars
• Ribose
• Deoxyribose

Pentose sugars
5 ”
5”
HOCH2 OH HOCH2 OH
O O

H H H H 1’
4’ 1’ 4’

H H H H
3’ 2’ 3’ 2’
OH H OH OH

Deoxyribose (in DNA) Ribose

Ribose (in RNA)
(in RNA)
4.21
 Nucleotide Polymers (DNA/RNA)
5’ end
 Nucleotide
5’C
polymers 3’C
O

• Are made up of
Phosphate
nucleotides linked O

by the –OH group

on the 3´ carbon of
one nucleotide and O

the phosphate on
the 5´ carbon on
5’C Sugar
the next O

3’C
3’ end
OH
4.20
Nucleic Acid Chain
 Adenosine Triphosphate (ATP)
 A nucleic acid
• One nucleoside + 3 phosphates

4.22
 Adenosine Triphosphate (ATP)
 ATP stores energy
• Energy is released from ATP when the terminal
phosphate bond is broken

P P P

Cells Adenosine
use this energy
triphosphate (ATP)

to perform cellular
functions
HO 2

Energy

P i
+ P P

4.24 Adenosine diphosphate (ADP)