BIOL 101 General Biology I
Chapter 5
The Structure & Function of Large Biological Molecules
Rob Swatski Associate Professor of Biology
HACC – York Campus 1
2
small
molecules LARGE molecules
3
Bonds with variety of elements
Diverse sizes & shapes
Carbon-based
Many covalent
bonds
More insoluble in
water
Monomers Polymers
Properties of Organic Molecules
Macromolecules
Carbo-hydrates
Lipids Proteins Nucleic Acids
4
5
Condensation (Dehydration) Synthesis
Dehydration
Short polymer Unlinked monomer
Longer polymer
HO
HO
HO
H2O
H
H H
4 3 2 1
1 2 3
6
7
Hydrolysis
Hydrolysis
HO
HO HO
H2O
H
H
H 3 2 1
1 2 3 4
8
9
3 Major Groups of Carbohydrates
Mono-saccharides
Disaccharides Polysaccharides
10
Carbohydrate Characteristics
C-H2O
Classify by location of carbonyl (C=O)
Aldoses or Ketoses
#C atoms in skeleton
11
Carbohydrates:
General Functions
Energy Synthesis Storage
12
Monosaccharides
C6H12O6
Dihydroxyacetone
Ribulose
Fructose
Glyceraldehyde
Ribose
Glucose Galactose
Hexoses (C6H12O6)
Pentoses (C5H10O5)
Trioses (C3H6O3)
13
(a) Linear and ring forms
(b) Abbreviated ring structure 14
15
Disaccharides
Glycosidic linkage
1–2 glycosidic
linkage
16
Dehydration reaction: Sucrose synthesis
Sucrose Fructose Glucose
Maltose
1–4 glycosidic
linkage
17
Dehydration reaction: Maltose synthesis
Glucose Glucose
18
Polysaccharides
Largest carb
Polymer: 100’s of mono’s
Storage and structure
Classified by its monomer & linkages
Glycogen
19
Storage Polysaccharides
Starch
Glucose polymer
Plant plastids
Glycogen
Glucose polymer
Animal liver & muscle
Glycogen
Starch
Amylose
Chloroplast
Starch
Amylopectin
Mitochondria Glycogen granules
20
21
Structural Polysaccharides
Cellulose
Glucose polymer
Plant cell walls
Alpha () & beta () rings
beta ()
beta-Glucose monomer
Cellulose
Microfibril
Cell walls
beta-Glucose = straight chain 22
23
and Glucose Ring Structures
Glucose Glucose
Starch: 1–4 linkage of glucose monomers
(Alpha) = All same side
24
25
Cellulose: 1–4 linkage of glucose monomers
(Beta) = Both sides
26
27
Insoluble Fiber
http://www.hulu.com/watch/
10304/saturday-night-live-
colon-blow
28
Symbiosis
29
Chitin
Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.
30
31
Hydrocarbons
C, H, O Hydrophobic
Nonpolar covalent
bonds No polymers
Glycerol & 1-3 fatty acids
Fats & oils
Lipids – General Characteristics
32
Lipid Structure
Fatty acid Glycerol
Dehydration synthesis of a fat
Ester linkage
Triglyceride 33
34
Triglyceride Structure
Fatty Acid Variation
Length
# and locations of
double bonds
Saturated fatty acids
Unsaturated fatty acids
35
Saturated Fats
Single covalent
bonds
Solid @ room temp
Mostly animal fats
36
37
Unaturated Fats
Cis double covalent
bond
Liquid @ room temp
Mostly plant & fish fats
39
Carotid artery plaque
Hydrogenation
trans fat
40
41
Adipose Tissue
Energy storage
Cushions organs
Insulation
42
Head
Polar
Hydrophilic
Glycerol & phosphate
Tails
Nonpolar
Hydrophobic
2 Fatty acids
Phospholipid Structure
Fatty acids
Choline
Phosphate
Glycerol
Hyd
rop
ho
bic
tai
ls
Hyd
rop
hili
c h
ead
43
44
Phospholipid Bilayer
45
46
Cholesterol = precursor
47
Steroids
48
49
50
Proteins
C, H, O, N
Diverse shapes &
sizes
Polypeptides (polymers)
Amino acids (monomers)
51
Enzymatic Structural Storage
Transport Hormonal Receptor
Contractile & Motor
Defensive
Types of Proteins
52
Structural support
Storage
Transport Communication
Movement Immune defense
Functions of Proteins
Keratin: structural
protein
53
60 m
Collagen
Connective tissue
Structural proteins
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.
54
GABA receptor
protein 55
Signaling molecules
Receptor protein
Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.
56
57
Actin & Myosin: contractile proteins
Muscle tissue
Actin Myosin
100 m
Contractile and motor proteins
Function: Movement
Examples: Motor proteins are responsible for the
undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of
muscles.
58
59
Antibodies: defensive proteins
Defensive proteins
Virus
Antibodies
Bacterium
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
60
Substrates
Active Site
Enzyme
61
Enzymatic proteins = Catalysts
Enzymatic proteins
Enzyme
Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.
Function: Selective acceleration of chemical reactions
62
Substrate (sucrose)
Fructose
Glucose
OH
H O
H2O
63
Enzyme (sucrase)
64
Amino Acids
Amino group
- NH2
Carboxyl group
- COOH
R group
Amino group
Carboxyl group
65
Side chain
Glycine (Gly or G)
Alanine (Ala or A)
Valine (Val or V)
Leucine (Leu or L)
Isoleucine (Ile or I)
Methionine (Met or M)
Phenylalanine (Phe or F)
Tryptophan (Trp or W)
Proline (Pro or P)
Nonpolar Amino Acids (hydrophobic)
66
Serine (Ser or S)
Threonine (Thr or T)
Cysteine (Cys or C)
Tyrosine (Tyr or Y)
Asparagine (Asn or N)
Glutamine (Gln or Q)
Polar Amino Acids (hydrophilic)
67
Acidic (negatively charged)
Basic (positively charged)
Aspartic acid (Asp or D)
Glutamic acid (Glu or E)
Lysine (Lys or K)
Arginine (Arg or R)
Histidine (His or H)
Electrically Charged Amino Acids (hydrophilic)
68
Peptide bond
New peptide bond forming
Side chains
Back- bone
Amino end (N-terminus)
Peptide bond
Carboxyl end (C-terminus) 69
70
Functional Proteins
Ribbon model of lysozyme
Space-filling model of lysozyme
Groove Groove
71
Antibody protein Protein from flu virus
72
73
Primary
Secondary
Tertiary Quaternary
Levels of Protein Structure
Amino acid subunits
+H3N
Amino end
25
20
15
10
5
1
74
Primary Structure
Primary structure Amino acids
Amino end
Carboxyl end Primary structure of transthyretin 75
pleated sheet
helix
Secondary Structure
76
Hydrogen bond
helix
pleated sheet
strand, shown as a flat arrow pointing toward the carboxyl end
Hydrogen bond
Secondary Structure
77
78 Silk = pleated sheet
79
too freakin’ cute…
…it has eyelashes for crying out loud!
Transthyretin polypeptide
Tertiary Structure
80
Hydrogen bond
Disulfide bridge
Polypeptide backbone
Ionic bond
Hydrophobic
interactions and
van der Waals
interactions
81
Transthyretin protein
(four identical polypeptides)
Quaternary Structure
82
Collagen 83
84
Collagen
Hemoglobin
Heme
Iron
subunit
subunit
subunit
subunit
85
86
Sickle-Cell Disease
Glutamic acid Valine (mutation)
No interaction between
molecules
Normal hemoglobin 7 6 5 4 3 2 1
Glu Val His Leu Thr Pro Glu
87
Normal hemoglobin
(top view)
Sickle-cell hemoglobin
Sickle-cell hemoglobin 7 6 5 4 3 2 1
Val Val His Leu Thr Pro Glu
Exposed hydrophobic
region
88
Interaction between
molecules = crystal fiber
Primary Structure
Secondary and Tertiary Structures
Quaternary Structure
Function Red Blood Cell Shape
subunit
subunit
Exposed hydrophobic region
Molecules do not associate with one another; each carries oxygen.
Molecules crystallize into a fiber; capacity to carry oxygen is reduced.
Sickle-cell hemoglobin
Normal hemoglobin
10 m
10 m
Sic
kle
-cell h
em
og
lob
in
No
rma
l h
em
og
lob
in
1
2
3
4
5
6
7
1
2
3
4
5
6
7
89
90
Physical & Chemical Conditions Affect Protein Structure
pH changes
Salt concentration
Temperature
Denaturation
Denaturation
Renaturation
91
92
Protein Folding in the Cell
Chaperonin
The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide.
Polypeptide
Correctly folded protein
Steps of Chaperonin Action:
An unfolded poly- peptide enters the cylinder from one end.
The cap comes off, and the properly folded protein is released.
3 2
1
Steps of Chaperonin Action
93
X-ray Crystall-
ography of Proteins
94
95
Nuclear Magnetic Resonance (NMR) spectroscopy
96
97 CoA Binding Site in Staphylococcus aureus
EXPERIMENT
RESULTS
X-ray source X-ray
beam
Diffracted X-rays
Crystal Digital detector X-ray diffraction pattern
RNA polymerase II
RNA
DNA
98
99
Bioinformatics
Predicts protein structure from AA sequence
100
101
C, H, O, N, P Polymer of nucleotides
DNA and RNA Molecular
biology
Regulates cell activities
Guides protein synthesis
Nucleic Acids
102
mRNA
1. Synthesis of mRNA in the
nucleus
DNA
NUCLEUS
mRNA
CYTOPLASM
2. mRNA moves into cytoplasm
via nuclear pore
Ribosome
Amino acids Polypeptide
3. Synthesis of protein
103
Nucleotides
Nitrogenous Base
Pentose Sugar
Phosphate Group
5' end
5'C
3'C
5'C
3'C
3' end
Polynucleotide (Nucleic Acid)
Nucleotide
Nucleoside
Nitrogenous base
3'C
5'C
Phosphate group Sugar
(pentose)
104
Ribose (in RNA) Deoxyribose (in DNA)
Sugars of the Nucleotide
105
Nitrogenous Bases of the Nucleotide
Purines
Guanine (G) Adenine (A)
Cytosine (C) Thymine (T, in DNA)
Uracil (U, in RNA)
Pyrimidines
106
107
108
DNA
Double helix
Antiparallel
A---T
C---G
Sugar-phosphate backbones
3' end
3' end
3' end
3' end
5' end
5' end
5' end
5' end
Base pair
Old strands
New strands
109
Sugar-phosphate backbones
Hydrogen bonds
Base pair joined by hydrogen bonding
Base pair joined by hydrogen
bonding
(b) Transfer RNA (a) DNA
5 3
5 3
110