Download Biological Molecules

Chapter 3
Biological Molecules
Great and Small
Chapter Goal: Understanding how cells use small building
blocks to build larger molecules and how
some of those molecules then fold into
3-D shapes
Key Questions
• How do organisms use carbon atoms
decorated with functional groups to build
basic molecules of life?
• What are the categories of building block
molecules?
• What reactions link and unlink building
blocks?
• How are fatty acids, polysaccharides,
nucleic acids and proteins formed?
Biological Molecules
• Size: either small (MW<300) or large
(MW>10,000)
• Organic molecules based on hydrogen,
carbon, nitrogen, oxygen, rarely
phosphorus and sulfur
• Are built of subunits — “building blocks”
Biological Molecules are Organic Compounds
Common elements in living systems:
• C, H, O, N are the great majority atoms (96.3%) in living things.
• Important ions: Na, K, Mg, Ca, P, S, Cl,
• Trace ions and minerals: Zn, Cu, Mn, Fe, I, and others
Element Symbol
Percent of Approximate percent
human body of Earth’s crust by
by weight
weight
Oxygen
O
65.0
46.6
Carbon
C
18.5
0.03
Hydrogen
H
9.5
0.14
Nitrogen
N
3.3
Trace
Calcium
Phosphor
us
Potassium
Ca
1.5
3.6
P
1.0
0.07
K
0.4
2.6
Sulfur
S
0.3
0.03
Chlorine
Cl
0.2
0.01
Sodium
Magnesiu
m
Na
0.2
2.8
Mg
0.1
2.1
Important Functions
Necessary for cellular respiration, component of
water
Backbone of organic molecules
Electron carrier, component of water and most
organic molecules
Component of all proteins and nucleic acid
Component of bones and teeth, trigger for many
cellular functions
Backbone of nucleic acids, important in energy
transfer
Principal positive ion in cells, important for nerve
function
Component of most proteins
Principal negative ion bathing cells
Principal positive ion bathing cells, important in
nerve function
Critical component of many energy-transferring
enzymes
Subunits and Macromolecules
•
•
•
•
Sugars
Lipids
Amino acids
Nucleotides
•
•
•
•
Polysaccharides
Fats and cholesterol
Proteins
DNA and RNA
Carbon
• Carbon chains
and rings are
linked by single
and double
covalent bonds
Carbon Rings
• Carbon rings can be flat
• Carbon rings can be “boat” or “chair”
Chemical Interactions of Molecules
• Determined by:
– Shape
– Charge distribution
– Interactions with water
– Interactions with other molecules
Functional Groups
• Small groups of atoms
• Contribute to the chemical properties of
a molecule
• Usually attached to the carbon
backbone
Examples of Functional Groups
•
•
•
•
•
•
-OH hydroxyl
-C=O carbonyl
-COOH carboxyl
-NH2 amine
-SH sulfhydryl
-PO4 phosphate
Shapes of Biomolecules
• Lipids do not form chains of subunits
• Proteins, nucleic acids and
carbohydrates can form long chains
• Carbohydrate chains may be branched
Linking Subunits to
Make Macromolecules
• Macromolecule
subunits are linked
by removing
water —
dehydration
condensation
Breaking Macromolecules
• Subunits are broken
apart by adding
water to a bond —
hydrolysis
Macromolecules
Lipids
• Contain high levels of chemical energy
• Do not dissolve in water
• Have few polar functional groups
• Major component of biological
membranes
The 6 Lipids Used in Cells
Fatty Acids
• Are amphipathic —
contain some polar
groups
• Saturated (no
double bonds) or
unsaturated (some
double bonds)
Health Effects
• Saturated fats increase cholesterol
levels in the blood
• Unsaturated fats have less effect on
cholesterol levels
• Omega-3 fatty acids (from fish and sea
weed) inhibit inflammation response in
blood vessels and joints
Forming Triglycerides
• Subunits
– Glycerol
– 3 fatty acids
• Linked by
condensation
reactions
Forming Phospholipids
• Subunits
– Glycerol
– 2 fatty
acids
–“Head” with phosphate group
•Amphipathic
•Linked by condensation reactions
Phospholipids in Membranes
• Amphipathic structure causes formation of a
bilayer
• Charged groups associate with water
• Hydrophobic tails clump together
Steroids
• Structure is 4 rings
• Based on cholesterol
• Functional groups determine biological
activity
Carbohydrates
• Fundamental energy storage molecule
• Subunits are simple sugars — 3 ~ 9 Carbons
monosaccharides
– Ex. Glucose, fructose, ribose, deoxyribose
• Linked by dehydration condensation into
disaccharide and polysaccharides –
glycosidic bond
– Disaccharide: sucrose (table sugar)
– Polysaccharide: starch, cellulose, glycogen,chitin
Formation of Polysaccharides
• 2 sugars link to form
disaccharide
– Ex. sucrose
• Several sugars —
oligosaccharide
• Long chains of
sugars —
polysaccharide
– Ex. Starch in bread
– Cellulose in wood and
paper
Structure of Carbohydrates
• Chemical formula:
(CH2O)n
• For each carbon:
– 1 oxygen
– 2 hydrogens
• Many hydroxyl groups
make sugars hydrophilic
• Ribose and deoxyribose:
building blocks for RNA
and DNA
Carbohydrates and Energy
• Glucose (blood sugar) is the basis of
most energy releasing reactions
• Short term energy — mono- and disaccharides
• Long term energy storage — glycogen
in animals, starch in plants
• Sugar in coke (15 square sugars or 28g
sugar/can)
Carbohydrates and Structure
• Glycogen
– Animal energy, branched
• Starch
– Plant energy, branched or unbranched
– Amyrose unbranched, amylopectin branched
• Cellulose
– Structural support for plant cells
– Glucose polysaccharide with bonds in straight orientation
• Chitin
– Exoskeleton of arthropods such as butterfly and crab
– Modified sugars in chains
Carbohydrates in Plants
Glycoproteins and Glycolipids
• Glycoproteins have short chains of sugars
attached to proteins
• Glycolipids have short chains of sugars
attached to lipids
• Both found on the exterior surface of cells
• Glycoproteins are signs that help cells to
recognize one another and communicate,
• Glycoproteins attached to newly made proteins
act as address labels to tell a cell where to
ship new proteins
Polypeptides
•Protein: working molecules of a cell, carry out biological activities encoded by
genes
•Classifications of Functions of Proteins:
-Enzymes: catalysts that accelerate the rates of biological reactions.
oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase
-Regulatory proteins: sensors and switches, control protein activity and gene
functions
hormones, insulin, transcriptional factor, lac repressor
-Transport proteins: control the flow of materials across cellular membrane.
Mb & Hb (O2), ion channel, serum albumin (FA: from adipose tissue to organs)
-Storage proteins: as a reservoir of an essential nutrients.
ovalbumin (egg white), casein (酪蛋白，milk), zeins (corn), ferritin (Fe2+)
-Motor proteins: cause motion, cell division, muscle contraction, cell motility.
myosin, actin, tubulin, dynein/kinesin
-Structural proteins: provide structural rigidity and protection to the cells and
tissues.
keratin, collagen, elastin, fibroin
-Signaling proteins: transmit external signals to the cell interior.
receptors, protein kinase/phosphatase, two component system
-Protective or exploitive protein: play active role in cell defense, protection
Ig (antibody), thrombin (blood-clotting protein), antifreeze protein, toxin
Polypeptides
• Structure
– Unbranched chains
of amino acids
– Bend into unique
shapes
Amino Acids
• Subunits of
polypeptides
• 20 different types
• Structure:
– Amino group
– Carboxyl (acid)
group
– R groups differ
Amino Acids
Formation of Polypeptides
• Linked by
dehydration
condensation
• Bonds are
peptide bonds
Protein Shapes
• Globular — irregular
shapes, non-repeating
amino acid sequence
– Hemoglobin
• Fibrous — regular
shapes, repeating
sequences
– Keratin, collagen, elastin
Protein Structure
• 4 levels of folding
– Primary structure is sequence of amino acids
Protein Structure
• Secondary — coils
or folds of sections
of protein
– Alpha helix
– Beta sheet
– Stabilized by
hydrogen bonds
– Collagen helix: three
polypeptide chains
wound around each
other
Protein Structure
• Tertiary
– 3-dimensional
conformation of
entire protein
– Stabilized by
covalent, hydrogen
and ionic bonds
Protein Structure
• Quaternary
– Multiple peptide
chains fitted together
to make 1 functional
protein
Levels of Protein Folding
Protein Folding
• Some proteins fold spontaneously into
their correct 3-dimensional shape
• Some proteins need chaperone proteins to
fold correctly
Nucleic Acids
• Functions:
– Contain genetic information (DNA and RNA)
– Some nucleotides used for energy storage:
ATP
– Some nucleotide used as signal transduction:
cAMP, cGMP
Nucleic Acids
• Structure
– Subunits —
nucleotides
– 3 building blocks for
each nucleotide:
• Sugar
• Phosphate
• Nitrogenous base
Nitrogenous Bases
• 2 types:
– Pyrimidines, single
ring
– Purines, 2 rings
• Differ in functional
groups attached to
the rings
Sugars and Phosphates
• 5 carbon sugars
– Ribose in RNA (ribonucleic acid)
– Deoxyribose in DNA (deoxyribonucleic acid)
• Phosphate groups link nucleotides
together: phosphodiester bond
Formation of Nucleic Acids
• Linked by dehydration
condensation
• Bond is called a
phosphodiester
linkage
Nucleic Acid Structure
DNA Structure
Key Concepts
• 4 building blocks — lipids, sugars, amino
acids, nucleotides
• Functional groups determine chemistry
• Dehydration reactions link small molecules
• Protein shape is determined by R-groups