Transcript BIOLOGY 189 Fundamentals of Life Science Fall 2002

BIOLOGY 189
Foundations of Life Science
Spring 2004
The Molecules of Cells
Chapter 3
Introduction
 Ability to spin a web is
genetically
programmed …
 But so are the
properties of the silk
produced
 Structure of silk
proteins are
determined by DNA
Introduction
 Structure determines
function
 Elasticity results from
coiling and uncoiling of
silk fibers
 5 times stronger than
steel
 Industrial applications
 Surgical thread
 Fishing line
 Bulletproof vests
Introduction
 Spider DNA and spider silk represent two of the
four classes of molecules in living organisms
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Carbohydrates
Lipids
Proteins
Nucleic acids
 A nearly infinite variety of molecules can be
made from these four simple classes
1) Organic Compounds
 Next to water, compounds containing carbon are the
most abundant in an organism
 Organic compounds – compounds synthesized by cells
and containing carbon
 Large diversity of organic compounds, over 2M
described. Diversity stems from…
 Carbon’s ability to form 4 covalent bonds
 Molecules composed only of carbon and hydrogen are
called hydrocarbons
- Carbon atoms with
attached hydrogen atoms
can bond together in
chains of various lengths
- Lengths and shapes
determine function
- Carbon skeleton – the
chain of carbon atoms in
organic molecules
- Carbon skeletons may
or may not be branched,
and may / not have
multiple bonds
- Isomers – same
molecular formula, but
different structure
1) Organic Compounds
 Carbon skeletons may be arranged in
rings
 Ball and stick (3D) models are vastly
different from the structural formulas
Ethane
Cyclohexane
2) Functional Groups
 Functional groups – groups of atoms that usually
participate in chemical reactions
 Give a compound some of its unique properties
 Four common types in biological systems.
All are polar due to O or N. Therefore they are
usually hydrophilic (water-loving) and soluble
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Hydroxyl – appendage to C skeleton
Carbonyl – add a C to the C skeleton
Carboxyl – add a C to the C skeleton
Amino - appendage to C skeleton
2) Functional Groups
3) Macromolecules
 Macromolecules – gigantic biological molecules




Carbohydrates
Proteins
Lipids
Nucleic acids
 Polymers – large molecules consisting of many
identical or similar molecular subunits strung
together in a chain
 Monomers – the units that serve as the building
blocks of polymers
3) Macromolecules
 Immense diversity of polymers, and all are made from a
list of 40-50 common monomers. Alphabet example
 Examples: 20 amino acids, 4 nucleotides
 Arrangement / sequence is the key to diversity
 Dehydration synthesis – process by which cells link
monomers to form polymers
 Hydrolysis – process by which polymers are broken into
monomers
3) Macromolecules
4) Carbohydrates
 Carbohydrate – class of molecules ranging
from small sugar monomers to very long
polymers
 Monosaccharide – carbohydrate monomer
 The molecular formula of a monosaccharide is
usually a multiple of CH2O. Glucose= C6H12O6
 Monosaccharides possess several hydroxyl
groups and a carbonyl group
4) Carbohydrates
 Glucose and fructose
are isomers and…
 This gives these
monomers different
properties.
 Example: Fructose
tastes considerably
sweeter than glucose
4) Carbohydrates
 C skeleton can vary from
3 to 7 carbons
 Pentoses – 5 C
 Hexoses – 6 C
 Some monosaccharides
switch between linear
and ring forms in an
aqueous solution
 Monosaccharides are the
main fuel for cellular
work. Cells also use C
skeletons
4) Carbohydrates
 Disaccharide – a double
sugar constructed by a
cell, from two
monosaccharides.
Occurs via dehydration
synthesis
 Sucrose (table sugar) is
made from 1 glucose and
1 fructose
4) Carbohydrates
 The chemical structure of
a compound determines
its shape, which
determines how well it fits
into a taste receptor
 Compounds that bind
more tightly to a sweet
receptor are perceived as
being sweeter
 Artificial sweeteners may
bind to other types of
taste receptors, leaving
an aftertaste
4) Carbohydrates
 Polysaccharides – polymers of a few hundred to a few
thousand monosaccharides linked together by
dehydration synthesis
 Starch – storage polysaccharide in plant roots, ect. that
consists entirely of glucose monomers. Coiled / helical
 Cells can break starch down as needed to obtain
glucose. This is done via hydrolysis in the digestive
system
 Potatoes, grains, corn and rice are good sources
4) Carbohydrates
 Animals store excess sugar in the form of glycogen
 Glycogen – polysaccharide identical to starch, but
extensively branched
 Stored as granules in liver and muscle cells. These cells
hydrolyze glycogen to release glucose
 Our digestive system hydrolyzes glycogen in the meat
we eat
4) Carbohydrates
 The most abundant organic compound on Earth is
cellulose
 Cellulose – polysaccharide resembling starch and
glycogen, but forms unbranched fibrils supported by
hydrogen bonds
 Forms plant cell walls; major component of wood
 Cannot be hydrolyzed by most animals. Fiber or
roughage. Requires microorganisms (cows / termites)
5) Lipids
 Lipids – diverse compounds consisting of C and H
atoms linked by nonpolar covalent bonds
 Lipids do not include polymers. Exception among
macromolecules
 Lipids are hydrophobic (water fearing). Insoluble in
water and aren’t attracted to water
 Example: Salad dressing. Oil is a type of lipid. It
separates from vinegar (mostly water)
 Also…
5) Lipids
The feathers of
waterfowl are water
resistant!!
“Like water off a
duck’s back”
5) Lipids
 Fat – large lipid made from two types of smaller
molecules:
 glycerol
 fatty acids
 The main function of fat is energy storage.
 One gram of fat contains twice the energy of a
gram of starch.
 9 calories per gram of fat
 4 calories per gram of carbohydrate or protein
5) Lipids
 Glycerol – alcohol with 3 carbons, each with a hydroxyl group
 Fatty acid – molecule consisting of a carboxyl group and a carbon
chain with about 15 other carbons. Nonpolar and therefore
hydrophobic
 Fatty acids link to glycerol via dehydration synthesis
 Triglyceride – synonym for fat. Three fatty acid chains linked to
glycerol.
5) Lipids
 Fatty acid chains are often different
 Unsaturated – fatty acids and fats with double
bonds.
 Double bonds cause kinks in the carbon chain
and prevent the maximum number of H atoms
from bonding
 Saturated – single bonds, maximum H atoms
5) Lipids
 Kinks prevent molecules from packing tightly together and solidifying
at room temperature
 Oils are unsaturated fats (corn, vegetable, olive oil). Plant fats are
unsaturated
 Margarine and some vegetable oils are hydrogenated
 Animal fats are saturated (butter and lard)
 Health risk
(atherosclerosis) due to plaque build-up
5) Lipids
 There are other lipids of importance
 Phospholipids – major component of cell
membranes. Structurally similar to fats but…
 only have two fatty acid tails
 contain phosphorous
5) Lipids
 Waxes – consist of
one fatty acid linked
to an alcohol
 More hydrophobic
than fats
 Natural protective
coating
 Fruits
 Insects
 Plants
5) Lipids
 Steroids – lipids with a
carbon skeleton of four
fused rings
 Cholesterol is a common
steroid found in animal
cells
 Starting material for other
steroids (sex hormones)
 Too much leads to
atherosclerosis
 Anabolic steroids pose
health risks
 Mood swings
 Cardiovascular problems
 Decrease in natural
testosterone
6) Proteins
 Protein – biological polymer constructed
from amino acid monomers
 Extremely diverse and important
molecules
 Tens of thousands of different proteins in
the human body
 Each has a specific function
6) Proteins
 Seven classes of proteins. Different structures for different functions
 Structural – spider silk, mammal hair, fibers of tendons and ligaments
 Contractile - work with structural proteins, provide muscle movement
 Storage - ovalbumin (egg whites), source of AAs for developing embryo
 Defensive – antibodies, fight infections
 Transport - hemoglobin, carries oxygen around the body
 Signal - hormones, chemical messengers that coordinate body activities
 Enzymes – catalysts – change rate of chemical reactions without being
used up in the process. Most important class of proteins. Suffix -ase
6) Proteins
 Protein diversity is based on different arrangements of
20 universal amino acids
 Amino acid – has an amino group, a carboxyl group and
an R group
 R group – variable part of an amino acid
 R groups can be polar (hydrophilic) or nonpolar
(hydrophobic). This will determine an AA’s properties
6) Proteins
 Cells link amino acids by dehydration synthesis
 Peptide bond – connects the carboxyl group of
one AA to the amino-group of a second AA
 Multiple AAs connected in a chain
 Dipeptide
 Polypeptide, can be thousands of monomers or more!
 Peptide bonds are cleaved by hydrolysis
6) Proteins
 Protein shape determines
function
 Ribbon model of
lysozyme, an enzyme in
tears and WBCs
 Lysozyme has a globular
shape with a groove
 Groove fits over surface
molecule on bacteria.
Lysozyme recognizes
target as bacteria, and
destroys!
6) Proteins
 Space –filling model of
lysozyme
 Denaturation – unraveling of
polypeptide chain, usually
due to
 Extreme temperature
 Change in pH
 Change in salinity
 Denaturation alters the
specific shape of a protein
 As a result the protein loses
it’s function (fried egg ex.)
6) Proteins
 Four levels of structure
determining a protein’s specific
shape
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Primary (1°) structure
Secondary (2°) structure
Tertiary (3°) structure
Quaternary (4°) structure
 Transthyretin example.
Transport protein in blood
 It’s primary structure consists
of 4 polypeptide chains, each
127 AAs long
 Altering hemoglobin’s AA
sequence by one AA causes
sickle-cell disease
6) Proteins
 Secondary structure of
transthyretin consists of…
 Alpha helix – coiling of a
polypeptide chain
 Pleated sheet – folding of
a polypeptide chain
 These patterns are
maintained by H bonds
6) Proteins
 Tertiary structure – overall
3D shape of protein
 Two shapes
 Globular – helix and sheet
 Fibrous - helical
 Globular proteins in
aqueous solutions are
folded so that
hydrophobic R groups
are on the inside
6) Proteins
 Quaternary structure –
overall shape or structure
resulting from the
bonding interactions
among multiple
polypeptide chains
(subunits)
 Transthyretin has 4
identical subunits
 Hemoglobin has 4
subunits of 2 different
types
7) Nucleic Acids
 Nucleic acids – polymers that serve as
blueprints for proteins
 DNA – deoxyribonucleic acid. Inherited from parents
 RNA – ribonucleic acid
 Genes – specific stretches of DNA molecules
that program AA sequences (1° structure) of
proteins
 Genes ultimately determine the 3D structure of
proteins, and thus, their function
7) Nucleic Acids
 DNA works in conjunction with RNA
 Information from DNA is transcribed into RNA
 This information is translated into the 1°
structure of proteins
 More on this later in the course!
7) Nucleic Acids
 Nucleotides – monomers that
make up nucleic acids
 3 parts
 Pentose (5-C sugar)
 Phosphate group
 Nitrogenous base
 DNA nitrogenous bases
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Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
 Same for RNA, except Uracil
(U) instead of Thymine
7) Nucleic Acids
 Polynucleotide – polymer
formed from nucleotide
monomers via
dehydration synthesis
 To form a polynucleotide
the phosphate group of
one nucleotide bonds to
the sugar of the next
monomer
 The result is a repeating
sugar-phosphate
backbone
7) Nucleic Acids
 DNA forms a double helix,
RNA is a single polynucleotide
 Double helix – two
polynucleotide strands
wrapped around each other
 Nitrogenous bases protrude
into the center of the helix from
the sugar-phosphate backbone
 Nitrogenous bases pair up via
H bonds
 A pairs with T
 C pairs with G
7) Nucleic Acids