Embed Size (px)
Citation preview
5/13/2013
1
The Structure and Function of
Large Biological Molecules
Chapter 5
You should be able to:
1. List and describe the four major classes of
molecules
2. Describe the formation of a glycosidic
linkage and distinguish between
monosaccharides, disaccharides, and
polysaccharides
3. Distinguish between saturated and
unsaturated fats and between cis and trans
fat molecules
4. Describe the four levels of protein structure
You should be able to:
5. Distinguish between the following pairs: pyrimidine and purine, nucleotide and nucleoside, ribose and deoxyribose, the 5 end and 3 end of a nucleotide
5/13/2013
2
Overview: The Molecules of
Life
o All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids
o Within cells, small organic molecules are joined together to form larger molecules
o Macromolecules are large molecules composed of thousands of covalently connected atoms
o Molecular structure and function are inseparable
Macromolecules are polymers,
built from monomers
o A polymer is a long molecule consisting of many similar building blocks
o These small building-block molecules are called monomers
o Three of the four classes of life’s organic molecules are polymers: Carbohydrates, Proteins, Nucleic Acids
Molecule Covalent Bond Sharing valence electrons
Polymer:
A Big Molecule
• A condensation reaction (or
dehydration reaction) occurs when two
monomers bond together through the loss
of a water molecule: (2 H’s, 1 O)
• Enzymes are macromolecules, which
speed up the dehydration process
• Polymers are disassembled to monomers
by hydrolysis, essentially the reverse of
the dehydration reaction
The Synthesis and Breakdown of
Polymers
Animation: Polymers
5/13/2013
3
Dehydration reaction:
synthesizing a polymer
Short polymer Unlinked monomer
Dehydration removes a water molecule, forming a new bond.
Longer polymer
1 2 3 4
1 2 3
Hydrolysis: breaking down a polymer
Hydrolysis adds a water molecule, breaking a bond.
1 2 3 4
1 2 3
The Diversity of Polymers
o Each cell has thousands of different
macromolecules
o Macromolecules vary among cells of an
organism, vary more within a species, and
vary even more between species
o An immense variety of polymers can be built
from a small set of monomers
5/13/2013
4
Carbohydrates serve as fuel and
building material
o Carbohydrates include sugars and the
polymers of sugars
o The simplest carbohydrates are
monosaccharides, or single sugar molecules
o Carbohydrate macromolecules are
polysaccharides, polymers composed of
many sugar building blocks
o Monosaccharides have molecular formulas that are usually multiples of CH2O
o Glucose (C6H12O6) is the most common monosaccharide
o Monosaccharides are classified by
o The location of the carbonyl group (as aldose or ketose)
o The number of carbons in the carbon skeleton
Sugars
Fig. 5-3
Dihydroxyacetone
Ribulose
Fructose
Glyceraldehyde
Ribose
Glucose Galactose
Hexoses (C6H12O6) Pentoses (C5H10O5) Trioses (C3H6O3)
5/13/2013
5
o Though often drawn as linear skeletons, in
aqueous solutions many sugars form rings
o Monosaccharides serve as a major fuel for
cells and as raw material for building
molecules
(a) Linear and ring forms (b) Abbreviated ring structure
o A disaccharide is formed when a dehydration
reaction joins two monosaccharides
o This covalent bond is called a glycosidic
linkage
“Table Sugar”
Animation: Disaccharide
Polysaccharides
o Polysaccharides, the polymers of sugars,
have storage and structural roles
o The structure and function of a
polysaccharide are determined by its sugar
monomers and the positions of glycosidic
linkages
5/13/2013
6
Storage Polysaccharides
o Starch, a storage polysaccharide of plants,
consists entirely of glucose monomers
o Plants store surplus starch as granules
within chloroplasts and other plastids
o Glycogen is a storage polysaccharide in
animals
o Humans and other vertebrates store
glycogen mainly in liver and muscle cells
Fig. 5-6
(b) Glycogen: an animal polysaccharide
Starch
Glycogen Amylose
Chloroplast
(a) Starch: a plant polysaccharide
Amylopectin
Mitochondria Glycogen granules
0.5 µm
1 µm
Structural Polysaccharides
o The polysaccharide cellulose is a major
component of the tough wall of plant cells
o Like starch, cellulose is a polymer of
glucose, but the glycosidic linkages differ
o The difference is based on two ring forms
for glucose: alpha () and beta ()
Animation: Polysaccharides
5/13/2013
7
Fig. 5-7
(a) α and β glucose ring structures
α Glucose β Glucose
(b) Starch: 1–4 linkage of α glucose monomers (b) Cellulose: 1–4 linkage of β glucose monomers
oPolymers with glucose are helical
oPolymers with glucose are straight
o In straight structures, H atoms on one strand
can bond with OH groups on other strands
oParallel cellulose molecules held together
this way are grouped into microfibrils, which
form strong building materials for plants
Fig. 5-8
β Glucose monomer
Cellulose molecules
Microfibril
Cellulose microfibrils in a plant cell wall
0.5 µm
10 µm
Cell walls
5/13/2013
8
o Enzymes that digest starch by hydrolyzing
linkages can’t hydrolyze linkages in cellulose
o Cellulose in human food passes through the
digestive tract as insoluble fiber
o Some microbes use enzymes to digest cellulose
o Many herbivores, from cows to termites, have
symbiotic relationships with these microbes
o Chitin, another
structural
polysaccharide, is
found in the
exoskeleton of
arthropods
o Chitin also provides
structural support
for the cell walls of
many fungi
Chitin forms the exoskeleton of arthropods.
The structure of the chitin monomer
Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.
Lipids are a diverse group of
hydrophobic molecules
o Lipids are the one class of large biological
molecules that do not form polymers
o The unifying feature of lipids is having little
or no affinity for water
o Lipids are hydrophobic becausethey consist
mostly of hydrocarbons, which form
nonpolar covalent bonds: C-H
o The most biologically important lipids are
fats, phospholipids, and steroids
5/13/2013
9
Fats o Fats are constructed from two types of smaller
molecules: Glycerol and Fatty acids
o Glycerol is a three-carbon alcohol (C-O-H) with a hydroxyl group attached to each carbon
o A fatty acid consists of a carboxyl group attached to a long carbon skeleton
o In a fat, 3 fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride
o Fats separate from water because water molecules form hydrogen bonds with each other and exclude (push away) the fats
Fig. 5-11
Fatty acid (palmitic acid)
Glycerol
(a) Dehydration reaction in the synthesis of a fat
Ester linkage
(b) Fat molecule (triacylglycerol)
o Fatty acids vary in length (number of
carbons in the skeleton) and in the number
and locations of double bonds
o Saturated fatty acids have the maximum
number of hydrogen atoms possible and no
double bonds
o Unsaturated fatty acids have one or more
double bonds
Animation: Fats
5/13/2013
10
Saturated fat
Structural formula of a saturated fat molecule
Space-filling model of stearic acid, a saturated fatty acid
o Fats made from
saturated fatty
acids are called
saturated fats,
and are solid at
room
temperature
o NO DOUBLE
BONDS
o Most animal fats
are saturated
Unsaturated fat
Structural formula of an unsaturated fat molecule
Space-filling model of oleic acid, an unsaturated fatty acid
Cis double bond causes bending.
o Fats made from
unsaturated fatty
acids are called
unsaturated fats
or oils, and are
liquid at room
temperature
o HAVE DOUBLE
BONDS
o Plant fats and fish fats
are usually unsaturated
o A diet rich in saturated fats may contribute to
cardiovascular disease through plaque deposits
o Hydrogenation is the process of converting
unsaturated fats to saturated fats by adding
hydrogen
o Hydrogenating vegetable oils also creates
unsaturated fats with trans double bonds
o These trans fats may contribute more than
saturated fats to cardiovascular disease
5/13/2013
11
o Certain unsaturated fatty acids are not
synthesized in the human body
o These must be supplied in the diet
o These essential fatty acids include the omega-3
fatty acids, required for normal growth, and
thought to provide protection against
cardiovascular disease
o The major function of fats is energy storage
o Humans and other mammals store their fat
in adipose cells
o Adipose tissue also cushions vital organs
and insulates the body
Phospholipids o In a phospholipid, two fatty acids and a
phosphate group are attached to glycerol
o The two fatty acid tails are hydrophobic, but
the phosphate group and its attachments
form a hydrophilic head
5/13/2013
12
Fig. 5-13
(b)
Space-filling model (a)
(c)
Structural formula Phospholipid symbol
Fatty acids
Hydrophilic head
Hydrophobic tails
Choline
Phosphate
Glycerol
Hyd
rop
ho
bic
ta
ils
H
yd
rop
hil
ic h
ea
d
o When phospholipids are added to water, they
self-assemble into a bilayer, with the
hydrophobic tails pointing toward the interior
o The structure of phospholipids results in a
bilayer arrangement found in cell membranes
o Phospholipids are the major component of all
cell membranes
Hydrophilic head
Hydrophobic tail
WATER
WATER
Steroids o Steroids are lipids characterized by a carbon
skeleton consisting of four fused rings
o Cholesterol, an important steroid, is a component
in animal cell membranes
Estradiol
Testosterone
Some Other Steroids
5/13/2013
13
Proteins have many structures,
resulting in a wide range of functions o Proteins account for more than 50% of the
dry mass of most cells
o Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances
o Just about everything a Cell/Organism Does or Is is the result of Proteins
o Proteins are polymers of Amino Acids
Figure 5.15-a
Enzymatic proteins Defensive proteins
Storage proteins Transport proteins
Enzyme Virus
Antibodies
Bacterium
Ovalbumin Amino acids for embryo
Transport protein
Cell membrane
Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
Function: Storage of amino acids Function: Transport of substances
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.
Figure 5.15-b
Hormonal proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
High blood sugar
Normal blood sugar
Insulin secreted
Signaling molecules
Receptor protein
Muscle tissue
Actin Myosin
100 m 60 m
Collagen
Connective tissue
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.
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.
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.
5/13/2013
14
o Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions
o Like a tool, it is not destroyed doing its job
o Unlike a tool, the reaction could occur anyway, just more slowly
o Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life
Animation: Enzymes
Fig. 5-16
Enzyme (sucrase)
Substrate (sucrose)
Fructose
Glucose
OH
H O
H2O
Amino Acid Monomers
o Amino acids are organic molecules with carboxyl and amino groups
o Amino acids differ in their properties due to differing side chains, called R
groups Side chain (R group)
Amino group
Carboxyl group
carbon
5/13/2013
15
Figure 5.16 Nonpolar side chains; hydrophobic
Side chain (R group)
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)
Polar side chains; hydrophilic
Serine (Ser or S)
Threonine (Thr or T)
Cysteine (Cys or C)
Tyrosine (Tyr or Y)
Asparagine (Asn or N)
Glutamine (Gln or Q)
Electrically charged side chains; hydrophilic
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)
Polypeptides
o Amino acids are linked by peptide bonds
o Polypeptides are polymers built from the same set of 20 amino acids
o A protein consists of one or more polypeptides
o Polypeptides range in length from a few to more than a thousand monomers
o Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)
Figure 5.17
Peptide bond
New peptide bond forming
Side chains
Back- bone
Amino end (N-terminus)
Peptide bond
Carboxyl end (C-terminus)
5/13/2013
16
Protein Structure and Function
o The sequence of amino acids determines a
protein’s three-dimensional structure
o A functional protein consists of one or more
polypeptides twisted, folded, and coiled into
a unique shape
o A protein’s structure determines its function
Fig. 5-19
A ribbon model of lysozyme (a) (b) A space-filling model of lysozyme
Groove
Groove
Fig. 5-20
Antibody protein Protein from flu virus
5/13/2013
17
Four Levels of Protein Structure
o The primary structure of a protein is its
unique sequence of amino acids
o Secondary structure, found in most
proteins, consists of coils and folds in
the polypeptide chain
o Tertiary structure is determined by
interactions among various side chains (R
groups)
o Quaternary structure results when a protein
consists of multiple polypeptide chains Animation: Protein Structure Introduction
o Primary structure,
the sequence of
amino acids in a
protein, is like the
order of letters in a
long word
o Primary structure is
determined by
inherited genetic
information (via
DNA)
Primary structure
Amino acids
Amino end
Carboxyl end
Primary structure of transthyretin
o The coils and folds of secondary structure
result from hydrogen bonds between
repeating constituents of the polypeptide
backbone
o Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet
5/13/2013
18
Secondary structure
Hydrogen bond
helix
pleated sheet
strand, shown as a flat arrow pointing toward the carboxyl end
Hydrogen bond
o Tertiary structure is determined by
interactions between R groups, rather than
interactions between backbone constituents
o These interactions between R groups
include hydrogen bonds, ionic bonds,
hydrophobic interactions, and van der
Waals interactions
o Strong covalent bonds called disulfide
bridges may reinforce the protein’s
structure
Fig. 5-21f
Polypeptide backbone
Hydrophobic interactions and van der Waals interactions
Disulfide bridge
Ionic bond
Hydrogen bond
5/13/2013
19
o Quaternary structure results when two or
more polypeptide chains form one
macromolecule
Fig. 5-21g
Polypeptide chain
Chains
Heme
Iron
Chains
Collagen Hemoglobin
Hemoglobin is a globular protein consisting
of four polypeptides: two alpha and two
beta chains Collagen is a fibrous protein consisting of
three polypeptides coiled like a rope
Fig. 5-21
Primary
Structure
Secondary
Structure
Tertiary
Structure
pleated sheet
Examples of amino acid
subunits
+H3N Amino end
helix
Quaternary
Structure
5/13/2013
20
Sickle-Cell Disease: A Change in
Primary Structure
o A slight change in primary structure can
affect a protein’s structure and ability to
function
o Sickle-cell disease, an inherited blood
disorder, results from a single amino acid
substitution in the protein hemoglobin
Figure 5.21
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
-cel
l h
emog
lob
in
Norm
al
hem
og
lob
in
1
2
3
4
5
6
7
1
2
3
4
5
6
7
o In addition to primary structure, physical and chemical conditions can affect structure
o Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel
o This loss of a protein’s native structure is called denaturation
o A denatured protein is biologically inactive
What Determines Protein Structure?
5/13/2013
21
Figure 5.22
Normal protein Denatured protein
tu
Protein Folding in the Cell
o It is hard to predict a protein’s structure from its
primary structure
o Most proteins probably go through several
states on their way to a stable structure
o Chaperonins are protein molecules that assist
the proper folding of other proteins
o Diseases such as Alzheimer’s, Parkinson’s,
and mad cow disease are associated with
misfolded proteins
Figure 5.23
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.
Cap
Polypeptide
Correctly folded protein
Chaperonin (fully assembled)
Steps of Chaperonin Action:
An unfolded poly- peptide enters the cylinder from one end.
Hollow cylinder
The cap comes off, and the properly folded protein is released.
1
2 3
5/13/2013
22
o Scientists use X-ray crystallography to
determine a protein’s structure
o Another method is nuclear magnetic
resonance (NMR) spectroscopy, which does
not require protein crystallization
o Bioinformatics uses computer programs to
predict protein structure from amino acid
sequences
Nucleic acids store and transmit
hereditary information o The amino acid sequence of a polypeptide is
programmed by a unit of inheritance called a gene
o Genes are made of DNA, a nucleic acid, a polymer of nucleotides
o A Gene is a section of a long DNA molecule
o You inherit ½ of your genes (the instructions to make your proteins from each of your parents)
o So ½ of your Polypeptides have the sequence (primary structure) like your mom’s, ½ like your dad’s
The Roles of Nucleic Acids o There are two types of nucleic acids:
o Deoxyribonucleic acid (DNA)
o Ribonucleic acid (RNA)
o DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis
o 2-step process: DNA (in nucleus) → RNA (leaves nucleus) → Protein
o The sequence of bases along a DNA or mRNA
polymer is unique for each gene
o Sequence of DNA nucleotides means the
Sequence of Protein amino acids
o Like translating a code
5/13/2013
23
Fig. 5-26-1
mRNA
Synthesis of mRNA in the nucleus
DNA
NUCLEUS
CYTOPLASM
1
Fig. 5-26-2
mRNA
Synthesis of mRNA in the nucleus
DNA
NUCLEUS
mRNA
CYTOPLASM
Movement of mRNA into cytoplasm via nuclear pore
1
2
Fig. 5-26-3
mRNA
Synthesis of mRNA in the nucleus
DNA
NUCLEUS
mRNA
CYTOPLASM
Movement of mRNA into cytoplasm via nuclear pore
Ribosome
Amino acids Polypeptide
Synthesis of protein
1
2
3
5/13/2013
24
The Structure of Nucleic Acids o Nucleic acids are polymers called polynucleotides
o Each polynucleotide is made of monomers called nucleotides
o Each nucleotide consists of a
o nitrogenous base
o pentose sugar
o phosphate group
o The portion of a nucleotide without the phosphate group is
called a nucleoside
o Nucleoside = Nitrogenous base + Sugar
o Nucleotide = Nucleoside + Phosphate group
Figure 5.26
Sugar-phosphate backbone 5 end
5C
3C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
(b) Nucleotide
Phosphate group Sugar
(pentose)
Nucleoside
Nitrogenous base
5C
3C
1C
Nitrogenous bases
Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)
Adenine (A) Guanine (G)
Sugars
Deoxyribose (in DNA) Ribose (in RNA)
(c) Nucleoside components
Pyrimidines
Purines
Fig. 5-27c-2
Ribose (in RNA) Deoxyribose (in DNA)
Sugars
(c) Nucleoside components: sugars
In DNA, the sugar is deoxyribose; in RNA,
the sugar is ribose
5/13/2013
25
Nucleotide Monomers o There are two families of nitrogenous bases:
o Pyrimidines (cytosine, thymine, and uracil) have a
single 6-membered ring
o Purines (adenine and guanine) have a 6-membered
ring fused to a 5-membered ring
Fig. 5-27ab
5' end
5'C
3'C
5'C
3'C
3' end
(a) Polynucleotide, or nucleic acid
(b) Nucleotide
Nucleoside
Nitrogenous base
3'C
5'C
Phosphate group Sugar
(pentose)
Adjacent nucleotides are joined by covalent
bonds between the –OH group on the 3 carbon
of one nucleotide and the phosphate on the 5
carbon on the next
These links create a backbone of
sugar-phosphate units, with
nitrogenous bases as appendages
The Structures of DNA and RNA Molecules
o RNA molecules usually exist as single polypeptide
chains
o A DNA molecule has two polynucleotides spiraling
around an imaginary axis, forming a double helix
o In the DNA double helix, the two backbones run in
opposite 5 → 3 directions from each other, an
arrangement referred to as antiparallel
o One DNA molecules includes many genes
5/13/2013
26
oThe nitrogenous bases in DNA pair up and form
hydrogen bonds: adenine (A) always with thymine
(T), and guanine (G) always with cytosine (C)
oCalled complementary base pairing
oComplementary pairing can also occur between
two RNA molecules or between parts of the same
molecule
oIn RNA, thymine is replaced by uracil (U) so A
and U pair
Figure 5.27
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
Fig. 5-UN7
5/13/2013
27
DNA and Proteins as Tape
Measures of Evolution
o The linear sequences of nucleotides in DNA
molecules are passed from parents to
offspring
o Two closely related species are more similar
in DNA than are more distantly related
species
o Molecular biology can be used to assess
evolutionary kinship
Figure 5.UN02
Fig. 5-UN9
5/13/2013
28
Wheat Chex®
Fig. 5-UN4
Fig. 5-UN5
5/13/2013
29
Fig. 5-UN10
