Download Ch 5 Macromolecules

Chapter 5
The Structure and Function of
Large Biological Molecules
Overview: The Molecules of Life
• Four types:
– carbohydrates, lipids, proteins, nucleic acids
• Macromolecules: large molecules composed
of thousands of covalently connected atoms
• Molecular structure closely related to function
Macromolecules: polymers
built from monomers
• Polymer (polys “many”, meros “parts”): molecule
composed of many similar building blocks
• Monomers (mono “single”): small building block
molecules
• Three of the four classes of life’s organic
molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
Warm up 
• Have bozeman notes ready to be stamped
In your groups, create the two compounds:
• Make C2H6 and a CH3-OH
• Black = carbon
• White = hydrogen
• Red = oxygen
Combine the two molecules
• C2H6 + CH3-OH  C3H8
What molecule is left behind?
Synthesis and Breakdown of Polymers
• Dehydration synthesis: two monomers bond,
loss of a water molecule
– “Lose H2O to make”
• Hydrolysis: polymers disassemble; reverse of
dehydration synthesis, water molecule added
– “to break apart by adding H2O
(a) Dehydration reaction: synthesizing a polymer
1
2
3
Short polymer
Unlinked monomer
Dehydration removes
a water molecule,
forming a new bond.
1
2
3
4
Longer polymer
(b) Hydrolysis: breaking down a polymer
1
2
3
Hydrolysis adds
a water molecule,
breaking a bond.
1
2
3
4
QUICK CHECK
HO
How many molecules of H2O are needed to
completely hydrolyze a polymer that is 10
monomers long?
Carbohydrates: fuel & building
material
•
•
•
•
Carbohydrates: sugars, polymers of sugars
Monosaccharides: single sugars
Disaccharides: double sugars
Polysaccharides: macromolecules; polymers
composed simple sugar building blocks
Monosaccharides: simple sugars
• molecular formulas multiples of CH2O
• glucose (C6H12O6), galactose, fructose
– Isomers
• classified
– number of carbons in carbon skeleton
– location of carbonyl group
• aldose or ketose
Aldoses (Aldehyde Sugars)
Ketoses (Ketone Sugars)
Trioses: 3-carbon sugars (C3H6O3)
Aldose:
carbonyl group
at the end
Ketose:
carbonyl group
in the middle
Glyceraldehyde
Dihydroxyacetone
Pentoses: 5-carbon sugars (C5H10O5)
Ribose
Ribulose
Hexoses: 6-carbon sugars (C6H12O6)
Glucose
Galactose
Fructose
1
2
6
6
5
5
3
4
4
5
1
3
2
4
1
3
2
6
(a) Linear and ring forms
6
5
4
1
3
2
(b) Abbreviated ring structure
• Simple sugars often drawn as
linear skeletons, in aqueous
solutions many form rings
• Monosaccharides
• major fuel for cells
• raw material for building
molecules
Disaccharide
• dehydration synthesis reaction joins two
monosaccharides
– sucrose, maltose, lactose
• covalent bond called glycosidic linkage
• C12H22O11
1–4
glycosidic
1 linkage 4
Glucose
Glucose
Maltose
(a) Dehydration reaction in the synthesis of maltose
1–2
glycosidic
1 linkage 2
Glucose
Fructose
(b) Dehydration reaction in the synthesis of sucrose
Sucrose
Polysaccharides
• polymers of sugars
– energy storage & structural roles
– starch, glycogen, cellulose, chitin
• structure & function determined by
– sugar monomers
– positions of glycosidic linkages
Storage Polysaccharides
• Starch: storage polysaccharide of plants,
consists entirely of glucose monomers
– stored as granules w/in chloroplasts & other plastids
– Amylose: simplest form of starch, unbranched
– Amylopectin: branched form
• Glycogen: storage polysaccharide in animals
– stored in liver & muscle cells
– “Carbo” loading
Chloroplast
Starch granules
Amylopectin
Amylose
(a) Starch:
plant polysaccharide
Mitochondria
1 m
Glycogen granules
Glycogen
(b) Glycogen:
0.5 m
animal polysaccharide
Structural Polysaccharides
• Cellulose: major component of plant cell walls
• polymer of glucose, but the glycosidic linkages differ
– difference is based on two ring forms for glucose: alpha () and
beta ()
(a)  and  glucose
ring structures
 Glucose
 Glucose
(b) Starch: 1–4 linkage of  glucose monomers (c) Cellulose: 1–4 linkage of  glucose monomers
• Starch: polymers with  glucose are helical
• Cellulose: polymers with  glucose are straight
• H atoms on one strand can bond with OH groups
on other strands
• Parallel cellulose molecules held together this way
are grouped into microfibrils, which form strong
building materials for plants
Cellulose
microfibrils in
plant cell wall
Cell wall
Microfibril
10 m
0.5 m
Cellulose
molecules
 Glucose
monomer
• Enzymes that digest starch by hydrolyzing  linkages
can’t hydrolyze  linkages in cellulose
• Cellulose in human food passes through the digestive
tract as insoluble fiber
• Some microbes use enzymes to digest cellulose
• Many herbivores, from rabbits to termites, have
symbiotic relationships with these microbes
Structural Polysaccharides
Chitin
• provides structural
support for cell walls
of many fungi
• forms exoskeleton of
arthropods
• used as surgical
thread
Structure of
chitin
monomer
Chitin forms exoskeleton
of arthropods
Chitin makes strong & flexible
surgical thread that decomposes with healing
Lipids: diverse group of
hydrophobic molecules
• Lipids: do not
form polymers
– Hydrophobic:
hydrocarbons
form nonpolar
covalent bonds
• fats, steroids,
phospholipids
Fats
• glycerol and 3 fatty acids
– glycerol: three-carbon alcohol w/ hydroxyl
attached to each carbon
– fatty acid: carboxyl group attached to long
carbon skeleton
Fatty acid
(palmitic acid)
Glycerol
One of three dehydration reactions in the synthesis of a fat
• Fats separate from water because water molecules form
hydrogen bonds with each other and exclude the fats
• Three fatty acids are joined to glycerol by an ester
linkage, creating a triacylglycerol, or triglyceride
Ester linkage
Fat molecule (triacylglycerol)
• Fatty acids vary: length (# C), number &
locations of double bonds
– saturated fatty acids: have maximum number of
hydrogen atoms possible, no double bonds
• fat molecules can pack together tightly; solid at room temp
• saturated fats may contribute to cardiovascular disease
through plaque deposits
– unsaturated fatty acids: have one or more double
bonds
• double bonds cause a kink, can’t pack together; liquid at
room temp
• Saturated fats: solid at room temperature
– most animal fats - lard, butter
• Unsaturated fats: liquid at room temperature
– plant fats: olive oil, fish fats - cod liver oil
(a) Saturated fat
(b) Unsaturated fat
Structural
formula
Structural
formula
Space-filling model of
Stearic acid
Space-filling
Model of oleic
acid
Cis double bond
causes bending.
• Hydrogenation:
converts unsaturated
fats to saturated fats
by adding hydrogen
– Hydrogenating
vegetable oils creates
unsaturated fats with
trans double bonds
– trans fats may
contribute more than
saturated fats to
cardiovascular
disease
• certain unsaturated fatty acids not synthesized
in body, must be supplied in the diet
• omega-3 fatty acids: required for normal growth,
and thought to provide protection against
cardiovascular disease
• found in fish, nuts, vegetable oils
Functions of Fat
• energy storage, insulation, cushions internal organs
• humans, other mammals store their fat in adipose cells
Phospholipids
• two fatty acids & phosphate group attached to
glycerol
• fatty acid tails “hydrophobic”, the phosphate
group forms a “hydrophilic” head
Hydrophilic head
Hydrophobic tails
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
(a) Structural formula
(b) Space-filling model
(c) Phospholipid symbol
Phospholipids
• in water, self-assemble into a bilayer
– hydrophobic tails point toward the interior
• major component of all cell membranes
Hydrophilic
head
WATER
Hydrophobic
tail
WATER
Double Bubble
• Write a double bubble map comparing
and contrasting carbohydrates with fats
Steroids
• Steroids: carbon skeletons four fused rings
• Sex hormones: testosterone, estrogen, progesterone
• Cholesterol: component in animal cell membranes
– cholesterol essential in animals
– high levels in blood may contribute to cardiovascular disease
cholesterol
Compare the structure of a fat (triglyceride)
with that of a phospholipid.
Both have a glycerol molecule attached to fatty acids.
The glycerol of fat has 3 fatty acids attached,
whereas the glycerol of a phospholipid is attached to
2 fatty acids and 1 phosphate group.
Copy the structure of a SINGLE
amino acid:
Bozeman Video questions (left side of
notebook):
• What are the monomers (subunits) of a
protein?
• What is similar from each amino acid?
• What reaction combines one amino acid
to the next? What is this bond called?
• If you have a positive amino acid and a
negative amino acid in the same
polypeptide, what is going to happen?
Proteins: structural diversity
results in a wide range of functions
• Types:
– enzymes, defensive proteins, storage proteins,
transport proteins, hormones, receptor proteins,
contractile and motor proteins, structural
• Functions:
– catalysis, defense against foreign substances, store
a.a., transport, homeostasis, cellular communication,
movement, structural support
• Enzymes: proteins that act as catalysts,
speed up chemical reactions
• can be reused, since they are not
consumed in chemical reaction
Enzymatic proteins
Defensive proteins
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.
Antibodies
Enzyme
Virus
Bacterium
Storage proteins
Transport proteins
Function: Storage of amino acids
Function: Transport of substances
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.
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.
Transport
protein
Ovalbumin
Amino acids
for embryo
Cell membrane
Hormonal proteins
Receptor 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
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.
High
blood sugar
Insulin
secreted
Normal
blood sugar
Receptor
protein
Signaling
molecules
Contractile and motor proteins
Structural 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.
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.
Actin
Myosin
Collagen
Muscle tissue
100 m
Connective
tissue
60 m
Polypeptides
• Polypeptides:
unbranched polymers
built from our 20
amino acids
• Protein: biologically
functional molecule
that consists of one or
more polypeptides
Amino Acid Monomers
• Amino acids: organic molecules w/ carboxyl &
amino groups
– amino acids have different properties due to varying
side chains, called R groups
Side chain (R group)
 carbon
Amino
group
Carboxyl
group
Nonpolar side chains; hydrophobic
Side chain
(R group)
Glycine
(Gly or G)
Alanine
(Ala or A)
Methionine
(Met or M)
Isoleucine
(Ile or I)
Leucine
(Leu or L)
Valine
(Val or V)
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)
Electrically charged side chains; hydrophilic
Tyrosine
(Tyr or Y)
Asparagine
(Asn or N)
Glutamine
(Gln or Q)
Basic (positively charged)
Acidic (negatively charged)
Aspartic acid
(Asp or D)
Glutamic acid
(Glu or E)
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)
Amino Acid Polymers
• a.a. linked by peptide bonds
• Polypeptide: polymer of amino acids
– range in length from a few to more than a thousand
monomers
• each has unique linear sequence of a. a., with
carboxyl end (C-terminus) & amino end (Nterminus)
Peptide bond
New peptide
bond forming
Side
chains
Backbone
Amino end
(N-terminus)
Peptide
bond
Carboxyl end
(C-terminus)
Protein Structure & Function
• protein consists of one or more polypeptides
precisely twisted, folded, and coiled into a
unique shape
(a) A ribbon model
(b) A space-filling model
• sequence of amino acids determines protein’s
three-dimensional structure
• protein’s structure determines its function
Antibody protein
Protein from flu virus
Four Levels of Protein Structure
• Primary structure: unique sequence of a. a.
• Secondary structure: coils & folds in
polypeptide chain
• Tertiary structure: determined by
interactions among side chains (R groups)
• Quaternary structure: protein consists of
multiple polypeptide chains
Amino
acids
Primary structure:
• sequence of a. a.
in protein
Amino end
– determined by DNA
Carboxyl end
Tertiary
structure
Secondary
structure
Quaternary
structure
 helix
Hydrogen bond
 pleated sheet
 strand
Hydrogen
bond
Transthyretin
polypeptide
Transthyretin
protein
Secondary
structure:
• H bonds w/in
polypeptide
backbone
Hydrogen bond
 helix
–  helix: coil
Hydrogen bond
• Keratin: hair
–  pleated sheet:
folded structure
 strand: shown
as flat arrow
pointing to
carboxyl end
• Silk, spider web
 pleated sheet
What type of secondary structure forms spider webs?
Tertiary structure: R group interactions
• H bonds, ionic bonds,
hydrophobic & Van
der Waals interactions
• disulfide bridges
(strong covalent bonds)
reinforce protein
structure
a
b.
c.
d.
Identify R group interactions
Quaternary structure:
• two or more polypeptide chains form one
macromolecule
– collagen: fibrous protein consisting of three
polypeptides coiled like a rope
– hemoglobin: globular protein consisting of four
polypeptides: two alpha and two beta chains
Heme
Iron
 subunit
 subunit
 subunit
 subunit
Hemoglobin
Sickle-Cell Disease: Change in
Primary Structure
• change in primary structure can affect a
protein’s structure & it’s ability to function
• Sickle-cell disease: inherited blood disorder,
results from a single amino acid substitution in
the protein hemoglobin
Sickle-cell hemoglobin
Normal hemoglobin
Primary
Structure
1
2
3
4
5
6
7
Secondary
and Tertiary
Structures
Quaternary
Structure
Function
Molecules do not
associate with one
another; each carries
oxygen.
Normal
hemoglobin
 subunit

Red Blood
Cell Shape

10 m


1
2
3
4
5
6
7
Exposed
hydrophobic
region
Sickle-cell
hemoglobin

 subunit

Molecules crystallize
into a fiber; capacity
to carry oxygen is
reduced.


10 m
Considering the chemical characteristics of the amino acids
valine and glutamic acid, propose a possible explanation for
the dramatic effect on the protein function that occurs when
valine is substituted for glutamic acid.
The R group on glutamic acid is acidic and hydrophilic, wheras the R
group on valine is nonpolar and hydrophibic. Therefore, it is unlikely that
valine can participate in the same intramolecular interactions that
glutamic acid can. A change in these interactions causes a disruption of
the molecular structure.
What Determines Protein Structure?
• primary structure, physical & chemical conditions
– changes in pH, salt concentration, temperature
• denaturation: bonds w/in protein destroyed
– denatured protein is biologically inactive
Normal protein
Denatured protein
Protein Folding in the Cell
• Chaperonins: protein molecules that assist
the proper folding of proteins
• Diseases: Alzheimer’s, Parkinson’s, & mad
cow disease associated with misfolded
proteins
Polypeptide
Correctly
folded
protein
Cap
Hollow
cylinder
Chaperonin
(fully assembled)
Steps of Chaperonin
Action:
1 An unfolded polypeptide enters the
cylinder from
one end.
2 The cap attaches, causing 3 The cap comes
the cylinder to change
off, and the
shape in such a way that
properly folded
it creates a hydrophilic
protein is
environment for the
released.
folding of the polypeptide.
Why does a denatured protein no longer function?
The function of a protein is a consequence of its specific
shape, which is lost when a protein becomes denatured.
Where would you expect a polypeptide region that is
high in the nonpolar amino acids valine, leucine, and
isoleucine to be located in the folded polypeptide?
These are all nonpolar amino acids, so you would expect
this region to be located in the interior of the folded
polypeptide, where it would not contact the aqueous
environment inside the cell.
Nucleic acids: store, transmit, &
express hereditary information
• a. a. sequence of polypeptide programmed
by genes
– units of inheritance
– composed of DNA
The Roles of Nucleic Acids
• types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• DNA provides directions for its own replication
• DNA directs synthesis of messenger RNA
(mRNA) and, through mRNA, controls protein
synthesis
• Protein synthesis occurs on ribosomes
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
Components of Nucleic Acids
• polynucleotides: polymers of nucleic acids
– made of monomers called nucleotides
– Nucleotide:
– nitrogenous base, a pentose sugar, and one or more
phosphate groups
– nucleoside: portion of nucleotide w/out phosphate
group
Nucleoside
Phosphate
group
Nitrogenous
base
Sugar
(pentose)
Nitrogenous bases & Pentose sugars
Nitrogenous bases
• Pyrimidines (cytosine, thymine, and uracil) single six-membered
ring
• Purines (adenine and guanine) six-membered ring fused to fivemembered ring
Pentose sugars:
• DNA: deoxyribose
• RNA: ribose
5 end
5C
3C
Nucleotide Polymers
Sugar-phosphate
backbone
• nucleotides joined by
covalent bonds
– Between OH group on 3
carbon of one nucleotide
and the phosphate on 5
carbon of the next
• backbone of sugarphosphate units
5C
3C
3 end
– nitrogenous bases as
appendages
DNA and RNA
• DNA
– Nucleus,
chromosomes
– Double helix
– Deoxyribose
– Bases: adenine,
guanine, cytosine,
thymine
– Base pairing: A-T, C-G
– antiparallel: two
backbones run in
opposite 5→ 3
• RNA
– Cytoplasm; mRNA,
tRNA, rRNA
– Single strand
– Ribose
– Bases: adenine,
guanine, cytosine,
uracil
– Base pairing: A-U, C-G
5
3
Sugar-phosphate
backbones
Hydrogen bonds
Base pair joined
by hydrogen
bonding
3
5
(a) DNA
Base pair joined
by hydrogen bonding
(b) Transfer RNA
1) One side of a DNA strand has this sequence of
nitrogenous bases. Copy this strand, then determine
it’s complementary strand. Label 5’ and 3’.
ATGCATAAG
2) Use the new DNA strand to transcribe mRNA
5’ ATGCATAAG 3’
3’ TACGTATTC 5’
mRNA
AUGCAUAAG
For Lab Test:
• No Prelab needed, but read through and
make a chart explaining what each test
indicates and how to test for it : Biurets,
iodine, benedicts
• Data:
Copy the following data table:
Solution #
Test
1
Buirets
2
Iodine
3
Benedict’s
4
Brown
Paper
Original
color
Final color
Type of
molecule
• Answer Questions from results and conclusion with
the following mods:
Results:
• Skip 3,6,9,10, and 12
2: Draw one amino acid and circle the carboxyl group
and amino group
5. Explain the difference between sucrose vs. glucose
7. What is the polysaccharide stored called?
8. Draw diagram and answer
11. What the reactive groups? (don’t draw)
Conclusion:
2. Skip
Construct a table that organizes the following
terms. Determine labels for the columns and rows.
•
•
•
•
•
•
Phosphodiester linkages
Peptide bonds
Glycosidic linkages
Ester linkages
Polypeptides
Triacylglycerols
•
•
•
•
•
•
Polyneucleotides
Polysaccharides
Monosaccharides
Nucleotides
Amino acids
Fatty acids
Monomers/
subunits
Polymer
Type of
linkage
Carbohydrates
Monosaccharides
Polysaccharides
Glycosidic
linkages
Lipids
Fatty acids
glycerol
Triacylglycerols
Ester linkages
Proteins
Amino acids
Polypeptides
Peptide bonds
Nucleic acids
Nucleotides
Polyneucleotides
Phosphodiester
linkages