Download Unit 3 Macromolecules, enzymes, and ATP

Mrs. Stahl
AP Biology
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Living organisms consist mostly of carbon-based
compounds
Carbon is unparalleled in its ability to form large,
complex, and varied molecules
Proteins, DNA, carbohydrates, and other molecules
that distinguish living matter are all composed of
carbon atoms bonded to one another and to other
elements (H, O, N, S, and P).
Carbon enters the planet through plantsphotosynthesis. Plants take CO2 from the atmosphere
and transform it into usable forms of energy – glucose
(C6H12 O6) and O2, which are passed along to animals
through the process of cellular respiration.
Carbon can
form up to
four
covalent
bonds!
Carbon can bond to four other atoms or
groups of atoms, making a large variety of
molecules possible.
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The electron configuration of carbon
gives it covalent compatibility with many
different elements
The valences of carbon and its most
frequent partners (hydrogen, oxygen,
and nitrogen) are the building code for
the architecture of living molecules.
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Carbon atoms can partner with
atoms other than hydrogen; for
example:
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Carbon dioxide: CO2
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Urea: CO(NH2)2
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Carbon chains form the skeletons of most
organic molecules.
Carbon chains vary in length and shape.
(c) Double bond position
(a) Length
Ethane
Propane
(b) Branching
Butane
1-Butene
2-Butene
(d) Presence of rings
2-Methylpropane
(isobutane)
Cyclohexane
Benzene
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Hydrocarbons are organic molecules consisting of
only carbon and hydrogen. Very common on Earth.
Attached to carbon skeleton, wherever electrons are
available for covalent bonding
Many organic molecules, such as fats, have
hydrocarbon components that serve as stored fuel for
animals
Hydrocarbons can undergo reactions that release a
large amount of energy
Major components of petroleum. Petroleum is called
a fossil fuel because it is partially made up of
decomposed remains that lived millions of years ago.
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NONPOLAR- do they dissolve in water?
Hydrophobic
Have the potential to release a lot of energy
through reactions
The gas in your car is made up if them
Nucleus
Fat droplets
10 μm
(a) Part of a human adipose cell
(b) A fat molecule
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Carbon and Hydrogen have similar
electronegativities with evenly distributed electrons
that is why they are nonpolar.
There are other biological molecules in cells that
contain other atoms with different electronegativities
that are partially positive and negative, making them
polar.
These groups can be referred to as the C-H core
group where other molecules known as functional
groups can attach to.
-OH is a common functional group, aka hydroxyl
group
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The seven functional groups that are
most important in the chemistry of life
Hydroxyl group
 Carbonyl group
 Carboxyl group
 Amino group
 Sulfhydryl group
 Phosphate group
 Methyl group
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Chemical Group
Hydroxyl group (—OH)
Compound Name
Examples
Alcohol
Ethanol
Carbonyl group (
C＝O)
Ketone
Aldehyde
Acetone
Carboxyl group (—COOH)
Propanal
Carboxylic acid, or
organic acid
Acetic acid
Amino group (—NH2)
Amine
Glycine
Sulfhydryl group (—SH)
Thiol
Cysteine
Phosphate group (—OPO32−)
Organic
phosphate
Glycerol phosphate
Methyl group (—CH3)
Methylated
compound
5-Methyl cytosine
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Isomers are compounds with the same molecular
formula but different structures and properties
 Structural isomers have different covalent
arrangements of their atoms (carbon skeleton).
Example-glucose
 Stereoisomers (Cis-trans isomers / Geometric
Isomers-)- have the same carbon skeleton but
differ in how the groups are attached / three
dimensional shape in space.
 Enantiomers are isomers that are mirror images
of each other
(a) Structural isomers
Pentane
2-methyl butane
(b) Cis-trans isomers
cis isomer: The two Xs are
on the same side.
trans isomer: The two Xs are
on opposite sides.
(c) Enantiomers
CO2H
CO2H
C
H
C
NH2
CH3
L isomer
NH2
H
CH3
D isomer
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All living things are made up of four classes
of large biological molecules: carbohydrates,
lipids, proteins, and nucleic acids
Macromolecules are large molecules and are
complex
Large biological molecules have unique
properties that arise from the orderly
arrangement of their atoms
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A polymer is a long molecule consisting of many
similar building blocks
The repeating units that serve as building blocks
are called monomers
Three of the four classes of life’s organic
molecules are polymers
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Carbohydrates
Proteins
Nucleic acids
Polymer= molecule that contains many
Monomers bonded together.
Monomer=
small
molecular
subunit
How many monomers are above?
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Enzymes are specialized macromolecules that
speed up chemical reactions such as those that
make or break down polymers
A dehydration reaction occurs when two
monomers bond together through the loss of a
water molecule
Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the
reverse of the dehydration reaction. Water is
added to break the bond.
Carbohydrates
 Lipids
 Proteins
 Nucleic Acids
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Fruits, grains, sugars, starches
Monosaccharides, Disaccharides and Polysaccharides
Mono= 1, saccharide= sugar, Di=2, Poly = many
The simplest carbohydrates are monosaccharides, or
simple sugars / glucose
Composed of carbon, hydrogen, and oxygengenerally in a 1:2:1 ratio
Function: When broken down they provide a source
of usable chemical energy for cells / main source of
energy (due to the high number of C-H bonds which
release energy when oxidation occurs)
Major part of plant cell structure too!!!
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Monosaccharides have molecular formulas
that are usually multiples of CH2O
They have to have at least three carbons, but
those that play the role in energy storage have
six carbons
Glucose (C6H12O6) is the most common and the
most important monosaccharide
They can exist in a straight chain form but
when dissolved in an aqueous solution they
almost always form rings.
Depending on the orientation of the carbonyl group (C=O) when the ring is
closed, glucose can exist in two different forms: 𝛂 glucose and 𝛃 glucose
𝛂 Glucose
(a) 𝛂 and 𝛃 glucose ring structures
𝛃 Glucose
They differ in
the orientation
of the –OH
bound to
carbon 1
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Glucose is not the only sugar that has the formula
C6H12O6
Structural isomers and stereoisomers of the six
carbon sugar exist in nature:
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Fructose is the structural isomer that differs in the position
of the carbonyl carbon (C=O); galactose is a stereoisomer
that differs in the position –OH and –H groups relative to
the ring.
These differences result in functional differences:
 Ex- taste buds can tell them apart. Fructose tastes much
sweeter than glucose even though their chemical composition
is the same.
 Ex- enzymes act on different sugars and they can also
distinguish between the two.
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Found in milk, whey, human body, mothers milk
Contributes to vital information and control
processes in the body. It also functions as
fundamental and structural substances for cells, cell
walls, and the intracellular matrix
Blood types- blood types A and B only differ from
blood type O by the presence of an additional
monosaccharide, N-acetylgalactosamine for Type A
and galactose for Type B. Blood types O and B differ
only by one galactose molecule. This small difference
can be between life and death for a human organism
in need of a blood transfusion.
Aldoses (Aldehyde Sugars)
Ketoses (Ketone Sugars)
Trioses: 3-carbon sugars (C3H6O3)
Glyceraldehyde
Dihydroxyacetone
Pentoses: 5-carbon sugars (C5H10O5)
Ribose
Ribulose
Hexoses: 6-carbon sugars (C6H12O6)
Glucose
Galactose
Fructose
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Serve as transport molecules in plants and
provide nutrition in animals
A disaccharide is formed when a dehydration
reaction joins two monosaccharides
This covalent bond is called a glycosidic linkage
Serve as effective reservoirs of glucose because
the enzymes that normally use glucose in the
organism cannot break the bond linking the two
monosaccharide subunits. These enzymes are
usually found only in the tissue that uses
glucose.
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When glucose forms a disaccharide bond with structural
isomer fructose, sucrose (table sugar) is the result.
Sucrose is the form that most plants use to transport
glucose and is the sugar that most humans and other
animals eat. Sugarcane and sugar beets = rich in sucrose
Glucose links with stereoisomer galactose, lactose is
made (milk sugar). Lactose is often transferred to young
via breast milk.
Adults typically have reduced amounts of the enzyme
lactase, which breaks down lactose. This leads to
inadequate digestion and metabolizing of lactose,
causing a lactose intolerance.
Lactose is a main energy source for offspring in
mammals.
Maltose- sugar used in grain for storage
(a) Dehydration reaction in the synthesis of maltose
1−4
glycosidic
linkage
Glucose
H2 O
Glucose
Maltose
(b) Dehydration reaction in the synthesis of sucrose
1−2
glycosidic
linkage
Glucose
H2 O
Fructose
Sucrose
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Polysaccharides, the polymers of sugars, have
storage and structural roles
Ex- Cellulose, starches, glycogen, and chitin
The architecture and function of a polysaccharide is
determined by its sugar monomers and the positions
of its glycosidic linkages
Starches- storage polysaccharide, made up of 𝛂 glucose
 Cellulose- structural polysaccharide, made up of 𝛃 glucose
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Starch, a storage polysaccharide of plants, consists
entirely of glucose monomers
Plants store surplus starch as granules within
chloroplasts and other plastids (part of the plant cell
used for storage)
The simplest form of starch is amylose
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Composed of hundreds of 𝛂 glucose molecules linked
together in long unbranched chains. Linkage occurs
between carbon 1 (C-1) of one glucose and the C-4 of
another, creating a 𝛂 - (1---4) linkages. These chains coil
up in water, making it insoluble. Potato starch is about 20%
amylose.
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Animals
Glycogen is stored mainly in liver and
muscle cells
Hydrolysis of glycogen in these cells
releases glucose when the demand for
sugar increases
Insoluble polysaccharides
Longer average chain length and more
branches than plant starch
Glycogen
granules in
muscle
tissue
1 µm
(b) Glycogen
Glycogen (branched)
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The polysaccharide cellulose is a major
component of the tough wall of plant cell walls
and cannot be broken down by most creatures.
Some animals, like cows, are able to break down
cellulose by means of symbiotic bacteria and
protists in their digestive tracts.
Like starch, cellulose is a polymer of glucose, but
the glycosidic linkages differ.
The difference is based on two ring forms for
glucose: alpha () and beta ()
Cellulose microfibrils
in a plant cell wall
Microfibril
0.5 µm
(c) Cellulose
Cellulose molecule
(unbranched)
Hydrogen bonds
Cell
wall
Plant cell,
10 µm
surrounded
by cell wall
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Chitin, another structural polysaccharide, is
found in the exoskeleton of arthropods (crabs,
insects, etc).
Chitin also provides structural support for the
cell walls of many fungi.
Few organisms are able to digest chitin, but
most possess a chitinase enzyme, probably to
protect against fungi.
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► Chitin is used to
make a strong
and flexible
surgical
thread.
The structure
of the chitin
monomer
Chitin, embedded in proteins,
forms the exoskeleton of
arthropods.
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Lipids are the one class of large biological molecules that does
not include true monomers or polymers.
The unifying feature of lipids is that they mix poorly, if at all,
with water / insoluble. Fats separate from water because
water molecules hydrogen-bond to each other and exclude
the fats
Lipids are hydrophobic because they consist mostly of
hydrocarbons (lots of C-H bonds), which form nonpolar
covalent bonds
The most biologically important lipids are fats (triglycerides),
phospholipids, and steroids
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Examples: fats, oils (coconut, olive, corn), waxes,
cholesterol, steroids, fatty acids, glycerol,
Function- Some are broken down for cell use,
some are stored for later energy use, and others
are parts of cell structures.
Humans and other mammals store their long-term
food reserves in adipose cells.
Adipose tissue also cushions vital organs and
insulates the body.
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Fats are constructed from two types of smaller
molecules: glycerol and fatty acids
Glycerol is a three-carbon alcohol with a hydroxyl
group attached to each carbon
A fatty acid consists of a carboxyl group (COOH) at
one end, attached to a long carbon skeleton
A fat molecule contains three fatty acids attached to a
glycerol and is commonly called a triglyceride
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Each fatty acid is typically different from the others and the
hydrocarbon chains vary in length (14-20 carbons)
The plethora of C-H bonds of fats serve as long term energy
storage. Connected by dehydration synthesis X 3 (ester
linkages)
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Saturated: occurs when all of the internal carbon
atoms are bonded to at least two hydrogen atoms.
Has all the hydrogen atoms possible.
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Unsaturated: one or more double bonds between the
carbon atoms.
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Solid at room temperature
Most animal fats are saturated
No double bonds between carbon
Not saturated with hydrogen atoms
Liquid at room temperature
Plant fats and fish fats are usually unsaturated
Polyunsaturated: two or more double covalent
bonds
 Good fatty acids
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A diet rich in saturated fats may contribute to
cardiovascular disease through plaque deposits
Hydrogenation is the process of converting unsaturated
fats to saturated fats by adding hydrogen
Hydrogenating vegetable oils also creates unsaturated
fats with trans double bonds
These trans fats may contribute more than saturated fats
to cardiovascular disease because they elevate lowdensity lipoprotein (LDL= “bad cholesterol”) and lower
high –density lipoprotein (HDL= “good cholesterol”)
Can lead to atherosclerosis= “hardening of the arteries” > plaque hardens on the to the lining of blood vessels,
blocking blood flow. Sometimes fragments can break off
and clog arteries to the brain, causing a stroke.
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Certain unsaturated fatty acids are not
synthesized in the human body
These must be supplied in the diet
These essential fatty acids include the omega-3
fatty acids, which are required for normal
growth and are thought to provide protection
against cardiovascular disease
(a) Saturated fat
(b) Unsaturated fat
Structural
formula
of a saturated
fat molecule
Space-filling
model of
stearic acid,
a saturated
fatty acid
Structural
formula of an
unsaturated
fat molecule
Space-filling
model of oleic
acid, an
unsaturated
Cis double
fatty acid
bond causes
bending.
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Modified triglyceride- phosphate replaces one of
the fatty acids
In a phospholipid, two fatty acids and a
phosphate group are attached to glycerol
The two fatty acid tails are hydrophobic, but the
phosphate group and its attachments form a
hydrophilic head
Molecule has both hydrophobic and hydrophilic
tendencies = amphipathic
Also known as the phospholipid bilayer, aka cell
membrane
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Glycerol- three carbon alcohol and forms the
backbone of the molecule
Fatty Acids- long chains of –CH2 groups
(hydrocarbon chains) ending in a carboxyl (--COOH)
group. Fatty acids attach to the glycerol backbone.
Phosphate Group- attached to one end of the glycerol
(usually has an organic molecule attached to it such
as choline, ethanolamine, or the amino acid serine.
AKA- heads and tails
Heads= polar, phosphate group and glycerol
 Tails= non-polar, fatty acids
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Hydrophilic head
Hydrophobic tails
Choline
Hydrophilic
head
Phosphate
Hydrophobic
tails
Glycerol
(c) Phospholipid symbol
Fatty acids
Kink due to cis
double bond
(a) Structural formula
(b) Space-filling model
(d) Phospholipid bilayer
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Steroids are lipids characterized by a carbon skeleton
consisting of four fused rings
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Presence of different functional groups leads to different
functions
Cholesterol, a type of steroid, is a component in
animal cell membranes and a precursor from which
other steroids are synthesized
A high level of cholesterol in the blood may
contribute to cardiovascular disease
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The amino acid sequence of a polypeptide is programmed by a unit of
inheritance called
a gene.
Genes consist of DNA, a nucleic acid made of monomers called
nucleotides (sugar= pentose, phosphate, and a nitrogenous base)
Nitrogen bases always pair up in the same way
 For DNA: A – T, C – G
 For RNA: A – U, C – G (thymine in RNA is replaced with uracil)
There are two 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. This process is called gene expression
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There are two families of nitrogenous bases
Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring
 Purines (adenine and guanine) have a six-membered ring
fused to a five-membered ring
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They are able to serve as templates for producing
precise copies of themselves, which allows genetic
information to be preserved during cell division and
reproduction.
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Forms a polymer by binding the phosphate end of
one nucleotide to the hydroxyl group from the
pentose sugar of another, releasing water which
forms a phosphodiester bond by dehydration
synthesis.
Nucleic Acid is defined as a chain of five carbon
sugars linked together by phosphodiester bonds with
a nitrogenous base protruding from each sugar.
The chains have different ends: a phosphate on one
end and an –OH from a sugar on the other end.
These ends are referred to as 5’(five prime, --PO4-)
and 3’ (three prime,-- OH) from the carbon
numbering of the sugar.
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
NITROGENOUS BASES
Pyrimidines
Cytosine
(C)
Thymine
(T, in DNA)
Purines
Adenine (A)
Uracil
(U, in RNA)
Guanine (G)
(c) Nucleotide components
5′ end
Sugar-phosphate backbone
(on blue background)
5′C
3′C
Nucleoside
Nitrogenous
base
5′C
1′C
5′C
3′C
Phosphate
group
3′C
Sugar
(pentose)
(b) Nucleotide
3′ end
(a) Polynucleotide, or nucleic acid
SUGARS
Deoxyribose
(in DNA)
Ribose (in DNA)
(c) Nucleotide components
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DNA molecules have two polynucleotides
spiraling around an imaginary axis, forming a
double helix
The backbones run in opposite 5 → 3
directions from each other, an arrangement
referred to as antiparallel
One DNA molecule includes many genes
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Only certain bases in DNA pair up and
form hydrogen bonds: adenine (A)
always with thymine (T), and guanine
(G) always with cytosine (C)
This is called complementary base
pairing
This feature of DNA structure makes it
possible to generate two identical copies
of each DNA molecule in a cell preparing
to divide
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RNA, in contrast to DNA, is single stranded
Complementary pairing can also occur between
two RNA molecules or between parts of the
same molecule
In RNA, thymine is replaced by uracil (U) so
A and U pair
While DNA always exists as a double helix,
RNA molecules are more variable in form
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
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Sequences of genes and their protein products
document the hereditary background of an
organism
Linear sequences of DNA molecules are passed
from parents to offspring
We can extend the concept of “molecular
genealogy” to relationships between species
Molecular biology has added a new measure to
the toolkit of evolutionary biology
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Most diverse
Proteins account for more than 50% of the dry
mass of most cells
Some proteins speed up chemical reactions
Other protein functions include defense, storage,
transport, cellular communication, movement, or
structural support
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
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.
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 membranes, as shown here.
Ovalbumin
Amino acids
for embryo
Transport
protein
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
Signaling
molecules
Receptor
protein
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
30 µm
Connective
60 µm
tissue
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Monomer- Amino Acids
Polymer - Proteins
Proteins are all constructed from the same set of 20
amino acids
Amino acids are thought to have derived from the
ocean and possibly among the first molecules to
show up on Earth
Polypeptides are unbranched polymers built from
these amino acids
A protein is a biologically functional molecule that
consists of one or more polypeptides
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Comprised of an amino group (-NH2) and an
acidic carboxyl group (-COOH)
R- group= functional group and determines the
unique character of each amino acid
The specific order of amino acids determines
the proteins structure and function
Side chain (R group)
𝛂 carbon
Amino
group
Carboxyl
group
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1. Nonpolar amino acids- R groups often have
CH2 or CH3
2. Polar uncharged – R groups have oxygen or
–OH
3. Charged amino acids –R groups that contain
acids or bases that can ionize
4. Aromatic amino acids- R groups have an
organic carbon ring with alternating single and
double bonds
5. Amino acids that have special functions have
unique properties
Nonpolar side chains; hydrophobic
Side chain (R group)
Glycine
(Gly or G)
Methionine
(Met or M)
Alanine
(Ala or A)
Valine
(Val or V)
Phenylalanine
(Phe or F)
Leucine
(Leu or L)
Tryptophan
(Trp or W)
Isoleucine
(Ile or I)
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
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)
Nonpolar side chains; hydrophobic
Side chain (R group)
Glycine
(Gly or G)
Methionine
(Met or M)
Alanine
(Ala or A)
Valine
(Val or V)
Phenylalanine
(Phe or F)
Leucine
(Leu or L)
Tryptophan
(Trp or W)
Isoleucine
(Ile or I)
Proline
(Pro or P)
Polar side chains; hydrophilic
Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Tyrosine Asparagine Glutamine
(Tyr or Y) (Asn or N) (Gln or Q)
Electrically charged side chains; hydrophilic
Basic (positively charged)
Acidic (negatively charged)
Aspartic acid Glutamic acid
(Asp or D)
(Glu or E)
Lysine
Arginine
(Lys or K) (Arg or R)
Histidine
(His or H)
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Two amino acids are linked by covalent bonds called
peptide bonds
A polypeptide is a polymer of amino acids
Polypeptides range in length from a few to more
than a thousand monomers
Each polypeptide has a unique linear sequence of
amino acids, with a carboxyl end and an amino end.
They are not free to rotate around the N-C bond
because the peptide has a partial double bond
character. This lack of rotation is what makes each
amino acid unique in shape.
Peptide bond
H2O
Side
chains
Backbone
Peptide
Amino end
bond
(N-terminus)
Carboxyl end
(C-terminus)
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

The specific activities of proteins result from
their intricate three-dimensional architecture
A functional protein consists of one or more
polypeptides precisely twisted, folded, and
coiled into a unique shape
Four levels
1. Primary
 2. Secondary
 3. Tertiary
 4. Quaternary




The sequence of amino acids determines a
proteins three-dimensional structure
A proteins structure determines how it works
The function of a protein usually depends on
its ability to recognize and bind to some other
molecule




The primary structure of a protein is its unique
sequence of amino acids
Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide
chain
Tertiary structure is determined by interactions
among various side chains (R groups)
Quaternary structure results when a protein
consists of multiple polypeptide chains



The primary structure of a protein is its
sequence of amino acids
Primary structure is like the order of letters in a
long word
Primary structure is determined by inherited
genetic information
Primary Structure
Amino
acids
1
5
10
20
15
Amino end
30
25
35
45
40
50
Primary structure of transthyretin
70
65
60
55
75
80
85
90
95
115
120
110
105
100
125
Carboxyl end



The coils and folds of secondary structure
result from hydrogen bonds between repeating
constituents of the polypeptide backbone
Hydrogen bonds can be with water or other
peptide groups
Typical secondary structures are a coil called
an  helix and a folded structure called a 
pleated sheet
Secondary
Structure
𝛂 helix
Hydrogen bond
𝛃 strand
Hydrogen
bond
𝛃 pleated sheet



Tertiary structure, the overall shape of a
polypeptide, results from interactions between
R groups, rather than interactions between
backbone constituents
These interactions include hydrogen bonds,
ionic bonds, hydrophobic interactions, and
van der Waals interactions
Strong covalent bonds called disulfide bridges
may reinforce the protein’s structure
Tertiary
Structure
Transthyretin
polypeptide
Hydrogen
bond
Hydrophobic
interactions and
Van der Waals
interactions
Disulfide
bridge
Ionic bond
Polypeptide
backbone



Quaternary structure results when two or
more polypeptide chains form one
macromolecule
Collagen is a fibrous protein consisting of three
polypeptides coiled like a rope
Hemoglobin is a globular protein consisting of
four polypeptides: two alpha and two beta
chains
Collagen
Heme
Iron
𝛃 subunit
𝛂 subunit
𝛂 subunit
𝛃 subunit
Hemoglobin


A slight change in primary structure can affect
a protein’s structure and ability to function
Sickle-cell disease, an inherited blood
disorder, results from a single amino acid
substitution in the protein hemoglobin
Normal
Primary
Structure
1
2
3
4
5
6
7
Secondary
and Tertiary
Structures
Normal 𝛃
subunit
Quaternary
Structure
Function
Normal
hemoglobin
Proteins do not associate
with one another; each
carries oxygen.
𝛃
𝛂
5 µm
Sickle-cell
𝛃
1
2
3
4
5
6
7
Red Blood Cell
Shape
Sickle-cell 𝛃
subunit
𝛂
Sickle-cell
hemoglobin
Proteins aggregate into a
fiber; capacity to
carry oxygen
is reduced.
𝛃
𝛂
𝛃
𝛂
5 µm




In addition to primary structure, physical and
chemical conditions can affect structure
Alterations in pH, salt concentration,
temperature, or other environmental factors
can cause a protein to unravel
This loss of a protein’s native structure is
called denaturation
A denatured protein is biologically inactive
Normal protein
Denatured protein
Normal protein
Denatured protein




It is hard to predict a proteins structure from its
primary structure
Most proteins probably go through several stages on
their way to a stable structure
Chaperone proteins are protein molecules that assist
the proper folding of other proteins. This is how cells
avoid having their proteins clump into a mass.
Ex- Heat shock proteins= produced when cells are
exposed to elevated temperatures. The high temps
cause the protein to fall apart, and the heat shock
proteins help the cell’s to refold properly


Diseases such as Alzheimer’s, Parkinson’s,
and mad cow disease are associated with
misfolded proteins. Look these up!
Cystic fibrosis- hereditary disorder in which a
mutation disables a vital protein that moves
ions across the cell membrane. Results in
people having thicker than normal mucus
which created breathing problems and lung
disease.




The proteins environment is altered or changed
which can cause the proteins shape to change
or unfold.
Denatured when the pH, temperature, or ionic
concentration of the surrounding solution
changes.
Result= inactivated proteins
Extremely important when dealing with
enzymes because almost every chemical
reaction is catalyzed by a specific enzyme.
 The
energy needed to get
things started



Most of the time the activation energy for a
chemical reaction comes from an increase
in temperature-> sometimes the process is
very slow.
In order to speed the process up,
substances called catalysts decrease the
activation energy needed to start the
chemical reaction. In the end it increases
the chemical reaction.
When a catalyst (ex- enzymes) is present
less energy is needed and products form a
lot faster.
 1.
Decrease activation
energy
 2. Increase reaction time.






Definition= catalysts for chemical reactions in
living things (made by proteins)
Reactants are usually found at very low
concentrations in the body, but really need to
occur quickly.
Almost all are proteins= long chains of amino
acids
Each one depends on its structure to function
Temperature, concentration, and pH can affect
the shape, function, rate, and activity of the
enzyme.
Work best at normal body temperature


If temperature is a little elevated
then the hydrogen bonds will fall
apart, the enzymes structure will
change, and its ability to function
will be lost.
This is the reason why a high
temperature / fever are very
dangerous to a person.




The structure is so important because each
enzyme’s shape is specific to a certain
reactant= allows them to fit perfectly
together just like a key fits into a lock
Specific reactant an enzyme acts on are
called substrates
The sites where substrates bind to enzymes
are called active sites.
Enzymes bring substrate molecules close
together, then they decrease activation
energy, substrates attach together and their
bonds are weakened, and then the catalyzed
reaction forms a product that is released
from the enzyme.




An important organic phosphate is adenosine
triphosphate (ATP)
ATP consists of an organic molecule called
adenosine attached to a string of three
phosphate groups
ATP stores the potential to react with water,
a reaction that releases energy to be used by
the cell
The cells main energy currency and is utilized
in the mitochondria of the cell
Adenosine
Reacts
with H2O
P
P
P
Adenosine
ATP
Pi
Inorganic
phosphate
P
P
Adenosine
ADP
Energy