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BIO 107 PRINCIPLES OF BIOLOGY

Chapter 5:
Biological Macromolecules

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Ben Benton, Ph.D.
Macromoleculesincorporating carbons
molecular diversity into cellular work.
Cells make a huge number of large molecules
from a limited set of small molecules.
These macromolecules come in four classes:
Carbohydrates
Lipids
Proteins
Nucleic Acids

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Macromoleculespolymerization of smaller
chemical units
A polymer is a long molecule consisting of many
identical or similar building blocks strung
together.
Glucose
(monomer)

Cellulosea polymer

A monomer is a building block of a polymer.


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Macromoleculesdiversity of polymers

Living cells make a vast number of different polymers


(macromolecules) from as few as 40-50 common
monomers.

Carbohydrate

Lipid

Nucleic Acid
Protein (DNA)
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Macromoleculesdiversity of polymers

One trillion (1,000,000,000,000)


proteins exist in nature from only
20 amino acids.
Our unique genetic identity is
formed from only 4 different
building blocks polymerized into
DNA.
This variety of polymers accounts
for the uniqueness of each
organism!

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Macromoleculesformation of polymers

Dehydration reaction: link two monomers (and/or


polymers) by removing a water molecule

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Macromoleculesformation of polymers

Hydrolysis reaction: break polymer linkages by


adding water.

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Macromoleculesformation of polymers

Dehydration and hydrolysis reactions require the


help of special proteins (macromolecules!) called
enzymes.

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Macromolecules I: Carbohydrates

Carbohydrates are a class of molecules


containing carbon, hydrogen, and oxygen
The primary chemical stores of energy in a cell.
Carbohydrates range from the simple sugars in
soft drinks to large polysaccharides such as
starch.

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Macromolecules I: Carbohydrates

Monosaccharides are the basic building blocks of


carbohydrates.
Monosaccharides have a general molecular
formula (CH2O)n. They can range from (CH2O)3 to
(CH2O)7
For example, honey consists mostly of the
monosaccharide isomers glucose and fructose.

C6H12O6 = (CH2O)6

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Macromolecules I: Carbohydrates

C6H12O6 = (CH2O)6
Hexoses = 6 carbons in sugar

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Macromolecules I: Carbohydrates

In water, carbohydrates usually form ring


structures.

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Macromolecules I: Carbohydrates

Cells construct disaccharides by linking 2


monosaccharides in a dehydration reaction:

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Macromolecules I: Carbohydrates

Other Disaccharides
Sucrose

Lactose

glucose fructose

glucose

galactose

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Lactose Intolerance
Milk and other dairy
products have long
been recognized as
highly nutritious foods.
Milk is rich in proteins
and minerals
necessary for healthy
teeth and strong
bones.
Milk also contains the
disaccharide lactose.

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Lactose Intolerance

Lactose can be digested by the enzyme lactase to more


useful forms of sugars.

Lactase

+H20 +

Galactose Glucose

Lactose

Convert to cellular energy


or use for other processes
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Lactose Intolerance

The best diet for infants is


breast milk which has all of the
essential nutrients for growth.
Infants have high levels of the
enzyme lactase which digests
the major carbohydrate in
breast milk.
Around age 2, most humans
lose the ability to produce
lactase because they get their
sugar energy elsewhere.

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Lactose Intolerance

X
Lactase
+
+H20

Lactose Intolerance
Galactose Glucose

Lactose

Convert to cellular energy


or use for other processes

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Lactose Intolerance

Thus, the normal condition


for adult humans is Lactose
Intolerance!
Indeed, 75% of African-
Americans and Native
Americans and 90% of
Asian-Americans are
lactose intolerant.
So, why is lactose
tolerance so prevalent in
the U.S.?

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Lactose Tolerance
an evolutionary adaptation!
Only 15% of people of
European descent are
lactose intolerant.
The remaining 85% have a
mutation that does not shut
off lactase at age 2.
This mutation was selected
for in Europe about 9,000
years ago as the population
became dairy herders and
farmers.

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Macromolecules I: Carbohydrates

Polysaccharides are polymers of


monosaccharides linked in long chains by
dehydration reactions.
Polysaccharides can consist of unbranched or
branched chains.

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Macromolecules I: Carbohydrates
Different Forms of Glucose Polysaccharides

Energy
Storage

Structural
Support

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Structural vs Energy-Storing Polysaccharides

Stereoisomers of Glucose

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Structural vs Energy-Storing Polysaccharides

Starch ( configuration) is largely helical

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Structural vs Energy-Storing Polysaccharides

Cellulose molecules ( configuration) are straight


and unbranched
Hydrogen bonding between
hydroxyls of adjacent chains
accounts for celluloses fibrous
structure

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Structural vs Energy-Storing Polysaccharides

Enzymes that digest starch by hydrolyzing


linkages cant hydrolyze linkages in cellulose
The cellulose in human food passes through the
digestive tract as insoluble fiber
Some microbes use enzymes to digest cellulose
Many herbivores, from cows to
termites, have symbiotic
relationships with these microbes

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ChitinAnother Structural Polysacchairde

Chitin, another structural polysaccharide, is found


in the exoskeleton of
arthropods
Chitin also provides
structural support for
the cell walls of many
fungi

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Macromolecules II: Lipids

Lipids are the one class of large


biological molecules that does not
include true polymers
The unifying feature of lipids is that
they mix poorly, if at all, with water
Lipids are hydrophobic because they
consist mostly of hydrocarbons, which
form nonpolar covalent bonds
The most biologically important lipids
are fats, phospholipids, and steroids
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Structure of Fat

Glycerol

Fat is a large lipid made from


two types of molecules: glycerol
and fatty acids. Oils are just
liquid forms of fat.

The main function of fat is


energy storage.

Fatty Acids
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Structure of Fat

Dehydration reactions link fatty acids to the


glycerol backbone

Fat aka Triglyceride=


tri- for the 3 fatty acids
-glyceride for the glycerol
backbone

The fatty acids in a fat can be all the same or of


two or three different kinds
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Structure of Fat

Fatty acids vary in length (number of carbons) and


in the number and locations of double bonds
Double bonds cause a
structural bending of the
hydrocarbon chain
preventing close packing.

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Structure of Fat

Saturated fatty acids have the maximum number


of hydrogen atoms possible and no double bonds
Saturated fats (containing only
saturated fatty acids) are
solid at room temperature
because they can pack
at a higher density (no kinks)
Most animal fats are saturated
(beef, pork, chicken)

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Structure of Fat

Unsaturated fatty acids have one or more


double bonds
Unsaturated fats contain at least
one unsaturated fatty acid and
are liquid at room temperature
because the fats cannot pack at
high density due to kinks.
Unsaturated fats are commonly
called oils.
Plants and fish are sources of oils.
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Function of Fat

The major function of fats is energy storage


Humans and other mammals store
their long-term food reserves
in adipose (fat) cells
Adipose tissue also cushions
vital organs and insulates the
body

Photo Credit:
2014 Pearson Education, Inc. http://www.vetmed.vt.edu/education/curriculum/vm8054/Labs/Lab5/Lab5.htm
Structure of Phospholipids

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
Because of this
dual nature we call
the molecule
amphipathic.
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Phospholipids Form Biological Membranes

When phospholipids are


added to water, they
self-assemble into
double-layered structures
called bilayers
At the surface of a cell, phospholipids are also
arranged in a bilayer, with the hydrophobic tails
pointing toward the interior
The structure of phospholipids
results in a bilayer arrangement
found in cell membranes
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Cholesterol and Steroids

Cholesterol belongs to
the steroid class of lipids.
The steroid carbon
skeleton consists of 4
fused rings.
Cholesterol is a
component of animal cell
membranes.
It regulates the fluidity
and permeability of the
membrane.
http://www.uic.edu/classes/bios/bios100/lectf03am/cholesterol.jpg
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Cholesterol and Steroids

Cholesterol is also the basic


building block of steroids.

Steroids are hormones that


regulate various physiological
functions like sex development
and immune response.

estradiol testosterone
(female sex hormone) (male sex hormone)

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Lipids and Cardiovascular Health

While cholesterol is needed


to maintain healthy
membranes, too much
cholesterol builds up in
particles and clogs arteries.
Good cholesterol = HDL,
scavenges excess
cholesterol and takes it to
the liver for disposal.
Bad cholesterol, LDL, sticks
to the walls of your arteries
and blocks them.

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Lipids and Cardiovascular Health

Saturated fats (e.g., animal


fat) induce the production of
LDL (bad).

Unsaturated fats (e.g., plant


and fish oils) induce the
production of HDL (good)>

FYI: www.hsph.harvard.edu/nutritionsource/what-should-you-eat/fats-full-story/index.html
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Macromolecules III: Proteins
Hormones

Proteins are the


workhorses of the cell.

Antibodies Transporters

Enzymes

Receptors

Cell support
Transcription factors structures

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Storage protein
Macromolecules III: Proteins

Proteins are all constructed from the same set of


20 amino acids
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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Amino Acid Monomers

Amino acids are organic molecules with amino


and carboxyl groups
Amino acids differ in their properties due to
differing side chains, called R groups

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Amino Acid Monomers
Hydrophobic (Non-Polar) Side Chains
Side chain (R group)

Glycine Alanine Valine Leucine Isoleucine


(Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I)

Methionine Phenylalanine Tryptophan Proline


(Met or M) (Phe or F) (Trp or W) (Pro or P)

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Amino Acid Monomers
Hydrophilic (Polar) Side Chains

Serine Threonine Cysteine


(Ser or S) (Thr or T) (Cys or C)

Tyrosine Asparagine Glutamine


(Tyr or Y) (Asn or N) (Gln or Q)

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Amino Acid Monomers
Electrically Charged (Hydrophilic) Side Chains

Basic (positively charged)

Acidic (negatively charged)

Aspartic acid Glutamic acid Lysine Arginine Histidine


(Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)

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Polypeptides (Amino Acid Polymers)

Amino acids are linked by covalent bonds called


peptide bonds
A polypeptide is a
polymer of amino
acids
Each polypeptide has a
unique linear sequence of
amino acids, with a
carboxyl end (C-terminus)
and an amino end
(N-terminus)
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Protein Structure and Function

A proteins specific shape determines its


function

Lysozyme: Groove is formed to VDAC-1: What might its function be?


fit only a specific substrate.
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Protein Structure and Function

The sequence of amino acids determines a


proteins three-dimensional structure
Interactions among amino acid side chains (R-
groups) and the peptide backbone promote folding
of a polypeptide into a three-dimensional shape.

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Four Levels of Protein Structure

The primary structure of a protein is its unique


sequence of amino acids
Each protein has a unique
amino acid sequence that
is determined by inherited
genetic information

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Four Levels of Protein Structure

Secondary structure, found in most proteins,


consists of coils and folds in the polypeptide chain
Secondary structure results
from hydrogen bonds between
repeating constituents of the
polypeptide backbone
Typical secondary structures
are a coil called an helix
and a folded structure called
a pleated sheet

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Four Levels of Protein Structure

Tertiary structure, the overall shape of a


polypeptide, results from interactions between
R groups, rather than interactions between
backbone constituents

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Four Levels of Protein Structure

Tertiary structure interactions include hydrogen


bonds, ionic bonds, hydrophobic interactions,
and van der Waals interactions
Strong covalent
bonds called
disulfide bridges
may reinforce
the proteins
structure

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Four Levels of Protein Structure

Quaternary structure results when a protein


consists of multiple polypeptide chains

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Other Examples of Quaternary Structure

Collagen is a fibrous protein consisting of three


polypeptides coiled like a rope

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Other Examples of Quaternary Structure

Hemoglobin is a globular protein


consisting of four polypeptides:
two alpha and two beta chains

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Unique Protein Structure = Unique Function
A protein unique primary structure leads to unique
folding patterns (unique amino acid interactions)
Unique folding leads to unique structure
Unique structure = unique function

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Sickle-Cell Disease: A Change in Primary
Structure
A slight change in primary structure can affect a
proteins structure and ability to function
Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in the
protein hemoglobin

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Figure 5.19

Secondary
Primary Quaternary Function Red Blood Cell
and Tertiary
Structure Structure Shape
Structures
1 Normal Normal Proteins do not associate
subunit hemoglobin with one another; each
2
carries oxygen.
3

Normal

4
5
6
7 5 m

1 Sickle-cell Sickle-cell Proteins aggregate into a


subunit hemoglobin fiber; capacity to
2
carry oxygen
3
Sickle-cell

is reduced.
4
5
6
7 5 m

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Environmental Factors Affecting Protein
Structure
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 proteins native structure is
called denaturation
A denatured protein is biologically inactive

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Protein Denaturation and Renaturation

Normal protein

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Protein Denaturation and Renaturation

Normal protein Denatured protein

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Protein Denaturation and Renaturation

Normal protein Denatured protein

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Protein Folding in the Cell

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
Chaperonins are protein molecules that assist
the proper folding of other proteins
Diseases such as Alzheimers, Parkinsons,
and mad cow disease are associated with
misfolded proteins

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Chaperonin-Assisted Protein Folding

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Enzyme Function

Enzymes are usually proteins that speed up


chemical reactions
Remember, chemical reactions are the
rearrangement of atoms
Not only is matter rearranged, but energy is also
involved.

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Chemical Energy and Cellular Work

Chemical energythe potential


energy stored in the structure of Chemical Energy
(energy stored in bond
that restricts motion)
molecules.
Kinetic energythe energy of Energy In Energy out
movement
Workthe transfer of energy Kinetic energy Kinetic energy
(free motion of atoms

Life depends on the fact that


and molecules)

cells work!

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Energy and Chemical Reactions

Chemical reactions are of two types:


They require an input of energy--endergonic
They release energy--exergonic
Chemical Energy
(energy stored in bond
that restricts motion)

Endergonic Energy In Energy out Exergonic

Kinetic energy Kinetic energy


(free motion of atoms
and molecules)
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Energy and Chemical Reactions

Another way to look at exergonic and endergonic


reactions

Breakdown of complex molecules to Synthesis of complex molecules from


simpler forms are exergonic reactions: simpler forms are endergonic reactions:

Example: Cellular respiration Example: Photosynthesis.

C6H12O6 + 6 O2 6 CO2 + 6 H2O 6 CO2 + 6 H2O 6 O2 + C6H12O6

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Energy of Activation

Why dont macromolecules with large stores of chemical


energy (and order) spontaneously hydrolyze to release
energy?

Chemical Energy
(energy stored in bond
that restricts motion)

Energy In Energy out

Kinetic energy Kinetic energy


(free motion of atoms
and molecules)
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Energy of Activation

Because there is an energy barrier that must be overcome


for a chemical reaction to begin.

This is the Energy of Activation for a chemical reaction.

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Enzymes assist chemical reactions

The energy of activation prevents most reactions from


occurring quickly in the cell.

So, how do cells respond quickly to stimuli to do work?

Trypsin

Cells have enzymes that assist chemical reactions by


lowering the activation energy.

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Enzymes assist chemical reactions

Cells have enzymes that assist chemical reactions


by lowering the activation energy.

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Enzymes assist chemical reactions
Enzymes are biological catalysts

increase the rate of a chemical reaction

are not consumed by the reaction.

Thus, only small amounts of enzyme is required to sustain


a chemical reaction because it can be reused on multiple
reactants.

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A specific enzyme catalyzes each
cellular reaction
As a protein, an enzyme has a specific 3-D shape
that determines which chemical reaction the
enzyme catalyzes.
Hexokinase

Lysozyme
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A specific enzyme catalyzes each
cellular reaction
Induced fit model of enzyme action
Active sitesite in enzyme of chemical reaction
Substrate (reactant)molecules acted upon by enzyme

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A specific enzyme catalyzes each
cellular reaction
General model of enzyme-catalyzed reactions:

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Optimal Enzyme Conditions
Because a protein is dependent on its 3-D shape
for function, several factors must be optimized for
effective enzyme function

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Optimal Enzyme Conditions

Temperature
High temperatures can
denature (unfold) proteins
Optimal temperature for
human enzymes, 37 C

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Optimal Enzyme Conditions

pH
Excess H+ or OH- can
interfere with hydrogen-
bonding and prevent
proper protein folding

Optimal pH for most


human enzymes is
pH 6-8

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Optimal Enzyme Conditions

Some enzymes require co-factors, usually


inorganic metal ions or vitamins
e.g., Mg, Ca, Fe, Zn, Cu, Co ions
Vitamins such as biotin, niacin

Pyruvate Carboxylase with biotin

Choline kinase with Mg (green)

Jitrapakdee etal.,Biochem. J. (2008) 413 (369387)


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Enzyme Inhibitors
Enzyme inhibitors are molecules that interfere with an
enzymes activity.

Your cells have natural enzyme inhibitors to regulate


chemical reactions

Drug companies design enzyme inhibitors to treat


diseases.

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Enzyme Inhibitors

Competitive inhibitor
inhibits an enzymes activity by blocking substrates
from entering the enzymes active site.

can be overcome by increasing amount of substrate

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Enzyme Inhibitors

Non-competitive inhibitor
binds to enzyme in region outside active site and
changes enzymes shape so that it can no longer bind
substrate.

cannot be overcome by increasing amount of substrate

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Macromolecules IV: Nucleic acids

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

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The Roles of Nucleic Acids

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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Figure 5.23-1

DNA

1 Synthesis of
mRNA
mRNA

NUCLEUS
CYTOPLASM

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Figure 5.23-2

DNA

1 Synthesis of
mRNA
mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into
cytoplasm

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Figure 5.23-3

DNA

1 Synthesis of
mRNA
mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into Ribosome
cytoplasm

3 Synthesis
of protein

Amino
Polypeptide acids
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The Components of Nucleic Acids

Nucleic acids are polymers called


polynucleotides
Each polynucleotide
is made of monomers
called nucleotides

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The Components of Nucleic Acids

Each nucleotide consists of a nitrogenous base, a


pentose sugar, and one or more phosphate
groups

Nucleotide

The portion of a nucleotide without the phosphate


group is called a nucleoside
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