Transcript Carbon

Carbon &
Biochemistry
Chapter 4: Carbon and the Molecular Diversity of Life
Chapter 5: The Structure & Function of Large Biological Molecules
Chemistry of Life

Carbon is essential to life

 Although cells are 70–95% water, the rest


consists mostly of carbon-based compounds
An
is any carboncontaining compound
-named “organic” because first ones studied
came from living organisms
Organic compounds in living organisms:
-proteins, amino acids, carbohydrates, fats
(lipids), nucleic acids, etc…
Carbon Structure



Carbon
-Needs
to fill outer shell
-Enables carbon to form large molecules
Electron configuration is the key to an atom’s
characteristics
Electron configuration determines the kinds and
number of bonds an atom will form with other
atoms
Fig. 4-4
Valence Electrons
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
H
O
N
C
Carbon Backbones:
Hydrocarbons




are
organic molecules consisting of only
carbon and hydrogen
Many organic molecules, such as fats,
have hydrocarbon components
Hydrocarbons can undergo reactions
that release a large amount of energy
With four valence electrons, carbon
can form
with a variety of atoms
Fig. 4-6
Fat droplets (stained red)
100 µm
(a) Mammalian adipose cells
(b) A fat molecule
Hydrocarbon Bonding
1) C – H bonds
-only single bonds
2) C – C bonds (different shapes and numbers)
a)
b)
C-C Bond Numbers
C-C Bond Shapes
Chain
Branched
Ring
Single
Double
Triple
Carbon - Carbon
Bond Numbers

= each carbon
bonded to four other atoms has
a tetrahedral shape

= two carbon
atoms are joined by a double
bond, the molecule has a flat
shape

= two carbon
atoms are joined by a triple
bond, the molecule has a linear
shape
Carbon - Carbon
Bonding Types
Straight Chains
Branched Chains
Rings
Fig. 4-3
Name
(a) Methane
(b) Ethane
(c) Ethene
(ethylene)
Molecular
Formula
Structural
Formula
Ball-and-Stick
Model
Space-Filling
Model
Isomers

Isomers are compounds with
the same molecular formula but
and
properties:

isomers have
different covalent
arrangements of their atoms

isomers have
the same covalent
arrangements but differ in
spatial arrangements

are isomers
that are mirror images of each
other
Chemical
Formula
Structural
Formula
Hexane:
C6H14
CH3CH2CH2CH2CH2CH3
Isohexane:
C6H14
CH3
l
CH3CH2CHCH2CH3
Enantiomers
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Enantiomers are important in the
industry
Two enantiomers of a drug may have different
effects
Differing effects of enantiomers demonstrate that
organisms are sensitive to even subtle variations
in molecules
Example: L-dopa is used to treat symptoms of
Parkinson’s disease, while R-dopa (its enantiomer)
has no effect
Functional Groups


Functional groups
are the components of
organic molecules that
are
The number and
arrangement of
functional groups give
each molecule its
unique properties
Functional Groups

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
Fig. 4-10a
CHEMICAL
GROUP
Hydroxyl
Carbonyl
Carboxyl
STRUCTURE
(may be written HO—)
NAME OF
COMPOUND
In a hydroxyl group (—OH), a
hydrogen atom is bonded to an
oxygen atom, which in turn is
bonded to the carbon skeleton of
the organic molecule. (Do not
confuse this functional group
with the hydroxide ion, OH–.)
The carbonyl group ( CO)
consists of a carbon atom
joined to an oxygen atom by a
double bond.
When an oxygen atom is
double-bonded to a carbon
atom that is also bonded to
an —OH group, the entire
assembly of atoms is called
a carboxyl group (—COOH).
Alcohols (their specific names
usually end in -ol)
Ketones if the carbonyl group is
within a carbon skeleton
Carboxylic acids, or organic
acids
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
EXAMPLE
Ethanol, the alcohol present in
alcoholic beverages
Acetone, the simplest ketone
Acetic acid, which gives vinegar
its sour taste
Propanal, an aldehyde
FUNCTIONAL
PROPERTIES
Is polar as a result of the
electrons spending more time
near the electronegative
oxygen atom.
A ketone and an aldehyde may
be structural isomers with
different properties, as is the
case for acetone and propanal.
Can form hydrogen bonds with
water molecules, helping
dissolve organic compounds
such as sugars.
These two groups are also
found in sugars, giving rise to
two major groups of sugars:
aldoses (containing an
aldehyde) and ketoses
(containing a ketone).
Has acidic properties
because the covalent bond
between oxygen and hydrogen
is so polar; for example,
Acetic acid
Acetate ion
Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion (here,
specifically, the acetate ion).
Fig. 4-10b
CHEMICAL
GROUP
Amino
Sulfhydryl
Methyl
(may be
written HS—)
STRUCTURE
NAME OF
COMPOUND
Phosphate
The amino group
(—NH2) consists of a
nitrogen atom bonded
to two hydrogen atoms
and to the carbon
skeleton.
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
Amines
Thiols
In a phosphate group, a
phosphorus atom is bonded to
four oxygen atoms; one oxygen
is bonded to the carbon skeleton;
two oxygens carry negative
charges. The phosphate group
(—OPO32–, abbreviated P ) is an
ionized form of a phosphoric acid
group (—OPO3H2; note the two
hydrogens).
Organic phosphates
A methyl group consists of a
carbon bonded to three
hydrogen atoms. The methyl
group may be attached to a
carbon or to a different atom.
Methylated compounds
EXAMPLE
Glycine
Because it also has a
carboxyl group, glycine
is both an amine and
a carboxylic acid;
compounds with both
groups are called
amino acids.
FUNCTIONAL
PROPERTIES
Acts as a base; can
pick up an H+ from
the surrounding
solution (water, in
living organisms).
(nonionized) (ionized)
Ionized, with a
charge of 1+, under
cellular conditions.
Glycerol phosphate
Cysteine
Cysteine is an important
sulfur-containing amino
acid.
In addition to taking part in
many important chemical
reactions in cells, glycerol
phosphate provides the
backbone for phospholipids,
the most prevalent molecules in
cell membranes.
Two sulfhydryl groups
can react, forming a
covalent bond. This
“cross-linking” helps
stabilize protein
structure.
Contributes negative charge
to the molecule of which it is
a part (2– when at the end of
a molecule; 1– when located
internally in a chain of
phosphates).
Cross-linking of
cysteines in hair
proteins maintains the
curliness or
straightness
of hair. Straight hair can
be “permanently” curled
by shaping it around
curlers, then breaking
and re-forming the
cross-linking bonds.
Has the potential to react
with water, releasing energy.
5-Methyl cytidine
5-Methyl cytidine is a
component of DNA that has
been modified by addition of
the methyl group.
Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects
expression of genes.
Arrangement of methyl
groups in male and female
sex hormones affects
their shape and function.
ATP
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One phosphate molecule, adenosine triphosphate
(ATP), is the primary
in the cell
ATP consists of an organic molecule called adenosine
attached to a string of three phosphate groups
Energy is
when a phosphate group is
from ATP to form ADP (adenosine diphosphate)
Energy is
when a phosphate group
is
to ADP to form ATP
Reacts
with H2O
P
P
P Adenosine
ATP
Pi
P
Inorganic
phosphate
P
Adenosine
ADP
Energy
Macromolecules


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
All living things are made up of four classes of
large biological molecules:
Within cells, small organic molecules are joined
together to form larger molecules
Macromolecules are large molecules
composed of thousands of covalently connected
atoms
One key concept is that
Macromolecules




A
is a single subunit
(building block)
A
is a long molecule
consisting of many similar monomers
Macromolecules are polymers, and identified
by their specific subunits (monomers)
Monomers are covalently bonded in
reactions to make
macromolecules
The Synthesis and
Breakdown of Polymers
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A condensation
reaction, or more
specifically dehydration
synthesis, occurs when
two monomers bond
together through the
Polymers are digested to
monomers by
,a
reaction that breaks apart
by adding water
Fig. 5-2a
HO
1
2
3
H
Short polymer
HO
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
HO
1
2
H
3
H2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
Fig. 5-2b
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
1
2
3
(b) Hydrolysis of a polymer
H
H
H2O
HO
H
Macromolecules Types
The four types of macromolecules include:

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
Carbohydrates
Lipids (fats)
Proteins
Nucleic Acids
Carbohydrates
Carbohydrates include
sugars and the polymers of
sugars
 Sugar polymers made of
carbon, hydrogen, & oxygen
in a
 The simplest carbohydrates
are
, or
single sugars
 Simple to complex:
Monosaccharides 
Disaccharides 
Polysaccharides

Carbs may be as much as 70%
of an Endurance Athlete’s Diet!
Lance Armstrong
Michael Phelps
6500Kcal/day
8400 Kcal/day
Our Primary Energy Source

from monosaccharides
- glucose, fructose, galactose
from polysaccharides

-glycogen (in animals)
-starch (in plants)

Other
-structural components of cells (ex. cellulose in
plant cell walls)
-Fiber in our diets
Monosaccharides
mono- “




”
saccharide- “
Monosaccharides have
molecular formulas that are
usually multiples of CH2O
(C6H12O6) is the
most common
monosaccharide (right) and
our
Another is fructose
(C6H12O6)
Monosaccharides serve as a
major fuel for cells and as
raw material for building
molecules
”
Glucose and Fructose
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Monosaccharides
Isomers
C6H12O6
Glucose is the form of
sugar carried in our
blood
Fructose is the sweet
sugar found in most
fruits and sweets
Hexoses (C6H12O6)
Glucose
Galactose
di- “
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Disaccharides
” -saccharide “
”
Disaccharides are 2 monosaccharides bonded together by
dehydration synthesis
This covalent bond is called a
Molecular formula of
Examples include:
 Sucrose (glucose + fructose)
 This is table sugar
 Lactose (glucose + galactose)
 This is a milk sugar
 Maltose (glucose + glucose)
 This is a grain sugar
Fig. 5-5
1–4
glycosidic
linkage
Glucose
Glucose
Maltose
(a) Dehydration reaction in the synthesis of maltose
1–2
glycosidic
linkage
Glucose
Fructose
(b) Dehydration reaction in the synthesis of sucrose
Sucrose
Polysaccharides
poly-: “
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

” -saccharides: “
Polysaccharides are long sugar
chains
Often not water soluble due to
great size
Used primarily for

(Plants
store surplus starch as
granules within chloroplasts
and other plastids)

(Humans
and other vertebrates store
glycogen mainly in liver and
muscle cells)
”
Polysaccharides: Glycogen and Starch
Cellulose
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The polysaccharide cellulose is a
major component of the tough wall
of plant cells
Like starch, cellulose is a
, but the
glycosidic linkages differ
Cellulose in human food passes
through the digestive tract as
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What evidence do we have of this?
Many herbivores, from cows to
termites, have symbiotic
relationships with microbes that use
enzymes to digest cellulose
Cellulose
Chitin


Chitin, another
structural
polysaccharide, is
found in the
Chitin also
provides
structural support
for the cell walls
of many
Lipids
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
Lipids are the one class of large
biological molecules that do not
form polymers
The unifying feature of lipids is
having
Lipids are
because they consist mostly of
hydrocarbons, which form
The most biologically important
lipids are fats, phospholipids,
and steroids
4.5 Kcal/g in carbs
VS.
9 Kcal/g in fats
Lipids

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The major function of fats is
Humans and other mammals store
their fat in
Adipose tissue also
vital organs and
the body
Energy storage
-Stored mostly as
Other functions
-Steroid hormones
-Plasma membrane structural
stability
Fats
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Fats are constructed from two types
of smaller molecules: glycerol and
fatty acids
is a threecarbon alcohol with a hydroxyl group
attached to each carbon
A
consists of
a carboxyl group attached to a long
carbon skeleton
 Many C-H bonds
Structure is a fatty acid chain bonded
to a carboxyl group
2 Types:
1) saturated
2) unsaturated
Most common form
of a fat is a
triglyceride
Triglycerides
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
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

Joined by an
Our primary lipid storage molecule
Form through dehydration synthesis
Fats separate from water because water molecules form
hydrogen bonds with each other and exclude the fats
Fig. 5-11b
Ester linkage
Fat molecule (triacylglycerol)
Fats
Saturated

Maximum number of C-H
bonds as possible, so
“saturated” with hydrogen
chain
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

vs.


Generally
temperature
at room

Example:
butter
fats;

Unsaturated
One or more C=C, so less
hydrogen
chain (b/c of
C=C bonds)
Generally
at
room temperaure
Example
fats; vegetable oil
Fats
Triglycerides & Trans Fats
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
A diet rich in saturated fats may contribute to
through plaque deposits
is the process of converting
unsaturated fats to saturated fats by adding
hydrogen
Hydrogenating vegetable oils also creates
unsaturated fats with trans double bonds (trans
fats)
Trans fats
levels “bad” cholesterol and
levels of “good” cholesterol
These trans fats may contribute more than
saturated fats to cardiovascular disease
Phospholipids




Make up
of a cell
In a phospholipid, two fatty acids and a phosphate
group are attached to glycerol
The two fatty acid tails are
, but
the phosphate group and its attachments form a
head
 Hydrophobic (“water fearing”) tail
-nonpolar
 Hydrophilic (“water loving”) head
-polar
The nucleus, mitochondria and endomembrane system
all are surrounded by their own phospholipid bilayers
Hydrophobic tails
Hydrophilic head
Fig. 5-13
(a) Structural formula
Phospholipid
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
(b) Space-filling model
(c) Phospholipid symbol
TEM Image: Plasma
Membrane
Phospholipids
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When phospholipids are added to water,
they self-assemble into a bilayer, with the
hydrophobic tails pointing toward the
The structure of phospholipids results in a
bilayer arrangement found in cell
membranes
Phospholipids are the major component of
all cell membranes
Fig. 5-14
Hydrophilic
head
Hydrophobic
tail
WATER
WATER
Steroids
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are lipids characterized by a carbon
skeleton consisting of four fused rings
, an important steroid, is a
component in animal cell membranes
Although cholesterol is essential in animals, high levels in
the blood may contribute to cardiovascular disease
In plasma membranes, cholesterol provides extra
structural support
are similar in structure to cholesterol
1)Testosterone
2)Estrogen
 Cholesterol

(form
other steroids from it)
Made into sex hormones
Estrogen
Testosterone
Anabolic Steroids
Mimic
First used for anemia and
muscle disease
Abused by athletes
Misuse can cause
Facial bloating/acne
Violent mood swings
Liver damage
Increased
Reduced
Testosterone
Anabolic Steroid
Proteins
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Proteins account for
of the
dry mass of most cells
Provide structural support (about 15% of our mass)
-muscle, cartilage, ligaments, skin, hair
Strengthen immune system (
)
Chemical messengers (
)
Carry oxygen (
)
Cell growth and repair
– Most Important
Table 5-1
Proteins

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

Proteins are
(subunits or
building blocks)
 20 different amino acids
 Amino acids are like letters while proteins are like
words
 Amino acids have an amino group, carboxyl group,
and an R group (side chain) bound to its original
carbon
Amino acids are joined by
through
to create proteins
They fold and twist to form shapes unique to each
protein
Reminder: The
of a molecule determines
its
!
Fig. 5-UN1
carbon
Amino
group
Carboxyl
group
Fig. 5-17
Nonpolar
Glycine
(Gly or G)
Valine
(Val or V)
Alanine
(Ala or A)
Methionine
(Met or M)
Leucine
(Leu or L)
Trypotphan
(Trp or W)
Phenylalanine
(Phe or F)
Isoleucine
(Ile or I)
Proline
(Pro or P)
Polar
Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Tyrosine
(Tyr or Y)
Asparagine Glutamine
(Asn or N) (Gln or Q)
Electrically
charged
Acidic
Aspartic acid Glutamic acid
(Glu or E)
(Asp or D)
Basic
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)
Amino Acid Polymers



There is no such thing as a
monopeptide since one amino
acid by itself is not a protein
Dipeptides are
linked together
A polypeptide is a


Polypeptides range in
length from a few to more
than a thousand
monomers
Each polypeptide has a
unique linear sequence of
amino acids
Protein Functions

The function of a protein is
dependent on its structure
In almost every case, the
function depends on its
ability to

Example: antibody and
antigen interaction in
the body (right)
Of all protein types, we will
focus a bit more on
enzymes because of their
value in biological sciences.


Enzymes

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
Enzymes are a type of protein that acts
as a catalyst to
They can either build up or break down
substances (called substrates or reactants)
Enzymes can perform their functions
repeatedly, functioning as workhorses that
carry out the processes of life
Enzyme animation
Fig. 5-16
Substrate
(sucrose)
Glucose
OH
Fructose
HO
Enzyme
(sucrase)
H2O
Protein Structure




A
protein consists of one or
more polypeptides twisted, folded, and coiled
into a
The sequence of amino acids determines a
protein’s three-dimensional structure
Again, a protein’s structure determines its
function
There are 4 levels of protein structure




Primary
Secondary
Tertiary
Quaternary
Protein Structure
Primary Structure
Amino Acid
protein
Primary structure, the
of amino acids
in a protein, is like the order
of letters in a long word
Primary structure is
determined by inherited
genetic information
Animation
Secondary Structure
The coils and folds of
secondary structure
result from
between
repeating constituents of
the polypeptide backbone
Typical secondary
structures are a coil
called an
and a folded structure
called a
Tertiary Structure
Tertiary structure is
determined by
, rather
than interactions between
backbone constituents
These interactions between R
groups include hydrogen
bonds, ionic bonds,
hydrophobic interactions, and
van der Waals interactions
Strong covalent bonds called
may
reinforce the protein’s structure
Quaternary Structure
Quaternary structure
results when
form
one macromolecule

(connective tissue protein) is
a fibrous protein consisting of
three polypeptides coiled like
a rope

is a
globular protein consisting of
four polypeptides: two alpha
and two beta chains
Protein Structure
Disease
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
Denatured Proteins





When a protein loses its structural integrity, and its tertiary
(3-D) structure is destroyed
This loss of a protein’s native structure is called
A denatured protein is
Factors that cause protein denaturation include:
temperature (on the stove)
(in your stomach)
-salt concentration
As a result:
-Losses its ability to function
-Properties can change (become insoluble, or change
color)
Fig. 5-23
Denaturation
Normal protein
Renaturation
Denatured protein
Nucleic Acids



The amino acid sequence of a polypeptide is programmed
by a unit of inheritance called a gene
Genes are made of DNA, a nucleic acid
Nucleic acids are

Made up of approximately 30 atoms
They create the two types of nucleic acids:

(Deoxyribonucleic Acid)
 Our genetic code (DNA)

(Ribonucleic Acid)
 Information for protein formation (RNA)
Tour into DNA



Nucleic acids & proteins are the only macromolecules
containing
Nucleotide Structure

Pentose (5-carbon)
sugar (ribose or
deoxyribose)



(Adenine, Cytosine,
Guanine, Thymine, or
Uracil)
connects the
nucleotides together
Pentose (5-C) Sugars
Nitrogenous Bases
There are two families
of nitrogenous bases:

(cytosine, thymine, and
uracil) have a single sixmembered ring

(adenine and guanine)
have a six-membered
ring fused to a fivemembered ring
Nucleic Acids

Nucleic acids are polymers called
polynucleotides
The portion of a nucleotide without the
phosphate group is called a
Nucleoside = nitrogenous base + sugar

Nucleotide = nucleoside + phosphate group

In DNA, the sugar is




RNA, the sugar is
; in
In DNA, nitrogenous bases are adenine (A),
cytosine (C), guanine (G), and thymine (T)
In RNA,
DNA and RNA
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
DNA
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DeoxyriboNucleic Acid - DNA
DNA is a recipe book for proteins
Genes direct the order of amino
acids
One strand has 100’s to 1000’s of
genes
DNA is arranged into a structure
called a
 2 strands of polynucleotides
 Nitrogenous bases bonded to
each other by

, vice versa

, vice versa
DNA Double Helix



A DNA molecule has two
polynucleotides spiraling around an
imaginary axis,
In the DNA double helix, the two
backbones run in opposite 5 → 3
directions from each other, an
arrangement referred to as
The nitrogenous bases in DNA pair
up and form hydrogen bonds:
adenine (A) always with thymine
(T), and guanine (G) always with
cytosine (C)
Race for the Double Helix



James Watson and
Francis Crick
(pictured right) are
credited with the
discovery of DNA
as a double helix
Proposed in 1953
Rosalind Franklin
may have played a
major role but
never received
credit
RNA



RiboNucleic Acid RNA
RNA is a
of
nucleotides
Many types of RNA
are used to help
create
Review Questions
1.
2.
3.
4.
5.
6.
7.
8.
Explain the importance of carbon as a compound of life.
Define organic compounds and hydrocarbons.
Define isomers and differentiate between the 3 different types.
Differentiate between 7 different biological functional groups.
Explain the use and functioning of ATP.
Name the 4 different classes of macromolecules and the subunits of each.
Differentiate between dehydration (condensation) synthesis and hydrolysis.
Describe carbohydrates, noting the functions and differences within the three
main categories, along with multiple examples of each.
9. Differentiate between starch, glycogen, chitin, and cellulose.
10. Describe lipids, noting the functions and differences within the three main
categories, along with multiple examples of each.
11. Describe 3 differences between unsaturated and saturated fats, naming an
example of each.
12. Describe the importance of phospholipids, along with their parts.
13. Define steroids and differentiate between the 3 examples discussed in class.
14. Describe proteins, including 6 different examples and their respective
functions.
15. Identify and describe the parts of an amino acid.
Review Questions cont’d
16. Discuss the importance of enzymes to life processes.
17. Differentiate between the 4 levels of protein structure and organization.
18. Describe denaturation and name factors that cause protein denaturation.
19. Identify and describe the 3 parts of a nucleotide.
20. Differentiate between the functions of DNA and RNA.
21. Describe 3 structural differences between DNA and RNA.
22. Differentiate between purines and pyrimidines.
23. Name 3 people important to the discovery of DNA as a double helix.