Chapter 21 Biochemistry
Name:
21.1 Introduction to Proteins
1.To learn about proteins
2.To understand the primary structure of proteins
3.To understand the secondary structure of proteins
4.To understand the tertiary structure of proteins
5.To learn the functions of proteins
6.To understand how enzymes work
Date:
Period:
There are _____________ essential elements that are essentials to human life and the first row transition
elements are found in _________________ amounts in the human body.
•Protein – natural _____________________, making up _______% of the body
–Types and Functions
•__________________ – structural integrity and strength
–Main components of ___________________, _________________,
_____________________
A. Proteins
•Globular – ______________________ ________________________
–_________________________ and________________ oxygen and nutrients
–Act as ________________________
–Fight ______________________ of body
–______________________ systems
–______________________ electrons
B. Primary Structure of Proteins
amino acids – _________________________________________________________
R groups (side chains)
__________________________________________________________________________________________
____
Amino group is always attached to the _______________________ the one next to the
______________________ group.
1
How do we build a protein?
Reactions between _____ ________________ __________ to form a di____________. Longer chains are
called _____________________________.
Primary structure the order or sequence of ____________ __________________. 3 letter codes. (Lys-ala-leu)
Example:
C. Secondary Structure of Proteins- arrangnment in space of the ____________ of long molecules.
Types
–helix
–pleated sheet
D. Tertiary Structure of Proteins
2
Disulfide linkage-linkage between 2 cysteine amino acids,which stabilizes the tertiary structure
E. Functions of Proteins
Denaturation – process of breaking down the 3-D structure of a protein
F. Enzymes
Enzymes – proteins that catalyze specific biological reactions
Lock and key model – model for how an enzyme works
–Substrate – reacting molecule
–Active site – part of the enzyme where the substrate attaches
Section 21.1: Team Learning Worksheets
1. Which statement (a–d) is false with respect to proteins?
a. Primary structure refers to the sequence of amino acids.
b. Secondary structure includes a-helixes.
c. Tertiary structure includes disulfide bonds.
d. The overall shape of a protein is related to the tertiary structure.
e. All are true.
2. Which of the following statements are correct in describing the primary structure of proteins? There may be
more than one answer.
a. Primary structure refers to the order of amino acids.
b. Primary structure refers to the arrangement of the chain in the long molecule.
c. Primary structure refers to the overall shape of the protein.
d. Primary structure is determined by the types of bonds it contains.
e. Primary structure is determined by the side chains.
3
3. Which of the following statements are correct about a pleated sheet arrangement of proteins? There may be
more than one answer.
a. A pleated sheet arrangement is found in muscle fibers.
b. A pleated sheet arrangement contains interchain hydrogen bonds.
c. A pleated sheet arrangement is found in silk fibers.
d. A pleated sheet arrangement results when hydrogen bonds occur between protein chains.
4. Draw the structures of the simple dipeptides gly-ala and ala-gly.
5. How are proteins able to provide a buffering action?
6. What is meant by inhibition of an enzyme? What happens when an enzyme is irreversibly inhibited?
21.2 Carbohydrates, Nucleic Acids, and Lipids
1.To understand the fundamental properties of carbohydrates
2.To understand nucleic acid structures
3.To learn the four classes of lipids
A. Carbohydrates
Simple sugars (monosaccharides) - aldehydes or ketones with multiple hydroxyl substituents.
-General formula CH2O
4
Slide 4
Ring formation- ____________usually for ring structures.
Slide 5
______________________- are a combination of 2 monosaccharides, sucrose is a _______________________
formed from_______________________ and ______________________.
Slide 6
________________________ are polymer of many monosaccharide units. s_________ is an example of one.
Slide 7
B. Nucleic Acids
_______________________ _________ (DNA) this is a type of polymer that ___________ and
_______________ genetic information.
_______________________ _________ (RNA) is a type of polymer that __________________ to
____________________ genetic material.
Slide 8
Nucleotides are biological molecules that form the building blocks of nucleic acids (DNA and RNA) and serve
to carry packets of energy within the cell (ATP).
5
Nucleotides are fundamental unit of both _________ and ____________.
The three parts are: _________________ , which contains the _______________ base.
Five-______________ ________________
____________________ group
Slide 9
Five carbon sugars both are nucleic acids and polymers.
-deoxyribonucleic acid (DNA) is a huge molecule which contains deoxyribose. DNA stores and transmits and
carries genetic information needed for synthesis of various proteins. DNA has a very high molar mass as high
as several billon grams.
Ribonucleic acid (RNA) functions to transport genetic information and is found in the cytoplasm outside the
cell nucleus. RNA is much smaller than DNA polymers, with molar mass of about 20,000-40,000 grams.
Slide 10
Organic bases-Organic base molecules found in the nucleotides of DNA and RNA are shown below. To form
the DNA and RNA polymers, the nucleotides are hooked together.
Slide 11,12,13, & 14
B. Nucleic acids
6
Double helix
Slides 15, 16, &17 DNA and Protein Synthesis
Protein synthesis Gene Ribosomes
RNA

Complimentary base

Replication during cell
division
Transfer RNA
Messenger RNA-
Slides 18
c. Lipids
 Defined in terms of
solubility characteristics
-Fat
7
Common Fatty Acids.
Saturated
Unsaturated
Saponification-

Soap cleaning action
- Miculles
•
•
Polar

Nonpolar
Phospholipids-

Waxes-

Steroids-
8

Cholesterol-

Hormones-

Bile acids
Section 21.2: Team Learning Worksheet
1. Differentiate between monosaccharide and disaccharide. Provide an example of each.
2. Sketch a representation of sucrose and clearly label the portion that originates from glucose, the portion that
originates from fructose, and the glycoside linkage between the rings.
9
3. What is a polysaccharide? What monomer unit makes up starch and cellulose?
4. Describe the structure of a typical nucleotide.
5. Sketch the structures of the sugars ribose and deoxyribose. Which molecule, RNA or DNA, contains each
sugar?
6. Sketch the general structure of a triglyceride. What are the components that go into making a typical
triglyceride?
7. Describe the mechanism by which fatty acid salts are able to exert a cleaning action.
10
Section 21.1: Team Learning Worksheet ANWSERS
1. The correct answer is “e,” all statements are true.
2. The only correct answer is “a.”
3. All of the given statements are correct concerning pleated sheet arrangement of proteins.
4.
H
H
O
H
H
O
N
C
C
N
C
C
H
H
H
CH3
OH
gly-ala
H
H
O
H
H
O
N
C
C
N
C
C
H
CH3
OH
ala-gly
H
5. Proteins contain both acidic (—COOH) and basic (—NH2) groups in their side chains, which can neutralize
both acids and bases.
6. An enzyme is inhibited if a molecule other than the enzyme’s correct substrate blocks the active sites of the
enzyme. If the inhibition is irreversible, the enzyme can no longer function (it is inactivated).
Section 21.2: Team Learning Worksheet ANSWERS
1. Monosaccharides are simple sugars. They are aldehydes or ketones that contain several hydroxyl
substituents. Glucose and fructose are two common examples. Disaccharides are the result of the
combination of two monosaccharides. Sucrose (table sugar) is a common example.
2. The structure of sucrose is shown in Figure 21.10c in the text.
3. Polysaccharides are large polymers containing many monosaccharide units. Starch and cellulose are each
made by the combination of many glucose rings. The linkage of the glucose rings is different in each case.
4. A nucleotide consists of three components: a five-carbon sugar, a nitrogen-containing organic base, and a
phosphate group. The phosphate and the nitrogen base are each bonded to respective sites on the sugar, but
are not bonded to each other.
5. Ribose is found in RNA molecules, and deoxyribose is found in DNA molecules. The structures are given in
Figure 21.12 in the text.
6. A triglyceride typically consists of a glycerol backbone, to which three separate fatty acid molecules are
attached by ester linkages.
O
R
C
O
C
O
R"
C
O
O
CH2
O
C
R'
CH2
7. This is described in the text, but the students should explain it in their own words, and with relevant
structures.
11
Section 21.2: Team Learning Worksheet ANWSERS
Section 21.2: Team Learning Worksheet
1. Monosaccharides are simple sugars. They are aldehydes or ketones that contain several hydroxyl
substituents. Glucose and fructose are two common examples. Disaccharides are the result of the
combination of two monosaccharides. Sucrose (table sugar) is a common example.
2. The structure of sucrose is shown in Figure 21.10c in the text.
3. Polysaccharides are large polymers containing many monosaccharide units. Starch and cellulose are
each made by the combination of many glucose rings. The linkage of the glucose rings is different in
each case.
4. A nucleotide consists of three components: a five-carbon sugar, a nitrogen-containing organic base,
and a phosphate group. The phosphate and the nitrogen base are each bonded to respective sites on
the sugar, but are not bonded to each other.
5. Ribose is found in RNA molecules, and deoxyribose is found in DNA molecules. The structures are given in
Figure 21.12 in the text.
6. A triglyceride typically consists of a glycerol backbone, to which three separate fatty acid molecules
are attached by ester linkages.
O
R
C
O
C
O
R"
C
O
O
CH2
O
C
R'
CH2
7. This is described in the text, but the students should explain it in their own words, and with relevant
structures.
12
Chapter 21
Biochemistry
1.
Oxygen is the element present in the human body in the largest percentage by mass (65%). Other
elements present in the body and their uses are given in Table 21.1.
2.
Proteins represent biopolymers of -amino acids used for many purposes in the human body (structure,
enzymes, antibodies, etc.). Proteins make up about 15% of the body by mass.
3.
Molar masses of proteins range from a few thousand amu to over 1 million amu. Such molar masses are
consistent with proteins being large polymeric molecules.
4.
Fibrous proteins provide the structural material of many tissues in the body, and are the chief
constituents of hair, cartilage, and muscles. Fibrous proteins consist of lengthwise bundles of
polypeptide chains (a fiber). Globular proteins have their polypeptide chains folded into a basically
spherical shape and tend to be found in the bloodstream, where they transport and store various needed
substances, act as antibodies to fight infections, act as enzymes to catalyze cellular processes, participate
in the body’s various regulatory systems, and so on.
5.
The general structural formula for the -amino acids is
O
NH2
CH
C
OH
R
All -amino acids contain the carboxyl group (–COOH) and the amino group (–NH2) attached to the carbon atom as indicated. In this general formula, R represents the remainder of the amino acid molecule
(side chain): It is this portion of the molecule that differentiates one amino acid from another.
6.
The structures of the amino acids are given in detail in Figure 21.2. Generally a side chain is nonpolar if
it is mostly hydrocarbon in nature (e.g., alanine, in which the side chain is a methyl group). Side chains
are polar if they contain the hydroxyl group (–OH), the sulfhydryl group (–SH), or a second amino (–
NH2) or carboxyl (–COOH) group.
7.
Since most proteins exist in aqueous media (water) in living creatures, the presence of hydrophobic
(water-fearing) and hydrophilic (water-loving) side chains on the amino acids in a protein will greatly
influence how that protein’s chain interacts with water. In particular, the three-dimensional structure of
the protein is greatly influenced by what types of side chains are present in its constituent amino acids.
8.
There are six tripeptides possible.
9.
cys–ala–phe
ala–cys–phe
phe–ala–cys
cys–phe–ala
ala–phe–cys
phe–cys–ala
a.
ile–ala–gly
13
O
O
H2N
CH
C
NH
b.
C
NH
CH2
C
OH
CH3
CH
H3C
CH
O
CH2CH3
gln–ser
O
O
CH
H2N
C
CH
NH
CH2
CH2
CH2
OH
C
C
OH
O
H2N
c.
ser–gln
O
O
H2N
CH
C
CH
NH
CH2
CH2
OH
CH2
C
C
OH
O
H 2N
d.
cys–asn–gly
.
O
H2N
CH
C
O
NH
CH
CH2
CH2
SH
C
C
O
NH
CH2
C
OH
O
H2N
10.
phe–ala–gly
O
H2N
N terminal
CH
CH2
C
O
O
NH
CH
CH3
C
NH
CH2
C
OH
C terminal
phe–gly–ala
14
O
H2N
N terminal
CH
C
O
O
NH
CH2
C
NH
CH
C
CH3
CH2
OH
C terminal
ala–phe–gly
O
H2N
N terminal
CH
C
O
O
NH
CH
C
NH
CH2
C
CH2
CH3
OH
C terminal
ala–gly–phe
O
H2N
N terminal
CH
C
O
O
NH
CH2
C
NH
CH3
CH
C
OH
C terminal
CH2
gly–phe–ala
O
H 2N
N terminal
CH2
C
O
O
NH
CH
CH2
C
NH
CH
CH3
C
OH
C terminal
gly–ala–phe
15
O
H2N
N terminal
CH2
C
O
O
NH
CH
CH3
C
NH
CH
CH2
C
OH
C terminal
11.
The secondary structure of a protein describes, in general, the arrangement in space of the protein’s
polypeptide chain. The most common secondary structures are the -helix and the -pleated sheet.
12.
Long, thin, resilient proteins, such as hair, typically contain elongated, elastic -helical protein
molecules. Other proteins, such as silk, which in bulk form sheets or plates, typically contain protein
molecules having the -pleated sheet secondary structure. Proteins that do not have a structural function
in the body, such as hemoglobin, typically have a globular structure.
13.
In the pleated-sheet secondary structure, a large number of similar polypeptide chains are arranged
lengthwise next to each other to form a wide sheet of protein. Because the individual polypeptide chains
contain the normal bond angles associated with the atoms involved, they are not themselves linear, and
when several chains are arranged next to each other to form a sheet, there are ripples (“pleats”) in the
overall sheet of protein due to this. A drawing of the pleated sheet is given in the text on page 756. Silk
and muscle fibers have the pleated-sheet structure.
14.
The secondary structure, in general, describes the arrangement of the long polypeptide chain of the
protein. In the -helical secondary structure, the chain forms a coil or spiral, which gives proteins
consisting of such structures an elasticity or resilience. Such proteins are found in wool, hair, and
tendons.
15.
The tertiary structure of a protein represents its specific, overall shape when it occurs in its natural
environment and is influenced by that environment. To distinguish between the secondary and tertiary
structures, consider this example: a given protein has an -helical secondary structure (the protein’s own
amino acid chain coils in a helix); in the body, however, this helix itself is folded and twisted by
interactions with the protein's environment until it forms a tight sphere. The fact that the helical protein
is folded into a tight sphere indicates the tertiary structure of the protein.
16.
Cysteine, an amino acid containing the sulfhydryl (–SH) group in its side chain, is capable of forming
disulfide linkages (–S–S–) with other cysteine molecules in the same polypeptide chain. If such a
disulfide linkage is formed, this effectively ties together two portions of the polypeptide, producing a
kink or knot in the chain, which leads in part to the protein’s overall three-dimensional shape (tertiary
structure). Cysteine, and the disulfide linkages it forms, is responsible for the curling of hair (whether
naturally or by a permanent wave).
17.
Denaturation of a protein represents the breaking down of the protein’s tertiary structure. If the
environment of a protein is changed from the normal environment of the protein, the specific folding
and twisting of the protein’s polypeptide chain will change to accommodate the new environment. If the
protein’s tertiary structure is changed, the protein most likely will no longer have whatever function in
the body it ordinarily possesses. Cooking of an egg (adding heat to the environment of the protein)
causes the protein albumin in the white of the egg to coagulate. Adding heavy metal ions (lead or
16
mercury, for example) can disrupt the inter-chain linkages that contribute to the protein’s tertiary
structure. A permanent hair wave works by deliberately changing the hair protein’s structure.
18.
Collagen has an -helical secondary structure. Collagen functions in the body as the raw material of
which tendons are constructed. The long, springy structure of the -helix is responsible for collagen’s
strength and elasticity.
19.
Proteins that catalyze biochemical processes are called enzymes.
20.
Antibodies are special proteins that are synthesized in the body in response to foreign substances such as
bacteria or viruses. Although there are usually specific antibodies for specific invaders, the antibody
interferon offers general protection against invasion by viruses.
21.
Antibodies are special proteins that are synthesized in the body in response to foreign substances such as
bacteria. Interferon is a protein that helps to protect cells against viral infection. The process of bloodclotting involves several proteins.
22.
In a permanent wave, cross-linkages between adjacent polypeptide chains of the protein are broken
chemically, and then re-formed chemically in a new location. The primary cross-linkage involved is a
disulfide linkage between cysteine units in the polypeptide chains. It is primarily the tertiary structure of
the hair protein that is affected by a permanent wave, although if the waving lotion is left on the hair too
long, the secondary structure can also be affected (making the hair very “frizzy”).
23.
Enzymes are typically 1 to 10 million times more efficient than inorganic catalysts. Enzymes are much
more efficient than any inorganic catalyst.
24.
The molecule acted upon by an enzyme is referred to as the enzyme’s substrate. When we say that an
enzyme is specific for a particular substrate, we mean that the enzyme will catalyze the reactions of that
molecule and that molecule only.
25.
The action of an enzyme on its substrate takes place at a specific portion of the polypeptide chain called
the active site.
26.
Figure 21.8 illustrates the lock-and-key model clearly. The lock-and-key model for enzyme action
postulates that the structures of the enzyme and its substrate are complementary, such that the active site
of the enzyme and the portion of the substrate molecule to be acted upon can fit together very closely.
The structures of these portions of the molecules are unique to the particular enzyme–substrate pair, and
they fit together much as a particular key is necessary to work in a given lock.
27.
Simple sugars typically contain several hydroxyl (–OH) groups, as well as the carbonyl (C=O) function
(making the sugar either an aldehyde or a ketone, as well as a polyalcohol).
28.
Sugars contain an aldehyde or ketone functional group (carbonyl group), as well as several –OH groups
(hydroxyl groups).
29.
In solution, functional groups at opposite ends of the simple sugar molecules react with each other,
forming the sugar into a ring or cyclic structure (see Figure 21.9 in the text for the structure).
30.
a.
glucose
17
CHO
H
C
OH
HO
C
H
H
C
OH
H
C
OH
CH2OH
b.
ribose
CHO
H
C
OH
H
C
OH
H
C
OH
CH2OH
c.
ribulose
CH2OH
C
O
H
C
OH
H
C
OH
CH2OH
d.
galactose
CHO
H
C
OH
HO
C
H
HO
C
H
H
C
OH
CH2OH
18
31.
Deoxyribonucleic acid (DNA) is the molecule responsible for coding and storing genetic information in
the cell, and for subsequently transmitting that information. DNA is found in the nucleus of each cell.
The molar mass of DNA depends on the complexity of the plant or animal species involved, but human
DNA may have a molar mass as large as 2 billion grams.
32.
Uracil (RNA only); cytosine (DNA, RNA); thymine (DNA only); adenine (DNA, RNA); guanine (DNA,
RNA)
33.
In a strand of DNA, the phosphate group and the sugar molecule of adjacent nucleotides become bonded
to each other. The chain portion of the DNA molecule, therefore, consists of alternating phosphate
groups and sugar molecules. The nitrogen bases are found sticking out from the side of this phosphate–
sugar chain, being bonded to the sugar molecules.
34.
When the two strands of a DNA molecule are compared, it is found that a given base in one strand is
always found paired with a particular base in the other strand. Because of the shapes and side atoms
along the rings of the nitrogen bases, only certain pairs are able to approach and hydrogen-bond with
each other in the double helix. Adenine is always found paired with thymine; cytosine is always found
paired with guanine. When a DNA helix unwinds for replication during cell division, only the
appropriate complementary bases are able to approach and bond to the nitrogen bases of each strand. For
example, for a guanine–cytosine pair in the original DNA, when the two strands separate, only a new
cytosine molecule can approach and bond to the original guanine, and only a new guanine molecule can
approach and bond to the original cytosine.
35.
A given section of the DNA molecule called a gene contains the specific information necessary for
construction of a particular protein.
36.
Messenger RNA molecules are synthesized to be complementary to a portion (gene) of the DNA
molecule in the cell, and serve as the template or pattern upon which a protein will be constructed (a
particular group of nitrogen bases on mRNA is able to accommodate and specify a particular amino acid
in a particular location in the protein). Transfer RNA molecules are much smaller than mRNA, and their
structure accommodates only a single specific amino acid molecule: transfer RNA molecules “find”
their specific amino acid in the cellular fluids, and bring it to mRNA where it is added to the protein
molecule being synthesized.
Rather than having some common structural feature, substances are classified as lipids based on their
solubility characteristics. Lipids are water-insoluble substances that can be extracted from cells by
nonpolar organic solvents such as benzene or carbon tetrachloride.
37.
38.
Saturated: butyric acid, caproic acid, lauric acid, stearic acid
Unsaturated: oleic acid, linoleic acid, linolenic acid
Most unsaturated fatty acids are derived from vegetable matter (plants).
39.
Saponification is the production of a soap by treatment of a triglyceride with a strong base such as
NaOH.
triglyceride + 3NaOH  glycerol + 3Na+soap–
19
O
CH2
O
C
R
O
CH
O
C
R'
+ 3NaOH
O
CH2
O
C
CH2
OH
CH
OH + R'COONa
CH2
OH
RCOONa
R''COONa
R''
40.
Soaps have both a nonpolar nature (due to the long chain of the fatty acid) and an ionic nature (due to
the charge on the carboxyl group). In water, soap anions form aggregates called micelles, in which the
water-repelling hydrocarbon chains are oriented toward the interior of the aggregate, with the ionic,
water-attracting carboxyl groups oriented toward the outside. Most dirt has a greasy nature. A soap
micelle is able to interact with a grease molecule, pulling the grease molecule into the hydrocarbon
interior of the micelle. When the clothing is rinsed, the micelle containing the grease is washed away.
See Figures 21.19 and 21.20.
41.
Cholesterol is the naturally occurring steroid from which the body synthesizes other needed steroids.
Since cholesterol is insoluble in water, it is thought that having too large a concentration of this
substance in the bloodstream may lead to its deposition and buildup on the walls of blood vessels,
causing their eventual blockage.
42.
44.
46.
48.
50.
52.
54.
56.
58.
60.
62.
v
t
x
q
k
y
c
n
e
s
h
43.
45.
47.
49.
51.
53.
55.
57.
59.
61.
63.
i
m
u
f
g
r
p
o
b
d
a
20