Download Chapter 3 Chemical Basis of Life II. Biological Molecules

CHAPTER 3 THE CHEMICAL BASIS OF LIFE
II:ORGANIC MOLECULES
The Carbon Atom and the Study of Organic Molecules
Formation of Organic Molecules and Macromolecules
Four types of Biological Molecules
 Carbohydrates
 Lipids
 Proteins
 Nucleic Acids
Learning Outcome
3.1 The Carbon Atom and the Study of Organic Molecules

Explain the properties of carbon that make it the focal point of organic compounds.

Compare and contrast different types of isomeric compounds.
3.2 Formation of Organic Molecules and Macromolecules

List the four major classes of biological macromolecules.

Describe each biological macromolecule, and how monomers of each class are brought together to form the
macromolecules.

Describe the relationship between functional groups and macromolecules.

Appreciate the variety and chemical characteristics of common functional groups of organic compounds.
3.3 Carbohydrates

Name the different forms of carbohydrate molecules.

Relate the structure of polysaccharides to their functions.
3.4 Lipids

Understand the structure of triglycerides.

Explain how fats function as energy-storage molecules.

Apply knowledge of the structure of phospholipids to the formation of membranes.
3.5 Proteins

Describe the possible levels of protein structure.

Understand the relationship between amino acid sequence and their three-dimensional structure.

Give examples of several different proteins and the general types of functions they carry out in a cell.
3.6 Nucleic Acids

Describe the structure of nucleotides.

Compare and contrast the structures of DNA and RNA.

Explain the functions of DNA and RNA.
2
Nucleus
First shell is filled
with 2 electrons
–
Spherical s
orbital of second
shell is filled with
2 electrons
–
–
–
–
Other energy orbitals
of second shell
contain 1 or 0
electrons
–
(a) Orbitals
–
–
–
–
+ +
+ +
+
+
–
–
(b) Simplified depiction of energy shells
3
4
5
6
Isomers
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
(b) Two types of stereoisomers
2-methyl butane
H
H
C
H
H
C
C
H
Pentane
H
H OH H
Isopropyl alcohol
H
H
C
C
H
C
OH
H
H
H
Propyl alcohol
(a) Structural isomers
(a) Structural isomers
(b) having the same covalent arrangements but
differ in spatial arrangements
H
H
H
H
H
H
H
cis
isomer:
The
two
Xs
areH trans
isomer:
TheHtwo Xs
H
C C
C
C
H
C C
C
C
on the same side.
are on opposite sides.
H
H
cis-butene
Cis–trans isomers
Molecule
H
H
H
trans-butene
Mirror image
(b) Enantiomers
Enantiomers
7
Dehydration (minus water) Synthesis and
Hydrolysis (water-split)
Water Removed
H2O
Monomers
HO
H
+
H
HO
H2O
HO
H2O
H
HO
HO
H
HO
H
HO
H
H
(a) Polymer formation by dehydration reactions
HO
HO
H
H2O
H
HO
HO
H
H
HO
H2O
H
HO
H
+
HO
H
H2 O
Water Added
(b) Breakdown of a polymer by hydrolysis reactions
8
Four major types of organic molecules
and macromolecules
1.
2.
3.
4.
Carbohydrates
Lipids
Proteins
Nucleic acids
9
Carbohydrates
Monosaccharides
Composed of carbon, hydrogen, and
oxygen atoms
Cn(H2O)n
Most of the carbon atoms in a
carbohydrate are linked to a hydrogen
atom and a hydroxyl group
10
6
5
HO
H
H
HO
H
H
H
1
2
3
4
5
6
H
C
C
OH
C
H
C
6
OH
C
OH
OH
H
D-glucose
(linear)
3
H
1
H
H
2
OH
-D-galactose
H
C
O OH
H
OH
4
O
CH2OH
6
CH2OH
5
O H
H
OH
4
HO
3
H
1
H
OH
2
OH
β-D-glucose
(ring)
H
6
CH2OH
5
O OH
H
OH
4
HO
3
H
1
H
H
H
2
H
OH
-D-glucose
5
HO O
1
2
OH
CH2OH
H
OH
H
4
HO
3
H
-L-glucose
Enantiomers
•Linear and ring structures
of -D-glucose
(b) Isomers of glucose
11
Disaccharides
Carbohydrates composed of two monosaccharides
Joined by dehydration or condensation reaction to form Glycosidic bond
Broken apart by hydrolysis
Examples − sucrose, maltose, lactose
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
CH2OH
CH2OH
O H
H
H
OH
H
HO
+
H
H
OH
O
HO
OH
H
OH
Glucose
OH
CH2OH
H
Fructose
12
CH2OH
CH2OH
O H
H
H
OH
H
HO
+
H
H
OH
O
HO
CH2OH
Glucose + Fructose
OH
H
OH
OH
Glucose
H
Fructose
CH2OH
O H
H
H
OH
H
H
OH
Glycosidic
bond
HO
O
CH2OH
H
H
OH
+
H2O
Sucrose + Water
O
HO
H
Sucrose
CH2OH
13
14
Lipids


Fats
Composed predominantly of hydrogen and
carbon atoms
Defining feature of lipids is that they are
nonpolar and therefore very insoluble in water




Also known as triglycerides or triacylglycerols
Formed by bonding glycerol to three fatty acids
Joined by dehydration or condensation reaction
Broken apart by hydrolysis
15
Fats: saturated vs. unsaturated fatty acid
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
HO
C CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2 CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2 CH2
CH2
CH2
CH2
CH3
Saturated fatty acid
(Stearic acid)
O
HO
C CH2
CH2
CH2 CH
CH
CH2
CH
CH
CH2
CH3
Unsaturated fatty acid
(Linoleic acid)
16
Phospholipids
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Charged
nitrogencontaining
region
CH3
N+
CH3
CH3
Hydrophilic
P head
CH2
CH2
Hydrophobic
FA tails
O
O
Phosphate
Glycerol
backbone
Ends of
fatty acids
Polar head
(hydrophilic)
O–
P
O
H2 C
H
C
O
O
C
O C
H2 C
CH2
H2 C
CH 2
O
CH2
H2 C
H2 C
CH 2
H2C
CH 2
H2C
CH 2
H2C
CH 2
H2C
CH 2
H2C
H3 C
Polar
heads
Schematic
drawing of a
phospholipid
CH 2
Nonpolar
tails
Membrane
bilayer
CH2
H2 C
CH2
H2 C
CH2
Nonpolar tail
(hydrophobic)
H2 C
Polar
heads
CH2
H2 C
Nonpolar
fatty acid
tails
CH2
H2 C
CH2
H3 C
Chemical
structure
Space-filling
model
(a) Structure and model of a phospholipid
Polar
heads
(b) Arrangement of phospholipids in a bilayer
17
Steroids


Four interconnected rings of carbon atoms
Usually not very water soluble
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
CH3
H3 C
CH3
CH2
CH
CH2
CH2
H
CH3
CH
CH3
3
HO


H
H
Cholesterol
All steroids come from a common precursor cholesterol
Tiny differences in chemical structure can lead to profoundly
different biological properties: Estrogen vs. testosterone
18
CH3
H3C
CH3
CH2
CH
CH2
CH3
CH
CH2
H
CH3
H
3
H
Cholesterol
HO
H3C
OH
H3C
OH
H
CH3
H
H
H
H
HO
H
O
Estrogen
Female cardinal
Testosterone
Male cardinal
b: © Adam Jones/Photo Researchers; c: © Adam Jones/Photo Researchers
19
Fig. 4-9
Functional groups are particular groupings of atoms
That give organic molecules unique properties
A-roid
Estradiol
Testosterone
Proteins : polymers of amino acids
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
R
H
H
N+
H
O
C
C
H
O–
-carbon
A typical amino acid
21
3.12 Proteins are made from amino acids linked by
peptide bonds
• Protein diversity is based on different arrangements of a
common set of 20 amino acid monomers
•
Each amino acid contains
A carboxyl group and an amino group
An R (variable)
group, which
distinguishes each
of the 20 different
amino acids
H
O
H
N
C
H
C
OH
R
Amino
-carbon
group
Figure 3.12A
Carboxyl (acid)
group
Nonpolar
Glycine
(Gly or G)
Alanine
(Ala or A)
Methionine
(Met or M)
Leucine
(Leu or L)
Valine
(Val or V)
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)
Peptide
bond
Side chains
(a)
Peptide
bond
Backbone
Amino end
(N-terminus)
(b)
Carboxyl end
(C-terminus)
Final Protein Product
Protein Structure
Primary Secondary
Tertiary Quaternary
25
Primary structure


Amino acid sequence
Determined by genes
Sequence alignment
Consensus key
* fully conserved residue
: conservation of strong groups
. conservation of weak groups
no consensus (blank)
INS_BOVIN MAL--WTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREV
INS_SHEEP MAL--WTRLVPLLALLALWAPAPAHAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREV
INS_PIG
MAL--WTRLLPLLALLALWAPAPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREA
INS_PANTR MAL--WMRLLPLLVLLALWGPDPASAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREA
INS_HUMAN MAL--WMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREA
INS_CHICK MAL--WIRSLPLLALLVFSGPGTSYAAANQHLCGSHLVEALYLVCGERGFFYSPKARRDV
:***..**:***:.** :**** *. :
INS_BOVIN EGPQVGALELAGGPG-----AGGL---EGPPQKRGIVEQCCASVCSLYQLENYCN
INS_SHEEP EGPQVGALELAGGPG-----AGGL---EGPPQKRGIVEQCCAGVCSLYQLENYCN
INS_PIG
ENPQAGAVELGGGLGG--LQALAL---EGPPQKRGIVEQCCTSICSLYQLENYCN
INS_PANTR EDLQVGQVELGGGPGAGSLQPLAL---EGSLQKRGIVEQCCTSICSLYQLENYCN
INS_HUMAN EDLQVGQVELGGGPGAGSLQPLAL---EGSLQKRGIVEQCCTSICSLYQLENYCN
INS_CHICK EQPLVSS-PLRGEAG--VLPFQQE---EYEKVKRGIVEQCCHNTCSLYQLENYCN
******
*.: :*:.***
26
Secondary & Tertiary Structure
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
NH3+
Chemical and physical
interactions cause
folding
O
CH2
C
O–
+
NH3
CH2
CH2
CH2
CH2
Repeating patterns
HC
COO–
CH3
CH2
CH3
CH2 OH
CH2
O
NH2 C CH2
CH2
CH2
α helices and β pleated sheets
Key determinants of a protein’s
characteristics
S
S
CH2
“Random coiled regions”
Not α helix or β
pleated sheet
Shape is specific
and important to
function
27
Tertiary structure
Folding gives complex three-dimensional shape
 Final level of structure for single polypeptide
chain

Green fluorescent protein (GFP)
Quaternary structure

Made up of 2 or more polypeptides
subunits – individual polypeptides
 Multimeric proteins – proteins with multiple parts
 Protein
28
Fig. 5-22
Normal hemoglobin
Primary
structure
Sickle-cell hemoglobin
Primary
structure
Val His Leu Thr Pro Glu Glu
1
2
3
Secondary
and tertiary
structures
4
5
6
7
subunit
Secondary
and tertiary
structures
Val His Leu Thr Pro Val Glu
1
2
3
Exposed
hydrophobic
region
Quaternary
structure
Normal
hemoglobin
(top view)
Quaternary
structure
Sickle-cell
hemoglobin
Function
Molecules do
not associate
with one
another; each
carries oxygen.
Function
Molecules
interact with
one another and
crystallize into
a fiber; capacity
to carry oxygen
is greatly reduced.
10 µm
Red blood
cell shape
Normal red blood
cells are full of
individual
hemoglobin
moledules, each
carrying oxygen.
4
5
6
7
subunit
10 µm
Red blood
cell shape
Fibers of abnormal
hemoglobin deform
red blood cell into
sickle shape.
5 factors promoting protein folding and
stability
1.
2.
3.
4.
5.
Hydrogen bonds
Ionic bonds and other polar interactions
Hydrophobic effects
Van der Waals forces
Disulfide bridges
30
Please note that due to differing
operating systems, some animations
will not appear until the presentation is
viewed in Presentation Mode (Slide
Show view). You may see blank slides
in the “Normal” or “Slide Sorter” views.
All animations will appear after viewing
in Presentation Mode and playing each
animation. Most animations will require
the latest version of the Flash Player,
which is available at
http://get.adobe.com/flashplayer.
31
Protein-protein interactions
32
Anfinsen Showed That the Primary Structure of
Ribonuclease Determines Its Three-Dimensional
Structure



Prior to the 1960s, the mechanisms by which proteins
assume their three-dimensional structures were not
understood.
Christian Anfinsen, however, postulated that proteins
contain all the information necessary to fold into their
proper conformation without the need for organelles
or cellular factors
He hypothesized that proteins spontaneously assume
their most stable conformation based on the laws of
chemistry and physics
HYPOTHESIS Within their amino acid sequence, proteins contain all the information needed to fold into their correct, 3-dimensional shapes.
KEY MATERIALS Purified ribonuclease, RNA, denaturing chemicals, size-exclusion columns.
Experimental level
1
Conceptual level
Incubate purified
ribonuclease in test tube
with RNA, and measure its
ability to degrade RNA.
Numerous H bonds
(not shown) and 4
S—S bonds. Protein
is properly folded.
S
S
S
Purified
ribonuclease
S
S S
S
S
2
-mercaptoethanol
+
Urea
Denature ribonuclease
by adding -mercaptoethanol
(breaks S—S bonds) and
urea (breaks H bonds and
ionic bonds). Measure its
ability to degrade RNA.
No more H bonds,
ionic bonds, or S—S
bonds. Protein is
unfolded.
SH
SH
SH
SH
SH
SH
Denatured
ribonuclease
SH
3
-mercaptoethanol
Mixture from
step 2 containing
denatured
ribonuclease,
-mercaptoethanol,
and urea
Layer mixture from step 2
atop a chromatography
column. Beads in the column
allow ribonuclease to escape,
while -mercaptoethanol and
urea are retained. Collect
ribonuclease in a test tube
and measure its ability to
degrade RNA.
Column containing
beads suspended
in a watery solution
Urea
Beads have
microscopic pores
that trap -mercaptoethanol and urea, but
not ribonuclease.
Denatured
ribonuclease
Collection port
with filter to prevent
beads from escaping
Solution of
ribonuclease
Renatured
ribonuclease
4
THE D ATA
5
100
Ribonuclease
function (%)
Activity restored
6
50
0
Purified
ribonuclease
(step 1)
Denatured
Ribonuclease
ribonuclease after column
(step 2)
chromatography
(step 3)
CONCLUSION Certain proteins, like ribonuclease, can
spontaneously fold into their final,
functional
shapes without assistance from other cellular
structures or factors. (Howeve r , as described in your text, this is not
true of many other proteins.)
SOURCE Habe r , E., and Anfinsen, C.B. 1961. Regeneration of
enzyme activity by air oxidation of reduced
subtilisin-modified ribonuclease.
Journal of
Biological Chemistry 236:422–424.
Proteins Contain Functional Domains Within Their
Structures
STAT
protein
HN3+
COO–
Nucleic Acids


Responsible for the storage, expression, and
transmission of genetic information
Two classes
 Deoxyribonucleic acid (DNA)
 Store genetic information coded in the sequence of their monomer
building blocks
 Ribonucleic acid (RNA)
 Involved in decoding this information into instructions for linking
together a specific sequence of amino acids to form a polypeptide
chain
36
Mononucleotide
Monomers linked into
polymer with a sugarphosphate backbone
Monomer is a nucleotide
Made up of phosphate
group, a five-carbon sugar
(either ribose or
deoxyribose), and a single
or double ring of carbon
and nitrogen atoms known
as a base
37
Bases
Backbone
Adenine
NH2
N
O
P
O–
N
H
O–
O
5
CH2
N
O
1
4
Phosphate H
H
H
3
N
Guanine
Sugar
O
H
P
O–
ATP has 3
phosphate
groups
N
H
N
O
O
H
N
2•
H
5
O CH 2
NH2
N
O
Cytosine
4
H
H
3
1
H
H
NH2
2
H
N
N
O
O
P
O–
O
5
CH2
O
4
H
H
3
1
H
2
H
CH3
Cyclic AMP
Has only one
phosphate
which is linked
to ribose in a
cyclic form.
Thymine
H
N
O
O
P
O–
O
5
CH2
4 H
H
3
OH
N
O
H
1
H
2
H
38
DNA vs. RNA
DNA
RNA
Deoxyribonucleic acid
Ribonucleic acid
Deoxyribose
Ribose
Thymine (T)
Uracil (U)
Adenine (A), guanine (G), cytosine (C)
used in both
2 strands- double helix
Single strand
Large
Small
Location to be found? Location to be found?
39
40
ETYMOLOGY OF KEY TERMS
enantioopposite; mirror image (from the Greek enantios- in
opposition)
-gen
that which produces (from the Greek genes- born or produced)
glycoof, or relating to, sugar (from the Greek glykys- sweet)
hydroof, or pertaining to, water (from the Greek hydor- water)
isoequal; same (from the Greek isos- equal)
macro- large; large enough to be seen with the naked eye (from the Greek
makros- long)
peptide compound containing two or more amino acids (modern derivative of
peptic and pepsin, which is from the Greek peptikos- conducive to digestion)
phobic
fear or aversion to (from the Greek phobos- fear or panic)
polymany (from the Greek polys- many)
stereoin three dimensions (from the Greek stereos- solid)
41
Biomolecules
Enzymes
_______
Structural
________
Transport
________
Functions
Sub-unit
Bond between
monomers
________
Protein
________
Structure
Primary
______
Place the letter in the appropriate
blank
a. Valine
b. Pro-Val-Ser-Thr
c. α-helix
d. DNA polymerase
e. Keratin
f. Hemoglobin
g. Peptide
h. Disulfide bonds
i. R-groups interactions
j. Hydrophobic exclusion
Secondary
________
Tertiary
Polar & non-polar
________
Cysteine
_______
_________