Chemistry 3

 Overview: The Molecules of Life
 Another level in the hierarchy of biological organization is
reached when small organic molecules are joined together
 Macromolecules
 Are large molecules composed of smaller molecules
 Are complex in their structures
 Include proteins, carboydrates, lipids, and nucleic acids like
DNA

Three of the classes of life’s organic
molecules are polymers
 Carbohydrates
 Proteins
 Nucleic acids

A polymer
 Is a long molecule consisting of many similar
building blocks called monomers

 Monomers form larger molecules by condensation
reactions also called dehydration reactions
Short polymer
Unlinked monomer

HO 1 2 3 OH HO H

Dehydration removes a water
molecule, forming a new bond H2O

HO 1 2 3 4 H

Longer polymer
(a) Dehydration reaction in the synthesis of a polymer

 Polymers can disassemble by
 Hydrolysis (also called digestion)

HO 1 2 3 4 H

Hydrolysis adds a water H2O
molecule, breaking a bond

HO 1 2 3 OH HO H

(b) Hydrolysis of a polymer

 Each class of polymer
 Is formed from a specific set of monomers
 All living organisms are composed of the same
types of polymers made up of the same monomer
types – proteins, carbohydrates and nucleic acids.
 However, each organism is composed of many
unique polymers (unique proteins, carbohydrates
and nucleic acids) based on the arrangement of
monomers
 An immense variety of polymers can be built from a
small set of monomers

 Carbohydrates
 Include both simple sugars and their polymers
 Monosaccharides (simple sugars)
 Are the simplest sugars
 Can be used for fuel - glucose
 Can be converted into other organic molecules
 Nucleotides include a 5 carbon sugar, ribose or deoxyribose
 Can be combined into polymers

 Examples of monosaccharides
Triose sugars Pentose sugars Hexose sugars
(C3H6O3) (C5H10O5) (C6H12O6)
H O H O H O H O
C C C C
H C OH H C OH H C OH H C OH

Aldoses
H C OH H C OH HO C H HO C H
H H C OH H C OH HO C H
H C OH H C OH H C OH
Glyceraldehyde
H H C OH H C OH
Ribose H H
Glucose Galactose

H H H
H C OH H C OH H C OH
C O C O C O
Ketoses

H C OH H C OH HO C H

H H C OH H C OH
Dihydroxyacetone H C OH H C OH

H H C OH
Ribulose H
Fructose

 Monosaccharides
Notice the carbons
 May be linear are numbered and
 Can form rings this numbering
system remains
when they form a ring
in water.
H C O 6CH OH
1 6CH OH
2 2
CH2OH
H 2C OH 5C H 5C
O O 6
H H H H H O
HO 3C H 5 H
4C H 1C 4C H 1C H
OH OH 4 OH 1
4 H H
H C OH O HO 3 2 OH
5 OH 2C OH 3C 2C OH
H C OH
3 C
H OH
6 H OH H OH
H C OH

H

(a) Linear and ring forms. Chemical equilibrium between the linear and ring
structures greatly favors the formation of rings. To form the glucose ring,
carbon 1 bonds to the oxygen attached to carbon 5.

(a) Dehydration reaction
in the synthesis of
maltose. The bonding CH2OH CH2OH CH2OH CH2OH
of two glucose units O O O O
forms maltose. The H H H H H H 1–4 H H
H H H 1 glycosidic 4 H
glycosidic link joins
OH H OH H OH H linkage OH H
the number 1 carbon OH HO OHOH
of one glucose to the HO HO O OH
number 4 carbon of
the second glucose. H OH H OH H OH H OH
Joining the glucose H2O
monomers in a Glucose Maltose
Glucose
different way would
result in a different
disaccharide.
CH2OH CH2OH
CH2OH CH2OH
H O O H O H 1–2 O
H H H
H H 1 glycosidic 2
(b) Dehydration reaction OH H H HO OH H linkage H HO
OH HO
in the synthesis of HO CH2OH HO O CH2OH
sucrose. Sucrose is
a disaccharide formed H OH OH H H OH OH H
from glucose and fructose.
Notice that fructose,
H2O
though a hexose like Glucose Fructose Sucrose
glucose, forms a
five-sided ring.
In living systems, these reactions Notice that the chemical
are always done by enzymes. reactions take place at
Cellular enzymes are controlled the functional groups

 Polysaccharides
 Are polymers of sugars
 Serve many roles in organisms
 Storage
 Starch is a polymer of glucose only
 Glycogen is also a polymer of glucose
 Cell wall - structure
 Cellulose is a polymer of glucose
 Chitin

Chloroplast Starch

 Is the major storage
form of glucose in
plants

1 m

Amylose Amylopectin

(a) Starch: a plant polysaccharide

 Glycogen
 Consists of glucose monomers
 Is the major storage form of glucose in animals

Mitochondria Glycogen
granules

0.5 m

Glycogen

(b) Glycogen: an animal polysaccharide

H O
CH2O C CH2O
H H
O H C OH H O OH
H H
H H
4
OH H HO C H 4 1
OH H
HO OH HO H
H C OH

Which type of bond H OH
H C OH
H OH

glucose H C OH glucose

depends on the
(a) and glucose ring structures
enzyme CH2O CH2O CH2O CH2O
H H H H
O O O O
which is controlled by OH
1
O
4
OH
1
O
4
OH
1
O
4
OH
1
O
HO
the cell. OH OH OH OH
(b) Starch: 1– 4 linkage of glucose monomers
CH2O CH2O
OH OH
H H
O O
O OH O OH
OH 1 4 O OH
HO OH
O O
CH2O CH2O
OH OH
H H
(c) Cellulose: 1– 4 linkage of glucose monomers

 Is a major component of the tough walls that enclose
plant cells
About 80 cellulose
molecules associate
to form a microfibril, the
Cellulose microfibrils main architectural unit
in a plant cell wall Microfibril the plant cell wall.
of
Cell walls

0.5 m

Plant cells

CH2OH OH CH2OH OH
O O O O
OH OH OH OH
O O O O O
O CH OH OH CH2OH
H
2 Cellulose
CH2OH OH CH2OH OH molecules
O O O O
OH OH OH OH
Parallel cellulose molecules are O O O O O
O CH OH OH CH2OH
held together by hydrogen H
2

bonds between hydroxyl CH2OH OH CH2OH OH
O O O O
groups attached to carbon OH OH
O OH O O
OH O
atoms 3 and 6. O CH OH O A cellulose molecule
OH CH2OH
H
2
is an unbranched
Figure 5.8 Glucose glucose polymer.
monomer

 Cellulose is difficult to digest
 Cows have microbes in their stomachs to facilitate this
process

What do these microbes
have that will allow them to
break down cellulose?

 Chitin, another important structural polysaccharide
 Is found in the exoskeleton of arthropods
 Can be used as surgical thread

CH2O
H
H O OH
H
OH H
OH H
H NH
C O
CH3

(a) The structure of the (b) Chitin forms the exoskeleton (c) Chitin is used to make a
chitin monomer. of arthropods. This cicada strong and flexible surgical
is molting, shedding its old thread that decomposes after
exoskeleton and emerging the wound or incision heals.
in adult form.

 Lipids
 Are the one class of large biological molecules that do
not consist of polymers
 Share the common trait of being hydrophobic
 Include
 Fats
 Phospholipids
 steroids

H H H H H H H H
O H H H H H H H H
H C OH C C C C C C C C H
C C C C C C C C
HO
H H H H H H H
H H H H H H H H
H C OH
Fatty acid
H C OH (palmitic acid)
H Again, notice where the
Glycerol
(a) Dehydration reaction in the synthesis of a fat chemical reaction takes
Ester linkage place.
H O H H H H H H H
H H H H H H H H
H C O C C C C C C C C H
C C C C C C C C
H H H H H H H
H H H H H H H H
O H H H H H H H
H H H H H H H H
C C C C C C C C
H H H H H H H
H H H H H H H H

O H H H H H H H
H H H H H H H H
C C C C C C C C
H H H H H H H H
H H H H H H H H

(b) Fat molecule (triacylglycerol)

Saturated fatty acids
 Have the maximum number of hydrogen atoms possible (saturated with hydrogen)
 Have no double bonds

Stearic acid

(a) Saturated fat and fatty acid
Oleic acid

•Unsaturated fatty acids
--Have one or more double
(b) Unsaturated fat and fatty acid
cis double bond
bonds
causes bending

A single bond allows
rotation, is longer and
not a strong as a
double bond

A double bond is
stronger, shorter, and
more rigid.

Bonds help to
determine the 3-D
shape of a molecule.

 Consists of a hydrophilic “head” and
hydrophobic “tails”

CH2 + )
N(CH
3 3 Choline
CH2
O
O P O–
Phosphate
O
CH2 CH CH2
Glycerol
O O
C O C O

Fatty acids

Hydrophilic
head
Hydrophobic
tails

(c) Phospholipid
(a) Structural formula (b) Space-filling model
symbol

 The structure of phospholipids
 Results in a bilayer arrangement found in cell
membranes

WATER
Hydrophilic
head

WATER
Hydrophobic
tail

 One steroid, cholesterol
 Is found in cell membranes
 Is a precursor for some hormones
H3C CH3
When written as a
CH3
ring, all points are CH3

carbon unless
CH3
written in
otherwise. Is this molecule polar or
nonpolar?
HO

Cholesterol fills in the spaces left by the kinks; stiffens the bilayer and
makes it less fluid and less permeable.

How do you think bacteria,
Do concept which do not use cholesterol,
check 5.3 adjust the fluidity of their cell
membrane?

Both saturated and trans
fats correlate with heart
problems and high levels
or blood cholesterol.
Atherosclerosis
Animal fats found in meat, butter, and cream are usually
saturated, and solid at room temperature.
Plant oils like corn oil contain more unsaturated fatty
acids.
Peanut and olive oil contain monounsaturated fatty
acids.

 Enzymes
 Are often a type of protein that acts as a
catalyst, speeding up chemical reactions

1 Active site is available for 2 Substrate binds to
a molecule of substrate, the enzyme.
Substrate
reactant on which the enzyme acts. (sucrose)

Is this part of the
protein polar or
nonpolar? Glucose
Enzyme
OH (sucrase)
H2O
Fructose

Enzyme remains H O

unchanged, ready
to work again.
4 Products are released. 3 Substrate is converted
to products.

 Polypeptides
 Are polymers of amino acids
 A protein
 Can consist of only one large polypeptide
 Can consists of more than one polypeptides (subunits)
bound together by non-covalent interactions
 Hemoglobin
 Some very small polypeptides are referred to as peptides
 Amino acids
 Are organic molecules possessing both carboxyl and amino
groups
 Differ in their properties due to differing side chains, called
R groups

Proteins are composed of
amino acid building blocks
and are diverse in structure
(shape) and function.
Amino acids have an amino
group and an acid group
bound to a central carbon.
This central carbon forms 4
Amino single bonds. One with the
Acid group
group amino group, one with the
carboxylic acid, one with
hydrogen, and the last with a
variety of different chemical
groups (R group).

 20 different amino acids make up proteins

CH3
CH3 CH3

CH3 CH3 CH CH2
H CH3 CH3 CH2 H3C CH
O O O O O
H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C
O– O– O– O– O–
H H H H H
Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)
Nonpolar

CH3
CH2
S
H2C CH2
NH O
CH2
H2 N C C
CH2 O CH2 CH2 O–
O O H
H3N+ C C H3N+ C C H3N+ C C
O– O– O–
H H H
Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro)

Know the structure of an amino acid, not all the R groups.

OH NH2 O
NH2 O C
OH SH C CH2
Polar OH CH3
CH2 CH CH2 CH2 CH2 O CH2
O O O O O
H3N+ C C H3N+ C C H3N+ C C H3 N+ C C H3N+ C C H3 N+ C C
O– O– O– O– O– O–
H H H H H H
Cysteine Tyrosine Asparagine Glutamine
Serine (Ser) Threonine (Thr) (Gln)
(Cys) (Tyr) (Asn)

Acidic Basic

NH3+ NH2 NH+
–O O O– O
C C CH2 C NH2+
NH
Electrically CH2
CH2 O CH2 CH2 CH2
charged O
H3N+ C C CH2 CH2 CH2 H3 N+ C C
O
O– CH2 O–
H3N+ C C O CH2 H
H
O–
H H3N+ C C CH2 O
O–
H H3N+ C C
O–
H
Aspartic acid Glutamic acid Lysine (Lys) Arginine (Arg) Histidine (His)
(Asp) (Glu)

Know both the name and abbreviation of all amino acids along
with their chemical nature – polar, nonpolar, charged, acidic, . . .

The formation of a peptide bonds in a tetrapeptide

 Amino acids
 Are linked by peptide bonds between the amino group of
one amino acid and the acid group of the other amino acid

OH
Peptide
bond
OH SH Each peptide
CH2 CH2 CH 2 bond is in a
H H H
The chemical H
N
C C N C C OH H N C C OH plane. This
reaction again takes H O H O contributes to
H O DESMOSOMES

place at the (a) HO
2 the shape of
functional groups! OH
the protein.
DESMOSOMES
DESMOSOMES Side
OH SH
Peptide chains
CH2 CH2 bond CH2
H H H
H N C C N C C N C C OH Backbone
H O H O H O

Amino end Carboxyl end
(b) (N-terminus) (C-terminus)

 Two models of protein
conformation Groove

(a) A ribbon model

A protein’s specific
conformation (shape
and chemical nature)
Groove

determines how it
functions.
(b) A space-filling model

 Primary structure
 Is the unique sequence of amino acids in a
polypeptide +
HN 3
Gly ProThr Gly
Thr
Gly Amino acid
Amino LeuPro
Cys LysSeu
Glu
subunits
end Met
Val

Covalent bonds
Lys
Val
Leu
Asp
AlaVal Arg Gly
Ser
Pro
Ala

Peptide backbone
imposes some Glu Lle
Asp
Thr
Lys

restrictions on the Gly
lle
Leu Ala
Lys Trp Tyr
Ser

folding of a protein.
Ser
ProPhe
His Glu
His
Ala
Glu
Val
Ala Thr PheVal

Why?
Asn
lle
Thr
Asp Tyr Ala
Arg
Ser Arg Ala
Gly Pro
Leu
Leu
Ser
Pro
SerTyr
Tyr
ThrSer
Thr
Ala
Val o
Val LysGlu c
Thr
AsnPro o–
Carboxyl end

 Secondary structure
 Is the folding or coiling of the polypeptide into a
repeating configuration
 Includes the helix and the pleated sheet

pleated sheet O H H O H H O H H O H H
R R R
Amino acid C C N C C N C C N C C N
C N C C N C C N C C N C C
subunits R R R R
H O H H OH H OH H O

R R R R
O C O O C O H
C H H H C
H C N HC H H
C N HC N N C NH C N C N HC N
helix C H
O C H O C H O C H
O C
R R R
R H R H
C C
H
N O C
N H
N H O C
All based on hydrogen
N H
O C
H C R H C
O C
H C R H C R bonds between the
R
N H O C N H
O C peptide bonds of
O C N H O C N H
R
C
H R
C
H
different amino acids

 Tertiary structure
 Is the overall three-dimensional shape of a
polypeptide after it “folds” into a stable form.
 Results from interactions between amino acids
and R groups
Hydrophobic
interactions and
van der Waals
What are CH
CH22 CH
interactions
H3C CH3
these? Hydrogen
O
H H3C CH3 Polypeptide
bond O CH backbone
HO C
CH2 CH2 S S CH2
Disulfide bridge
O
CH2 NH3+ -O C CH2
Ionic bond

The distribution of polar and nonpolar amino acids is important
in how a protein folds. The nonpolar side chains tend to
cluster in the interior of a molecule, avoiding contact with
water, while the polar side chains arrange themselves near the
outside.

Hydrophobic areas also tend to be found spanning the
lipid bilayer of membranes like the plasma membrane.

Transmembrane proteins often cross the membrane in an alpha
helix because the peptide bond itself is hydrophic unless all
partial charges are equalized in an alpha helix or beta sheet.

Is the overall protein
structure that results
from the aggregation
of two or more
polypeptide subunits

Hemoglobin contains
two alpha globin subunits and
two beta globin subunits.

There are
many
Heme is the large
site where multi-
oxygen is subunit
carried proteins in
cells.

Larger protein molecules may contain more than one
polypeptide chain or subunit. The region that interacts with
another molecule through
noncovalent bonds is the
binding site.

Normal β Sickle-cell β
Primary hemoglobin Primary Val hemoglobin Glu . . .
Val His Leu Thr Pro Glul Glu . . . His Leu Thr Pro Val Exposed
structure 1 2 3 4 5 6 7 structure 1 2 3 4 5 6 7 hydrophobic
region
Secondary Secondary
and tertiary subunit and tertiary subunit
structures structures

Quaternary Hemoglobin A Quaternary
structure structure Hemoglobin S

Function Molecules
interact with
Function Molecules do one another to
not associate crystallize into a
with one fiber, capacity to
another, each carry oxygen is
carries oxygen. 10 m 10 m greatly reduced.
Red blood Normal cells are
Red blood
cell shape full of individual
cell shape
hemoglobin Fibers of abnormal
molecules, each hemoglobin
carrying oxygen deform cell into
Figure 5.21 sickle shape.
The sickle-cell hemoglobin does not fold into the proper
shape because the amino acid sequence (Primary structure) is incorrect.

 Depends on
 the sequence of amino acid side chains (with R groups) and
 the physical and chemical conditions of the protein’s environment
 Denaturation is when a protein unravels and loses its native
conformation
Increased temperature

Denaturation Change in pH
What kinds of bonds are Organic solvent (hydrophobic)
broken here?

Normal protein Denatured protein

What kinds of bonds are not
Renaturation
broken here?

 Most proteins
 Probably go through several intermediate states on
their way to a stable conformation.
 Many proteins are being made in the cell all of the
time. How do the fold correctly, how do they interact
with their subunits correctly?

 Chaperonins
 Are protein molecules that assist in the proper folding
of other proteins

Correctly
folded
Polypeptide
protein
Cap

Hollow
cylinder

Chaperonin Steps of Chaperonin 2 The cap attaches, causing 3 The cap comes
(fully assembled) Action: the cylinder to change shape in off, and the properly
1 An unfolded poly- such a way that it creates a folded protein is
peptide enters the hydrophilic environment for the released.
cylinder from one end. folding of the polypeptide.

 X-ray crystallography
 Is used to determine a protein’s three-dimensional
structure
X-ray
diffraction
pattern
Photographic film
Diffracted X-rays
X-ray X-ray
source beam

Crystal Nucleic acid Protein
Do concept
check 5.4

Figure 5.24 (a) X-ray diffraction pattern (b) 3D computer model

 Genes
 Are the units of inheritance
 Code for the amino acid sequence of polypeptides
 Are made of nucleic acids
 There are two types of nucleic acids
 Deoxyribonucleic acid (DNA)
 Ribonucleic acid (RNA)

 Stores information for the synthesis of specific proteins –
DNA

DNA is the “ genetic material” inherited from parents
1
 Directs RNA synthesis Synthesis of
mRNA in the nucleus mRNA
 Directs protein synthesis
indirectly NUCLEUS through messenger

RNA CYTOPLASM

2 Movement of mRNA
mRNA into cytoplasm
via nuclear pore Ribosome

3
Synthesis
of protein

Amino
Polypeptide acids

 Nucleic acids
5’ end  Exist as polymers called polynucleotides
 Each polynucleotide
5’C O
 Consists of monomers called
3’C
nucleotides
O

Nucleoside

O Nitrogenous
base

O 5’C
5’C O P O CH2
O O
O
3’C
Phosphate
3’ end group
3’C
Pentose
OH
sugar
(a) Polynucleotide,
or nucleic acid (b) Nucleotide

 Are made up of nucleosides and phosphate
groups pyrimidines
Nitrogenous bases
Pyrimidines
NH2 O O
C C CH3 C
N CH HN C HN CH
C CH C CH C CH
O N O N O N
H H H
Cytosine Thymine (in DNA) Uracil (in RNA)
Uracil (in RNA)
Nucleoside C T U
U

Nitrogenous Purines
base NH2 O
N CC N C C
N NH
HC HC
O 5’C N C CH N C
NH2
N N
H H
O P O CH2 Adenine Guanine
O
A G
O
Phosphate Pentose sugars
3’C 5” 5”
group Pentose HOCH2 O OH HOCH2 O OH
sugar 4’ H H 1’ H H 1’
4’
H 3’ 2’ H H H
3’ 2’
(b) Nucleotide OH H OH OH
Deoxyribose (in DNA) Ribose (in RNA)

Figure 5.26 (c) Nucleoside components

Nucleotide polymers
are made up of
nucleotides linked
by the–OH group
on the 3´ carbon of
one nucleotide and
the phosphate on
the 5´ carbon on
the next
So they “grow” at
the 3’ end.

 The sequence of
bases along a
nucleotide
polymer
 Is unique for
each gene

The DNA Double Helix

Anti-parallel

complementary

Complementary base pairs

Do concept
check 5.5

 Molecular comparisons
 Help biologists sort out the evolutionary connections
among species
 Ribosomal RNA gene sequence is conserved.
 Look for differences.

Chemistry 3

Recommandé

Recommandé

Contenu connexe

Tendances

Tendances (18)

En vedette

En vedette (6)

Similaire à Chemistry 3

Similaire à Chemistry 3 (20)

Plus de Blaschke's Class

Plus de Blaschke's Class (9)

Dernier

Dernier (20)

Chemistry 3