Transcript Slide 1

Lipids and Proteins
I.
Lipids
A. Fats
1. fatty acids
a. saturated
b. unsaturated
2. trans fats
B. Phosopholipids
C. Steroids
1. LDL
2. HDL
Lipids
Lipids are a diverse group of hydrophobic
molecules
 Lipids
– Are the one class of large biological
molecules that do not consist of
polymers
– Share the common trait of being
hydrophobic

Fats
– Are constructed from two types of smaller
molecules, a single glycerol and usually three
fatty acids
– Vary in the length and number and locations
of double bonds they contain
Fats
• Vary in the length and number and
locations of double bonds they
contain

Saturated fatty acids
– Have the maximum number of hydrogen
atoms possible
– Have no double bonds
Stearic acid
(a) Saturated fat and fatty acid
Figure 5.12

Unsaturated fatty acids
– Have one or more double bonds
– Mono-unsaturated or polyunsaturated
Oleic acid
Figure 5.12 (b) Unsaturated fat and fatty acid
cis double bond
causes bending

Monoacylglycerol

Diacyglycerol

Triacylglycerol
Ester
linkage
In unsaturated fatty acids, there are two
ways the pieces of the hydrocarbon tail
can be arranged around a C=C double
bond. In cis bonds, the two pieces of the
carbon chain on either side of the double
bond are either both “up” or both “down,”
such that both are on the same side of the
molecule. In trans bonds, the two pieces
of the molecule are on opposite sides of
the double bond, that is, one “up” and one
“down” across from each other
Naturally-occurring unsaturated vegetable
oils have almost all cis bonds, but using
oil for frying causes some of the cis bonds
to convert to trans bonds. If oil is used
only once like when you fry an egg, only a
few of the bonds do this so it’s not too
bad. However, if oil is constantly reused,
like in fast food French fry machines, more
and more of the cis bonds are changed
to trans until significant numbers of fatty
acids with trans bonds build up.
The reason this is of concern is that fatty
acids with trans bonds are carcinogenic,
or cancer-causing. The levels of trans fatty
acids in highly-processed, lipid-containing
products such as margarine are quite
high, and the government is considering
requiring that the amounts of trans fatty
acids in such products be listed on the
labels.

Phospholipids
– Have only two fatty acids
– Have a phosphate group instead of a
third fatty acid

Phospholipid structure
– Consists of a hydrophilic “head” and
hydrophobic “tails”
CH2
CH2
O
O
P
O–
+
N(CH3)3
Choline
Phosphate
O
CH2
CH
O
O
C
O C
CH2
Glycerol
O
Fatty acids
Hydrophilic
head
Hydrophobic
tails
Figure 5.13
(a) Structural formula
(b) Space-filling model
(c) Phospholipid
symbol

The structure of phospholipids
– Results in a bilayer arrangement found
in cell membranes
WATER
Hydrophilic
head
WATER
Hydrophobic
tail
Figure 5.14

Steroids
Steroids
– Are lipids characterized by a carbon skeleton
consisting of four fused rings
H 3C
CH3
CH3
Figure 5.15
HO
CH3
CH3

One steroid, cholesterol
– Is found in cell membranes
– Cholesterol is the precursor to our sex
hormones and Vitamin D. Vitamin D is
formed by the action of UV light in sunlight on
cholesterol molecules that have “risen” to
near the surface of the skin.
– Our bodies make about 2 g of cholesterol per
day, and that makes up about 85% of blood
cholesterol, while only about 15% comes from
dietary sources.
Lipoproteins are clusters of proteins and lipids
all tangled up together. These act as a means of
carrying lipids, including cholesterol, around in
our blood. Two main categories of lipoproteins
distinguished by how compact/dense they are.
1. LDL or low density lipoprotein is the “bad
guy,” being associated with deposition of
“cholesterol” on the walls of someone’s arteries.
2. HDL or high density lipoprotein is the
“good guy,” being associated with carrying
“cholesterol” out of the blood system, and is
more dense/more compact than LDL.
FYI only!!! An emulsifying agent is a
substance which is soluble in both oil and
water, thus enabling the two to mix. A
“famous” phospholipid is lecithin which is
found in egg yolk and soybeans. Egg yolk
is mostly water but has a lot of lipids,
especially cholesterol, which are needed
by the developing chick. Lecithin is used
to emulsify the lipids and hold them in
the water as an emulsion. Lecithin is the
basis of the classic emulsion known as
mayonnaise
Proteins
Proteins have many structures,
resulting in a wide range of
functions
 Proteins do most of the work in
cells and act as enzymes
 Proteins are made of monomers
called amino acids


5.1
An overview of protein functions

Enzymes
– Are a type of protein that acts as a catalyst,
speeding up chemical reactions
Active site is
available for
a molecule of
substrate, the
reactant on which the
enzyme acts.
2
1
Substrate
binds to
enzyme.
Substrate
(sucrose)
Enzyme
(sucrase)
Glucose
OH
H O
Fructose
Figure 5.16
H 2O
3 Substrate is converted
to products.
4 Products are
released.

Amino acids
– Are organic molecules possessing both
carboxyl and amino groups
– Differ in their properties due to differing
side chains, called R groups
Twenty Amino Acids

20 different amino acids make up proteins
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
H
Glycine (Gly)
O–
C
H3N
C
H
+
O–
C
CH2
CH2
O
H 3N
C
H
Valine (Val)
Alanine (Ala)
CH
CH3
CH3
O
CH3
CH3
C
+
O–
O
C
H
Leucine (Leu)
H3C
H3N
+
O–
CH
C
O
C
H
Isoleucine (Ile)
O–
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
H3N+
C
O–
Methionine (Met)
Figure 5.17
CH2
O
C
H
CH2
O
C
O–
Phenylalanine (Phe)
H3N+
C
H
O
C
H2C
CH2
H2
N
C
O
C
H
O–
Tryptophan (Trp)
Proline (Pro)
O–
OH
OH
Polar
H3N
+
CH2
C
O
C
H
CH
H3N
O–
Serine (Ser)
C
+
O
C
H3N
O–
H
+
CH2
C
H
O
C
CH2
H3N
O–
C
+
O
C
H
Electrically
charged
H3N
+
C
+
O–
O–
O
NH3+
NH2
C
CH2
C
CH2
CH2
CH2
CH2
CH2
CH2
O
H
O–
H3N
+
CH2
C
O
C
H
O–
H3N
+
CH2
C
H
Aspartic acid
(Asp)
O–
+
CH2
C
O
C
H
O–
Glutamine
(Gln)
Asparagine
(Asn)
C
C
C
H3N
Basic
O
C
CH2
O
H
Acidic
–O
CH2
H3N
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
NH2 O
Glutamic acid
(Glu)
O–
Lysine (Lys)
NH2+
H3N
+
CH2
O
C
NH+
H3N
+
CH2
C
H
NH
CH2
O
C C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
Amino Acid Polymers

Amino acids
– Are linked by peptide bonds
Polypeptides

Polypeptides
– Are polymers (chains) of amino acids

A protein
– Consists of one or more polypeptides
Protein Conformation and
Function

A protein’s specific conformation (shape)
determines how it functions
Four Levels of Protein Structure

Primary structure
+H
– Is the unique
sequence of amino
acids in a polypeptide
3N
Amino
end
Amino
acid
subunits
Gly ProThrGly
Thr
Gly
Glu
Cys LysSeu
LeuPro
Met
Val
Lys
Val
Leu
Asp
AlaVal ArgGly
Ser
Pro
Ala
Glu Lle
Leu Ala
Gly
Asp
Thr
Lys
Ser
Lys TrpTyr
lle
Ser
Pro Phe
His Glu
AlaThrPhe Val
Asn
His
Ala
Glu
Val
Thr
Asp
Tyr
Arg
Ser
Arg
Gly Pro
lle
Ala
Ala
Leu
Leu
Ser
Pro
SerTyr
Tyr
Ser
Thr
Thr
Ala
Val
Val
Glu
Thr Pro Lys
Asn
Figure 5.20
c
o
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
Amino acid
subunits
O H H
C C N
C N
H
R
R
O
C
C
R
N H
C
H
R
O C
O C
N H
N H
N H
O C
O C
H
H C R H C R
H C R
C
R
N H O C
N H
O C
O C
H
C
O
N H
N
C
C
H
R
H
R
Figure 5.20
C
R
O H H
C C N
C C N
O H H
R
R
O H H
C C N
C C N
OH H
R
O
O
C
H
H
C
H
N HC N H C N H C N
C
H
H
C
O
C
O
R
R
H
 helix
R
R
O H H
C C N
C C N
OH H
R
O
C
H
H
NH C N
C
H
O C
R
R
C C
O
R
H
C
N HC N
H
O C

Tertiary structure
– Is the overall three-dimensional shape of a
polypeptide
– Results from interactions between amino
acids and R groups
Hydrogen
bond
CH22
CH
O
H
O
H 3C
CH
CH3
H 3C
CH3
CH
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
HO C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+-O C CH2
Ionic bond

Quaternary structure
– Is the overall protein structure that results
from the aggregation of two or more
polypeptide subunits
Polypeptide
chain
Collagen
 Chains
Iron
Heme
 Chains
Hemoglobin
Review of Protein Structure
+H
3N
Amino end
Amino acid
subunits
helix
Sickle-Cell Disease: A Simple
Change in Primary Structure

Sickle-cell disease
– Results from a single amino acid
substitution in the protein
hemoglobin
Primary
structure
Normal hemoglobin
Val
His Leu Thr Pro Glul Glu
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Red blood
cell shape
Figure 5.21
Val
His
Leu Thr Pro


Molecules do
not associate
with one
another, each
carries oxygen.
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen


Val
Glu
structure 1 2 3 4 5 6 7
Secondary
 subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Function
Sickle-cell hemoglobin
. . . Primary
Quaternary
structure
Function
10 m
...
Exposed
hydrophobic
region
 subunit




10 m
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity
to carry oxygen
is greatly
reduced.
Red blood
cell shape
Fibers of
abnormal
hemoglobin
deform cell into
sickle shape.
What Determines Protein
Conformation?
Protein conformation Depends on
the physical and chemical
conditions of the protein’s
environment
 Temperature, pH, etc. affect
protein structure

•Denaturation is when a protein
unravels and loses its native
conformation
(shape)
Denaturation
Normal protein
Figure 5.22
Denatured protein
Renaturation
The Protein-Folding Problem

Most proteins
– Probably go through several
intermediate states on their way to a
stable conformation
– Denaturated proteins no longer work in
their unfolded condition
– Proteins may be denaturated by
extreme changes in pH, temperature,
salinity or heavy metals

Chaperonins
– Are protein molecules that assist in the proper
folding of other proteins
Cap
Polypeptide
Correctly
folded
protein
Hollow
cylinder
Steps of Chaperonin
Chaperonin
(fully assembled) Action:
An unfolded poly1
peptide enters the
cylinder from one
Figure 5.23
end.
The cap attaches, causing
The cap comes
3
the cylinder to change shape off, and the
in
properly
such a way that it creates a
folded protein is
hydrophilic environment for
released.
the folding of the polypeptide.
2
Prions
Prions are slow-acting, virtually
indestructible infectious proteins that
cause brain diseases in mammals
 Prions propagate by converting normal
proteins into the prion version
 Scrapie in sheep, mad cow disease, and
Creutzfeldt-Jakob disease in humans are
all caused by prions

What happens if a protein
isn’t folded correctly?
Prions are formed – misfolded
versions of normal proteins

X-ray crystallography
– Is used to determine a protein’s threedimensional structure
X-ray
Photographic
film
Diffracted
X-
rays
X-ray
source
diffraction
pattern
X-ray
beam
Crystal Nucleic acid Protein
Figure 5.24
(b) 3D computer model
(a) X-ray diffraction pattern
Nucleic Acids
Nucleic acids store and transmit
hereditary information
 Genes

– Are the units of inheritance
– Program the amino acid sequence of
polypeptides
– Are made of nucleotide sequences on
DNA
The Roles of Nucleic Acids

There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
Deoxyribonucleic Acid

DNA
– Stores information for the synthesis of
specific proteins
– Found in the nucleus of cells
DNA Functions
– Directs RNA synthesis (transcription)
– Directs protein synthesis through RNA
DNA
(translation)
1 Synthesis of
mRNA in the nucleus
NUCLEUS
2 Movement of
mRNA into cytoplasm
via nuclear pore
mRNA
CYTOPLASM
mRNA
Ribosome
3 Synthesis
of protein
Figure 5.25
Polypeptide
Amino
acids
The Structure of Nucleic Acids

5’ end
Nucleic acids
– Exist as polymers called
polynucleotides
5’C
O
3’C
O
O
5’C
O
3’C
(a) Polynucleotide,
or nucleic acid
Figure 5.26
OH
3’ end

Each polynucleotide
– Consists of monomers called nucleotides
– Sugar + phosphate + nitrogen base
Nucleoside
Nitrogenous
base
O

O
P
5’C
O
CH2
O
O
Phosphate
group
Figure 5.26
(b) Nucleotide
3’C
Pentose
sugar
Nucleotide Monomers

Nucleotide monomers
Nitrogenous bases
Pyrimidines
NH2
O
O
C
C
CH
C
3
N
CH
C
CH HN
HN
CH
C
CH
C
C
CH
N
N
O
N
O
O
H
H
H
Cytosine Thymine (in DNA)Uracil
(in RNA)
RNA)
Uracil (in
U
C
U
T
– Are made up of
nucleosides (sugar +
base) and phosphate
groups
Purines
O
NH2
N C C
N C C
NH
N
HC
HC
C
CH
N C
N
NH2
N
N
H
H
Adenine
Guanine
A
G
5”
Pentose sugars
HOCH2 O
4’
OH
H H
1’
5”
HOCH2 O OH
4’
H H
1’
H
H
H 3’ 2’ H
3’ 2’
OH H
OH OH
Deoxyribose (in DNA) Ribose (in RNA)
Figure 5.26
(c) Nucleoside components
Nucleotide Polymers

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
Gene

The sequence of bases along a nucleotide
polymer
– Is unique for each gene
The DNA Double Helix

Cellular DNA molecules
– Have two polynucleotides that spiral around
an imaginary axis
– Form a double helix

The DNA double helix
– Consists of two antiparallel nucleotide strands
5’ end
3’ end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
A
3’
end
Nucleotide
about to be
added to a
new strand
5’ end
3’ end
Figure 5.27
5’ end
New
strands
3’ end
A,T,C,G

The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary
fashion (A with T only, and C with G only)
DNA and Proteins as Tape
Measures of Evolution

Molecular comparisons
– Help biologists sort out the
evolutionary connections among
species
The Theme of Emergent Properties
in the Chemistry of Life: A Review

Higher levels of organization
– Result in the emergence of new
properties

Organization
– Is the key to the chemistry of life