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BSC 2010 - Exam I Lectures and Text Pages
• I. Intro to Biology (2-29)
• II. Chemistry of Life
–
Chemistry review (30-46)
–
Water (47-57)
–
Carbon (58-67)
–
Macromolecules (68-91) continued…proteins and nucleic acids
• III. Cells and Membranes
–
Cell structure (92-123)
–
Membranes (124-140)
• IV. Introductory Biochemistry
–
Energy and Metabolism (141-159)
–
Cellular Respiration (160-180)
–
Photosynthesis (181-200)
Proteins
• Proteins have many structures, resulting in a
wide range of functions
– Proteins
• Have many roles inside the cell
• Make up 50% of the dry weight (after
removal of water) of cells.
• Have amino acids as their monomer
Proteins have many functions in the cell.
Table 5.1
1
Enzymes – Structure is Important to Function
• Enzymes
– Are a type of protein that acts as a catalyst,
speeding up chemical reactions
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
2 Substrate binds to
enzyme.
Glucose
OH
Enzyme
(sucrase)
H2O
Fructose
H O
4 Products are released.
Figure 5.16
3 Substrate is converted
to products.
Polypeptides
• Polypeptides
– Are polymers of amino acids
• A protein
– Consists of one or more polypeptides
Amino Acid Monomers
• Amino acids
– Are organic molecules possessing both
carboxyl and amino groups
– Differ in their properties due to differing side
chains, called R groups (can be polar,
nonpolar, or charged)
2
• 20 different amino acids make up proteins
H
H3N+
CH3
O
H3N+
C
C
O–
H
Glycine (Gly)
H3N+
C
H
Alanine (Ala)
CH
CH3
CH3
O
C
O–
C
CH2
CH2
O
H3N+
C
O–
H
Valine (Val)
CH3
CH3
CH3
CH3
H3C
O
C
CH
H3N+
C
H
Leucine (Leu)
C
O
C
O–
O–
H
Isoleucine (Ile)
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
CH2
O
C
H3N+
C
H3N+
C
C
O–
H
CH2
O
C
O
C
O–
H
C
O–
H
Phenylalanine (Phe)
Methionine (Met)
C
CH2
O
O–
H
H2C
H2N
Proline (Pro)
Tryptophan (Trp)
Figure 5.17
OH
OH
Polar
CH2
H3N+
C
CH
O
H3N+
C
O–
H
Serine (Ser)
C
CH2
O
H3N+
C
O–
H
NH2 O
C
CH2
O
C
O–
H
H3N+
C
CH2
O
H3N+
C
C
O–
H
CH2
H3N+
C
O
NH2
CH2
C
CH2
CH2
CH2
O
CH2
C
O–
H3N+
H
C
CH2
O
O
C
O–
H
Glutamine
(Gln)
O–
H3N+
C
H3N+
CH2
O
C
O–
H
CH2
H3N+
C
H
Lysine (Lys)
Glutamic acid
(Glu)
NH+
NH2+
CH2
CH2
C
H
Aspartic acid
(Asp)
O–
C
Basic
NH3+
C
O–
O
C
Electrically
charged
CH2
H3N+
C
Asparagine
(Asn)
Acidic
–O
CH2
O
H
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
NH
CH2
O
C C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
Peptide
bond
OH
OH
SH
CH2
CH2
H
N
H
CH2
H
C C
H
N C C OH H N C
H O
H O
H
(a)
C OH
O DESMOSOMES
H2O
OH
DESMOSOMES
DESMOSOMES
SH
Peptide
CH2 bond CH2
OH
CH2
H
H N C C
H O
Figure 5.18
(b)
Amino end
(N-terminus)
H
H
N C C
H O
N C C OH
Side
chains
Backbone
H O
Carboxyl end
(C-terminus)
3
Protein Conformation and Function
• A protein’s specific conformation
– Determines how it functions
• Conformation is determined at four different
levels.
Four Levels of Protein Structure
• Primary structure
– Is the unique sequence
of amino acids in a
polypeptide
+H N
3
Amino
end
GlyProThr Gly
Thr
Gly
Amino acid
subunits
Glu
CysLysSeu
LeuPro
Met
Val
Lys
Val
Leu
Asp
AlaVal Arg Gly
Ser
Pro
Ala
– Is what is coded for by
the DNA of genes.
GluLle
LeuAla
Gly
Asp
Thr
Lys
Ser
Lys Trp Tyr
lle
Ser
ProPheHisGlu
Ala Thr PheVal
Asn
His
Ala
Glu
Val
Thr
Asp
Tyr
Arg
Ser
Arg
GlyPro
Thr Ser
Tyr
lle
Ala
Ala
Leu
Leu
Ser
Pro
SerTyr
Thr
Ala
Val
Val
ThrAsnProLysGlu
Figure 5.20
c
o
o–
Carboxyl end
Secondary structure
– Is the folding or coiling of the polypeptide into a
repeating configuration caused by H-bonds between
peptide linkages.
– Includes the predictable shapes of the α helix and β
pleated sheet
β pleated sheet
Amino acid
subunits
O H H
C C N
C N
H
R
R
O H H
C C N
C C N
O H H
O
O H H
O H H
R
R
C C N
C C N
N
C C N
R C C
R C C
OH H
OH H
O
R
R
O
O
C
H
C
H
H
H C N HC
C N HC N
C
N
H
H
C
O
C
O
R
R
O
C
R
R
R
H
H
C
C
O C
O C
N H
N H
N H
N H
C
O C
H C R H C R
H C R H C
R
N H O C
N H
O C
O C
O C
N H
N H
C H
C H
R
R
R
O
C
H
H
NH C N
C
H
O C
R
R
H
C
N HC N
H
O C
α helix
Figure 5.20
4
Tertiary structure
– Is the overall three-dimensional shape of a
polypeptide
– Results from interactions between the R groups of
amino acids. Shapes are less predictable than 2’.
Hyrdogen
bond
CH
CH22
CH
O
H
O
H3C
H3C
CH3
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
β Chains
Iron
Heme
α Chains
Hemoglobin
The four levels of protein structure
• Amino acid sequence determines the way the
protein molecule forms the higher levels of structure.
Heat, pH, salinity can all affect the structure of the
molecule, and if it is changed too much, the protein is
said to be denatured.
• A change in amino acid sequence, as could be
caused by a mutation in the DNA, might result in a
non-functional molecule.
+
H3N
Amino end
Amino acid
subunits
α helix
5
Chaperonins
– Are protein molecules that assist in the proper
folding of other proteins
Correctly
folded
protein
Polypeptide
Cap
Hollow
cylinder
2 The cap attaches, causing 3 The cap comes
Steps of Chaperonin
the cylinder to change shape in off, and the properly
Action:
folded protein is
such a way that it creates a
1 An unfolded polyhydrophilic environment for the released.
peptide enters the
cylinder from one end. folding of the polypeptide.
Chaperonin
(fully assembled)
Figure 5.23
Denaturation
– When a protein unravels and loses its native
conformation
Denaturation
Normal protein
Denatured protein
Renaturation
Figure 5.22
Sickle-Cell Disease:
A Simple Change in Primary Structure
• Sickle-cell disease – a single change in one a.a.
Primary
structure
Normal hemoglobin
Val
His Leu Thr
Pro Glul Glu
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Sickle-cell hemoglobin
. . . Primary
Val
His
Leu Thr
Secondary
β subunit and tertiary
structures
Quaternary Hemoglobin A
structure
α
β
Function
Molecules do
not associate
with one
another, each
carries oxygen.
Red blood
cell shape
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen
β
α
Pro Val Glu
...
structure 1 2 3 4 5 6 7
Quaternary
structure
β subunit
α
β
β
α
Function
10 μm
10 μm
Red blood
cell shape
Exposed
hydrophobic
region
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced.
Fibers of abnormal
hemoglobin
deform cell into
sickle shape.
Figure 5.21
6
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 nucleic acids
The Roles of Nucleic Acid Polymers
• There are two types of polynucleotides
– Deoxyribonucleic acid (DNA) (genes)
• Stores information for the synthesis of
specific proteins
• Directs RNA synthesis
– Ribonucleic acid (RNA)
• Translates the DNA code into polypeptides
DNA to Protein
DNA
1
Synthesis of
mRNA in the nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
3 Synthesis
of protein
Figure 5.25
Polypeptide
Amino
acids
7
The Structure of Nucleic Acids
• Nucleic acids
– Exist as polymers called polynucleotides
5’ end
5’C
O
3’C
O
O
5’C
O
3’C
OH
3’ end
(a) Polynucleotide,
or nucleic acid
Figure 5.26
• Each polynucleotide
– Consists of monomers called nucleotides
Nucleoside
Nitrogenous
base
O
−
O
P
5’C
O
CH2
O
O−
Phosphate
group
Figure 5.26
3’C
Pentose
sugar
(b) Nucleotide
Nucleotide Monomers
Are made up of nucleosides and phosphate
groups
Nucleoside
Nitrogenous
base
O
−
O
P
Nitrogenous bases
Pyrimidines
O
O
C
C
CH3
CH
N
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
NH2
C
Purines
5’C
O
CH2
O
O−
Phosphate
group
3’C
Pentose
sugar
O
NH2
N C C
N CC
NH
N
HC
HC
C
CH
N C
N
NH2
N
N
H
H
Adenine
Guanine
A
G
5”
Pentose sugars
(b) Nucleotide
Figure 5.26
5”
HOCH2 O OH
H H 1’
H H 1’
4’
H
H
H 3’ 2’ H
3’ 2’
OH OH
OH H
Deoxyribose (in DNA) Ribose (in RNA)
HOCH2 O OH
Figure 5.26
4’
(c) Nucleoside components
8
Nucleotides
• Structure: nucleotides are made up of a nitrogenous
base, a pentose sugar, and a phosphate group.
• The sugar and nitrogenous base are also called a
nucleoside.
• The nitrogenous bases include:
–
The pyrimidines (single ring structure) cytosine and
thymine (and uracil in RNA)
–
The purines (double ring structure) adenine and guanine
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
5’ end
5’C
O
3’C
O
O
5’C
O
3’C
OH
3’ end
Figure 5.26
• The sequence of bases along a nucleotide
polymer
– Is unique for each gene
9
The DNA Double Helix
• Cellular DNA molecules
– Consists of two
antiparallel nucleotide
strands that spiral
around to form a
“double helix).
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
New
strands
5’ end
3’ end
Base-Pairing Rules
• The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary
fashion (A with T only, and C with G only)
• In RNA, Uracil is substituted for Thymine.
DNA and Proteins as Tape Measures of Evolution
• Molecular comparisons
– Help biologists sort out the evolutionary
connections among species
• The more closely related two species are the
more nucleic acid and protein sequences they
will have in common.
• Various classes of nucleic acids mutate at
characteristic rates.
10
Other nucleic acids
• There are other nucleic acids in the cell
(besides DNA and RNA) and they have other
functions:
a. energy transfer - AMP, ADP, ATP
b. coenzymes for metabolism - NAD and FAD
c. messenger within the cell - cAMP
Organic molecules may be formed in combinations
• Examples include:
– Lipoproteins: carry cholesterol in blood. LDL
(low density lipoprotein) = bad; HDL (high
density lipoprotein) = good
– Glycoproteins: (in cell membranes)
11