Chapter 3 : The Structures and Function of Macromolecules

Molecular Biology

Mochamad Untung Kurnia Agung, S.Kel., M.Si.

Marine Molecular Microbiologist
 • Macromolecules
– Are large molecules composed of smaller
molecules
– Are complex in their structures

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 Most macromolecules are polymers, built from
monomers
• Four of the classes of life’s organic
molecules are polymers
– Carbohydrates
– Lipid
– Proteins
– Nucleic acids

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 • A polymer
– Is a long molecule consisting of many similar
building blocks called monomers

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 The Synthesis and Breakdown of Polymers
• Monomers form larger molecules by
condensation reactions called dehydration
reactions

HO 1 2 3 H HO H

Short polymer Unlinked monomer

Dehydration removes a water

H2O
molecule, forming a new bond

HO 1 2 3 4 H
Longer polymer
Figure 5.2A (a) Dehydration reaction in the synthesis of a polymer

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 • Polymers can disassemble by
– Hydrolysis

HO 1 2 3 4 H

Hydrolysis adds a water

H2O
molecule, breaking a bond

HO 1 2 3 H HO H

Figure 5.2B (b) Hydrolysis of a polymer

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 PROTEIN
• Proteins have many structures, resulting in a
wide range of functions
– Proteins
• Have many roles inside the cell

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 • An overview of protein functions

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 • Enzymes
– Are 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)

Glucose
Enzyme
OH (sucrase)
H2O
Fructose

H O

4 Products are released. 3 Substrate is converted

Figure 5.16 to products.
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 Polypeptides
• Polypeptides
– Are polymers of amino acids

• A protein
– Consists of one or more polypeptides

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 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

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 • 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
H2N C C
CH2 O CH2 CH2 O–
O O H
H3N+ C C H3N+ C C H3 N+ C C
O– O– O–
H H H
Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro)

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 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 H3N+ C C H3N+ C C H3N+ 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 H3N+ 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)

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 Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
OH
Peptide
bond
OH SH
CH2 CH2 CH2
H H H
N
H C C N C C OH H N C C OH
H O H O H O DESMOSOMES
(a) H2O

OH
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

Figure 5.18 (b) (N-terminus) (C-terminus)

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 Determining the Amino Acid Sequence of a Polypeptide

• The amino acid sequences of polypeptides

– Were first determined using chemical means
– Can now be determined by automated
machines

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 Protein Conformation and Function
• A protein’s specific conformation
– Determines how it functions

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 • Two models of protein conformation

Groove

(a) A ribbon model

Groove

(b) A space-filling model

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 Four Levels of Protein Structure
• Primary structure
– Is the unique sequence of amino acids in a
polypeptide HN Amino acid
+
3
Gly ProThr Gly
Thr
Gly

Amino LeuPro
Cys LysSeu
Glu
subunits
end Met
Val
Lys
Val
Leu
Asp
AlaVal Arg Gly
Ser
Pro
Ala

Glu Lle
Asp
Thr
Lys
Ser
Lys Trp Tyr
Leu Ala
Gly
lle
Ser
ProPhe
His Glu
His
Ala
Glu
Val
Ala Thr PheVal
Asn
lle
Thr
Asp Tyr Ala
Arg
Ser Arg Ala
Gly Pro
Leu
Leu
Ser
Pro
SerTyr
Tyr
Thr Ser
Thr
Ala
Val o
Val LysGlu c
Thr
AsnPro o–
Carboxyl end

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 • 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
H H C H O C H
C O C O O C
R R R
R H R H
C C
N H O C N H O C
N H
O C O C
N H
 helix
H C R H C H C R H C R
R
N H O C N H
O C
O C N H O C N H
C C
R H R H

Figure 5.20
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 • Tertiary structure
– Is the overall three-dimensional shape of a
polypeptide
– Results from interactions between amino acids
and R groups Hydrophobic
interactions and
CH van der Waals
CH22
CH
H3C CH3 interactions
O
Hyrdogen 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

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 • 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

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 • The four levels of protein structure

+H
3N
Amino end

Amino acid
subunits
helix

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 What Determines Protein Conformation?
• Protein conformation
– Depends on the physical and chemical
conditions of the protein’s environment

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 • Denaturation
– Is when a protein unravels and loses its native
conformation
Denaturation

Normal protein Denatured protein

Figure 5.22 Renaturation

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 The Protein-Folding Problem
• Most proteins
– Probably go through several intermediate
states on their way to a stable conformation

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 • Chaperonins
– Are protein molecules that assist in the proper
folding of other proteins
Correctly
folded
Polypeptide
protein
Cap

Hollow
cylinder

Chaperonin Steps of Chaperonin
(fully assembled) Action:
1 An unfolded poly-
peptide enters the
Figure 5.23 cylinder from one end.
2 The cap attaches, causing 3 The cap comes
the cylinder to change shape in off, and the properly
such a way that it creates a folded protein is
hydrophilic environment for the released.
folding of the polypeptide.

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 • 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

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

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 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

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 The Roles of Nucleic Acids
• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)

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 • DNA
– Stores information for the synthesis of specific
proteins

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 – Directs RNA synthesis
– Directs protein synthesis through RNA
DNA

1 Synthesis of
mRNA in the nucleus mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into cytoplasm Ribosome
via nuclear pore

3 Synthesis
of protein

Amino
Polypeptide acids

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 The Structure of Nucleic Acids
• Nucleic acids
– Exist as polymers called polynucleotides
5’ end

5’C O

3’C

5’C O
3’C
3’ end
OH
(a) Polynucleotide,
Figure 5.26 or nucleic acid
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 • Each polynucleotide
– Consists of monomers called nucleotides

Nucleoside

Nitrogenous
base

O 5’C

O P O CH2
O
O
Phosphate
3’C
group Pentose
sugar

Figure 5.26 (b) Nucleotide

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 Nucleotide Monomers
• Nucleotide monomers
– Are made up of nucleosides and phosphate
groups Nitrogenous bases
Pyrimidines
NH2 O O
C C CH 3
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)
C T UU

Purines
NH2 O
N CC N C C
N NH
HC HC
N C CH N C
N N NH2
H H
Adenine Guanine
A G

Pentose sugars
5” 5”
HOCH2 O OH HOCH2 O OH
4’ H H 1’ 4’ H H 1’

H 3’ 2’ H H H
3’ 2’
OH H OH OH
Deoxyribose (in DNA) Ribose (in RNA)

(c) Nucleoside components

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 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

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 • The sequence of bases along a nucleotide
polymer
– Is unique for each gene

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 The DNA Double Helix
• Cellular DNA molecules
– Have two polynucleotides that spiral around an
imaginary axis
– Form a double helix

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 • 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

Nucleotide
about to be
added to a
new strand
A 3’ end

5’ end

3’ end New
strands

Figure 5.27 5’ end 3’ end

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 • The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary
fashion (A with T only, and C with G only)

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 DNA and Proteins as Tape Measures of Evolution
• Molecular comparisons
– Help biologists sort out the evolutionary
connections among species

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Next Chapter 4 :
DNA