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Biochem Lec4 Macromolecules

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20 views67 pages

Biochem Lec4 Macromolecules

Uploaded by

btttrinhhcmiu
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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You are on page 1/ 67

The Structure and

Function of
Macromolecules

1
The Molecules of Life
• Overview:
– Another level in the hierarchy
of biological organization is
reached when small organic
molecules are joined together
– Atom ---> molecule ---
compound

2
Macromolecules
– Are large molecules composed of
smaller molecules
– Are complex in their structures

3
Macromolecules
•Most macromolecules are
polymers, built from monomers
• Four classes of life’s organic
molecules
– Carbohydrates
– Proteins
– Nucleic acids
– Lipids

4
• A polymer
– Is a long molecule consisting of many
similar building blocks called monomers
– Specific monomers make up each
macromolecule
– E.g. amino acids are the monomers for
proteins

5
The Synthesis and Breakdown of
Polymers
• Monomers form larger molecules by
condensation reactions called
dehydration synthesis
HO 1 2 3 H HO H

Short polymer Unlinked monomer

Dehydration removes a water


H 2O
molecule, forming a new bond

HO 1 2 3 4 H
Longer polymer
Dehydration reaction in the synthesis of a polymer

6
The Synthesis and Breakdown of
Polymers
• Polymers can disassemble by
– Hydrolysis (addition of water
molecules)
HO 1 2 3 4 H

Hydrolysis adds a water


H 2O
molecule, breaking a bond

HO 1 2 3 H HO H

Hydrolysis of a
polymer
7
• Although organisms share
the same limited number
of monomer types, each
organism is unique based
on the arrangement of
monomers into polymers
• An immense variety of
polymers can be built from a
small set of monomers

8
Carbohydrates
• Serve as fuel and building
material
• Include both sugars and
their polymers (starch,
cellulose, etc.)

9
Sugars
• Monosaccharides
– Are the simplest sugars
– Can be used for fuel
– Can be converted into other
organic molecules
– Can be combined into polymers

10
• Examples of monosaccharides
Triose sugarsPentose 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
11
• Monosaccharides
– May be linear
– Can form rings
H O
1C CH2OH
6 6
CH2OH
2 CH2OH
H C OH 5C O H 5
C O 6
H H H H H O
HO
3
C H
5 H
H H H
4
C 1
C 4
C 1
C 4 1
4 OH H OH H OH
H C OH O HO 3 2 OH
OH 3 OH OH
5 C 2
C 3
C 2
C
H C OH
H OH
6 H OH H OH
H C OH

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.

12
• Disaccharides
– Consist of two
monosaccharides
– Are joined by a glycosidic
linkage

13
(a)
Dehydration reaction
in the synthesis of
CH2OH CH2OH CH2OH CH2OH
maltose. The bonding
of two glucose units O O O O
forms maltose. The H H H H H H H 1– 4 H H H
H H 1 glycosidic 4
glycosidic link joins O O
OH H OH H H linkage H
OHOH
the number 1 carbon OH HO H H
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 H2 O
monomers in a Glucose Maltose
Glucose
different way would
result in a different
disaccharide.
CH2O
CH2OH
H CH2OH CH2OH
H O O H O H 1–2 O
H H H H H
1 glycosidic 2
O H O linkage
(b)Dehydration reaction O H HO H H HO
H H HO H O
in the synthesis of H CH2OH HO CH2OH
sucrose. Sucrose is O
H O
a disaccharide formed OH H H OH OH H
from glucose and fructose. H
H2 O
Notice that fructose,
though a hexose like Glucose Fructose Sucrose
glucose, forms a
five-sided ring.

14
Polysaccharides
• Polysaccharides
– Are polymers of sugars
– Serve many roles in organisms

15
Storage Polysaccharides Chloroplas
Starch
t

• Starch
– Is a polymer
consisting
entirely of
glucose
monomers 1 m

– Is the major
storage form of
glucose in Amylose Amylopectin

plants
Starch: a plant polysaccharide

16
• Glycogen
– Consists of glucose monomers
– Is the major storage form of glucose in
animals Mitochondria Giycogen
granules

0.5 m

Glycogen

Glycogen: an animal polysaccharide


17
Structural
Polysaccharides
• Cellulose
– Is a polymer of glucose

18
– Has different glycosidic linkages than starch
H O
CH2O C CH2O
H O H O
H O H H C H O
H H
H H H
4
OH H C H 4 O 1
O O H H
H H
H C OH O H
O H
O
H C O H OH
H H
H
 glucose C O
H  glucose
H

(a)  and  glucose ring structures


CH2O CH2O CH2O CH2O
H H H H
O O O O
O 1 4 O 1 4 O 1 4 1
H O O O OH O
H H H
O
O O O O
H H H H
(b) Starch: 1– 4 linkage of  glucose monomers
CH2O O CH2O O
H H H H
O O
O O O O O O
H 1 4 H O H O
H H
O O O H
O CH2O CH2O
OH
H H H
(c) Cellulose: 1– 4 linkage of  glucose monomers
19
– Is a major component of the tough walls
that enclose plant cells

About 80 cellulose
Cellulose microfibrils molecules associate
in a plant cell wall Microfibril to form a microfibril, the
Cell walls main architectural unit
of the plant cell wall.


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 CH
held together by hydrogen 2 OH 2OH
H
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 
 Glucose glucose polymer.
monomer 20
• Cellulose is difficult to digest
– Cows have microbes in their stomachs
to facilitate this process

21
• Chitin, another important structural
polysaccharide
– Is found in the exoskeleton of
arthropods
– Can be used as surgical thread
CH2O
HO
H OH
H
OH H
OH H
H NH
C O
CH3

(a) The structure of


(b) Chitin forms the exoskeleton (c) Chitin is used to make a
the
of arthropods. This cicada strong and flexible surgical
chitin monomer.
is molting, shedding its old thread that decomposes after
exoskeleton and emerging the wound or incision heals.
in adult form.
22
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

23
Function of Lipids
• Fats store energy, help to
insulate the body, and
cushion and protect organs
Fats
• Are constructed from two types of smaller
molecules, a single glycerol and usually three
fatty acids

25
Fats
• Vary in the length and number and
locations of double bonds they contain

26
• Saturated fatty acids
– Have the maximum number of
hydrogen atoms possible
– Have no double bonds

Stearic acid

(a) Saturated fat and fatty acid


27
• Unsaturated fatty acids
– Have one or more double bonds

Oleic acid

cis double bond


(b) Unsaturated fat and fatty acid causes bending

28
• Phospholipids
– Have only two fatty acids
– Have a phosphate group instead of
a third fatty acid

29
• Phospholipid structure
– Consists of a hydrophilic “head”
and hydrophobic “tails”
Hydrophilic head

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

Fatty acids

Hydrophilic
head
Hydrophobic
tails

(c) Phospholipid
(a) Structural formula (b) Space-filling model
symbol
30
• The structure of phospholipids
– Results in a bilayer arrangement found
in cell membranes

WATER
Hydrophilic
head

WATER
Hydrophobic
tail

31
Steroids
• Steroids
– Are lipids characterized by a carbon
skeleton consisting of four fused rings

32
Steroids
Cholesterol is
the “base
steroid” from Cholesterol

which your body


produces other Estrogen
Testosterone
steroids

Estrogen & testosterone are also


steroids
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
34
Four Types of ProteinsStorage

Structur
al

Contractil
e
Transport
• An overview of protein functions

36
• 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)
H 2O
Fructose

H O

4 Products are released. 3 Substrate is converted


to products.
37
Polypeptides
• Polypeptides
– Are polymers (chains) of amino
acids
• A protein
– Consists of one or more
polypeptides

38
• Amino acids
– Are organic molecules possessing
both carboxyl and amino groups
– Differ in their properties due to
differing side chains, called R groups

39
Twenty Amino Acids
• 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 H3N H3N
H3N+ C C H3N+ C C C C C C 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 CH2 CH2 O–
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)

40
OH NH2 O
NH2 O C
OH CH3 SH C CH2
Polar OH
CH2 CH CH2 CH2 CH2 CH2
O O O O O O
H3N H3N H3N H3N H3N H3N
+
C C C C +
C C C C +
C C +
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 CH2
CH2 O CH2
charged O
H3N CH2 CH2 H3N
C C O CH2 C C
+ +
O– H3N CH2 O–
C C O CH2 H
H +
H3N
O– C
H C CH2
+ O
O –
H3N
H +
C C
O–
H
Aspartic acid Glutamic acid Lysine (Lys) Arginine (Arg) Histidine (His)
(Asp) (Glu)

41
Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds

42
Protein Conformation and
Function
• A protein’s specific conformation
(shape) determines how it functions

43
Four Levels of Protein
Structure
• Primary structure +H3 N
Amino
GlyProThrGly

LeuPro
Thr

CysLysSeu
Gly
Glu
Amino
acid
end
Met
subunits
– Is the unique
Val
Lys
Val
Leu
Asp
AlaVal ArgGly
Ser

sequence of amino
Pro
Ala

acids in a
polypeptide
GluLle
Asp
Thr
Lys
Ser
LysTrpTyr
LeuAla
Gly
lle
Ser
ProPhe
HisGlu
His
Ala
Glu
Val
AlaThrPheVal
Asn
lle
Thr
Asp Tyr Ala
Arg
Ser Arg Ala
GlyPro
Leu
Leu
Ser
Pro
SerTyr
Tyr
ThrSer
Thr
Ala
Val o
Val
Thr ProLys
Glu c
Asn o–
Carboxyl end

44
• Secondary structure
– Is the folding or coiling of the
polypeptide into a repeating
configuration
– Includes the  helix and the  pleated
 pleated sheet
sheet Amino
O H H
C C N R
O H H
C C N R
O H H
C C N
R
O H H
C C N
acid C N R C C N R
C C N
R C C N R C C
subunits H O H H OH H OH H O

R R R R
O O C O C O H
C H H H C
H H
C N HC N H C N H C 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 N H
O C O C  helix
H C R H C H C R H C R
R
N H N H
O C O C
O C N H O C N H
C C
R R
H H

45
• Tertiary structure
– Is the overall three-dimensional shape
of a polypeptide
– Results from interactions between
amino acids and R groups
Hydrophobic
interactions
and
CH2
CH CH van der Waals
2
H3 C CH3
O interactions
Polypeptid
Hyrdogen H H3 C CH3
e
bond O CH
backbone
HO C
CH2 CH2 S S CH2
Disulfide bridge
O
CH2 NH3+-O C CH2
Ionic bond

46
• Quaternary structure
– Is the overall protein structure that
results from the aggregation of two or
more polypeptide subunits

Polypeptid
e
chain

Collage
n
 Chains

Iron
Heme
 Chains
Hemoglobin
47
Review of Protein Structure

+
H3 N
Amino end

Amino acid
subunits
helix

48
Sickle-Cell Disease: A Simple
Change in Primary Structure

• Sickle-cell disease
– Results from a single amino
acid substitution in the protein
hemoglobin

49
Normal Sickle-cell
Primary hemoglobin Primary Valhemoglobin
Val His Leu Thr Pro Glul Glu . . . His Leu Thr Pro Val Glu . . . Exposed
structure 1 2 3 4 5 6 7 structure1 2 3 4 5 6 7 hydrophobic
region
Secondary Secondary
and tertiary  subunit and tertiary  subunit
structures structures

 
QuaternaryHemoglobin A Quaternary  
structure structure  Hemoglobin S
  Molecules

Function interact with
one another to
Function Molecules do crystallize into
not associate a fiber,
with one capacity to
another, each
Normal cells carry oxygen is
carries
are oxygen. 10 m 10 m greatly
Red blood full of reduced.
cell shape individual Red blood
hemoglobin cell shape
molecules, Fibers of
each abnormal
Figure 5.21 carrying hemoglobin
oxygen deform cell into
sickle shape.
50
What Determines Protein
Conformation?
• Protein conformation
Depends on the physical and
chemical conditions of the
protein’s environment
• Temperature, pH, etc. affect
protein structure

51
•Denaturation is when a
protein unravels and loses its
native conformation
Denaturation
(shape)

Denatured
Normal protein
protein

Renaturation

52
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 or
temperature

53
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

54
The Roles of Nucleic Acids
• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)

55
Deoxyribonucleic Acid
• DNA
– Stores information for the
synthesis of specific proteins
– Found in the nucleus of cells

56
DNA Functions
– Directs RNA synthesis (transcription)
– Directs protein synthesis through RNA
(translation) DNA

1 Synthesis of
mRNA in the nucleus mRNA

NUCLEUS
CYTOPLASM

mRNA
2Movement of
mRNA into cytoplasm Ribosome
via nuclear pore

3 Synthesis
of protein

Amino
Polypeptide acids 57
The Structure of Nucleic
Acids
5’ end

• Nucleic acids 5’C O


– Exist as polymers called 3’C

polynucleotides
O

5’C
O

(a) 3’C
Polynucleo 3’ end
tide, OH
or nucleic acid 58
• Each polynucleotide
– Consists of monomers called nucleotides
– Sugar + phosphate + nitrogen base
Nucleoside

Nitrogenous
base

O 5’C

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

(b) Nucleotide

59
Nucleotide Monomers

• Nucleotide Nitrogenous bases


Pyrimidines

monomers
NH2 O O
C C CH 3
C
N CH HN C HN CH
C CH C CH C CH

– Are made up of O N O N O N
H H H
CytosineThymine (in DNA) Uracil (in RNA)
Uracil (in RNA)

nucleosides (sugar C T U

Purines
U

+ base) and N C
NH2
C
N C
O
C
N NH
phosphate groups HC
N C
H N
CH
HC
N
H
N
C
NH2

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
60
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

61
Gene
• The sequence of bases along a
nucleotide polymer
– Is unique for each gene

62
The DNA Double Helix
• Cellular DNA molecules
– Have two polynucleotides that spiral
around an imaginary axis
– Form a double helix

63
• 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
3’ new strand
A
end

5’ end

3’ end New
strands

5’ end 3’ end
64
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)

65
DNA and Proteins as Tape
Measures of Evolution

• Molecular comparisons
– Help biologists sort out the
evolutionary connections
among species

66
67

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