Macromolecules: Focus on

Proteins
AP Biology
 A P B io lo g y
Macromolecules: Focus on Proteins
S u n d a y , 0 3 O cto b e r 2 0 1 0
 Objective
Students will demonstrate understanding of protein


structure and folding by identifying chemical

properties in paper models.


Do Now (linking your homework to

yesterday’s work)
Draw the general structure of an amino acid (from

packet, pg 2)
(from HW): What are the 4 chemical types of

amino acids?
Thought Question (HARD): How can the structure
 A P B io lo g y
Macromolecules: Focus on Proteins
S u n d a y , 0 3 O cto b e r 2 0 1 0
 Objective

Students will demonstrate understanding of
macromolecules by identifying chemical properties in
paper models.


Homework
-Finish Macromolecules Packets #1 & 2

-Look at amino acid structures (textbook or

google):
-What are the 4 chemical categories of Amino

Acid R-groups?
 A P B io lo g y
Macromolecules: Focus on Proteins
S u n d a y , 0 3 O cto b e r 2 0 1 0
 Classwork

-Notes on protein structure

Question for class:

What are the “building blocks” (monomers) of proteins?



________________________?



-Work Time, packet #2


 -Summary of Chemistry / Preview of Next Week

 Functional Groups
• Functional groups are
the parts of molecules
involved in chemical CH3
OH

reactions Estradiol

• They Are the

chemically reactive HO
groups of atoms
within an organic Female lion

molecule CH3
OH

• Give organic molecules CH3

distinctive chemical
properties O
Testosterone
• Figure 4 . 9 Male lion
5
•
• Six functional groups are important in the
chemistry of life
– Hydroxyl
– Carbonyl
– Carboxyl
– Amino
– Sulfhydryl
– Phosphate

6
  Some important functional groups of organic
compounds
FUNCTIONAL
GROUP HYDROXYL CARBONYL CARBOXYL

O O
OH C C
(may be written HO ) OH

STRUCTURE In a hydroxyl group (—OH), a The carbonyl group

hydrogen atom is bonded to an
oxygen atom, which in turn is
( CO) consists of a
carbon atom joined to an
When an oxygen atom is double-
bonded to a carbon atom that is
bonded to the carbon skeleton oxygen atom by a double also bonded to a hydroxyl group, the
of the organic molecule. (Do bond. entire assembly of atoms is called
not confuse this functional a carboxyl group (—COOH).
group with the hydroxide ion,
OH–.)
Figure 4 . 10

7
 Some important functional groups of organic
compounds
Ketones if the carbonyl group is
NAME OF Alcohols (their specific Carboxylic acids , or organic
within a carbon skeleton
COMPOUNDS names usually end in -ol) acids
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
EXAMPLE H H H O H O
H C C OH H C C H C C
H OH
H H H C H
Ethanol , the alcohol
H
present in alcoholic H Acetic acid , which gives vinegar its
beverages sour tatste
Acetone , the simplest ketone

H H
O
H C C C
H H H
Figure 4 . 10 Propanal , an aldehyde

8
 • Some important functional groups of organic
compounds

AMINO SULFHYDRYL PHOSPHATE

H SH O
N (may be written HS ) O P OH
H OH

The amino group (—NH2) The sulfhydryl group

consists of a nitrogen atom
bonded to two hydrogen atoms
and to the carbon skeleton.
Figure 4 . 10
consists of a sulfur atom
bonded to an atom of hydrogen;
resembles a hydroxyl group in
shape.
In a phosphate group , a phosphorus
atom is bonded to four oxygen atoms;
one oxygen is bonded to the carbon
skeleton; two oxygens carry negative
charges; abbreviated P . The phosphate
group (—OPO32– ) is an ionized form of
a phosphoric acid group (—OPO3H2; note
the two hydrogens).

9
 Our life is maintained by molecular
network systems

Molecular network
system in a cell

(From ExPASy Biochemical Pathways; http://www.expasy.org/cgi-bin/show_thumbnails.pl?2)

Proteins play key roles in a living
system
• Three examples of protein functions
Alcohol
dehydrogenase
– Catalysis: oxidizes alcohols to
Almost all chemical reactions in a aldehydes or
ketones
living cell are catalyzed by protein
enzymes.

– Transport: Haemoglobin
Some proteins transports various carries oxygen
substances, such as oxygen, ions,
and so on.
Insulin controls the
– Information transfer: amount of sugar in
For example, hormones. the blood
 Amino acid: Basic unit of protein

R Different side chains, R,

+ - determin the properties of
NH3 C COO 20 amino acids.
Amino group Carboxylic
acid group
H
An amino acid
 20 Amino acids
Glycine (G) Alanine (A) Valine (V) Isoleucine (I) Leucine (L)

Proline (P) Methionine (M) Phenylalanine (F) Tryptophan (W) Asparagine (N)

Glutamine (Q) Serine (S) Threonine (T) Tyrosine (Y) Cysteine (C)

Asparatic acid (D) Glutamic acid (E) Lysine (K) Arginine (R) Histidine (H)

White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

Proteins are linear polymers of amino
acids
R1 R2
NH3 ＋ COO ー NH3 ＋ COO ー
C ＋ C ＋
H H
A carboxylic acid condenses
H2O H2O with an amino group with the
release of a water
R1 R2 R3

NH3 ＋ C CO NH C CO NH C CO
H Peptide bond H Peptide bond H
The amino acid sequence is
A
F
G S T D
K A
called as primary structure
N G S
Amino acid sequence is encoded by
DNA base sequence in a gene
DNA molecule ・ ・ DNA base
G C sequence
C G
G C
C G
＝ T A
T A
A T
A T
G C
C G
G C
C G
・ ・
 Amino acid sequence is encoded by
DNA base sequence in a gene
Second letter
T C A G
First T TTT Phe TCT Ser TAT Tyr TGT Cys T Thir
lette TTC TCC TAC TGC C d
r TTA Leu TCA TAA Stop TGA Stop A lette
TTG TCG TAG TGG Trp G r
C CTT Leu CCT Pro CAT His CGT Arg T
CTC CCC CAC CGC C
CTA CCA CAA Gln CGA A
CTG CCG CAG CGG G
A ATT Ile ACT Thr AAT Asn AGT Ser T
ATC ACC AAC AGC C
ATA ACA AAA Lys AGA Arg A
ATG Met ACG AAG AGG G
G GTT Val GCT Ala GAT Asp GGT Gly T
GTC GCC GAC GGC C
GTA GCA GAA Glu GGA A
GTG GCG GAG GGG G
Amino acid sequence is encoded by
DNA base sequence in a gene

From Traphagen, DiMarco, and Silliker, 2010

Gene is protein’s blueprint, genome
is life’s blueprint
DNA Genome

Gene Gene Gene Gene

Gene
Gene Gene Gene
Gene Gene Gene
Gene Gene Gene
Protein Gene

Protein
Protein Protein
Protein
Protein Protein
Protein Protein
Protein
Protein Protein Protein
Protein Protein
Gene is protein’s blueprint, genome
is life’s blueprint
Glycolysis network Genome

Gene Gene Gene

Gene
Gene Gene Gene
Gene Gene Gene
Gene Gene Gene
Gene

Protein
Protein Protein
Protein
Protein Protein
Protein Protein
Protein
Protein Protein Protein
Protein Protein
 In 2003, Human genome
• Genomesequence was
is the complete set deciphered!
of genes of a living thing.
• In 2003, the human genome sequencing was completed.
• The human genome contains about 3 billion base pairs.
• The number of genes is estimated to be between 20,000 to
25,000.
• The difference between the genome of human and that of
chimpanzee is only 1.23%!

3 billion base pair => 6 G letters

&
1 letter => 1 byte
The whole genome can be recorded in just 10 CD-ROMs!
Each Protein has a unique structure

Amino acid sequence

NLKTEWPELVGKSVEEA
KKVILQDKPEAQIIVLPVG
TIVTMEYRIDRVRLFVDK
LDNIAEVPRVG

Folding!
Basic structural units of proteins:
Secondary structure
α-helix β-sheet

Secondary structures, α-helix and β-sheet,

have regular hydrogen-bonding patterns.
Three-dimensional structure of
proteins

Tertiary structure

Quaternary structure
 Hierarchical nature of protein
structure
 Primary structure (Amino acid sequence)
 ↓
 Secondary structure （ α-helix, β-sheet ）
 ↓
 Tertiary structure （ Three-dimensional structure
formed by assembly of secondary structures ）
 ↓
 Quaternary structure （ Structure formed by more
than one polypeptide chains ）
 Close relationship between protein
structure andHormone
Example of enzyme reaction
its function
receptor Antibody
substrates
enzyme A enzyme

Matching the
Digestion of
shape to A
enzyme
A!

Binding to A
 Protein structure prediction has remained

elusive over half a century

“Can we predict a protein structure from



its amino acid sequence?”

•
 Now, impossible!
 Summary
• Proteins are key players in our living systems.
• Proteins are polymers consisting of 20 kinds of amino acids.
• Each protein folds into a unique three-dimensional structure
defined by its amino acid sequence.
• Protein structure has a hierarchical nature.
• Protein structure is closely related to its function.
• Protein structure prediction is a grand challenge of
computational biology.