Download Macromolecules 2: Proteins and Nucleic Acids Amino Acids differ

Macromolecules 2: Proteins
and Nucleic Acids
•  Finish Lipids
Amino Acids differ only by their
“R” group
•  20 kinds of amino acids
–  Phospholipids
–  soaps
–  Same chasis, different cargo
•  Proteins
Nonpolar
–  Amino Acids
–  Kinds of R groups
–  4 Levels of protein structure
Oil
Polar
OH
Charged
SH
R5
Duracell
•  Nucleic Acids
–  Nucleotide structure
–  Base pairing
Can Keep adding
to the end
10 Sept. 2012
Polar and Charged Amino Acids
Nonpolar Amino Acids
The amino and acid groups
couple the monomers together
Building a polypeptide
Carboxyl group
Amino group
•  Can make polymers that are 100s or 1000s of amino
acids long
R5
R1
R2
R3
Dehydration reaction
releases a water
molecule
R4
Can Keep adding
to the end
Like Fig 5.17
1
4 Levels of Structure
Primary Structure:
Amino acid sequence
Primary structure: amino acid sequence
Met - Ala - Cys - Glu - Ser - Thr - Val - Val - Leu - Cys - Arg
NP NP
Tertiary Structure:
3-D shape of one
polypeptide
P
-
P
P
Secondary structure is stabilized by
hydrogen bonding of peptide bonds
Secondary Structure
OPTIONAL
OPTIONAL
||
|
|
R
O
H
|
||
|
+
+
-
-
+
+
Hydrogen bonds
N - C - C - N - C - C - N - C - C - N - C - C - O|
H
|
|
||
H
R
O
-
||
O
+
-
+
+
-
-
+
+
-
+
|
R
-
|
H
+
H
-
|
+
H
|
H
-
\
H/
H
+
Secondary structure
" sheet
O
P
•  Length
•  Abundance of different A.A.s
•  Order of A.A.s
Secondary structure
! helix
R
NP
Individual Polypeptides (proteins) differ by
Quaternary Structure:
Assembly of several
polypeptides to form
one functional protein
Secondary Structure:
Local folding
! helix and " sheet
H
NP NP
R groups are NOT
involved in secondary
structure
2
R groups are on the outside
“Fuzzy can”
R-R--
--R
R
RR--
--R
-R
R-R
&
R groups are on the outside
Often, A.A.s are ordered so one side has
mostly polar R groups and the other has
mostly non-polar R groups. Why?
“Shag carpet”
R
R
|
R
R R | R |
|
|
|
R
|
R
R
R
|
R--
|
| R
R
R--
R
RR--
--R
R
-R
R--
|
R
R
R
|
|
| R
R
R
Means that the R groups can
interact with other molecules
Tertiary Structure
(3-D shape of the entire peptide)
R
R
|
R
R R | R |
|
|
|
--R
3D structure stabilized by
interactions among R groups
Ionic
bonding
•  Formed by interactions among R groups
• 
Hydrogen
bonding
Mostly !
helices
Hydrophobic
interactions
Mostly "
sheets
Disulfide
Bridges
Mixture
Quaternary Structure
•  Sometimes a single functional PROTEIN
is made of several POLYPEPTIDES that
work together as a unit
Hemoglobin
How do you curl hair?
Postassium Channel
3
Nucleotides have three components
Nucleic Acids
•  Sugar
•  Base
•  Phosphate
ATP
Purines
3’
Use dehydration
reactions to connect
these molecules
Pyrimidines
A, G
2’
Carbons in the sugar are
numbered with primes
The bases each have a polar edge for
hydrogen bonding
Thymine
Adenine
Cytosine
Guanine
C, T, U
Can you think of a good
mnemonic?
The nucleotide ATP is a common
energy carrier
Polynucleotide (DNA, RNA)
chains are assembled by yet
another type of dehydration
reaction
5’ end
These are high-energy phosphate bonds
•  Link the -OH on the 3’ carbon
of one nucleotide
•  to the phosphate on the 5’
carbon of the next.
Also GTP, CTP, etc.
3’ end
4
RNA
DNA
DNA copying
is the basis
of heredity
The
sequences of
bases is the
hereditary
information
Flow of information
DNA --> RNA --> Protein
5