1. Proteins

2. Amino Acids, Peptides and Proteins
Learning objectives
• Amino acids share a common structure
• R groups provide different chemical properties
• Amino acids can ionize in aqueous solutions
• Proteins can be purified and studied in a variety of
ways
• Protein structure has four levels of organization
• Sequence homology generally translates to shared
function

3. Proteins
• Proteins serve many functions:
– 1.Structure: collagen and keratin are the chief
constituents of skin, bone, hair, and nails.
– 2. Catalysts: virtually all reactions in living systems are
catalyzed by proteins called enzymes.
– 3. Movement: muscles are made up of proteins called
myosin and actin.
– 4. Transport: hemoglobin transports oxygen from the
lungs to cells; other proteins transport molecules across
cell membranes.
– 5. Hormones: many hormones are proteins, among
them insulin, oxytocin, and human growth hormone.

4. Proteins
– 6. Protection: blood clotting involves the protein
fibrinogen; the body used proteins called antibodies to
fight disease.
– 7. Storage: casein in milk and ovalbumin in eggs store
nutrients for newborn infants and birds; ferritin, a
protein in the liver, stores iron.
– 8. Regulation: certain proteins not only control the
expression of genes, but also control when gene
expression takes place.

5. Amino Acids
•Have an alpha- carbon
attached to:
• an amino group
• carboxyl group
• a hydrogen
• an R group

6. Chirality of Amino Acids
• With the exception of glycine, all protein-derived
amino acids have at least one stereocenter (the carbon) and are chiral.
– The vast majority of protein-derived amino acids have
the L-configuration

7. Each R group
determines the
properties of the amino
acid
R groups can be
polar, nonpolar,
acidic, basic
Hundreds of modified
amino acids

8. Each R group
determines the
properties of an amino
acid
R groups can be
polar, nonpolar,
acidic, basic

14. Proteins are made of 20 amino acids

15. amino acids can act as acids and bases
• Amino acids exist in solution as dipolar ions (Zwitterions)
• Like buffers, AA’s can act as proton donors or acceptors
– “Amphoteric” compounds or “amphoteric electrolytes”

16. titration of amino acids
Ex. Glycine Deprotonation
• Two distinct
plateaus, each
correspond to
deprotonation of glycine
• Titration curves can be
used to predict AA
charge at a given pH
• The isoelectric point (pI)
is the pH at 0 charge

17. proteins

18. formation of peptide bonds
Peptides and proteins are
polymers of amino acids
• Two amino acids are
covalently joined in
condensation reaction
N-terminal
C-terminal

19. Peptides: how aa are linked
• proteins are long chains of amino acids joined by amide
bonds.
peptide bond:
– amino acids become linked together to form peptide
bonds with the elimination of water
– The reaction takes place between the -COOH of one
amino acid and the -NH2

20. α-carbons separated by 3 covalent bonds
Partial sharing of
e-
• A small electric dipole results from the partial negative charge on
oxygen and the partial positive charge on nitrogen
• The shared electrons result in some double bond character and the
lack of rotation

21. planar nature of peptide bonds
• The N-Cα and Cα-C bonds can rotate

22. Primary Structure
• Just how important is the exact amino acid
sequence?
– Human insulin consists of two polypeptide chains
having a total of 51 amino acids.
– In the table are differences between four types of
insulin.
A Chain
positions 8-9-10
B Chain
position 30
Human
Cow
-Thr-Ser-Ile-Ala-Ser-Val-
-Thr
-Ala
Hog
Sheep
-Thr-Ser-Ile-Ala-Gly-Val-
-Ala
-Ala

23. Primary Structure
– Vasopressin and oxytocin are both nonapeptides but
have quite different biological functions.
– Vasopressin is an antidiuretic hormone.
– Oxytocin affects contractions of the uterus in childbirth
and the muscles of the breast that aid in the secretion
of milk.

24. proteins range in size

25. proteins contain prosthetic groups
Non-amino acid part of proteins

26. protein purification (chromatography)
Ion-Exchange
Size-Exclusion
Affinity
Uses protein characteristics, such as charge, size and binding affinity to separate the protein

27. electrophoresis (SDS-PAGE)
Purification steps
Stain and
blot the gel
Migration of charged proteins in an electric field
Gel slows migration in proportion to mass

28. 2D gel electrophoresis
1. Isoelectric focusing
2. SDS PAGE

29. Mass Spectrometry
1. First treat isolated
protein with a protease
2. Mixture is vaporized
and peptides
separated
3. One peptide is
selected and further
fragmented
4. MS measures m/z
ratios for all the
fragments

30. Mass spectrometer

31. Mass Spectrum of Ethanol

32. Levels of Structure
• Primary structure: the sequence of amino acids
• Secondary structure: conformations of amino acids
in localized regions of a polypeptide chain;
examples are -helix, -pleated sheet, and random
coil.
• Tertiary structure: the complete three-dimensional
arrangement of atoms of a polypeptide chain.
• Quaternary structure: the spatial relationship and
interactions between subunits in a protein that has
more than one polypeptide chain.

33. 4 levels of protein structure
• Primary – sequence of amino acids
• Secondary – interactions between adjacent amino
acids
• Tertiary – 3D folding of the polypeptide
• Quaternary – arrangements of multiple polypeptides

34. Secondary Structure
• conformations of amino acids in localized regions
of a polypeptide chain.
– The most common types of secondary structure are helix and -pleated sheet.
-Helix: a type of secondary structure in which a
section of polypeptide chain coils into a spiral, most
commonly a right-handed spiral.
-Pleated sheet: a type of secondary structure in which
two polypeptide chains or sections of the same
polypeptide chain align parallel to each other

35. -Helix
• The -helix structure: held together by hydrogen
bonds

36. -Helix
• In a section of -helix;
– The C=O group of each
peptide bond is hydrogen
bonded to the N-H group
of the peptide bond four
amino acid units away
from it.
– All R- groups point
outward from the helix.

37. secondary structure
• Note the position of the
purple R groups relative
to the backbone of the
polypeptide

38. all α helices are right handed
• But some
supramolecular
complexes are
left handed
(keratin, collage
n)
right-handed = clockwise

39. β sheet secondary structure
• More extended
• H-bonds may occur between amino acids some
distance from one another
• Adjacent chains can run parallel or anti-parallel
to each other

40. β sheets require β turns
• One third of amino acids are in turns or loops
• Gly and Pro are frequently found in turns

41. -Pleated Sheet
• In a section of -pleated sheet;
– The C=O and N-H groups of peptide bonds from
adjacent chains point toward each other so that
hydrogen bonding is possible between them.
– All R- groups on any one chain alternate, first
above, then below the plane of the sheet, etc.

42. Pleated Sheet Structure of
Proteins

43. secondary structure and function

44. Tertiary Structure
• the overall conformation of an entire polypeptide
chain.
• Tertiary structure is stabilized in several ways:
– Covalent bonds, as for example, the formation of disulfide bonds
between cysteine side chains.
– Hydrogen bonding between polar groups of side chains, as for
example between the -OH groups of serine and threonine.
– Electrostatic interaction or Salt bridges, as for example, the
attraction of the -NH3+ group of lysine and the -COO- group of
aspartic acid.
– Hydrophobic interactions, as for example, between the nonpolar
side chains of phenylalanine and isoleucine.

45. Cysteine
• The -SH (sulfhydryl) group of cysteine is easily
oxidized to an -S-S- (disulfide).

46. the permanent wave that isn’t
Heat
+
New S-S bonds

47. Tertiary Structure
• Forces that stabilize 3° structure of proteins

48. Tertiary Structures of Proteins
• the three dimensional shape of proteins that results
from further crosslinking, folding and interaction between
R groups

49. protein structure
ribbon
mesh
surface contour
Sperm Whale
Myoglobin
ribbon + side chains
space-filling model

50. relative compactness of proteins
• Hypothetical chain length of a protein if it were to
appear either as an α helix or β sheet

51. Common Motifs stable folding patterns in globular proteins

52. Common Motifs

53. Common Motifs
β microglobulin

54. Common Motifs

55. Common Motifs

56. Complex domain from simple motifs
immunoglobulin

57. quaternary structure

58. Quaternary Structure
• the arrangement of polypeptide chains into a
noncovalently bonded aggregation.
– The individual chains are held together by hydrogen
bonds, electrostatic interactions, and hydrophobic
interactions.
• Hemoglobin
– Adult hemoglobin: two chains of 141 amino acids
each, and two chains of 146 amino acids each.
– Each chain surrounds an iron-containing heme unit.

59. Hemoglobin
• The 4° structure of hemoglobin: made up of 4
subunits

60. Fibrous proteins: α keratin
• Evolved for strength (hair, wool, nails, claws, quills…)
• Right handed α helix
• Coiled-coil provides added strength (like a twisted rope)

61. Fibrous proteins: collagen
• Like keratin, collagen also evolved to provide strength
• Left-handed a chain (not an α helix)
• Right handed coiled coils – 3-stranded coil

62. Fibrous protein: silk
• Fibroin, the silk protein is in the β conformation
• Rich in Ala and Gly (for close packing)
• More extended than α helix conformation

63. Denaturation
• the process of destroying the native conformation
of a protein by chemical or physical means.
– Some denaturations are reversible, while others
permanently damage the protein.

65. protein folding and misfolding
• Molecular chaperones
assist in protein folding
for many
• Interact with partially
folded or improperly
folded polypeptides
• Misfolded proteins can
be lethal
Vacuoles
associated with
spongiform
encephalopathies

66. Protein Function
• Protein function often includes reversible binding
interactions with other molecules.
• Complementary interactions between proteins
and ligands are the basis of self vs non-self
recognition by the immune system.
• Specific protein interactions modulated by
chemical energy are the basis of muscle
movement.

67. oxygen-binding proteins have a
heme prosthetic group

68. oxygen-binding proteins have a
heme prosthetic group
hemoglobin
http://www.youtube.com/watch?v=5LjLFrmKTSA&feature=related

69. protein-ligand interactions can be measured
association equilibrium: Ka = [PL] / [P] [L]
dissociation equilibrium: Kd = [P] [L] / [PL]
O2 binding to myoglobin
θ = fraction of ligand-binding sites
occupied
Which protein (X or Y) has greater
affinity for ligand A?

70. Hemoglobin
Binds O2 is a cooperative process.
Binding affinity of Hb for O2 is increased by the O2
saturation of the molecule
with the first O2 bound influencing the shape of the
binding sites (conformation change) for the next O2

71. hemoglobin-O2 binding is influenced by pH
Hb, binds H+ and CO2 as well as
O2, but all at different sites.
Binding of H+ and CO2 is inversely
related to binding of O2.
Low pH = high [H+] = lower O2
binding.

72. hemoglobin-O2 binding allosterically
modulated by 2,3-bisphosphoglycerate
BPG reduces the affinity of
Hb for O2.
BPG binds at a site distant
from the O2-binding site
and regulates the affinity of
Hb for O2.

73. immune responses are mediated by protein
interactions that distinguish self and non-self
Cellular immune response - T cells destroy host cells infected by
viruses
Humoral immune response – B cells produce antibodies or
immunoglobulins against bacteria, viruses and foreign molecules

74. muscle contraction is also based on protein
interactions and conformational changes
Muscle contraction occurs by the
sliding of the thick (myosin) and thin
(actin) filaments past each other
Conformational
changes in the
myosin head
are coupled to
ATP hydrolysis
http://www.sci.sdsu.edu/movies/actin_myosin
_gif.html

75. 1.
What 2 functional groups are present in all amino acids?
2.
Name the simplest amino acid. Is it a chiral molecule?
3.
Approximately how many amino acids are needed to make the proteins found in the
body?

76. 5.
What is meant by the primary, secondary and tertiary structures of proteins?
6.
What type of bonds are responsible for the helix structure of some proteins?
5.
Linus Pauling and Robert Corey found that the C—N bond in the peptide link is
intermediate in length between a single and double bond. They also found that the
peptide bond is planar.
a) What does the length of the bond tell us about the strength and bond order?
b) What does the observations tell us about the ease of rotation about the C—N
peptide bond?

77. 9. What is the effect of the following changes on the O2 affinity of hemoglobin?
a)
Drop in pH of blood plasma
a)
A decrease of partial pressure of CO2 in the lungs
a)
Increase in BPG levels
a)
Increase in CO