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Chapter 22: Proteins

K. Dunlap

Chem 104
Human Proteins
• proteins contain C,
H, O, and N
• Made up of 20
amino acids
• amino acids written
in blue are essential
a...
Proteins
• Proteins serve many functions:
– 1.Structure: collagen and keratin are the chief
constituents of skin, bone, ha...
Proteins
– 6. Protection: blood clotting involves the protein
fibrinogen; the body used proteins called
antibodies to figh...
Amino Acids
•Have an alpha- carbon
attached to:
• an amino group
• carboxyl group
• a hydrogen
• an R group
Each R group
determines the
properties of the
amino acid
R groups can be
polar, nonpolar,
acidic, basic
Each R group
determines the
properties of an
amino acid
R groups can be
polar, nonpolar,
acidic, basic
Chirality of Amino Acids
• With the exception of glycine, all proteinderived amino acids have at least one
stereocenter (t...
Zwitterions

• amino acids can act as acids and bases
•
•

Amino acids exist in solution as dipolar ions (Zwitterions)
Lik...
Proteins are made of 20 amino acids
proteins
Peptides: how aa are linked
• proteins are long chains of amino acids joined by
amide bonds.
peptide bond:
– amino acids b...
formation of peptide bonds
Peptides and proteins are
polymers of amino acids
• Two amino acids are
covalently joined in
co...
Peptides
– Peptide: A short polymer of amino acids joined by
Peptide
peptide bonds; they are classified by the number of
a...
4 levels of protein structure

• Primary – sequence of amino acids
• Secondary – interactions between adjacent amino
acids...
Levels of Structure
• Primary structure: the sequence of amino
acids
• Secondary structure: conformations of amino
acids i...
1) Primary Structure
• the sequence of amino acids in a polypeptide
chain.
• The number peptides possible from the 20
prot...
Primary Structure
• The hormone
insulin consists of
two polypeptide
chains held
together by two
interchain disulfide
bonds...
Primary Structure
• Just how important is the exact amino acid
sequence?
– Human insulin consists of two polypeptide chain...
Primary Structure
– Vasopressin and oxytocin are both nonapeptides
but have quite different biological functions.
– Vasopr...
proteins range in size
2) Secondary Structure
• conformations of amino acids in localized
regions of a polypeptide chain.
– The most common types...
α-Helix
• The α-helix structure: held together by
hydrogen bonds
α-Helix
• In a section of α-helix;
– The C=O group of
each peptide bond is
hydrogen bonded to
the N-H group of the
peptide...
secondary structure
• Note the position of the
purple R groups relative
to the backbone of the
polypeptide
all α helices are right handed
• But some
supramolecular
complexes are
left handed
(keratin,
collagen)

right-handed = clo...
β sheet secondary structure
• More extended
• H-bonds may occur between amino acids some
distance from one another
• Adjac...
β-Pleated Sheet
• In a section of β-pleated sheet;
– The C=O and N-H groups of peptide bonds from
adjacent chains point to...
Pleated Sheet Structure of
Proteins
secondary structure and function
3) Tertiary Structure
• the overall conformation of an entire
polypeptide chain.
• Tertiary structure is stabilized in fou...
Cysteine
• The -SH (sulfhydryl) group of cysteine is easily
oxidized to an -S-S- (disulfide).
the permanent wave that isn’t
Heat
+

New S-S bonds
Tertiary Structure
• Forces that stabilize 3° structure of proteins
Tertiary Structures of Proteins
• the three dimensional shape of proteins that results
from further crosslinking, folding ...
relative compactness of proteins

• Hypothetical chain length of a protein if it were to
appear either as an α helix or β ...
4) Quaternary Structure
• the arrangement of polypeptide chains into a
noncovalently bonded aggregation.
– The individual ...
Hemoglobin
• The 4° structure of hemoglobin: made up of 4
subunits
Denaturation
• the process of destroying the native
conformation of a protein by chemical or
physical means.
– Some denatu...
Protein Function
• Protein function often includes reversible
binding interactions with other molecules.
• Complementary i...
oxygen-binding proteins have a
heme prosthetic group
oxygen-binding proteins have a
heme prosthetic group

hemoglobin

http://www.youtube.com/watch?
Hemoglobin

Binds O2 is a cooperative process.
Binding affinity of Hb for O2 is increased by the O2
saturation of the mole...
hemoglobin-O2 binding allosterically
modulated by 2,3-bisphosphoglycerate

BPG reduces the affinity of
Hb for O2.
BPG bind...
immune responses are mediated by protein
interactions that distinguish self and non-self
Cellular immune response - T cell...
muscle contraction is also based on protein
interactions and conformational changes
Muscle contraction occurs by the
slidi...
1. What 2 functional groups are present in all amino acids?

2. Name the simplest amino acid. Is it a chiral molecule?

3....
5. What is meant by the primary, secondary and tertiary
structures of proteins?

6. What type of bonds are responsible for...
Proteins
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Proteins

  1. 1. Chapter 22: Proteins K. Dunlap Chem 104
  2. 2. Human Proteins • proteins contain C, H, O, and N • Made up of 20 amino acids • amino acids written in blue are essential amino acids, meaning they can not be made and must be consumed
  3. 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 Transport 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. 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. 5. Amino Acids •Have an alpha- carbon attached to: • an amino group • carboxyl group • a hydrogen • an R group
  6. 6. Each R group determines the properties of the amino acid R groups can be polar, nonpolar, acidic, basic
  7. 7. Each R group determines the properties of an amino acid R groups can be polar, nonpolar, acidic, basic
  8. 8. Chirality of Amino Acids • With the exception of glycine, all proteinderived amino acids have at least one stereocenter (the α-carbon) and are chiral. – The vast majority of protein-derived amino acids have the L-configuration
  9. 9. Zwitterions • 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” • Isoelectric point – pH at which all the molecules have equal positive and negative charges
  10. 10. Proteins are made of 20 amino acids
  11. 11. proteins
  12. 12. 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
  13. 13. 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
  14. 14. Peptides – Peptide: A short polymer of amino acids joined by Peptide peptide bonds; they are classified by the number of amino acids in the chain. – Dipeptide: containing two amino acids joined by a Dipeptide peptide bond. – Tripeptide: containing three amino acids joined by Tripeptide peptide bonds. – Polypeptide: chain containing up to 50 amino acids Polypeptide – Protein: A biological macromolecule containing at Protein least 30 to 50 amino acids joined by peptide bonds.
  15. 15. 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
  16. 16. 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 α-helix, β-pleated sheet, and random coil. • Tertiary structure: the complete threedimensional 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.
  17. 17. 1) Primary Structure • the sequence of amino acids in a polypeptide chain. • The number peptides possible from the 20 protein-derived amino acids is enormous. – the number of peptides possible for a chain of n amino acids is 20n. – for a small protein of 60 amino acids, the number of proteins possible is 2060 = 1078
  18. 18. Primary Structure • The hormone insulin consists of two polypeptide chains held together by two interchain disulfide bonds.
  19. 19. 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 p ositions 8-9-10 B Chain p osition 30 H uman Cow -Thr-Ser-Ile-A la-Ser-Val- -Thr -Ala H og -Thr-Ser-Ile- -Ala Sh eep -Ala-G ly-Val- -Ala
  20. 20. 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.
  21. 21. proteins range in size
  22. 22. 2) Secondary Structure • conformations of amino acids in localized regions of a polypeptide chain. – The most common types of secondary structure are α-helix and β-pleated sheet. α-Helix: a type of secondary structure in which a section of polypeptide chain coils into a spiral, most commonly a right-handed spiral. β-Pleated sheet: a type of secondary structure in which two polypeptide chains or sections of the same polypeptide chain align parallel to each other
  23. 23. α-Helix • The α-helix structure: held together by hydrogen bonds
  24. 24. α-Helix • In a section of α-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.
  25. 25. secondary structure • Note the position of the purple R groups relative to the backbone of the polypeptide
  26. 26. all α helices are right handed • But some supramolecular complexes are left handed (keratin, collagen) right-handed = clockwise
  27. 27. 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
  28. 28. β-Pleated Sheet • In a section of β-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.
  29. 29. Pleated Sheet Structure of Proteins
  30. 30. secondary structure and function
  31. 31. 3) Tertiary Structure • the overall conformation of an entire polypeptide chain. • Tertiary structure is stabilized in four ways: – Covalent bonds, as for example, the formation of disulfide bonds bonds between cysteine side chains. – Hydrogen bonding between polar groups of side chains, as for example between the -OH groups of serine and threonine. – Salt bridges, as for example, the attraction of the -NH3+ bridges group of lysine and the -COO- group of aspartic acid. – Hydrophobic interactions, as for example, between the interactions nonpolar side chains of phenylalanine and isoleucine.
  32. 32. Cysteine • The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S- (disulfide).
  33. 33. the permanent wave that isn’t Heat + New S-S bonds
  34. 34. Tertiary Structure • Forces that stabilize 3° structure of proteins
  35. 35. Tertiary Structures of Proteins • the three dimensional shape of proteins that results from further crosslinking, folding and interaction between R groups 1) disulfide linkages (-S-S-) b/w cysteins 2) dipole dipole interactions b/w polar groups 3) hydrogen bonding on side chains 4) London forces
  36. 36. relative compactness of proteins • Hypothetical chain length of a protein if it were to appear either as an α helix or β sheet
  37. 37. 4) Quaternary Structure • the arrangement of polypeptide chains into a noncovalently bonded aggregation. – The individual chains are held together by hydrogen bonds, salt bridges, 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.
  38. 38. Hemoglobin • The 4° structure of hemoglobin: made up of 4 subunits
  39. 39. 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.
  40. 40. 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.
  41. 41. oxygen-binding proteins have a heme prosthetic group
  42. 42. oxygen-binding proteins have a heme prosthetic group hemoglobin http://www.youtube.com/watch?
  43. 43. 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
  44. 44. 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.
  45. 45. 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
  46. 46. 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/
  47. 47. 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? 4. What element is present in proteins but not in sugars or fats?
  48. 48. 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?

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