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Proteins

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The Function of Proteins Amino Acids The Peptide Bond Structure of Proteins Myoglobin, Hemoglobin and Oxygen Overview of Protein Structure and Function – PowerPoint PPT presentation

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Title: Proteins


1
Proteins
  • The Function of Proteins
  • Amino Acids
  • The Peptide Bond
  • Structure of Proteins
  • Myoglobin, Hemoglobin and Oxygen
  • Overview of Protein Structure and Function
  • Effect of Temperature and pH

2
  • Proteins are among the essential compounds
    necessary for the normal functioning of a living
    system.
  • The name is derived from the Greek word
    Proteios, meaning first.
  • All proteins are made from amino acids.

3
The function of proteins
  • Enzymes Biological catalysts.
  • Antibodies They fight off infection.
  • Transport Move materials around
  • Ex. hemoglobin for O2.
  • Regulatory As hormones, they control
    metabolism.
  • Structural coverings and support
  • skin, tendons, hair, nails, bone.
  • Movement muscles, cilia, flagella.

4
Proteins are often gigantic in size
  • Insulin Molecular Wt 5700
  • Hemoglobin Molecular Wt 64,000
  • Virus Proteins Molecular Wt 40,000,000

5
Amino acids
  • All these proteins are made from the same
    building blocks.
  • Twenty common amino acids.
  • All are ?-amino acids except proline.
  • A primary amine is attached to the ? carbon.
  • ?-carbon - the carbon just after the acid.
  • H
  • R-C-COOH
  • NH2

6
Amino acids
  • Because an acid and base are both present, an
    amino acid can form a /- ion, called a
    zwitterion.
  • H H
  • R-C-COOH R-C-COO-
  • NH2 NH3
  • How well it happens is based on pH and the type
    of amino acid.

7
?-Amino acids
  • Except for glycine, the ? carbon is attached to
    four different groups - it is a chiral center.
  • For Carbohydrates
  • We used the D- form.
  • For Amino Acids
  • We use the L- form.

COO- H3N - C - H
R

The amino group is on the left side of the
fischer projection.
8
Classification of amino acids
  • The ?-amino acid group is the same in each of the
    amino acids.
  • They are classified by the polarity of the side
    chain (R).
  • Hydrophobic - water fearing
  • non-polar side chains
  • Hydrophilic - water loving
  • polar, neutral chains
  • negatively charged
  • positively charged

9
Neutral, nonpolarside chains
10
Neutral, nonpolarside chains
H -CH2-C-COO-
NH3
H3C H
H3C-CH2-CH-C-COO-
NH3
isoleucine
phenylalanine
proline
H2C CH-COO- H2C
NH2 H2C
11
Polar, neutral amino acids
H
HO-CH2-C-COO-
NH3
HO H CH3-CH-C-COO-
NH3
serine
threonine
tyrosine
tryptophan
H -CH2-C-COO-
NH3
H
CH2-C-COO- NH3
HO-
N
12
Polar, neutral amino acids
H HS-CH2-C-COO-
NH3
cysteine
O H
H2N-C-CH2-CH2-C-COO-

NH3
O H
H2N-C-CH2-C-COO-
NH3
glutamine
asparagine
13
Acidic, polar side chains
  • Based on having a pH of 7.

O H
-O-C-CH2-CH2-C-COO-
NH3
glutamic acid
O H
-O-C-CH2-C-COO-
NH3
aspartic acid
14
Basic, polar side chains
  • Based on a pH of 7.

H

H3N-CH2-CH2-CH2-CH2-C-COO-

NH3
lysine
NH2 H

H2N-C-N-CH2-CH2-CH2-C-COO-

NH3
arginine
H CH2-C-COO-
NH3
histidine
H
N
N
H
H

15
Essential Amino Acids
  • Proteins are constantly being produced in the
    body for growth and repair.
  • Of the 20 amino acids found in these proteins, 10
    cannot be synthesized by the body.
  • Arginine Methionine
  • Histidine Phenylalanine
  • Isoleucine Threonine
  • Leucine Tryptophan
  • Lysine Valine

16
  • Histidine is an essential amino acid for infants,
    but apparently not for adults.
  • Arginine is produced in the body but not in
    sufficient quantities to meet protein demand.

17
  • Complete or Adequate Proteins supply all of the
    essential amino acids. (Animal Proteins)
  • Incomplete Proteins Low in one or more of the
    essential amino acids (Vegetable Proteins)
  • Animal Proteins
  • Source Type of Protein Missing AA
  • Egg Complete None
  • Milk(Dairy) Complete None
  • Meat, fish Complete None

18
  • Vegetable Proteins
  • Source Type of Protein Missing AA
  • Wheat Incomplete Lysine
  • Corn Incomplete Lysine
  • Tryptophan
  • Rice Incomplete Lysine
  • Beans Incomplete Methionine
  • Tryptophan
  • Peas Incomplete Methionine
  • Quinoa Complete
  • Hemp Complete

19
  • A complete assortment of amino acids can be
    obtained from a vegetable diet by pairing a
    vegetable protein missing one essential amino
    acid with a vegetable that contains it.
  • The two vegetable proteins are called
    complementary proteins.
  • Ex. Rice and Beans

20
  • Kwashiorkor A condition where diet is deficient
    in protein. Child fails to grow, develops a
    fatty liver, abdomen becomes enlarged due to
    edema.

21
Amphoteric Properties of Amino Acids
  • Amphoteric substances act as acids or bases.
  • They are acids when they donate protons.
  • They are bases when they accept protons.
  • Amino acids can act as acids or bases.
  • When placed in an acidic solution (low pH), they
    act as bases by accepting protons and becoming
    positively charged.
  • In basic solutions (high pH), they act as acids
    by donating protons and becoming negatively
    charged.

22
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23
  • Amino Acids function as buffers because they can
    neutralize small increases of acid or base.
  • Proteins are one of the major buffering systems
    in the body.

24
ISOELECTRIC POINT (pI)
  • A Zwitterion, which is electrically neutral
    overall, can only exist at a specific pH value.
  • This pH value, called the isoelectric point, is
    different for each amino acid.
  • Amino acids with hydrocarbon R groups attain
    their isoelectric point between pH 5.0 and 7.0
  • ex. Leucine pH 6.0
  • Basic amino acids need high pH values to reach
    their isoelectric points.
  • ex. Arginine pH 10.8

25
  • Acidic amino acids need low pH values.
  • ex. Aspartic acid pH 3.0
  • Proteins also have isoelectric points depending
    on the amino acids that make them up.
  • At their pH, proteins become insoluble in water,
    clump together, and precipitate out of solution.

26
  • Ex. Adding acid to milk eventually causes casein
    (pI 4.7) to become insoluble, solidify, and
    separate. (curds)

Yogurt and cheese are made by adding a bacteria
to milk that produces an acid.
27
The peptide bond
  • Proteins are polymers made up of amino acids.
  • Peptide bond - how the amino acids are
  • linked together to make a protein.

This is a condensation reaction H2O is
eliminated.
28
  • This bond between the two amino acids is called a
    peptide bond.
  • Two amino acids joined like this give what is
    called a dipeptide.

These 2 amino acids could also link the other way.
29
  • Any two amino acids can be joined in a similar
    manner to form dipeptides.
  • It doesnt end here ! Each dipeptide still has a
    COOH and an NH2 that can form new peptide bonds.
  • Adding a 3rd amino acid gives us a tripeptide.
  • This process can be continued to get a
    tetrapeptide, a pentapeptide, and so on until we
    have a chain of hundreds or even thousands of
    amino acids.

30
  • The chains of amino acids are the proteins.
  • The shorter chains are often called polypeptides.
  • Ex. Glucagon with 21 amino acids is a large
    polypeptide.
  • Insulin with 51 amino acids is a very small
    protein.
  • We will consider a protein to be a peptide chain
    with a minimum of 30 amino acids.

31
Primary structureof proteins
  • Primary Structure What are the amino acids that
    make up the protein and how are they arranged in
    the chain ? (The amino acid sequence)

32
  • The amino acids in a chain are often referred to
    as residues.
  • Ex. Ala-gly-lys 3 residue amino acids
  • The amino acid residue with the free COOH group
    is called the C-terminal, and the amino acid
    residue with the free NH2 group is called the
    N-terminal.
  • Peptide and protein chains are always written
    with the N-terminal residue on the left.

33
Peptides
N-terminal residue
C-terminal residue
peptide linkages
34
  • The continuing pattern of peptide linkages is
    called the backbone of the protein molecule.

The R groups are called the side chains.
The 20 different amino acid side chains provide
variety and determine the chemical and physical
properties.
35
  • The isoelectric point of a protein occurs at a pH
    where the positive and negative charges are
    balanced.
  • The number of COO- groups equals the number of
    NH3 groups.
  • At any pH above the pI, the protein molecules
    have a net negative charge.
  • At any pH below the pI, the protein has a net
    positive charge.

36
  • Just like the amino acids, proteins are soluble
    when they have a net or - charge.
  • At the pI, the repulsive forces between these
    charges are at a minimum.
  • The protein molecules clump together and can be
    precipitated from solution.

37
  • Each peptide and protein molecule in biological
    organisms has a different sequence of amino
    acids.
  • It is this sequence that allows the protein to
    carry out its function, whatever it might be.
  • The number of different protein possibilities is
    staggering.
  • Ex. A tripeptide can have 20 different amino
    acids at each position.
  • 20 x 20 x 20 8000 possible tripeptides

38
  • A typical protein with 60 amino acid residues can
    have up to 2060 different arrangements.
  • This means that there would be 1 x 1078
    possibilities.
  • 1,000,000,000,000,000,000,000,000,000,000,000,000,
    000,000,000,000,000,000,000,000,000,000,000,000,
    000,000.

39
Secondary structureof proteins
  • Long chains of amino acids will commonly fold or
    curl into a regular repeating structure.
  • Structure is a result of hydrogen bonding between
    amino acids within the protein.
  • Common secondary structures are
  • ? - helix
  • ? - pleated sheet
  • Secondary structure adds new properties to a
    protein like strength, flexibility, ...

40
?-Helix
One common type of secondary structure. Propertie
s of ?-helix include strength and low solubility
in water. Originally proposed by Pauling and
Corey in 1951.
41
?-Helix
Every amide hydrogen and carbonyl oxygen is
involved in a hydrogen bond. There are 3.6 amino
acids in each turn. Multiple strands may entwine
to make a protofibril.
The R groups extend out from the helical portion
of the ?-helix
42
?-Helix example
myosin head
myosin tail
ATP and actin binding sites
thick filament thin filament
actin
myosin/actin structure Proteins used in muscle
troponin
43
?-Pleated sheets
  • Another secondary structure for protein.
  • Held together by hydrogen bonding between
    adjacent sheets of protein.

44
?-Pleated sheets
  • Silk fibroin - main protein of silk is an example
  • of a ? pleated sheet structure.

Composed primarily of glycine and alanine. Stack
like corrugated cardboard for extra strength.
45
Linus Pauling
http//www.youtube.com/watch?vyh9Cr5n21EE
46
Collagen
  • Family of related proteins.
  • About one third of all protein in humans.
  • Structural protein
  • Provides strength to bones, tendon, skin, blood
    vessels.
  • Forms triple helix - tropocollagen.

47
  • Collagen consists of 3 protein chains each wound
    about its own axis in a left handed helix.
  • It is much more open than the coiled alpha helix
    chains.
  • Hydrogen bonds between chains hold them together.
  • Collagen chains are somewhat cross-linked by
    covalent bonds.

48
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49
  • As an animal grows older, the extent of
    cross-linking increases and the meat gets
    tougher.
  • Treatment with boiling water converts collagen to
    gelatin. Therefore, cooking meat converts part
    of the tough connective tissue to gelatin, making
    the meat more tender. (ex. Stewing chickens)

50
  • Tanning hides increases the degree of
    cross-linking, converting skin to leather.

51
  • Wool, hair and muscle are all formed from strands
    of alpha helixes.
  • These proteins can be stretched because the
    hydrogen bonds can be elongated and then return
    to the original configuration.
  • This is especially true for wool.

52
  • In hair, horn, nails and muscles, the adjacent
    helices are not precisely parallel but are wound
    around each other like strands of a rope.
  • These ropes are called protofibrils and there may
    be 3 or 7 alpha helices as strands.
  • Horns, nails, and claws have less flexibility due
    to more extensive cross linking by disulfide
    bridges.

53
DISULFIDE BRIDGES
  • Disulfide bridges are covalent bonds formed when
    2 cysteine units are oxidized to form a cystine
    unit.

SH SH
S
oxidation
S
reduction
The strength of this bond is much greater than
that of a hydrogen bond.
54
Collagen and Vitamin C
  • Major use of vitamin C is for making collagen.
  • Vitamin C ascorbic acid
  • Proline and lysine in collagen are converted to
    4-hydroxyproline and 5-hydroxylysine using this
    vitamin.
  • Scurvy - disease from lack of Vitamin C results
    in skin lesions, bleeding gums and fragile blood
    vessels.

55
  • Fibrous proteins
  • insoluble in water
  • form used by connective tissues
  • silk, collagen, ?-keratins
  • Globular proteins
  • soluble in water
  • form used by cell proteins
  • 3-D structure - tertiary

56
Tertiary structure of proteins
  • This refers to how the molecule is folded. It
    makes the molecule very compact.
  • Results from interaction of side chains.
  • Protein folds into a tertiary structure.
  • This is typical of proteins called globular.
  • Found in egg and serum albumin, hemoglobin and
    myoglobin, and enzymes and antibodies.

57
Types of tertiary bonding
  • Possible side chain interactions
  • - Similar solubilities
  • - Ionic attractions
  • - Attraction between ? and ?- sidechains
  • - Covalent bonding

58
Tertiary structureof proteins
59
Side chain interactions Help maintain specific
structure. Oxidation of cysteine - crosslink
formation.
covalent disulfide bond
oxidation O
60
  • Hydrophobic attractions
  • Attractions between R groups of non-polar amino
    acids.
  • Hydrogen bonding
  • Interaction between polar amino acid
  • R groups.
  • Ionic bonding
  • Bonding between oppositely charged amino acid R
    groups.

61
Quaternary structureof proteins
  • Many proteins are not single peptide strands.
  • They are combinations of several proteins
  • - aggregate of smaller globular proteins.
  • Conjugated protein - incorporate another type of
    group that performs a specific function.
  • - prosthetic group

62
Quaternary structureof proteins
Aggregate structure This example shows
four different proteins and two
prosthetic groups.
63
Examplecytochrome C 550
Ring structure Contains Fe2 Used in
metabolism.
Aggregate of several types of proteins
and structures.
64
Hemoglobin and myoglobin
  • Hemoglobin
  • oxygen transport protein of red blood cells.
  • Myoglobin
  • oxygen storage protein of skeletal muscles.
  • Both proteins rely on the heme group as the
    binding site for oxygen.

65
Myoglobin
Heme
66
Hemoglobin
2 ? chains
4 heme
2 ? chains
67
Hemoglobin and oxygen transport
  • In the lungs, there is an abundance of O2 so
    oxygen is picked up by the hemoglobin.
  • When blood reaches the cells, there is a lack of
    O2 so oxygen is given up by the hemoglobin.

Hb 4 O2 Hb(O2)4
Hb 4 O2 Hb(O2)4
68
Sickle cell anemia
  • Defective gene results in production of mutant
    hemoglobin - one misplaced amino acid. Glutamate
    is replaced by valine at 2 of the 547 positions.
  • Still transports oxygen but results in deformed
    blood cells - elongated, sickle shaped.
  • Difficult to pass through capillaries.
  • Causes organ damage, reduced circulation.
  • Affects 0.4 of American blacks.

69
Sickled cells
70
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71
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72
Comparison of normal andsickle cell hemoglobin
Normal
Sickle
73
Summary ofprotein structure
primary
secondary
tertiary
quaternary
74
Effect of temperature and pH on proteins
  • Both will alter the 3-D shape of a protein if you
    go beyond a normal range.
  • Disorganized protein will no longer act as
    intended - denatured. They become biologically
    inactive.
  • They will clump together - coagulate.
  • Examples - frying an egg
  • HCl in stomach

75
Denaturing of a protein
denatured coagulated
heat or acid
heat or acid
76
  • Changes in pH or temperature may not break any of
    the peptide bonds.
  • The primary structure is maintained.
  • If denaturation occurs under extremely mild
    conditions, the protein may be restored to its
    original shape.

77
  • COAGULATION
  • Most changes are so drastic that the protein
    remains denatured.
  • Protein strands become insoluble and precipitate
    out of solution (coagulate).
  • Effects of coagulation are irreversible.

78
Hydrolysis
  • Will result in protein being reduced to simpler
    peptides and amino acids.
  • Amount of hydrolysis depends on pH, time and
    temperature.

H or OH-
79
Effect of pH on proteins
lower pH
raise pH
Changing pH will alter charge on protein. This
alters their solubility and may change their
shape.
-COO-
80
  • Proteins are often biologically active only at
    certain pH ranges.
  • For most enzymes, the optimum pH is 7.0 to 7.5
  • Two exceptions are the digestive enzymes pepsin
    and trypsin.
  • Pepsin in acidic stomach pH 2.0
  • Trypsin in small intestine pH 8.0

81
  • The effect of acid or base is to add or remove H
    to ionic side groups.
  • Salt bridges and hydrogen bonds are disrupted.
  • When a protein is placed in a strong acid or
    base, coagulation may also occur.
  • Ex. Cheese made from acid coagulated protein
    (casein) which forms curds.

82
  • Tannic acids in burn ointments cause protein
    coagulation at the site of the burn.
  • This forms a protective coating which acts as a
    barrier to further loss of fluids.
  • A household source of tannic acid is Tea.
  • Applying dampened tea bags to a burn will
    precipitate protein and form a protective barrier
    over the wound.

83
Heat and UV Light
  • Optimum temperature for most proteins is 37C.
  • Very few proteins remain biologically active
    above 50 C. (Some bacteria have protein that
    remains stable up to 70 C and higher)
  • Increased Thermal activity (heat or UV) disrupts
    some of the hydrogen bonds and attractions
    between non-polar side groups that maintain
    secondary and tertiary structures.

84
  • When you cook food, you are denaturing protein.
  • Ex. Boiling an egg, frying a steak.
  • High temperatures are used to disinfect surgical
    instruments, gowns, and gloves.
  • AUTOCLAVE.

85
ORGANIC SOLVENTS
  • Solvents like Ethanol, isopropyl alcohol, and
    acetone disrupt the hydrogen bonding of proteins
    by forming their own hydrogen bonds with the
    protein.
  • These solvents are used as disinfectants.
  • A 70 solution of ethanol or IPA can pass thru
    cell walls of bacteria
  • Once inside, they cause coagulation of the
    bacterial proteins within the cell.
  • A 90 solution isnt nearly as effective. Why?

86
Heavy Metal Ions
  • Metal ions like Ag, Pb 2, Hg 2, etc.. cause
    denaturation of protein.
  • The heavy metals react with the disulfide bonds
    and the carboxyl groups of acidic amino acids.
  • The denatured protein is insoluble and
    precipitates out of solution.
  • Ex. 1 AgNO3 placed in eyes of newborn to kill
    the bacteria that causes gonorrhea.

87
  • When these ions are ingested, stomach proteins
    are severely disrupted.
  • The antidote is high protein foods like eggs,
    milk, or cheese.
  • The food protein ties up the metal ions until the
    stomach can be pumped or vomiting induced.

88
Other Methods of Denaturation
  • Agitation Violent whipping action causes a
    stretching of globular proteins which turns egg
    whites into meringues and whipping creams into
    toppings. How does cream of tartar work?
  • Which would be best for beating eggs into
    meringue a glass bowl or a copper bowl?
  • Why can canned pineapple be used in gelatin
    deserts while fresh pineapple cant be used?

89
  • Alkaloidal Reagents Many naturally occurring
    organic bases with nitrogen in their structure
    affect salt bridges and hydrogen bonding.
  • The Tannic acid mentioned earlier is an example.
    It is called an alkaloid reagent because it was
    originally used to study the structures of
    alkaloids.
  • Reducing Agents Compounds that disrupt the
    disulfide bridges formed between cysteine groups.
    (Permanent Waves use ammonium thioglycolate)

90
Protein hormone examples
  • Source Action
  • Gastrin Stomach Causes stomach to
  • secrete HCl
  • Glucagon Pancreas Stimulates liver to
  • metabolize glycogen
  • Insulin Pancreas Control of glucose in
  • blood
  • Prolactin Pituitary Stimulates lactation
  • Vasopressin Pituitary Decreases level of urine
  • prodction

91
Size of some important proteins
  • Molecular Number of amino
  • Protein weight acid residues
  • Insulin 6,000 51
  • Cytochrome c 16,000 104
  • Hemoglobin 65,000 574
  • Gamma globulin 176,000 1320
  • Myosin 800,000 6100

92
Protein gallery
Human growth hormone 596 residues Originally
obtained from human cadavers. It would cost
20,000 per year to treat one child. Now
produced by genetically engineered bacteria.
93
Protein gallery
  • Immunoglobin FC - 262 residuals
  • A Y shaped protein actually composed of 4
    protein chains linked by disulfide bonds.

antigen-binding site
94
Protein gallery
Lipoprotein 116 residues 2 helical strands
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