The Nitrogen Cycle What Are Proteins?

Nitrogen-fixing
bacteria
 Large molecules
Air
Nitrogen
Soil
Nitrates
 Made up of chains of amino acids
denitrifying
bacteria
 Are found in every cell in the body-the chief constituents of
Synthesis
all cells in the body
Soluble
 Are involved in most of the body’s functions and life
Nitrogen Plant processes
Proteins and Amino Acids compounds
in soil
Protein

 The sequence of amino acids is determined by DNA

decay

Digestion &
synthesis
Animal
Animal
Waste
Protein
products

metabolism

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Best Sources of Protein

Best Sources of Protein How Does the Body Use Protein?
 Proteins are abundant in  “protein” is derived from the Greek word “_________” ~
• __________ of first importance
• __________
• __________  Functions of protein
• Provide structural and mechanical support:
• Meat alternatives such as __________, __________, - Building of new cells
_________and __________ - Maintenance of existing cells
 3 oz serving of cooked meat, poultry, or fish - Replacement of old cells
- Muscular activity (contraction)
• Provides _________ grams of protein - Components of skin, hair, nails, connecting and supporting tissues
• About _______ • Source of energy (when necessary):
• About the size of a ____________ - 1 g protein ~ 4 kcal energy
- 1 g carbohydrate ~ 4 kcal energy
• Adequate amount for one meal - 1 g lipid ~ 9 kcal energy

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How Does the Body Use Protein? Structure of Proteins

• Regulation of metabolic processes
- Catalysis of biochemical reactions : enzymes
- Regulation of metabolic processes: hormones
• Help maintain acid base balance: Blood buffers
• Transport nutrients (e.g. hemoglobin: oxgyen)
• Transmission of impulses: Nerves
• Transmission of hereditary characteristics: nucleoproteins
• Assist the immune system
- Defense against infection: antibodies
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 Made up of chains of amino acids; classified by number of
amino acids in a chain
• Peptides: fewer than 50 amino acids
- Dipeptides: _____ amino acids
- Tripeptides: _____ amino acids
- Polypeptides: more than ____ amino acids
• Proteins: more than 50 amino acids
- Typically _____ to ________ amino acids linked
together
 Chains are synthesized based on specific bodily ______
 Amino acids are composed of ______, _______, _______,
and ________
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Structural Differences Between Carbohydrates,
Lipids, and Proteins
The Anatomy of an Amino Acid
Peptide Bonds Link Amino Acids
 Form when the acid group (COOH) of one amino acid joins
with the amine group (NH2) of a second amino acid
 Formed through ___________
 Broken through ___________

Figure 6.1 Figure 6.2b © 2010 Pearson Education, Inc.

Condensation and Hydrolytic Reactions

Essential, Nonessential, and Conditional
 ____________ – must be consumed in the diet
 ____________ – can be synthesized in the body
 _____________________ – cannot be synthesized due to
illness or lack of necessary precursors
• Premature infants lack sufficient enzymes needed to
create arginine

Figure 6.3 © 2010 Pearson Education, Inc.

The 20 Amino Acids Found in Proteins Stereoisomers of -amino acids

Stereochemistry of -amino acids

All amino acids in

proteins are L-amino
acids, except for
____________, which
is achiral.
 RS Nomenclature System (Cahn, Ingold, Properties of Cysteine Side Chain
Prelog System) Alternative Representation of Amino Acids

SH
pKa = 8.2 Side chains with -SH or
S
All L-amino acids in proteins are S, except for + H+ -OH can ionize, making
H3N COO H3N COO
cysteine, which is R. them more nucleophilic.

CH3
H3N (S) COO H3N COO H3N COO
H C CH3
Leucine CH2 = =
HS
oxidation
+ 2H+
Oxidation between pair of
H3N C COO S
H
H3N (S) COO
S + 2e-
cysteine side chains results
SH reduction in disulfide bond formation.
H3N COO
H3N COO

SH
Cysteine CH2
=
SH
=
H3N (R) COO
H3N C COO
H
H3N (R) COO SH Disulfide bonds are mainly found in extracellular proteins; the ~5 mM
glutathione (g-Glu-Cys-Gly) makes the inside of the cell a highly
reducing environment.

Hydroxyl-Containing Amino Acid Side Chains Tyrosine, Serine and Threonine Can Be Modified or Unusual Amino Acids
Phosphorylated in Proteins
pKa = 13
OH O
+ H+ Example: Tyrosine
Serine H3N COO H3N COO

:Base-Enzyme (Kinase)
O H

pKa = 13
HO CH3 O CH3 N
H
H+
Threonine H3N COO H3N COO
+ O

Tyrosyl Residue in a Protein

O O
NH2 P
O O
O N
N

O O O N N
OH pKa = 10.1 O + O P O P O P O O
O O O N
Tyrosine + H+ N
H OH OH
H
O
O Mg2+
H3N COO Phosphotyrosyl Residue
H3N COO
+ ADP

Amphoteric Nature Isoelectric Point The Isoelectric Points of Some Proteins

Amino acids are aphoteric
compounds ~ they can act
as either acid or base
When an amino acid is placed in
a basic solution, it forms a
negatively charged ion that
will be attracted toward a
positively charged electrode
When an amino acid is placed in
an acidic solution, it forms a
positively charged ion that
will be attracted toward a
negatively charged electrode
A certain pH where an amino At a protein’s isoelectric point:
acids will not migrate __________ solubility
toward either positive or __________ viscosity
negative electrode : __________ osmotic pressure
~ amino acids become neutral; Above isoelectric point:
~equal number of positive and More ___________ charges
Amphoterism accounts for the ability
than ___________ charges
of amino acids to act as __________ negative ions
in the blood
Isoelectric point vary from each Below isoelectric point:
kind of proteins More ___________ charges
than ___________ charges
Isoelectric Focusing Formation of a Peptide

Electrophoresis through polyacrylamide gel in

which there is a pH gradient.

cis and trans Isomers

Planarity of Peptide (Amide) Bond

The ______ isomer is generally more

stable because of ___________ of
side chains in the cis isomer.

Examples of Oligopeptides
N- and C-Termini May Be Modified in
Proteins
 Structure of the Protein Denaturing
Molecular Data on Some Proteins
 Four levels of structure  Alteration of the protein’s shape and thus functions
• ______________ structure through the use of
• ______________ structure • __________
• ______________ structure • __________
• ______________ structure • __________
• __________
• ___________________
Any alteration in the structure or sequencing changes  Primary structure is unchanged by denaturing
the shape and function of the protein

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Primary Structure Primary Structure of Bovine Insulin Secondary Structures

– ___________________________________________ - regular recurring arrangement of the amino acid chain;
- local spatial arrangement of a polypeptide’s backbone atoms
First protein to be fully sequenced (by (without regard to side chain conformation);
-ala-glu-val-thr-asp-pro-gly- … Fred Sanger in 1953). For this, he won his - main-chain H-bonds that define short-range order in structure
first Nobel Prize (his second was for the
• Can be determined by amino acid sequencing of the protein Sanger dideoxy method of DNA Forms:
sequencing).
• Can also be determined by sequencing the gene and then  , 310,  helices
using the codon information to define the protein sequence  pleated sheets and the strands that comprise them
• Amino acid analysis means percentages; (less informative  Beta turns
than the sequence)
 More specialized structures like collagen helices

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Characteristics of  helices Alpha helix

 Amino acids form a coil or spiral Other helices
 The coils consist of loops of amino acids held  310 helix is NH to C=O three residues
together by hydrogen bonds (between the –H earlier
of the –NH2 of one amino acid and the O of • More kinked; 3 residues per turn
the C=O of the acid part of another amino acid • Often one H-bond of this kind at N-
 Each turn of the helix contains an average of terminal end of an otherwise -helix
3.6 amino acids 
 Flexible and elastic   helix: even rarer: NH to C=O five
 Amino acid side chains face outward residues earlier
 ~ 10 residues long in globular proteins
Most helices are ____________ because of the
Examples: L-configuration of naturally occurring amino
Alpha-keratin (hair, wool, nails, …) acids

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 Beta strands
 Consists of parallel strands of polypeptides
held together by H-bonds
 Flexible but not elastic
 No defined interval in sequence number
between amino acids involved in H-bond
Example: Silk (strong but resistant to stretching)
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Sheets: roughly planar
 Folds straighten H-bonds
 Side-chains roughly
perpendicular from sheet plane
 Consecutive side chains up,
then down
 Minimizes intra-chain
collisions between bulky side
chains
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Anti-parallel
beta sheet
 Neighboring strands extend in opposite
directions
 Complementary C=O…N bonds from top to
bottom and bottom to top strand
 Slightly pleated for optimal H-bond strength
Example: Silk fibrion
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Silk fibroin Parallel Beta Sheet Beta turns

 Antiparallel beta  Abrupt change in direction
sheets running  N-to-C directions are the same for both strands
 , angles are
parallel to the silk  You need to get from the C-end of one strand
fiber axis to the N-end of the other strand somehow characteristic of beta
 Multiple repeats of  H-bonds at more of an angle relative to the  Main-chain H-bonds maintained
(Gly-Ser-Gly-Ala- approximate strand directions almost all the way through the
Gly-Ala)n  Therefore: more pleated than anti-parallel turn
sheet  Jane Richardson and others have
characterized several types

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Collagen Triple Helix

TIM barrel
Tertiary Structure
 Alternating ,  creates parallel -pleated
 Refers to sheet
___________________________________  Bends around as it goes to create barrel
_______
 Three left-handed helical  The overall 3-D arrangement of atoms in a
strands interwoven with a single polypeptide chain
specific hydrogen-bonding
interaction  Described in terms of sequence, topology,
overall fold, domains
 Every 3rd residue approaches
other strands closely: so  Gives proteins their specific biologic
they’re glycines activity

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 Quaternary Structure
 Stabilized by
 Occurs when two or more protein units (each with
• Salt bridges its own primary, secondary, and tertiary structure) Not all proteins have all four levels of structure
- Formed between positively and negatively charged groups within the
combine to form a complex unit
protein structure (example: carboxyl and amino side chains found in
glu, lys, arg, asp
 Monomeric proteins don’t have quaternary
 Spatial arrangement of subunits of proteins structure
• van der Waals interactions, composed of multiple polypeptides (protein
complexes)  Tertiary structure: subsumed into 2ndry
• Hydrogen bonds (can form between different segments of the coil) structure for many structural proteins
• Disulfide bonds (can form between cysteine groups in the different  Individual chains can be identical or different (keratin, silk fibroin, …)
parts of the coil) • If they’re the same, they can be coded for by the same gene
• If they’re different, you need more than one gene  Some proteins (usually small ones) have
• Hydrophobic bonds (can be formed in nonpolar amino acids no definite secondary or tertiary structure;
folded on the “inside” of the protein)
they flop around!
• Polar group interactions (formed between polar amino acids on
the “outside” of the protein molecule and water molecules)

The hemoglobin
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Percent Composition
Categories of Proteins
 The amount of protein present in food is determined
by determining the amount of N present  Simple = _____________ + ______________
 The average %N in a protein is 16% or 1/6 of the
amount of protein.  Conjugated = _____________ + _____________
Example:
A 100g sample of food yields 4 g of N on chemical
 Derived – produced by the action of chemicals,
analysis. What is the amount of protein? enzymes, or physical forces on either simple or
conjugated proteins
Answer: Example: proteoses, peptones, polypeptides, tripeptides,
dipeptides

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Classification of Proteins  Nucleoproteins

 Classification According to Composition
• Based on solubility, composition, function or shape • Conjugated proteins are classified based on the  Glycoproteins
 Classification According to Solubility nature of non-protein portion of the molecule • (carbohydrate: hexoses, mannose, galactose,
Type Non-protein Portion of Examples
pentoses arabinose and xylose, and sialic acids)
Type of Solubility Coagulated Examples the molecule • Glucose is not found in glycoproteins except for
Protein by Heat Nucleoproteins Nucleic acid Chromosomes collagen
Albumins Soluble in water and salt Yes Egg albumin, serum
solutions albumin, lactalbumin
Glycoproteins Carbohydrate Mucin in saliva
• Human cell membranes are 5% carbohydrate
Phosphoproteins Phosphate Casein in milk
Globulins Slightly soluble in water; soluble Yes Serum globulin, present in glycoproteins and glycolipids
Chromoproteins Chromophore group Hemoglobin, hemocynin,
in salt solutions lactoglobulin, vegetable Examples:
(color-producing group) flavoproteins, cytochrome
globulin
Lipoproteins Lipids Fibrin in blood - glycophorin – found in membranes of human
Albuminoids Insoluble in all neutral solvents No Keratin in hair, nails,
and in dilute acid and alkali feathers, collagen Metalloproteins Metals Ceroplasmin (contains Cu) erythrocytes
Histones Soluble in salt solutions; No Nucleohistones in
and siderophilin (contains - Heparin – inhibits blood clotting
Fe) in blood plasma
insoluble in very dilute NH4OH thymus gland, globin in
hemoglobin

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 • Structural glycoproteins: collagen
• Lubricants: mucin and mucous
secretions
• Transportation molecules:
• Immunoglobulins: interferon
• Hormones: thyrotropin (TSH)
• Enzymes: hydrolases and nucleases
• Hormone receptor sites
• Specification of human blood types
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• VLD lipoproteins
- Transport TAG synthesized by the liver to other
parts of the body
- Note: the breakdown of VLDL produce
intermediate density lipoproteins (IDL) and low
density lipoprotein (LDL)
- LDL provides cholesterol for cellular needs; in
excess, thought to promote coronary heart
disease by clogging coronary artery walls and
eventually develop into atherosclerotic plaque
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 Classification According Shape
• Globular proteins – consists of polypeptides
folded into shape of a “ball”; soluble in water or
form colloidal dispersions
- Length to width ration: <10
Examples: hemoglobin, albumins, globulins
• Fibrous proteins – consists of parallel
polypeptide chains that are coiled and stretch
out; insoluble in water
- Length to width ration: >10
Examples: collagen, fibrin, myosin
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 Lipoproteins (proteins containing lipids; part of cell • Chylomicrons
membranes)
- Produced in the intestinal mucosa used to
• Plasma lipoproteins (consist of a neutral lipid core of transport dietary lipids into the blood plasma via
TAG and cholesterol ester that is surrounded and the thoracic lymph duct
stabilized by free cholesterol, protein, and
phospholipid. - Removed from the plasma with a half life of 5-15
min
- The relative proportions of nonpolar lipid, protein,
and polar lipid determine the density, size, and - Responsible for the creamed-tomato-soup
appearance of the blood following a meal
charge f the resulting lipoproteins
containing fats
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 Classification According Function
• HD lipoproteins (HDL)
- Involve in the catabolism of other lipoproteins Type of Example Use
Protein
• Lipoprotein (a) Structural Collagen Structure of connective tissue
- Recently detected lipoprotein with similar Keratin Structure of hair and nails
structure as that of human plaminogen Contractile Myosin, actin Muscle contraction
Storage Ferritin Storage of iron needed to make
- Links atherosclerosis and thrombosis but found to hemoglobin
be an independent risk factor for coronary heart Transport Hemoglobin Carrying oxygen
disease Serum albumin Carrying fatty acids
Hormones Insulin Metabolism of carbohydrates
↑ LDL: increases risk of coronary artery disease
Enzymes Pepsin Digestion of proteins
↑ HDL: reduces the risk of coronary artery disease in women
Women HDL: 55 mg/100 mL Men HDL: 45 mg/100 mL Protective Gamma globulin Antibody Formation
Fibrinogen Blood clotting
 HDL is increased by aerobic exercise and running
Toxins Venoms Poisons
Marathon runner average HDL: 65 mg/100 mL
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Properties Denaturizing Agents
 Colloidal Nature (forms colloidal dispersion with water)  Alcohol can coagulate all proteins except prolamines
• Can pass through a filter paper but not a membrane • Forms hydrogen bonds that compete with naturally
- Proteins present in the blood stream cannot pass through occurring H-bonds in the polypeptide; irreversible
capillaries and should remain in the blood stream otherwise  Salts of Heavy Metals
there is damage with the membranes of the kidneys -
nephritis • very poisonous when ingested
 Denaturation (unfolding and rearrangement of the • Disrupt the salt bridges and disulfide bonds in the protein
secondary and tertiary structures of a protein without • irreversible
breaking the peptide bonds - Bichloride of mercury: HgCl2 (Antidote: egg white
• Protein loses its biological activity and must be removed from the body through emetic)
• Reversible denaturation – the protein can be restored to its - Lunar caustic: AgNO3 (mild sol’n: disinfectant in the
original conformation by reversing the conditions that caused eyes of neonates; strong solutions: cauterize fissures
denaturation else its irreversible and destroy excessive granulation tissues
• Primary structure is unchanged by denaturing
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 Heat
 pH  Oxidizing and reducing agents
• Disrupts intermolecular interactions
• Change in pH can disrupt H-bonds and salt bridges • Irreversible; disrupts disulfide bonds
- Mild: reversible
- Acids - Oxidizing agent: HNO3
- Intense: irreversible
- Bases - Reducing agents: sulfides and oxalates
• Testing urine for presence of protein is done by heating
• Casein in milk is coagulated in the stomach to form curd  Salting Out
 Alkaloidal Reagents when comes in contact with HCl. • Proteins are insoluble in saturated salt solutions and
• Irreversible; disrupts H-bonds and salt bridges • Heller’s Ring test: Testing urine for presence of albumin precipitate out unchanged.
- Tannic acid (used for treatment of burns) with HNO3 (white ring) - Proteins can be separated from a mixture by saturated
- Picric acid • Long period of exposure to acid or base, peptide bonds solution of salt where they coagulate and removed
 Radiation can coagulate proteins are broken through filtration and purified via dialysis
• Can be irreversible if H-bonds and hydrophobic bonds  Mechanical agitation
are disrupted
- UV, X-ray
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Denaturing a Protein
Deamination How Much Protein Do You Need?
 When the amino acid pool reaches capacity the amino acids  Healthy, nonpregnant adults
are broken down to their component parts for other uses • Should consume enough to replace what is used every
 First _________________ must occur day
 Carbon-containing remnants are • The goal is ___________________
• Converted to __________, if they are glucogenic amino  Pregnant woman, people recovering from surgery or injury,
acids, through _________________ and growing children
• Converted to fatty acids and stored as triglycerides in • Should consume enough to build new tissue
adipose tissue

Figure 6.5 © 2010 Pearson Education, Inc. © 2010 Pearson Education, Inc.

Nitrogen Balance and Imbalance

Not All Protein Is Created Equal Protein Quality
 High quality protein  Complete proteins
• _______________ • Contain all ________ essential amino acids
• _____________________________ • Usually __________ source are complete proteins
• _____________________________ • Are considered higher quality
 It helps to be aware of:  Incomplete proteins
• Amino acid score • Low in one or more essential amino acid
• Limiting protein • Usually ____________ sources are incomplete
• Protein digestibility corrected amino acid score
(PDCAAS)
• Biological value of protein rates absorption and retention
of protein for use

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Protein Needs Protein Bars Eating Too Much Protein
 Protein intake recommendations  Are marketed as convenient and portable  Risk of heart disease
• _______% of total daily kilocalories  Can be  Risk of kidney stones
• Adults over 18 • High in saturated fat and/or sugar  Risk of calcium loss from bones
- ______ g/kg daily • Low in fiber  Risk of colon cancer
• Expensive  Displacement of other nutrient-rich, disease preventing
 American College of Sports Medicine, the American  A peanut butter sandwich is portable and lower in saturated foods
Dietetic Association, and other experts advocate fat and sugar and higher in fiber than some protein bars
• ________% more protein for competitive athletes
participating in endurance exercise or resistance exercise
• Typically this population eats more and therefore gets
additional protein

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Eating Too Little Protein Too Little Protein Types of PEM: Kwashiorkor
 Severe protein deficiency
 Protein-energy malnutrition (PEM)  Without adequate protein • Generally result of a diet high in
• Protein is used for energy rather than its other functions • Cells lining the GI tract are not sufficiently replaced as grains and deficient in protein
in the body they slough off  Symptoms range from
• Other important nutrients are in short supply • Digestive function is inhibited • Edema in legs, feet, and stomach
• More prevalent in infants and children • Absorption of food is reduced • Muscle tone and strength
- 17,000 children die each day as a result • Intestinal bacteria gets into the blood and causes diminish
septicemia • Hair is brittle and easy to pull out
• Immune system is compromised due to malnutrition and • Appear pale, sad, and apathetic
cannot fight infection • Prone to infection, rapid heart
rate, excess fluid in lungs,
pneumonia, septicemia, and
water and electrolyte imbalances
(Image from http://www.thachers.org/pediatrics.htm)

© 2010 Pearson Education, Inc. © 2010 Pearson Education, Inc. © 2010 Pearson Education, Inc. Figure 6.16

Types of PEM: Marasmus Types of PEM: Marasmic Kwashiorkor Treatment for PEM
 Results from a severe deficiency
in kilocalories  Chronic deficiency in kilocalories  Medical and nutritional treatment can dramatically reduce
• Frail, emaciated appearance and protein mortality rate
• Weakened and appear apathetic • Have edema in legs and arms  Should be carefully and slowly implemented
• Many cannot stand without • Have a “skin and bones” • Step 1 – Address life-threatening factors
support appearance - Severe dehydration
• Look old • With treatment the edema - Fluid and nutrient imbalances
• Hair is thin, dry, and lacks subsides and appearance becomes
more like someone with marasmus • Step 2 – Restore depleted tissue
sheen - Gradually provide nutritionally dense kilocalories and
• Body temperature and blood high-quality protein
pressure are low • Step 3 – Transition to foods and introduce physical
• Prone to dehydration, activity
infections, and unnecessary
blood clotting
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Vegetarian Diet Potential Benefits, Risks of a Vegetarian Diet
 People choose vegetarian diets for a variety of reasons  Benefits of a healthy vegetarian diet
• Ethical • Reduced risk of
• Religious - Heart disease - Cancer
• Environmental - High blood pressure - Stroke
• Health - Diabetes - Obesity

 Vegetarians must consume adequate amounts of a variety  Potential risks of a vegetarian diet
of food and should plan meals well • Underconsumption of certain nutrients
- Protein
- Vitamin B12

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Vegetarian Food Guide Pyramid

Soy Putting It All Together
 Soy is increasing in popularity in the United States  Majority of daily kilocalories should come from
• High-quality protein source carbohydrate-rich foods
• Low in saturated fat  Fat intake should be no more than about one-third of daily
• Contains isoflavones kilocalories
 Protein should provide the rest of the daily kilocalories
• Phytoestrogens
• May reduce risk of heart disease
• Some research suggests it may reduce the risk of cancer
• Some concern it may promote breast cancer

© 2010 Pearson Education, Inc. Figure 6.18 © 2010 Pearson Education, Inc. © 2010 Pearson Education, Inc.