Biochemistry
Intro to Macro molecules
2 main types of tertiary structures
 Globular
 form ball-like structures where hydrophobic parts
are towards the centre and hydrophilic are towards
the edges
 Structure=water soluble
 Found in watery environments
o cells, tissue fluid, or in fluids being transported
(blood or phloem)
 metabolic roles
 Ex: enzymes in all organisms, plasma proteins and
antibodies in mammals
 Fibrous
 form long fibres
 mostly consist of repeated sequences of amino acids
which are insoluble in water
 usually have structural roles
 Ex.
 Collagen in bone and cartilage
 Keratin in fingernails and hair
Special Proteins
Globular
Fibrous
 Spherical 3D shape
 Do not curl up in 3D ball
 Ex. Haemoglobin, insulin,
 Long, thin molecules
enzymes
 Water soluble
 Physiologically active
 Metabolic and transport
roles
 Molecules lie side-by-side
to form fibres
 Insoluble in water
 Not physiologically active
 STRUCTURAL roles
Haemoglobin
 Water soluble globular protein
 Structure
 two α polypeptide chains
 two β polypeptide chains
 Hydrophobic R groups face inwards (toward centre)
Helps maintain 3D shape
 Hydrophilic R groups face outwards
 Maintain solubility
 Each beta polypeptide chain has similar structure to myoglobin
 4 inorganic prosthetic groups
 Haem (heme) group
 Contains Iron (Fe2+) ion
 Oxygen is very attracted to Iron (think rust)
 Function
 carry oxygen around in the blood
 Due to presence of haem group

One Complete Haemoglobin molecule
 4 haem groups
 Each with one Fe2+ ion
 Carry 4 oxygen molecules
(O2)
 Total of 8 oxygen atoms
 Haem group responsible for
color of blood
 Purple NO oxygen with
the Fe
 Red oxygen has combined
with the Fe ion…
“oxyhaemoglobin”
Sickle Cell Anemia
 One of the polar AA (glutamic acid) in
the beta polypeptide chain is replaced with
AAValine (has a non-polar R group)
 Non-polar R group in the beta polypeptide
chain (which is found on outside of
molecule) makes haemoglobin much less
soluble
 Causes clots
 RBC inefficient at delivering Oxygen
 “Anemia” is when there is a lower than normal
RBC count
 Sickle RBC live only 10-20 day (normal RBCs
live about 120)
 Bone marrow cannot replace fast enough
Collagen: Fibrous protein
 Structure
 Three polypeptide chains wound
around each other
 Helical but NOT alpha helix (not tight
enough)
 Every third AA is a glycine
 Collagen molecule=3 polypeptide chains
wrapped around each other
 Hydrogen bonds form between these
coils, which are around 1000 amino
acids in length, which gives the
structure strength (tensile strength)
 Collagen Molecule
 When 3 collagen peptide chains
 Collagen Fibrils
 When collagen molecules wrap around
each other
 Collagen Fibres
 When many collagen fibrils wrap around
each other
 Covalent cross links
 Form between R groups of lysines in
the collagen molecules parallel to each
other
 Holds together collagen fibres
Collagen functions
 Form the structure of bones
 Makes up cartilage and
connective tissue
 Prevents blood that is being
pumped at high pressure
from bursting the walls of
arteries
 Is the main component of
tendons, which connect
skeletal muscles to bones
Haemoglobin vs. Collagen
 Haemoglobin may be compared with Collagen as such:
 Basic Shape - Haemoglobin is globular while Collagen is fibrous
 Solubility - Haemoglobin is soluble in water while Collagen is
insoluble
 Amino Acid Constituents - Haemoglobin contains a wide range
of amino acids while Collagen has 35% of it primary structure made
up of Glycine
 Prosthetic Group - Haemoglobin contains a haem prosthetic group
while Collagen doesn't possess a prosthetic group
 Tertiary Structure - Much of the Haemoglobin molecule is wound
into α helices while much of the Collagen molecule is made up of left
handed helix structures
Testing For Proteins
 Biuret Test
 to show the presence of peptide bonds
 basis for the formation of proteins.
 Peptide bonds will make the blue Biuret reagent turn purple.
 This color change is dependent on the number of peptide bonds in
the solution
 more protein, the more intense the change = longer polypeptide chain
 Procedures
 Create a control for the protein test (water and Biurets reagent)
 Add 5 mL of protein solution into test tube
 Add 5 drops of Biurets Reagent (very basic so do NOT get on hands or
clothing)
 Gently shake/roll test tube between your hands
 Record color changes
Denaturation
 Unraveling/unfolding of protein
 Why would this be a problem?
 When protein loses its 3-D shape and thus its specific function
 Caused by:
 Unfavorable changes in pH, temperature or other environmental
condition
 Disrupts the interactions between side chains and causes loss of shape
 Examples:
 Frying an egg
 Straightening your hair
Denaturation
 involves the disruption and possible destruction of both the
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secondary and tertiary structures
not strong enough to break the peptide bonds
primary structure (sequence of amino acids) remains the
same after a denaturation
Denaturation disrupts the normal alpha-helix and beta
sheets in a protein
Uncoils protein into a random shape= LOSS of FUNCTION
Denaturation
 Occurs b/c the bonding interactions responsible for the
secondary structure (hydrogen bonds to amides) and
tertiary structure are disrupted
 tertiary structure: four types of bonding interactions between
"side chains" that can be disrupted
 hydrogen bonding, salt bridges, disulfide bonds, and non-polar
hydrophobic interactions
 Variety of reagents and conditions can cause denaturation
 The most common observation in the denaturation process is
the precipitation or coagulation of the protein
Causes of Denaturation: HEAT
 Heat can be used to disrupt hydrogen bonds and non-polar
hydrophobic interactions
 occurs because heat increases the kinetic energy and causes the
molecules to vibrate so rapidly and violently that the bonds are
disrupted
 proteins in eggs denature and coagulate during cooking
 Other foods are cooked to denature the proteins to make it easier for
enzymes to digest them
 Medical supplies and instruments are sterilized by heating to denature
proteins in bacteria and thus destroy the bacteria
Causes of Denaturation: ALCOHOL
Alcohol Disrupts Hydrogen Bonding
 Hydrogen bonding occurs between amide groups in the secondary protein
structure
 Hydrogen bonding between "side chains" occurs in teriary protein
structure in a variety of amino acid combinations
 All disrupted by the addition of another alcohol
 A 70% alcohol solution is used as a disinfectant on the skin
 penetrates the bacterial cell wall and denature the proteins and enzymes inside of the
cell
 Why not 95%?
 95% alcohol solution merely coagulates the protein on the outside of the cell wall
and prevents any alcohol from entering the cell
 Alcohol denatures proteins by disrupting the side chain intramolecular
hydrogen bonding
 New hydrogen bonds are formed instead between the new alcohol molecule
and the protein side chains.
Causes of Denaturation: ACIDS/BASES (changing pH)
 Salt bridges result from the neutralization of an acid and amine on
side chains
 Final interaction= ionic bond b/t the + ammonium group and the acid group
 Acids and bases disrupt salt bridges held together by ionic charges
 Double replacement reaction occurs where the positive and
negative ions in the salt changes partners with the positive and
negative ions in the new acid or base added
 Occurs in the digestive system, when the acidic gastric juices cause the
curdling (coagulating) of milk
Causes of Denaturation: Heavy Metals
 Heavy metal salts act to denature proteins in much the same manner as acids and bases
 Heavy metal salts usually contain:
 Hg+2, Pb+2, Ag+1 Tl+1, Cd+2 (and other metals with high atomic weights)
 Since salts are ionic they disrupt salt
 Heavy metal + protein insoluble metal protein salt
 Used for its disinfectant properties in external applications
 Silver nitrate, AgNO3
 used to prevent gonorrhea infections in the eyes of new born infants
 to treat nose and throat infections,
 cauterize wounds
 Mercury salts administered as Mercurochrome or Merthiolate have similar properties in
preventing infections in wounds
 Used in reverse in cases of acute heavy metal poisoning
 a person may have swallowed a significant quantity of a heavy metal salt
 As an antidote, a protein such as milk or egg whites may be administered to precipitate the
poisonous salt followed by an emetic is given to induce vomiting so that the precipitated
metal protein is discharged from the body
Causes of Denaturation: Heavy Metals
 Heavy metals disrupt disulfide bonds
 They have high affinity/attraction for sulfur denaturation of proteins
 Have a positive charge (really want e-)
 Reducing Agents Disrupt Disulfide Bonds (things that can
accept electrons)
 Oxidation - involves the loss of electrons or hydrogen OR gain of oxygen
Oxidizing agent is the one thing that LOSES electrons
 Reduction - involves the gain of electrons or hydrogen OR loss of oxygen
 Reducing agent is the one thing that GAINS electrons
 Disulfide bonds are formed by oxidation of the sulfhydryl (-SH) groups on cysteine
 Hold together chains or loops within a single protein chain
 Reducing agents would do the opposite...break DISUPLHIDE BRIDGES (denaturation)
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Classification of Proteins According to biological
function.
Type:
Example:
Enzymes- Catalyze biological reactions
ß-galactosidase
Transport and Storage
Hemoglobin
Movement
Actin
And Myosin in muscles
Immune Protection
Immunoglobulins
(antibodies)
Regulatory Function within cells
Transeription Factors
Hormones
Insulin
Estrogen
Structural
Collagen
Path of a Protein in
the Body
 Check out this story!
Inorganic Ions
 Many important functions in
living systems
 Include:
 Nerve impulse transmission
 Excretion from the kidneys
 Enzyme function
 transport
Calcium Ion Ca2++
 Ions important in:
 transmission of electrical
impulses across synapses
 Muscle contraction
 Calcium phosphate
 Structural component of bones and
teeth
Sodium Na+
 Transmission or nerve
impulses along neurons
 Contribute to high
concentration built up by
loop of Henle in medulla of
kidney
 Enable concentrated
urine to be excreted so
water is conserved
 Sodium-potassium pump in
cells
• Filtering machines of the body
• As blood travels through the kidneys,
they remove waste products and excess
water
• Process about 200 liters of blood to sift
out about 2 liters of waste products and
extra water, everyday.
• The waste, along with the water is
turned into urine which travels through
the remaining components of the urinary
system and is excreted
• Food consumed provides energy and
helps repair cells
• Whatever the cells do not use in this
process must be eliminated from the
body
• It is combined with waste from the
breakdown of normal tissues in the blood
• The kidneys help rid the body of these
materials to prevent accumulation that
can damage the body
Potassium Ions K+
 Work with sodium ions
 Involved in transmission of
nerve impulses along
neurons
 Contribute to control of
turgidity of cells
 This controls opening and
closing of the stomata
 STOMOTA:
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Tiny openings on the
underside of cells
Surrounded by guard cells
Close up to conserve water
Three sodium ions enter the pump and attach to binding sites.
ATP binds to the pump.
One phosphate bond in the ATP molecule breaks, releasing its energy to the pump protein. The pump
protein changes shape, releasing the sodium ions to the outside.The new shape reduces its ability to bind to
sodium ions and it increases its ability to bind potassium ions. The two potassium binding sites are exposed
to the outside, allowing two potassium ions to enter the pump.
When the phosphate group detaches from the pump, the pump returns to its original shape. Its
ability to bind potassium ions is decreased and its ability to bind sodium ions is increased. The two
potassium ions leave, three sodium ions enter, and the cycle repeats itself.
Magnesium Ion, Mg2++
 Chlorophyll molecules contain
magnesium
 Active sites of ATP synthases contain
Magnesium ions
 ATP sythase ASE = enzyme
 Enzyme that helps add a phosphate group
(PO43-) to an adenosine diphosphate (ADP)
molecule to make adenosine triphosphate
(ATP)
Chloride ion Cl Works with sodium ions
 Contributes to the high concentration built up by the loop of
Henle in the medulla of the kidney
 Enables concentrated urine to be excreted so water is
conserved
 Help balance the positive charge of cations (Na+ and K+)
within and around cells
Nitrate ions, NO3 Plants use nitrogen from nitrate ions to make amino acids
and nucleotides
 Ion is able to be surrounded by water molecules and pulled
up into root hairs into xylem of plant and carried around the
plant
 This is why polarity of water is important…allows plants to
pull up important ions
Phosphate Ions, (PO43-)
 Used in making phospholipids (cell membrane)
 Used in the making of nucleotides (phosphate group)
 DNA
 RNA
 Combine with calcium to make calcium phosphate, that gives
strength to bone
 Component of ATP, energy currency of cells
Iron, Fe2+
 Hemoglobin contains this ion to attract oxygen molecule and
carry it to cells
 One hemoglobin contains 4 iron ions