1. Proteins Part 2
Review of protein structure, Types of Proteins, Testing for Proteins

2. Where are amino acids linked?
In living cell Ribosomes!
These reactions that occur on the ribosomes are controlled by ENZYMES (more on this later)

9. How are polypeptides broken?
Hydrolysis Reactions
Naturally occurs in stomach and small intestine
Protein in food is hydrolyzed into amino acids prior to being absorbed by the blood
Once in the blood, these AA can be restructured into polypeptides and then twisted and folded into functioning PROTEINS the cells in you body needs

10. Protein Structure the association of the polypeptide chains
Primary structure 1’
Order of amino acids in a polypeptide chain
Secondary structure 2’
Polypeptide chain folds because of interactions between amino acids
HYDROGEN BONDING
Tertiary Structure 3’
Gives proteins 3-D shape
VERY IMPORTANT to function of protein
Beta pleated sheets and alpha helices fold based on interactions between R-groups of a.a.
Hydrogen bonds, polar/non-polar interactions, acid/base interactions, disulfide bonds, van der Waals forces
Quaternary Structure 4’
the association of the polypeptide chains
some proteins contain more than one polypeptide chain
Each polypeptide chain in the protein is called a subunit
Two or more subunits come together for a specific function
HEMOGLOBIN
On Red blood cells
Its shape allows RBCs to carry oxygen all around your body!

11. Primary Structure Sequence of AA in a long polypeptide chain
AA= letters of alphabet
Sequence of AA= arrangement of letters to make words
HUGE amount of different primary structures
Changing ONE AA is polypeptide chain GREATLY changes the properties of the polypeptide chain and PROTEIN

12. Secondary Structure
Three possible 2o structures
Determined by order R-groups
No particular arrangement
Alpha helix
Polypeptide chains that coil tightly
Beta pleated sheet
Looser, straighter shape created by hydrogen bonds
The order of AA in polypeptide chain determine interactions between functional groups of AA
Functional groups interact via HYDROGEN BONDS
Attraction between oxygen in the –CO end of one AA and the hydrogen in the – NH end of another AA
H-bond easily broken
Change pH and change Temperature

14. Tertiary Structure Secondary structure gets coiled and folded
Precise 3D shape
Folding is determined by interactions between R-groups
Hydrogen bonds
Tryptophan
Arginine
Asparigine
Disulphide bonds
Between 2 cystine molecules
Ionic bonds
b/t R groups containing amine and carboxyl groups
Hydrophobic interactions
b/t R groups that are non-polar (hydrophobic)

16. 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
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

19. Quaternary Structure
Proteins are made up of multiple polypeptide chains, sometimes with an inorganic component (for example, a haem group in haemoglogin)
Prosthetic Group (inorganic component of protein)
These proteins will only be able to function if all subunits are present
Made by same bonds found in tertiary structure
Interactions between R-groups
Hydrogen bonds
Tryptophan
Arginine
Asparigine
Disulphide bonds
Between 2 cystine molecules
Ionic bonds
b/t R groups containing amine and carboxyl groups
Hydrophobic interactions
b/t R groups that are non-polar (hydrophobic)

22. Special Proteins Spherical 3D shape Ex. Haemoglobin, insulin, enzymes
Globular
Fibrous
Spherical 3D shape
Ex. Haemoglobin, insulin, enzymes
Water soluble
Physiologically active
Metabolic and transport roles
Do not curl up in 3D ball
Long, thin molecules
Molecules lie side-by-side to form fibres
Insoluble in water
Not physiologically active
STRUCTURAL roles

23. 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

25. 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”

26. Sickle Cell Anemia
One of the polar AA (glutamic acid) in the beta polypeptide chain is replaced with AA Valine (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 day (normal RBCs live about 120)
Bone marrow cannot replace fast enough

27. 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

30. 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

31. 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

32. 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

33. Practice Set 4 Grading C D A B