Protein - Week 2 Flashcards
What is an Amino Acid
A compound that contains both an Amino group and a carboxyl group. Where there are different side chains attached to the alpha carbon which gives the molecule its characteristics
What is Chirality
A molecule which contains a single bonded carbon bonded to 4 different groups (functional groups) is Chiral.
Such molecules are not superimposable on its mirror molecule
What is L Form
Where the amino group (-NH2) lies on the left side of a Fischer projection
What is D form
Where the amino group -NH2 lies on the right side of a Fischer projection
What is the zwitterion
AA with a neutral charge
What impacts the net charge of an AA
The pH of the solution
High pH makes the AA have a net negative charge as the increased -OH removed a H+
Low pH makes the AA have a net positive charge as the increase H30+ adds a H+ to NH2 to make it NH3+
What is the Isoelectric point and what is use for
The point along the pH scale at which a molecule exists with a neutral charge.
The more neutrally charged the AA is the less soluble it is and the more likely it is to precipitate out of solution
If a protein has a pI of 7 what is its charge at a low pH
Positive
If a protein has a pI of 7 what is its charge at a high pH
negative
How does pH change the charge of a protein
Causes the protein to under go hydrolysis where either the amino group will deprotonate or the carboxyl group will protonate changing the net charge of the protein. (NOTE: the side chain will impact this) (NOTE: only acidic and basic functional groups will be affected)
What is a peptide
A short chain of AA held together by peptide bonds (2-10 AA) - di peptide, tri peptide
By convention peptides are written from left beginning with the free -NH3+ (N-terminal) to the right ending with the free -COO- (C-terminal)
What is a Protein
A chain of many AA (more than 30)
Example of non polar AA
Alanine* (methane side chain)
Glycine (hydrogen)
Valine (methyl-ethane)
Example of polar AA
Serine* (methanol)
Cysteine* (CH2SH)
Threonine
Example of acidic AA
Aspartate* (ethanoic acid)
Glutamate (propanoic acid)
Example of basic AA
Lysine* (butamine)
Arginine
Histidine
What are the functions of Proteins (8)
- Structure
- Catalysts
- Movement
- Transport
- Signaling
- Protection
- Storage
- Regulation
Example of Protein Function: Structure
Collagen - supports skin, bone, teeth
Keratin - component of hair and nail
Example of Protein Function: Catalyst
Enzymes (Pyruvate kinase) - increases rate of organic reactions
Example of Protein Function: Movement
Myosin an Actin - protein in muscles
Example of Protein Function: Transport
Hemoglobin - transports oxygen from the lungs to cells
Example of Protein Function: Signaling
Insulin - regulates the production of glucose and lipids
Example of Protein Function: Protection
Fibrinogen - split apart into the active protein fibrin and then join to create an insoluble mesh which stabilises blood clots
Example of Protein Function: Storage
- Casein(kay-seen) is a protein in milk which stores nutrients for newborns
Example of Protein Function: Regulation
Transcription factors - involves proteins which control the expression of genes into RNA
What are the 3 classes of Proteins
- Fibrous Proteins
- Globular proteins
- Membrane proteins
What are Fibrous Proteins
- Simple chain primary structures
- mostly simple beta sheet or triple helix secondary structures
E.g. Collagen, Silk Fibroin, A-keratin
What are Globular proteins
- Complex primary and tertiary structures
- Completes complex roles 5-8
e.g. Hemoglobin
What are the types of membrane proteins
- Integral membrane protein (intrinsic)
- Peripheral Protein
What are integral membrane protein
- Proteins bounded to the into the cell membrane (reaches both sides)
- functions as ion channels which transport small molecules across the membrane
- Also functions as receptors where other noncellular molecules can attatch to
eg. Lactose permease which transports sugar across the membrane???
What are Peripheral proteins
- Proteins which is only attatched to the surface of the cell membrane
- functions to carry electrons
e.g. Cytochrome C - moves electrons in the final
What is the Primary structure of Proteins
initial sequence of amino acids in a polypeptide chain linked together by peptide bonds
What is the secondary structure of proteins
The connection/folding of the primary structure to create the backbone structure of a protein.
Created from the hydrogen bonds between the amide hydrogens and the carbonyl oxygens of the peptide bonds
Main types of secondary structures
alpha-helix
beta-pleated sheet
Example of a alpha helix
Alpha-keratin - fibrous protein
Example of a beta-pleated sheet
silk fibroin - antiparallel b-sheet
What are the tertiary structure of proteins
the 3D shape of the entire peptide chain where the regions of the secondary structure further fold on themselves.
Created by the bonds/ forces between the side chains
What are the bonds/forces which create tertiary structures of proteins
- Covalent bonds (disulphide bonds between 2 sulphides - cysteine (-CH2SH))
- Hydrogen bonding - H bonds - HFONs
- Salt bridges/ionic bonds - forces between oppositely charged side chain group (-NH3+ and -COO-)
- Hydrophobic interactions/ Dispersion forces - temporary dipole attractions between hydrophobic/ nonpolar side chains
Types of Tertiary Structures
- beta saddle
- beta Barrel
What are quaternary structures of Proteins
Some proteins are made up of multiple polypeptide chains also known as subunits, where when these subunits come together they give the protein its quaternary structure
e.g. Hemoglobin
What is the primary structure of collagen
Gly - X - Pro
Gly - Glycine
X = Any AA
Pro = Proline
What is collagen
- Fibrous Protein
- Most abundant protein in vertebrates (bones, connective tissues)
- provides structure and stability
What is the quaternary structure of collagen
Tertiary structure - triple helix
What is silk fibroin
- fibrous protein
- insoluble protein secreted by silkworm
What is the secondary structure of silk fibroin
- antiparallel beta-sheet
- using hydrogen bonds to hold the peptide chains together
What is alpha keratin
- fibrous fiber
- found in hair, nails and epithelial cells (gives skin colour)
Types of protein folding (2)
- spontaneous folding
- assisted folding
What is spontaneous folding
- proteins self assembling slowly using dispersion forces as they come out of the ribosome
- then interactions between side chains will create the secondary and tertiary structures
What is assisted folding
- uses chaperones (protein complex) which takes incorrectly folded proteins and assembles them into the right structure
What is protein denaturation
The process of destroying the structure of a protein by either chemical or physical means
Examples of protein denaturation using cellular organelles
- In Lysosomes (contains acid enzymes which breaks down protein)
- In Proteasomes (has a molecular channel which feeds protein to its enzymes)
How can protein be broken down into
- amino acids which can be re used again
- or AA further broken down through protein catabolism to create energy
Examples of protein denaturation using denaturing agents (7)
- Heat
- 6M aq Urea
- Surface-active agents (sodium dodecylsulfate)
- Reducing agents
- Heavy metal ions
- Alcohol
- Extreme pH
How does heat denature a protein
Increases vibrational motion inside the molecule which breaks the hydrogen bonding which holds the peptide chains together
How does 6M aq Urea denature a protein
C=O and NH2 form hydrogen bonds with the protein in turn weakening the strength of the hydrogen bonds between the AA chains
Impact of alcohol to a protein
The -OH hydroxyl group of the alcohol will disrupt and weaken the hydrogen bonds between the amino acid chain. Denaturing the protein
Impact of Hg, Pb (heavy metal ions) on proteins
Forms insoluble salts with Sulphur in turn disrupting the desulphated bridges - denaturing proteins
Give an example of a widely used therapeutic peptide
Oxytocin - a peptide hormone which reduces blood pressure and cotisol levels
How does the structure of hemoglobin relate to its function
Hemoglobin contains 4 globin subunits that provides its overall 3D structure. There is a heme group in each subunity and as a result there are 4 iron atoms in a molecule of hemoglobin, this allows it to have 4 binding sites for oxygen which means it can bind 4 molecules of oxygen at once.
Example to essential amino acids
Phenylalanine(fee -nile - a - luh - neen), lysine
What is the function of proteins such as lysozyme and lactoperoxidase in toothpaste
Lysozme breaks down bacteria cell walls in toothpaste, fighting against oral bacteria. WHile lactoperoxidase generates antimicrobial compounds in saliva, aiding in the prevention of bacteria growth in the mouth.
Example of a peripheral protein
Cytochrome C - transports electrons
What is the average life span of a protein
3 days
