Lecture 3 Flashcards
What is the structure of an amino acid?
An amino group joined to a central carbon and hydrogen, joined to an R side group, and joined to a carboxylic group.
What is a peptide bond?
- The carbon of the carboxyl group joins with the nitrogen of the amino group through dehydration synthesis. This bond is quite rigid and joins amino acids together to make a dipeptide
- Free N-terminal and C-terminal of a dipeptide react further to make larger polypeptides and eventually proteins
- Peptide bond is quite rigid, but adjacent R groups can rotate
What is the function of a side R group?
This is what differentiates between different amino acids. Gives an amino acid its chemical properties and reactivity
Non-polar amino acids?
- Their side chains are typically just hydrocarbons (H&C)
- Not reactive
- Hydrophobic
- The bigger the side chain, the more hydrophobic it gets, therefore the more electronegative it gets
Non-polar amino acid exceptions? Why do these exceptions work?
- Tryptophan (N), Cysteine (S), Methionine (S), Phenylalanine (N)
- S & N are relatively electronegative, therefore it doesn’t increase the polarity
Polar amino acids?
- Hydrophilic
- Uncharged
- More reactive
- Oxygen in their side group. O2 is way more electronegative than N&S, so it makes it polar
Acidic amino acids?
- Negative side chains at a neutral pH
- Long side chains
- Has O in their long side chain
Basic amino acids?
- Positive side chains at a neutral pH
- Long side chains
- Has N in their long side chain
What do the different levels of protein organisation mean?
They’re different ways that amino acids bond together to form different protein structures for various roles in your body
Primary structure?
The linear amino acid sequence. Peptide bonds. First level of protein organisation
Secondary structure?
Primary structures bonded together. Can either be a B-pleated sheet or an a-helix. Results from hydrogen bonding between amino acids
Tertiary structure?
Secondary structures bonded together. More folding occurs due to the covalent/hydrogen bonds between amino acids, and ionic bonds between the R groups
Dipeptide?
The amino group from one amino acid can react with the carboxylic acid from a second amino acid to form a dipeptide
Quaternary structure?
- More than 1 polypeptide
- Beta chain bonds to the alpha chain
Molecular chaperones?
- Assist the folding of proteins
- Specialised proteins
Why do proteins fold?
To change their function
Hsp60?
Transports and refolds proteins from the cytoplasm to the mitochondrial matrix
Hsp70?
Recognise exposed, unfolded regions of new protein chains. It binds to these regions, protecting them until productive folding reactions can occur
Hsp90?
Stabilises proteins against heat stress, aids in protein degradation, and stabilises a number of proteins required for tumour growth
The role of an enzyme?
Catalyse specific chemical reactions in our body, build (synthesis), or breakdown (digest)
How does an enzyme work?
Step 1: A pair of substrate molecules bind to the active site
Step 2: The substrate interacts, forming a product
Step 3: This product detaches from the active site, and bc the substrate of the enzyme hasn’t been affected, the entire process can be repeated
What are the 7 different functions of proteins?
Enzymes, Structural proteins, storage proteins, transport proteins, regulatory proteins, motile proteins, Productive proteins
What is the function of structural proteins?
Strength and protect cells and tissues
What is the function of storage proteins?
To store nutrients
What is the function of transport proteins?
Move substances between cells and across cell membranes
What is the function of regulatory proteins?
Control the activities of proteins, genes, cells and tissues ex: protein kinases: control activities of other proteins hormones (insulin)
What is the function of motile proteins?
Generate movement in cells and tissues ex: action/myosin muscle contractions
What is the function of protective proteins?
Defend against foreign invaders ex: antibodies
Explain the alpha helix.
- a delicate coil held together by hydrogen bonding between every fourth amino acid
- Each hydrogen bond forms between an oxygen with a partial negative charge and a hydrogen with a partial positive charge
- elasticity due to helical shape and hydrogen bonding
Explain the beta pleated sheet.
- held together by hydrogen bonds
- Each chain is fully extended as each has zigzag structure
- Strong and flexible but not elastic as the distance between the pleats is fixed
Why do proteins have different conformations?
Environment
- in vivo (inside) and ex-vivo (outside)
Specialised proteins
- molecular chaperons
What determines the biological role of a protein?
- It’s structure
- Different regions of a single protein can have different functions
- Some proteins have 2 or globular regions (domains connected by less compact regions so each domain can have different functions)
What are 3 things that cause a protein to become denatured?
- Heat
- pH change
- Chemical exposure
(causes proteins to unfold so they cant complete their function- disrupts the hydrogen + ionic bonding)
What is the lock and key model?
- Enzymes are specific to the substrate they bind to
- Specific enzyme for specific reaction
- Shape of protein
Proteins?
- Most enzymes are proteins
- Polymers
- Largely determine what a cell looks like and how it functions
What is conformation dictated by?
The amino acid sequence
What enzymes break down sucrose, proteins and lipids? What enzyme builds DNA?
Sucrose = sucrase Protein = protase Lipid = lipase DNA = DNA polymerase
What are the four properties of a tertiary structure?
- Disulphide bonds
- R groups are bonded through ionic bonds
- Amino groups are bonded through hydrogen covalent bonds
- Hydrophilic
