Q/A Session 1 Flashcards
How does and aa look as a zwitterion?
- Amine side is protonated
- CA is deprotonated (becoming a carboxylate)
Characteristics of a Non-Polar side chain
- Mainly composed of hydrocarbons
- Found in the core of the protein
- Hydrophibobic
Characteristics of Polar Groups
- Can either be charged or uncharged
- If the pH changes, can become charged/uncharged
- Surface of protein. Polar groups make the protein soluble
Characteristics of polar uncharged
-Polar groups in the side chains but uncharged at neutral pH
Characteristics of polar charged
- An O by itself indicates negative charge
- Positive charge on the N atom indicated a negative charge
What is produced when a peptide bond forms?
Water
-Condendsation reaction
Whats the configuration of an aa
Trans, minimises steric hinderance
Is there rotation around a peptide bond?
No
Characteristics of peptide bond
- Planar
- Rigid
- Linear
- Cannot rotate
Psi bond (trident shaped)
Goes between Calpha-C
Phi bond (O with slash)
Goes between C-N
Formation of secondary structure is called
Nucleation
What are secondary structures stabilised by
What hold them together which is hydrogen bonds
Where do amino acid side chains point
Outwards from the helix
What are the 2 unfavourable amino acids in the alpha helix formation?
- Glycine (too flexible)
- Proline (too bulky)
Explain the n+4 stabilising the alpha helix
Hydrogen bond goes between the Oxygen of Amino acid n ——– Hydrogen of amino acid n+4
O(n)—-hydrogen bond—-H(n+4)
How many strand in a beta sheet
2-10
What aa are used in turns on the beta sheets?
- Glycine due to flexibility
- Proline due to naturally occurring bend
What direction do antiparallel bond patterns tend to be (beta sheets)
vertical
What direction do parallel bond patterns tend to be (beta sheets)
diagonal
How are beta sheets pleated?
With a right hand twist
Turning clockwise
What are tertiary structures?
Collection of secondary structures making a 3D sturcute
Tertiary structures stabilised by:
- Metal ion coordination
- Hydrophobic interactions
- electrostatic interaction
- Hydrogen bonds
- Disulfide bond
What are quaternary structures made from
-Made up of 2+ tertiary structures
What are quaternary structrues held together by?
Weak/non covalent bonds
What are supersecondary structures?
Combinations of secondary structures that form recognisable patterns
What are domains?
Combinations of super secondary structures that form independently folded regions
-Have hydrophobic cores
What is a chaperone?
helps to assist with correct folding by passively preventing incorrect folding
- > no ATP required
- > hydrophobic molecules
What is a chaperonin?
Larger proteins that require ATP to function
What is protein folding driven by?
Hydrophobic interactions
What is the order of protein folding?
- Formation of secondary structures
- Several secondary structures come together and form super-secondary structures->domains
- Several domains come together and form almost tertiary
- Small conformational changes give final tertiary structure
What is pka?
pH at which an ionisable group is 50% ionised
Is pka for an amino group high or low?
High
Is pka for a carboxyl group high or low?
Low
