Session 4.3c - Lecture 1 - Protein Structure Flashcards
Slides 24-45
Fill in the gaps using these words. They can be used more one once.
Function
Sequence
Structure
________ determines _________
_________ determines ________
Sequence determines structure
Structure determines function
Fig. 24
What does this image show?
A DNA binding protein with two lobed halves.
DNA has _____ and _____ grooves.
Major and minor grooves
What structure do we often find in many DNA binding molecules?
A helix turn helix motif
What is the significance of the helix turn helix motif in DNA binding molecules?
They wrap around DNA and they’re specifically designed to do that to make these tight interactions
DNA has major and minor grooves.
Draw a simplistic view of a DNA binding molecule.
DNA binding molecule with two lobes
DNA in centre
What is important in the folding of proteins?
The backbone sequence, i.e. the bonds formed between the different amino acid residues
What are the bonds formed between different amino acid residues?
Peptide bonds
Describe the movement related to and around the peptide bond?
Peptide bond is rigid and planar
We can get flexibility and rotation around the other bonds on either side of the peptide bond
What is the significance of the flexibility of bonds around the peptide bond?
These bonds determine the overall 3D structure
What is the protein conformation for primary structure?
Covalent (peptide) bonds hold primary structure together
How do psi and phi bonds contribute to the protein folding?
Angles determine the conformation of peptide backbone and hence the ‘fold’ of the protein
Fig. 25
Label the image
- backbone peptide plane R1 R2 R3 - 1.45 A - 1.33 A - 1.52 A - 1.23 A
118o
120o
122o
116o
121o
123o
Different angle determine the conformation of peptide backbone and hence hte ‘fold’ of the protein
Draw a schematic representation of the protein conformation of primary structure
See Fig. 25
Name a common secondary structure conformation.
Alpha-helix
What is an alpha helix?
It is a right-handed helix.
What is a right-handed helix?
If you hold you right hand up in a thumbs up, the helix follows the direction of your hand
How many amino acids does an a-helix have per turn?
3.6 amino acid residues per turn
What is the pitch of the a-helix?
Distance you go as you go up 1 amino acid residue
= 0.54 nm
Fig. 26
What does this image show?
Ribbon-like cartoon of an alpha helix (secondary structure of a protein)
Draw the outline of an alpha-helix of a protein (second structure)
[WOULD NOT HAVE TO DRAW]
See Fig. 26
What holds the alpha-helix secondary structure together?
By hydrogen bonds (H-bonds)
Where do the hydrogen bonds in the alpha-helix secondary structure come from?
Between the amide-hydrogen (N-H) and carbonyl-oxygen (C=O)
How is the alpha-helix secondary structure stabilised?
H-bonds between N-H and C=O stabilise the structure of the a-helix.