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.
Fig. 27
Label the bond and fill in the key
- hydrogen bond
hydrogen (white) carbon (grey) nitrogen (blue) oxygen (red) R groups (purple)
Draw the secondary structure a-helix of a protein and show how it is stabilised.
[WOULD NOT HAVE TO DRAW]
See Fig. 27
Alpha helix structure
hydrogen (white) carbon (grey) nitrogen (blue) oxygen (red) R groups (purple)
hydrogen bonds between N-H and C=O bonds
Which amino acid residues are involved in the H-bond in alpha-helical secondary structure of proteins?
An interaction between 1 amino acid residue and 4 amino acids away.
Fig. 28
Caption this image
Secondary structure - the a-helix
Flattened conformation showing the backbone -C=O group of one residue is H-bonded to the -NH group of the residue four amino acids away
Draw the secondary structure of the alpha-helix in a flattened conformation, explaining which amino acids interact.
[WOULD NOT HAVE TO DRAW]
See Fig. 28
Ri
Ri+1
Ri+2 etc.
Ri –> Ri+4
Ri+1 –> Ri+5
What affects the a-helix stability?
The amino acid sequence
Why does the amino acid sequence affect a-helix stability?
Not all polypeptide sequences adopt a-helical structures; certain ones are more likely to form them than others.
Which residues are likely to form an a-helix?
Small hydrophobic residues such as Ala and Leu are strong helix formers
What is the significance of proline in a-helix stability?
Pro has its side chain bonded back into the amino group. This means it acts as a helix breaker because the rotation around the N-Ca bond is impossible (inflexible)
What is the significance of glycine in a-helix stability?
Gly acts as a helix breaker because the tiny R-group supports other conformations
Which amino acids are strong helix formers, and which are helix breakers?
Formers = small hydrophobic residues e.g. Ala, Leu
Breakers = Pro, Gly
Other than a-helices, what is the other common secondary structure?
β-strand
What is the conformation of a β-strand?
It is a fully extended conformation (an extended conformation like you’ve stretched out the protein sequence)
What is the distance between amino acids in β-strand conformation?
0.35 nm between adjacent amino acids (much more than we saw previously)
Where are the R groups for β-strands?
They alternate between opposite sides of the chain
Fig. 30
What does this image show?
β-strand secondary structure of a protein (extended conformation)
0.35 nm between adjacent amino acids
R groups alternate between opposite sides of the chain
Draw a β-strand secondary structure conformation.
[WOULD NOT HAVE TO DRAW]
See Fig. 30
What do 2 β-strands form?
A β-sheet
What is a β-sheet made up of?
β-strands
β-_______ make up a β-_____ in the secondary structure of proteins.
β-strands make up a β-sheet
How do two β-strands make a β-sheet?
2 β-strands come together in a side-by-side arrangement and stabilise themselves by forming Hydrogen bonds.
How are β-sheets arranged?
Side-by-side antiparallel β-strands coming together
What stabilises a β-sheet?
Hydrogen bonds (between the β-strands)
What is the general structure of β-sheets?
Antiparallel β-sheet or parallel β-sheet
What is an antiparallel β-sheet?
Adjacent β-strands run in opposite directions (i.e. one left to right and one right to left), with multiple inter-strand H-bonds stabilising the structure
Fig. 31
Label this image.
Antiparallel β-sheet: adjacent β-strands run in opposite directions, with multiple inter-strand H-bonds stabilising the structure
Draw an antiparallel β-sheet.
[WOULD NOT HAVE TO DRAW]
See Fig. 31
Yellow arrows: antiparallel
Boxes - show H-bonds between antiparallel β-sheets
Green lines - Hydrogen bonds
In an antiparallel β-sheet, where are the hydrogen bonds?
Between different strands
How does an antiparallel β-sheet appear from a side view?
You can see a sort of ‘wavy’ pattern
What is the key importance about antiparallel β-sheets?
The R groups are on opposite sides as we go through.
Fig. 32
Label and caption the image
(a) Antiparallel
Top view (top)
Side view (bottom)
Draw an antiparallel β-strand from top and side views.
[WOULD NOT HAVE TO DRAW]
1) Top - 3 β-strands on top of each other, stabilised by H-bonds. They run antiparallel to each other.
2) Side view - 3 β-strands forming a wavy pattern
What is a parallel β-sheet?
Where the two strands go in the same direction.
Describe the H-bonds of a parallel β-sheet in comparison to that of an antiparallel β-sheet.
In a parallel β-sheet, the H-bonds are slightly kinked so they are not quite as strong.
Fig. 33
Label this image.
A parallel β-sheet
Strands are going in the same direction
H-bonds are slightly kinked (not as strong)
(Note: would not have to draw)
Fig. 34
Label this image.
Parallel β-sheet
Top view (strands going in the same direction, kinked H-bonds)
Side view (strands on top of each other, wavy pattern)
Same sort of pattern as antiparallel β-sheet
(Note: would not have to draw)
What is a mixed β-sheet?
Where β-strands run in all directions (some same, some opposite)
Some β-sheets have both antiparallel and parallel layers. What are these called?
A mixed β-sheet
Fig. 35
Label this image.
Structure of a mixed β-sheet
Top two layers parallel (kinked H-bonds)
Bottom two layers antiparallel (strong H-bonds; straight)
(Note: would not need to draw)
How do we represent a-helices and β-sheets?
‘Cartoon’ versions:
a-helices: ribbon-like structure
β-strands/sheets: flat arrows
What is the function of ferritin?
It is an iron storage protein
Give an example of a protein that is largely a-helical in structure.
Ferritin
Give an example of a protein that is largely β-stranded in structure.
Fatty acid binding protein
Fig. 36 (Left)
Label this image.
Simple protein structure
Iron storage protein ferritin - largely a-helix
(Note: would not need to draw)
Fig. 36 (Right)
Label this image.
Simple protein structure
Fatty acid binding protein - largely b-sheet
(Note: would not need to draw)
In proteins, what does a ribbon-like coil represent?
A-helix
In proteins, what does a flat arrow represent?
B-strand (which makes up b-sheets)
What do a-helices and b-sheets fold up into?
The tertiary structure.
What is the tertiary structure?
The overall 3D structure of the protein.
What is myoglobin made up of (protein arrangement)?
Lots of a-helices (and ‘wiggly bits’)
What does the tertiary structure show?
The spatial arrangement of amino acids far apart in the protein sequence.
Fig. 37
Label this image.
Tertiary structure
Myoglobin
- made up of a-helices
- ‘wiggly bits’
- purple = haem group bound to the molecule
The spatial arrangement of amino acids far apart in the protein sequence.
What group binds to myoglobin?
Haem group
What types of protein can you get?
Globular and fibrous proteins
How big is a β-conformation
2000 X 5 A
How big is an a Helix?
900 x 11 A
How big are proteins generally in native globular form?
100 X 60 A
What are the measurements of β-conformation, a Helix and Native globular forms?
β Conformation = 2000 X 5 A
a Helix = 900 x 11 A
Native globular form = 100 X 60 A
What type of proteins are myoglobin and haemoglobin?
Globular proteins
Which proteins are more biologically relevant: fibrous or globular proteins?
Globular proteins do more stuff/have more function
Fibrous proteins tend to be more simple in structure and function and are there to provide structural support
What do globular proteins look like?
They are nicely folded up
Carbonic anhydrase is an example of a globular protein. What secondary structure types does it contain?
A mixture - a helices, b sheets, b strands etc.
Collagen is an important fibrous protein. What is its secondary structure like?
It has repeating structural motifs
What is the role of a fibrous protein?
Support, shape and protection
What is the role of a globular protein?
Catalysis, regulation
What is the shape of a fibrous protein?
Long strands or sheets
What is the shape of a globular protein?
Compact shape
What type of secondary structure does a fibrous protein contain?
Single type of repeating secondary structure
What type of secondary structure does a globular protein contain?
Several types of secondary structure
Give an example of a fibrous protein.
Collagen
Give an example of a globular protein.
Carbonic anhydrase
Fig. 38 (top)
Label the images
β Conformation = 2000 X 5 A
a Helix = 900 x 11 A
Native globular form = 100 X 60 A
Fig. 38 (bottom left)
Label the image
Collagen - Fibrous protein
(Fibrous proteins:
Role - support, shape, protection
Long strands or sheets
Single type of repeating secondary structure)
Fig. 38 (bottom right)
Label the image
Carbonic anhydrase - Globular protein
(Globular proteins:
Role - Catalysis, regulation
Compact shape
Several types of secondary structure)
What is collagen made up of?
3 alpha chains
(NOT a-helices; a-chains)
i.e. 3 polypeptide chains
What do the constituents of collagen make up?
3 alpha chains make up a triple helical sequence
triple helical arrangement of collagen chains
What sequence does collagen contain?
contain Gly - X - Y repeating sequence
Gly - any amino acid - any amino acid
What stabilises the interactions between collagen chains?
Hydrogen bonds between chains stabilise helical structure.
Give 3 facts about collagen.
- Triple helical arrangement of collagen chains
- Contain Gly - X - Y repeating sequence
- Hydrogen bonds stabilise interactions between chains
What do collagen molecules form?
Lots of collagen molecules come together to make a FIBRIL, which ultimately make a FIBRE.
Collagen _________ come together to form a ______, which ultimately form a _____
Molecules
Fibril
Fibre
What is a collagen fibre?
A BIG collagen structure made up of collagen fibrils (which are lots of collagen molecules)
How does collagen appear under an electron microscope?
Striated, due to staining of collagen molecules
How strong is collagen?
Really strong - stronger than steel
What is the function of collagen?
Strong structural support (it is stronger than steel!); hence why it is a key part of bone and skin.
Fig. 39 (top)
Label this image.
Collagen a chain
Draw a collagen a chain.
See Fig. 39
Fig. 39 (bottom)
Label this image.
- Heavy staining in regions with gaps
- Light staining in regions with no gaps
- Staggered arrangement of collagen molecules causes the striated appearance of a negatively stained fibril
What is negative staining?
Where the background is stained, so the actual specimen is untouched, and thus visible
(Positive staining = specimen stained)
Draw a single collagen molecule,
See. Fig. 39 (bottom)
LEFT
Draw the arrangement of collagen molecules in fibrils.
Staggered
See. Fig. 39 (bottom)
Second to left
Draw a single collagen fibril under an electron microscope, and explain.
Striated
- Light staining in regions with no gaps
- Heavy staining in regions with gaps
See. Fig. 39 (bottom)
Second to right
Draw how collagen fibrils look under an electron microscope, and explain.
- Staggered arrangement of collagen molecules causes the striated appearance of a negatively stained fibril
See. Fig. 39 (bottom)
RIGHT
What do globular proteins contain (structurally)?
A variety of tertiary structures, such as motifs and domains.
What is a motif?
Folding patterns (repeating elements) containing 1 or more elements of secondary structure.
Give 2 examples of motifs.
β-a-β loop
β-barrel
What is a β-barrel?
A type of motif where beta strands form a ‘rounded’ shape.
What are domains?
Part of a polypeptide chain that fold into a distinct shape. Often has a specific functional role.
What is the difference between a domain and motif?
Domains tend to be bigger parts of a protein where they’re folded up into specific 3D shapes in their own right - big proteins will often have several different domains which will do different things.
How can one protein do several different things?
Big proteins will often have several different domains which will do different things.
Give an example of a protein that has 2 domains.
Troponin has got 2 rather similar shaped domains
What is the role of troponin’s domains?
Bind calcium
Why is the role of troponin’s domains important?
They bind calcium which is important for function of troponin in muscle contraction.
Fig. 40 (left top)
Label the image.
β-a-β loop
Fig. 40 (left bottom)
Label the image.
β-barrel
Fig. 40 (right)
Label the image.
Calcium binding domains of troponin C
What causes a protein to fold up?
- Mainly due to ENTROPY
- Also so they can become the most stable form they can be (chemical properties)
What does a space filling model of a protein show?
A better representation as we can see the nature of the amino acids that make it up.
Which molecules do we get on the surface of water-soluble proteins?
Charged or polar molecules
What do we find on the interior of a protein if we do a cross-section?
Hydrophobic residues
Why do we find hydrophilic residues on the outside and hydrophobic residues in the middle?
Hydrophilic amino acid residues are on the outside interacting with water
Hydrophobic amino acid residues are in the middle packed away from water
Describe the folding of water soluble proteins.
Polypeptide chains fold to so that hydrophobic side chains are buried and polar, charged chains are on the surface
Fig. 41 (left)
Caption the image
Myoglobin
Ribbon diagram
Fig. 41 (A)
Caption the image and provide a key
Myoglobin
(A) Space filling model
Blue = charged, yellow = hydrophobic, white = other
Fig. 41 (B)
Caption the image and provide a key
Myoglobin
(B) Cross-section
Blue = charged, yellow = hydrophobic, white = other
Describe the folding of membrane proteins.
Membrane proteins often show “inside-out” distribution of amino acids
The middle of a membrane is very __________ due to ____________
The middle of a membrane is very hydrophobic due to lots of fatty acyl chains
Give an example of a membrane protein.
Porins
What do the hydrophobic residues interact with in porins?
Fatty acyl groups
What do the hydrophilic residues interact with in porins?
Water-filled cavity
hydrophilic residues = charged/polar
Fig. 42
Label the image.
Folding of membrane proteins, e.g. porins
- Largely hydrophobic exterior
- Water-filled hydrophilic channel
Describe the folding of a water-soluble protein and the folding of a membrane protein and explain why.
Water-soluble proteins:
- hydrophilic outside: interacts with water
- hydrophobic inside: hidden from water
Membrane proteins:
- hydrophobic outside: interact with fatty acyl chains
- hydrophilic inside: interacts with water-filled cavity
What is the quaternary structure?
Where we get further division - multi-subunit proteins
Give an example of a protein structure where we have a quaternary structure from a protein of the same type.
Haemoglobin (has 4 subunits)
What are the subunits of haemoglobin?
2 α subunits and 2 β subunits
Give an example of a protein structure where we have a quaternary structure from interactions with other macromolecules.
Ribosome (has its own subunits and interacts with RNA molecules)
What are the subunits of ribosome and what does it interact with?
55 protein subunits and 3 RNA molecules
forms an enormous complex
What is the difference in quaternary structures of haemoglobin and ribosomes?
Haemoglobin has a quaternary structure from proteins of the same type
Ribosomes have a quaternary structure including interacts from other macromolecules.
Fig. 43 (left)
Label the image.
Haemoglobin
2 α subunits and 2 β subunits
Fig. 43 (right)
Label the image.
Ribosome
55 protein subunits and 3 RNA molecules
What do I need to know?
- Structure of an amino acid.
(Remember it is not about memorising detail but applying these things)
Need to know generalised amino acid structure
e.g. COO-, NH3+, R groups etc
What do I need to know?
- Properties of side chains of amino acids - how they are classified
(Remember it is not about memorising detail but applying these things)
Don’t need to know which ones are which, but if showed an amino acid to say its properties e.g. hydrophobic, charged etc.
e.g. OH - hydrophilic
alkanes - hydrophobic
What do I need to know?
- Why some amino acids are charged and how to calculate relative proportions
(Remember it is not about memorising detail but applying these things)
Why some side groups are charged (can be a difficult concept)!
e.g. pKa
pI
Henderson-Hasselbalch
What do I need to know?
- Structure and properties of a peptide bond
(Remember it is not about memorising detail but applying these things)
Need to know the features
e.g. Rigid
Planar
Flexibility around the peptide bond
What do I need to know?
- Features and properties of secondary structure - including why the properties of a peptide bond contribute to this
(Remember it is not about memorising detail but applying these things)
Some features of secondary structure, and very generally a-helix, b-sheet, why they’re important
e.g. a-helix
b-sheet
How sequences affect these
What do I need to know?
- What is meant by tertiary and quaternary structure
(Remember it is not about memorising detail but applying these things)
What we mean by them
e.g. tertiary = spatial 3D arrangement
quaternary = >1 subunit
What do I need to know?
- The types of bonds involved in maintaining protein structure
(Remember it is not about memorising detail but applying these things)
The types of bonds
e.g. peptide bond
H-bond
covalent bond
