Biological macromolecules, protein structure and enzyme catalysis Flashcards
What are the roles of sugars and polysaccharides within the cell?
Food molecules and energy storage
Structural support in plant and bacteria cell walls
Cell protection
Cell-cell adhesion and mobility
Cell signalling
What is a sugar?
Straight chain polyhydroxy alcohols
They include an aldehyde or ketone group
Why is the Haworth projection of glucose misleading?
Glucose is puckered not planar
Which bond links 2 monosaccharides?
Glycosidic
Why is the reducing end of a disaccharide more reactive?
Ring can be opened to produce a free reducing group (aldehyde)
How reactive is sucrose?
Why is this?
Relatively inert
No reducing end
What is chitin?
Structural polysaccharide used for cell walls of fungi and exoskeletons of arthropods
What is the nitrogen containing group in chitin?
N acetyl glucosamine
What are oligosaccharides?
What is their function?
Complex carbohydrates that coat proteins and lipids on the cell surface
Protection
Cell-cell adhesion
Signalling
Where are oligosaccharides added to proteins?
Endoplasmic reticulum
Which amino acid side chains are oligosaccharides linked to?
N-linked to asparagine
O-linked to serine or threonine
What is the function of RNA?
Working template involved in gene expression
Information store in some viruses
Structural and functional role in ribosomes
Involved in catalysis
What type of sugar is deoxyribose?
Aldopentose
Which part of deoxyribose is incorporated into the DNA?
Beta-anomer
How many rings are in a purine molecule?
2
How many rings are in a pyrimidine molecule?
1
Which bases are purine?
Adenine and guanine
Which bases are pyrimidine?
Cytosine, thymine and uracil
In which direction do DNA bases bind down the backbone?
3’ - 5’
Why do purines only bind to pyrimidines?
Same distance between all base pairs so keeps a regular structure
How often is there a complete turn in the double helix of DNA?
Every 3.4nm
10 bases per turn
What are major and minor grooves in the DNA helix?
What is the function of these grooves?
Spaces between 2 strands
Provide access to the bases for DNA binding proteins n
What does the ribosome consist of?
RNA and protein
mostly RNA
Which amino acids have hydrophobic side chains
Proline
Alanine
Leucine
Glycine
Isoleucine
Valine
Which amino acids have charged side chains?
Histidine
Aspartic acid
Glutamic acid
Arginine
Lysine
Which amino acids have aromatic side chains?
Phenylalanine
Tryptophan
Which amino acids have sulphur-containing side chains?
Cysteine
Methionine
Which amino acid cannot form hydrogen bonds?
Why?
Proline
Side chain is covalently linked to the N in of the amino group
Where does rotation occur in a peptide bond?
Around the alpha carbon
Describe rotation in a peptide bond
Rotation of phi and psi around alpha carbon
What is amylose?
A polymer of maltose with repeating alpha glucose subunits
How is glycogen stored?
Granules in the liver
Can humans break down cellulose?
No
On which carbon is DNA deoxy?
2
Why do hairpin loops form in RNA?
Give an example of this
Some regions of single stranded RNA can be complementary to other regions of the same single stranded molecule
e.g. tRNA has 4 regions that are double stranded and forms a 3D structure recognisable by a ribosome
What form is the alpha carbon in the chiral centre?
L-form
When do amino acids form zwitterions?
At neutral pH
What can free cysteine side chains be involved in?
Metal binding
Do nucleotide bases point inwards or outwards?
Inwards
Is peptide bond planar or non-planar?
Why is this?
Planar due to electron delocalisation
In what order is the primary structure numbered?
N-terminus to C-terminus
What is the primary structure of a protein?
The linear sequence of amino acid residues
What was the first protein to have its primary structure determined?
Insulin
Describe the experiment that shows how primary structure alone provides all the information required for folding and formation of the tertiary structure?
- A pure sample of RNase was denatured in a test tube by adding urea and mercaptoethanol
- urea breaks hydrogen bonds
- mercaptoethanol reduces disulphide bonds
- Denaturing agents removed and protein spontaneously refolds
- Refolded structure was active showing that the native structure had reformed
What is the secondary structure?
Folding of regions of the protein into localised, regular arrangements of the backbone via hydrogen bonding between N-H and C=O groups
In what orientation is a hydrogen bond strongest?
Linear
What are the 2 main types of secondary structure?
Alpha helix and beta pleated sheet
How are secondary structures linked together?
Loop regions
What is shown by the Ramachandran plot?
All combinations of phi and psi angles found in proteins
What direction does the alpha helix turn?
Clockwise/right
How many amino acid residues are there per turn of the alpha helix?
3.5
Which form of the beta-sheet is more stable, parallel or anti-parallel?
Anti-parallel
What are the 5 types of interaction in the tertiary structure from strongest to weakest?
What are the relative strengths of these interactions?
Disulphide bonding (350-450kj/mol)
Ionic interaction (40-200kj/mol)
Hydrogen bonding (2-20kj/mol)
Hydrophobic interaction (3-10kj/mol)
van der Waal’s (0.4-4kj/mol)
Where do hydrogen bonds form between amino acids?
C=O and N-H groups
Between R groups
What are hydrophobic interactions?
Hydrophobic groups cluster in the core of the protein and interact with each other to avoid contact with water which would be entropically unfavourable
What are 2 other terms for ionic interactions?
Electrostatic interactions
Salt bridges
Why are ionic interactions stronger in the core of a protein?
No water to shield the charges
Why do vdW forces arise?
Asymmetric electron distribution induces a transient dipole in a neighbouring atom
What determines the strength of vdW forces?
Distance between atoms
Why don’t intracellular proteins exhibit disulphide bonding
disulphide bonds cannot form inside the cell because it is a reducing environment
Describe fibrous proteins
Regular, ordered structures with a strong repeat unit
Give examples of fibrous proteins
Collagen and keratin
What is the function of collagen?
Provides strength to skin, bone, cartilage and tendons
Describe the structure of collagen
Each chain forms a helix which twists around 2 others to form a ‘superhelix’
Why is collagen not an alpha helix?
It has only 3 residues per turn and is left handed
What are each of the 3 collagen chains made up of ?
Many copies of a 3 amino acid repeat:
Gly-X-Y
X is usually proline which causes tight bends in the backbone
Y is usually hydroxyproline which is generated by enzymatic modification of proline
Describe the orientation of the chains and the helix formed in collagen
Each chain is a left handed helix
The 3 chains are twisted into a right handed superhelix
What is the reason for the tensile strength of collagen?
Tightly packed triple helix structure
Where are the proline residues situated in collagen?
On the outside of the triple helix
Where is glycine situated in collagen?
Why is this?
On the inside of the triple helix
Its small size allows the 3 helices to pack closely
What is hydroxylation?
Addition of an -OH group
What is a collagen fibre made up of?
Many triple helices
What does proline hydroxylation enable?
Formation of another hydrogen bond (proline has no NH group)
How does a lack of vitamin C lead to scurvy?
The enzyme that makes hydroxyproline needs Fe2+ ions
Vitamin C maintains Fe2+ in the reduced state, allowing the enzyme to work
Scurvy is caused by a lack of vitamin C which leads to a lack of collagen
This leads to bleeding skin and gums and loss of teeth
What is more common? Fibrous or globular proteins?
Globular
Describe the structure of a globular protein
Hydrophobic side chains cluster in the centre and drive folding
Hydrophilic side chains are found on the surface and help to determine function
How is the b-a-b motif held together?
Hydrogen bonds between the strands and hydrophobic interactions between helix and strands
How are alpha helical hairpins held together?
Mostly by hydrophobic interactions, some ionic interactions
How are beta sheets in greek key motifs held together?
Hydrogen bonds between strands
What is a domain?
Part of a protein that forms a structurally independent unit with a hydrophobic core
Composed of several motifs together
What size is insulin?
5.6kDa
What links the 2 chains in insulin?
Disulphide bonding
What is a multidomain protein?
A single polypeptide chain which folds into multiple domains with linkers between
Give an example of a multidomain protein
Glyceraldehyde-3-phosphate dehydrogenase
2 domains come together to form a single globular entity
1 domain binds to NAD
Other domain contains active site
Describe the action of a DNA binding protein
Each domain independently binds to DNA by fitting into a separate place on the major groove
What is a multimeric protein?
A protein made up of many polypeptide chains (quaternary)
Give an example of a multimeric protein
HIV protease
2 subunits
What holds quaternary structures together?
Same interactions as tertiary
What do all antibody molecules contain?
4 polypeptide chains, 12 domains
4 light chain domains
8 heavy chain domains
What is a motif?
Commonly observed groupings of secondary structural elements
What stabilises the antibody tetramer?
Disulphide bonding (inter and intra)
