13 Amino Acids and Proteins Flashcards
What does the formation of hydroxy amino acid require and what can a defect in the structure of collagen lead to?
Formation requires Vitamin C
Scurvy leads to bleeding and tooth loss due to defective collagen
What do D and L describe in amino acids?
the configuration of the chiral centre in relation to D-glyceraldehyde
determined by looking at the position of the -OH group on the chiral carbon furthest from the C=O group
What are the lengths and locations of the secondary structure of proteins?
can vary between proteins
In proteins, what is the bonding between adjacent amino acids?
covalent bonding
Describe the structure of collagen and where it is found.
An extracellular protein of great tensile strength, found in skin, bone, tendon, cartilage and teeth
What 2 molecular shapes of proteins can we have?
globular or fibrous proteins
What are hydroxy amino acids formed from and how?
formed from proline and lysine
by enzymatic oxidation of the protein
In proteins, what is the bonding distant near amino acids and what does it result in?
non-covalent bonding
results in a compact three-dimensional folded shape
Fill in the following table on the document on the 20 amino acids and the categories they fit.
see document
Which amino acid is actually an im’IN’o acid?
prol’IN’e (which is not actually an amino acid)
How is the secondary structure of a protein described and maintained?
Describes regions of regular or ‘periodic’ structure
Maintained by hydrogen bonds occurring between
-C=O and -N-H atoms of peptide bond
Draw out the general structure of an L α-amino acid.
see document
Describe the secondary structure shown in the document.
a beta-barrel
Draw out a peptide and explain why in spite of the no rotation about the C-N bond, how a protein rotates.
(see document for drawing)
There is free rotation around the Cα-CO bond
There is free rotation around the Cα-NH bond
What is the primary structure of a protein?
A linear sequence of amino acids linked together by peptide bonds
What property does a globular protein have and where is it usually found and used for?
Usually of limited solubility or insoluble in water.
Found in skin, bone, tendons and teeth
Adapted for a structural function
On the following amine (on document) identify the N-terminus and C-terminus and state the amine shown on the document.
On the left is the N-terminus
On the right is the C-terminus
Eg. A hexapeptide containing six amino acids and five peptide bonds
State the 6 amino acids which have ionisable side-chains.
Tyra Aspired Glutes Like Argentinian History
Tyr - CH₂-C₆H₆-OH [Phenol ring structure]
Asp - CH₂-C=O(NH₂)
Glu - (CH₂)₂-C=O(NH₂)
Lys - (CH₂)₄-H₂N
Arg - (CH₂)₃-NH-C=NH-H₂N
His - CH₂-CH-CH(N)CH(NH) [Ring structure]
What is the importance of the quaternary protein structure?
This allows some proteins to execute complex biological functions
State what an essential amino acid is and state the 10 that are essential.
(Hint: all the ines, A TP MTV HILL)
cannot be produced in the body
obtained from food sources
Essential: Arginine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine
What is the quaternary structure of collagen?
It is a collagen triple helix held together by H-bonds between helices
Several of these triple helices then wind up to form a collagen fibre
Describe a β-turn and where it can be found.
A β-turn is a secondary motif in proteins that causes a change in direction of the polypeptide chain
Single chains contain a β-turn
Proline kinks protein chains often found in β turns
What are amino acids the primary products of?
protein degradation
What is the secondary structure of collagen?
A left handed helix, not an -helix
No H-bonds
3 residues per turn.
What is the tertiary structure of a protein?
proteins fold into compact three-dimensional structures
generally, the most stable structures in terms of intra-molecular bonds and a minimum surface area accessible to water
Describe the primary structure of collagen.
It is a simple repeat sequence (G X Y)n where X is any amino acid and Y is Proline or 4-Hydroxyproline.
How many naturally-occurring amino acids are there and how are they referred to?
20 amino acids
referred to by either their full names or a 3-letter code
How are peptides always written/drawn?
from the amino terminus at the (top) left to carboxyl terminus at the (bottom) right
In which case can peptides be synthesised chemically?
if the sequence is known
State the properties of the following:
a) amine groups
b) carboxylic acid
a) are basic and accept H⁺ as pH decreases
NH₂ + H⁺ ⇌ NH₃
b) a group that readily loses H⁺ as pH increases
COOH ⇌ COO- + H⁺
For the structure of an alpha-helices draw:
a) a ribbon diagram (and state how many amino acids are present per turn)
b) the main chain view
c) a side-chain diagram (also describe the structure)
a) see document 4 AAs per turn
b) see document
c) see document
Describe how side-chains and hydrogen bonds are located in the secondary structure of a protein.
Hydrogen bonds parallel to the axis of the helix
Sidechains project outwards from the helix – can accommodate large groups
For the tertiary structure of a protein, explain how each of the following intermolecular bonds stabilises the structure of a protein and give examples of groups where required:
a) Electrostatic interactions
b) Hydrogen-bonds
c) London/Van der Waal’s interactions
d) Hydrophobic interactions
e) Disulphide bonds
a) between oppositely charged side-chains, called an ion pair or salt bridge e.g. Glu + Lys
b) stabilise tertiary structure by H-bonding between side-chains. Most polar residues can H-bond eg Ser, Thr.
c) non-covalent forces of attraction between neutral molecules. All amino acids form these eg Leu, Tyr.
d) the most important effect in stabilising protein 3D shapes and involves burying the hydrophobic residues eg Ala, Val
e) forms between 2 cysteine residues as [methionine cannot form] (-SH + -SH → S-S)
Describe the ‘end-on’ view of a collagen molecule.
G in the middle (red) – small, no sidechain
Describe the interior and exterior structure of a globular protein.
Interior of the protein contains hydrophobic amino acids Exterior of the protein contains hydrophilic amino acids
What is the chemical composition of a conjugated protein? Provide an example of one.
often bigger: simple protein united with a non-protein factor – Prosthetic group, Cofactor, Lipids or Carbohydrates e.g. Glycoproteins (protein + carbohydrate)
Fill in the table with properties of amino acids by ticking the boxes.
Hint: Aliphatic (girls and vampires love Iceland) Aromatic (please try tomorrow) Sulphur (Easy) Basic (Laugh at her) Acidic (Allerton Grange) Bi-Polar (people try laughing at her) Non-polar (going so totally crazy atm) Hydrophilic (any voices lying in mind?) Hydrophobic (Gary and Victoria try lying in most profitable problems)
See table on document
For an amino acid with only 2 ionisable groups, what is pI?
the average of the 2 pKas
pI = (pK1 + pK2)/2
In proteins, what is the bonding between near amino acids and what does it result in?
non-covalent bonding
results in α-helices and β-sheets
What are amino acids the basic units of?
proteins
State what a conditionally essential amino acid is and state the 3 that are conditionally essential.
(Hint: The Grand Canyon)
essential in certain physiologic conditions
Conditionally essential: Cysteine, Glutamine, Tyrosine
What does the charge on amino acids and which groups (or sidechains) are protonated depend on?
the pH of the surroundings
In the amino acid shown on the document label the amino terminus and the carboxyl terminus and state the amino acid number at each end. Also, state one of the amino acid residues and number.
see document
What is cell pH?
7.0-7.4
For amino acids with ionizable side chains, what must be considered?
the structure as pH varies
What is the quaternary structure of a protein?
Many proteins exist as oligomers.
These are assemblies of two or more separate folded monomer subunits (single peptide chains).
Define ‘Isoelectric point, pI.’
the pH at which there is no charge and an equal amount of positive and negative charges present so the amino acid is neutral
How is the primary structure of a protein described and determined?
Determined by the gene encoding the protein
Changes to gene result in different amino acids in a protein
Lysine has pKas 2.2 (α-CO2H), 9.0 (α-NH3) and 10.5 (sidechain). Write out its equations, find its pI and state the net charge at each point.
see document for structure equations and net charges
pI = average of pKas of functional groups that are involved in equilibria with the neutral form
= (9.0+10.5)/2 = 9.75
Draw the structure of an example of a globular protein, state the main bonds within it and its approximate MW in Daltons.
see document for structures
Small protein MW ~ 6000 Daltons.
Two chains held together by disulfide bonds
What is the chemical composition of a small protein? Provide examples.
often smaller: chains of amino acid units joined by peptide bonds e.g. Albumins, globulins etc.
For the secondary structure of a protein draw and describe a beta-sheet and state what is meant by a ‘parallel’ and ‘anti-parallel’ β-sheet.
(see document for drawings)
Sidechains alternate above and below sheet.
Sheets can form from multiple chains side by side or a single chain
parallel: N-C repeated
anti-parallel: N-C and C-N alternating repeated
Describe the 3 features of the peptide/amide bond.
Permanent trans configuration in the –CO-NH- system because of the absence of free rotation
Partial double bond character
Trans configuration
For each of the functions of the following proteins, state how they work and provide examples of this:
a) Catalysis
b) Regulation and communication
c) Transport and storage
d) Motion
e) Mechanical support
f) Protection
a) as enzymes e.g. catalase
b) as hormones e.g insulin or receptors, e.g. 7-transmembrane receptors
c) e.g haemoglobin and myoglobin
d) as contractile proteins e.g. myosin
e) as structural proteins e.g. actin
f) as immunity proteins e.g. γ globulin antibodies
What groups are globular proteins divided and subdivided into? Give examples of each category.
Subdivided into elastic (coiled) and inelastic (extended – sheet structures)
Elastic – e.g. keratin, elastin, myosin
Inelastic – e.g. fibroin, collagen
What property do groups of amino acids have?
ionisable groups
Which type of amino acids are used in human metabolism?
L α-amino acids
What is a fibrous protein and what does it usually contain?
Highly elongated fibre-like structure.
Polypeptide chains are held together by inter-chain hydrogen bonds
For the following amino acid write out the equations for the ionisation of K1 and K2, the net charges at each point and the pI:
H₃N-CH₂-C=O-OH
(Also, include the proof for the equation you use to find pI)
see document for structure equations and net charges
k = [products]/reactants] K1 = [H₃N⁺CH₂CO₂-][H⁺]/[H₃N⁺CH₂CO₂H] K2 = [H₂NCH₂CO₂-][H⁺]/[H₃N⁺CH₂CO₂-]
At the isoelectric point [H₃N⁺CH₂CO₂H] = [H₃N⁺CH₂CO₂-]
Therefore:
K1 x K2 = [H⁺]^2
and:
pI = (pK1 + pK2)/2
How can mutations affect the primary structure of collagen and what can this result in?
can destabilise collagen fibres osteogenesis imperfecta (brittle bone disease)
What is a globular protein and what does it usually contain?
Compact and spheroidal shape.
Contain α-helices and β-sheets. Polypeptide chains are held together by intra-chain hydrogen bonds maintaining a compact shape
What do the different functions of proteins require?
different 3D shapes
In proteins, what is the bonding between different peptide and what does it result in?
non-covalent bonding
multisubunit protein
What are individual amino acids within a protein called and how are they numbered?
residues
are numbered in sequence
With pKas in what order do amino acids lose groups?
First a positive net charge to the most negative possible
State the 6 general ways amino acids can be categorised according to their R-group.
Size (large / small)
Shape (aliphatic / aromatic)
Hydrophobicity (polar / non-polar)
Charge at physiological pH (acidic / basic)
Sulphur-containing (cysteine & methionine)
Imino
State and draw the 2 most common types of secondary structure in a protein.
(see document for drawings)
α-helices
β-sheets
Which bonds are involved in the quaternary structure of a protein?
Non-covalent bonds, as listed for tertiary structure, hold the monomers together
Is there a repeating sequence motif in a globular protein or a fibrous?
None in a globular protein
Yes, usually one in a fibrous protein
State the interior and exterior of the tertiary structure of a protein and state the amino acid residues involved.
The interior of proteins is hydrophobic i.e. contains Leu, Val, Met, Phe etc. amino acid residues
The exterior of proteins is mostly hydrophilic i.e. contains Lys, Arg, Asp, Glu etc. amino acid residues – although most proteins do have small exposed hydrophobic regions
Draw out the orbital diagram of the amide/peptide bond and the reason for there being a partial double-bond character.
see document
Draw α L-glycine, D-glyceraldehyde (and its fisher projection).
see document
At cell pH, what do amino acids look like?
see document
If R has no potential for charge how does the amino acid exist in a living cell?
as neutral
What property does a globular protein have and where is it usually found and used for?
Water soluble
Usually found in solution, e.g. in the cytosol and blood. Functional uses rather than structural eg enzymes
State what a non-essential amino acid is and state the 10 that are non-essential.
(Hint: 3As, 3Gs, C, IMINE, S and T ending in ine)
can be produced in the body.
synthesised from essential amino acids or simpler precursors
uses and functions in the body are equally as important as the essential amino acids
Non-essential: Alanine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Proline, Serine, Tyrosine
