Flashcards in Proteins Deck (37):
Describe the functions of proteins
Proteins have a huge range of functions within the body.
o Control of gene expression
Define the primary structure of a protein
The sequence of amino acids in a polypeptide chain. This is the source of versatility in protein structure and function.
Define the secondary structure of a protein
The spatial arrangement of amino acid residues that are near each other in the linear sequence.
• Alpha Helices
A telephone cord shape held in place by H Bonds between the N-H group and the C=O group of the amino acid in the next turn of the helix.
• Beta Sheet
The pleated structure is held together by H bonds between the amide groups of linear polypeptide chains.
Define the tertiary structure of a protein
The spatial arrangement of amino acid residues that are far apart in the linear sequence. This depends on:
• Van der Waals
• Ionic Interactions
• Hydrogen Bonding
• Disulphide bridges
• Hydrophobic interactions
Define the quarternary structure of a protein
Refers to the spatial arrangement of individual polypeptide chains in a multi-subunit protein.
Define the 4 classes of naturally occurring amino acids.
Name some acidic amino acids
• Aspartic Acid
• Glutamic Acid
Name some basic amino acids
HAL is basic af
Name some uncharged polar amino acids
STTAG (e.g. stag horns)
Name some polar amino acids
Name some sulphur containing amino acids
Name some aromatic amino acids
Describe the basic structure of an amino acid
Amino acids are biologically important organic compounds containing amine (-NH2) and carboxylic acid (-COOH) functional groups, along with a side-chain (R group) specific to each amino acid
How many codons are there in the genetic code?
64, some redundancy
What occurs in protein denaturation?
• Denaturation of proteins involves the disruption and possible destruction of both the secondary and tertiary structures.
• Denaturation reactions are not strong enough to break the peptide bonds, so the primary structure remains the same after a denaturation process
What can cause protein denaturation?
• Solvents - Ethanol, methanol
• Cross linking reagents - Formaldehyde
• Chaotropic agents – Urea (disrupts hydrogen bonding between water molecules, affects stability of other molecules in solution)
• Disulphide bond reducers - 2 mercaptoethanol
What effects does denaturation have on proteins?
• Decreased solubility
• Altered water binding capacity
• Loss of biological activity
• Improved digestibility
Name the enzyme involved in protein degradation and describe its different activity
Peptidases - cleave peptide bonds
Endopeptidases - cleavage of internal bonds
Exopeptidases - cleave off one aa at a time
Carboxypeptidases - cleave from carboxylic end
Aminopeptidase - cleave at amine end
Describe the composition of a glycoprotein
Protein + carbohydrate
Formed by post translational modification reaction glycosylation, e.g. immunoglobulins
Describe glycosylation and where it occurs in a cell
• Glycosylation is the reaction in which a carbohydrate, i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor). In biology glycosylation mainly refers in particular to the enzymatic process that attaches glycans to proteins, lipids, or other organic molecules.
• Process occurs in the ER and Golgi network.
Describe lipoproteins and their function, including some examples
Protein and lipids that are either covalently or non-covalently bonded together. Their main function is for the transport of water-insoluble fats and cholesterol in the blood e.g. HDL, LDL
Describe some metalloproteins and their functions
Protein molecule with a bound metal ion. Functions include:
Importance can be seen in anaemia, when there is an iron deficiency that affects the functionality of haemoglobin.
Describe haemoglobin's structure, and the role of its structure in its function
Haemoglobin is the iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates as well as the tissues of some invertebrates.
The hemoglobin molecule is an assembly of four globular protein (2 x α + 2 x β) subunits. Each subunit is composed of a protein chain tightly associated with a non-protein heme group. Each protein chain arranges into a set of alpha-helix structural segments connected together in a globin fold arrangement, so called because this arrangement is the same folding motif used in other heme/globin proteins such as myoglobin. This folding pattern contains a pocket that strongly binds the heme group.
A heme group consists of an iron (Fe) ion (charged atom) held in a heterocyclic ring, known as a porphyrin.
Haem group at the centre of each polypeptide chain binds one molecule of oxygen.
So that one haemoglobin molecule can bind four molecules of oxygen
What is cooperative binding?
Seen in oxygen binding to haemoglobin.• The binding of O2 to one sub-unit alters its shape.
This in turn causes a change in the shape of the other sub-units, so that they bind O2 more easily.
Describe sickle cell anaemia, the properties of sickle cell haemoglobin, and its clinical features
Single base change (single point mutation, 1 base substitute) in the DNA chain A is swapped for T at postion 6 on the B chain. Causing the hydrophilic amino acid glutamic acid to be replaced with the hydrophobic amino acid valine at the sixth position.
Properties of Hb S:
o At low O2 levels forms crystals and polymerises to form long chains, causing the RBC to change shape (sickle shape)
o Severe haemolytic anaemia
o Hb S gives up oxygen in the tissues more easily than Hb A.
Describe some illnesses arising from an error in collagen production
• Vit C required to convert proline to hydroxyproline, and lysine to hydroxylysine
• Hydroxyproline and hydroxylysine are essential for stabilising the crosslinks between collagen chains
• Weaker collagen produced
• Glycine substituted for larger amino acid
• The protein no longer folds to form a tight coil
• Reduced interaction between fibrils
• Loss of secondary, tertiary structure
• Weakened and brittle collagen produced
What is the LDL receptor, what does it recognise, and name an illness associated with its dysfunction
The Low-Density Lipoprotein (LDL) Receptor is a mosaic glycoprotein that mediates the endocytosis of cholesterol-rich LDL. It is a cell-surface receptor that recognizes the apoprotein B100, which is embedded in the outer phospholipid layer of LDL particles.
What is Levinthal's paradox?
Levinthal’s paradox is that finding the native folded state of a protein by a random search among all possible configurations can take an enormously long time. Yet proteins can fold in seconds or less.
Therefore protein folding must be guided by local interactions and transition states.
What class of amino acids is proline in?
Other - connects to backbone twice to make it the only amino acid which forms a five membered nitrogen containing ring
What doesn't the central dogma account for?
Reverse flow of information from RNA to DNA
What two functional groups are found on amino acids?
Carboxylic acid (-COOH)
Also have specific R chains
Describe briefly peptide bond formation
Covalent bond between amine and carboxylic acid functional groups of two amino acids with the loss of water
Describe the formation of alpha helices
Hydrogen bonds between N-H and oxygen of C=O in next turn
Turns every 4 amino acid residues
Name some proteins who show alpha helical structures
Describe the formation of beta-sheets
H bonds between amide groups of linear polypeptide chains
Name some proteins which show beta sheet structure
Fatty acid binding protein