Lecture 5 and 6- Proteins

Pregunta	Respuesta
What are the monomers that form polypeptides?	Amino acids
How many different amino acids are there?	20
Draw the general formula of an amino acid	Image: aminoacid.gif (image/gif)
Which is the only amino acid that isn't chiral?	Glycine
What is an amino acid called if it has a positive and negative charge?	Zwitterion
What is the pH if both functional groups are protonated (NH3+ and COOH)?	Acidic
What is the pH is both functional groups are deprotonated (NH2 and COO-)?	Alkaline
What bond is formed between two cysteine molecules?	Disulphide bridge
Cysteine + Cysteine = ?	Cystine
What type of reaction occurs in the formation of cystine?	Oxidation
Which amino acid is always the first in a polypeptide chain?	Methionine
What bonds link amino acids together?	Peptide bonds
In which direction in a polypeptide sequence read?	From the N terminal (amino terminal residue) to the O terminal (carboxyl terminal residue)
What causes peptide bonds to be rigid and planar?	Bond resonance
Where is rotation possible in a polypeptide?	Image: rotat.gif (image/gif)
Why is the trans- form most common?	Rotation at C is limited due to steric clashes between R groups
When does the cis- form occur?	Glycine and 0
What are the four levels of protein structure?	Primary, Secondary, Tertiary and Quaternary
What is the primary structure?	The sequence of amino acids
What is the secondary structure?	The formation of alpha helices, beta sheets and loops/random coils due to the formation of hydrogen bonds
What is the tertiary structure?	Attractions cause the polypeptide to fold
What is the quaternary structure?	A protein consisting of two or more polypeptide chains assembled together
Why is the primary structure so important?	It dictates final protein structure because sequential arrangement of R groups will influence subsequent secondary, tertiary and quaternary structures. The protein structure then dictates the function.
What can lead to a change in the primary structure?	Genetic mutation
Feature of the alpha helix	Coiled like a spring, hydrogen bonds and amphipathic
Features of the beta sheet	Flat sheets, pleated, short runs of 5-10 amino acids, parallel or anti parallel, sheets held together by hydrogen bonds, the sheets are often connected by hairpin loops or turns
The difference between parallel and anti parallel beta sheets?	Image: Parallell_antiparallel_beta_sheet.GIF (image/GIF)
What are loops?	They connect secondary structure elements, not connected by hydrogen bonds, frequently form part of active sites and the difference between structurally similar proteins occur almost exclusively in loops.
What are motifs?	They are particular arrangements of secondary structures that occur frequently within a polypeptide and can be associated with a particular biological function.
What are domains?	A poly peptide chain (or part of a polypeptide chain) that folds independently into a stable structure with its own hydrophobic core. They are formed fro several simple motifs. Each domain is associated with a distinct biological function.
What bonds are responsible for the tertiary structure?	Hydrogen bonds between R groups, ionic bonds between COO- and NH3+ of R groups, disulphide bridges between cysteine groups and hydrophobic interactions (hydrophobic R groups cluster inside proteins to shield themselves from water)
What are Fibrous Proteins (Scleroproteins)?	Long parallel fibres of secondary structures
The Features of Fibrous Proteins	Usually insoluble and important for support and strength.
Features of Collagen	Superhelices of glycine rich alpha helices, main protein in connective tissue, most abundant protein, strong and elastic
What are alpha-keratins composed of?	Composed of coiled-coils of two alpha helices that assemble together in larger fibres
What is the structure of Beta Keratins: Fibroin?	Layers of anti-parallel beta sheets rich in Ala and Gly, Small side chains interdigitate (interlock like fingers) which allows close packing
What are Globular Proteins?	Mixture of irregularly folded secondary elements to form a compact 3-D spherical shape
What are Fibrous Proteins?	Long parallel fibres of secondary structures
Features of Globular Proteins	Usually soluble with inner hydrophobic core, transported easily in body fluids.
What interactions are responsible for the quaternary structure of a protein?	van der Waals
What is haemoglobin constructed from?	4 poly peptide chains (2 alpha, 2 beta) and 4 haem groups (porphyrin and Fe 2+)
What mutation results in sickle cell anaemia?	Beta chain mutation Glu becomes Val
What is Thalassaemia?	Underproduction of globin chains
What is Porphyria?	Underproduction of haem
What are immunoglobins?	Y-shaped proteins (antibodies) used by the immune system to identify and combat non-self .
What is the structure of immunoglobins?	4 chains linked by disulphide bridges ( 2 large heavy chains and 2 short light chains). The chain tips have variable structure and form specific binding sites for antigens.
What is the role of chaperone proteins?	Chaperone proteins assist the non-covalent folding of a protein.
What can occur when proteins aggregate?	Diseases can occur such as prion and amyloid disease (where soluble proteins become insoluble)
Is the structure or sequence more strongly preserved in evolution?	Structure
What are the properties of alpha keratins?	Strong and inextensible, insoluble and chemically inert
What bonds form between the coiled coils of alpha-keratins?	Disulphide bridges
Where is fibroin found?	Fibroin is found in silk cloth and spiders webs
How are the beta sheets in fibroin joined together?	Sheets joined by amorphous stretches which confer elasticity
Give some examples of globular proteins	Examples include: myoglobin, haemoglobin and immunoglobins
What do chaperone proteins prevent?	They prevent aggregation, repair misfolded/heat damaged units
Do chaperone proteins require ATP?	YES

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