AMINO ACID AND PROTEINS 1 Flashcards

Question

what is tertiary structure

Answer 1

-The 3-D structure of a particular protein /polypeptide. -Some include the arrangement of secondary structures – Super secondary structures or motifs -On average 27% are in alpha helix and 23% beta structures -But there are exceptions – there is 75-80% alpha helix in Myoglobin and Hemoglobin -Concanavalin A has only beta structures and no alpha helices. It is a lectin protein that binds selectively to carbohydrates (sugars, glycoproteins) found in plants, human etc. -Usually all hydrophobic aa are found in the protein interior (val, leu, met) -Polar and charged aa (glu, asp, his, lys) are found on the surface of the proteins – meets water molecules -Polar aa with no charge can be found inside or on the surface of globular proteins (ser, asn, tyr) -Usually globular proteins that are large (>200aa) have DOMAINs – for example, domain A & B (ex. Theenzyme glyceraldehyde 3-P DH, phosphoglycerate kinase)

Answer 2

-the peptide bond - its geometry -the hydrogen bond -hydrophobic interactions -electrostatic interactions -van der waals interactions -disulphide bond

Answer 3

-The C=O, C-N atoms are planar. -Degree of rotation depends on the size of the R groups of the amino acids in the peptide bond -It has a double bond characteristic. -The structure and geometry of the peptide bond limits the degree of rotation or conformational coiling that can take place.

Answer 4

-Occurs between side chains (R) that are hydrophobic in nature -Automatically/spontaneously avoids interaction with water (more stable) -Usually in the core of globular proteins

Answer 5

Occurs between side chains that are charged (ex: between -- COO- with --NH+ groups)

Answer 6

-Transient weak electrical attractions; electron clouds around molecule fluctuate and forms temporary electric dipoles -(ex: between two methyl groups, –CH3 )

Answer 7

Between side chains of cysteine residues linking together polypeptide chains (same or different chains)

Answer 8

-The fourth level of protein structure is concerned with the interaction of 2 or more polypeptide chains to associate to form a larger protein molecule. -Proteins with more than one polypeptide chain are said to be oligomeric, and the individual chains are called subunits or monomers of the oligomer. -The geometry of the molecule is its quaternary structure. Two subunits forms a dimer, three a trimer, four a tetramer etc. -The subunits (polypeptide chains) may be identical (homogeneous) e.g. muscle creatine kinase is a dimer of 2 identical subunits or non-identical e.g. haemoglobin is a tetramer and contains 2 alpha + 2 beta subunits (heterogeneous).

Answer 9

-The central dogma of protein folding – “The primary structure determines the tertiary structure” -Protein folding is spontaneous and probably starts with a local secondary (α-helix or β-structure) structure, which forms the nucleus/centre, around which the rest of the coil folds around. -Recently proteins called molecular chaperone or chaperone proteins have been discovered (originally called heat shocked proteins) which help in protein folding – although exactly how not known. -Probably protect certain exposed non-polar regions of developing polypeptide

Answer 10

keratin and collagen

Answer 11

myoglobin and hemoglobin

Answer 12

formed from parallel polypeptide chains held together by cross links. these form long, rope-like fibres, with high tensile strength and are generally insoluble in water

Answer 13

the main component of connective tissue such as ligaments, tendons, cartilage

Answer 14

the main component of hard structures such as hair, nails, claws and hooves

Answer 15

forms spiders' webs and silkworms cocoons

Answer 16

-Main structural component of hair (also nail, skin and horns etc). -Its basic unit is the a-helix polypeptide. -Two a-helices are twisted together to form a coiled-coil. -Two coiled-coils twist together to form a protofilament/protofibril. -Protofilaments are arranged in 9+2 fashion to form a microfibril -Many microfibrils are packed together form a macrofibril -Many macrofibrils pack together to form a fiber (a single hair)

Answer 17

-Rich in hydrophobic amino acids that promote a-helix formation. -Because R-groups are directed toward the outside of the helix, keratins are highly insoluble in water. -Lack helix-breaking proline residues. -Structure of protofilaments is stabilized by intermolecular hydrogen bonds and disulfide bridges. -The disulphide bonds can be reductively cleaved by mercaptans (ex. Ethyl or methyl mercaptans). -Hair so treated can be curled and set in a “permanent wave” by an oxidizing agent which reestablishes the disulphide bonds and the hair in a new conformation.

Answer 18

-Most abundant protein in vertebrates – 25% of all protein in body -Structural component of extracellular matrix, bone, teeth, tendons and blood vessels. -Basic structural unit is a collagen polypeptide that forms a left-handed helix -No α-helix or β-pleated sheet structure possible -The collagen molecule is a triple helix of three collagen polypeptides – ~ 3000A long

Answer 19

-structural protein with tensile strength -glycine-proline-alanine -3 polypeptide chains, each in the shape of helix -3rd amino acid is glycine (allows the coils to lie close to e/o) -triple strands wind around each other forming fibres -molecules within the fibre are joined by cross linkages

Answer 20

-usually have a spherical shape caused by tightly folded polypeptide chains -the chains are usually folded so that hydrophobic groups are on the inside, while the hydrophilic groups are on the outside. this makes many globular proteins soluble in water

Answer 21

-transport proteins ( haemoglobin, myoglobin, those embedded in membranes) -enzymes (lipase, DNA polymerase) -hormones (oestrogen, insulin)

Answer 22

-Myoglobin structure was elucidated by John Kendrew & Max Perutz (late 50s) using x-ray crystallography techniques. -Small in size (153 amino acid residues) and crystallizes easily – easy to study. -Has the ability to carry oxygen because it has a prosthetic group – haem (a tetrapyrrole – see below). -Myoglobin is extremely compact. -75% of polypeptide is in alpha helix – 8 helix segments, A, B, C, D, E, F, G & H.

Answer 23

-Hemoglobin (or haemoglobin, frequently abbreviated as Hb), which is contained in red blood cells, serves as the oxygen carrier in blood. -Hemoglobin also plays a major role in the transport of carbon dioxide from the tissues back to the lungs. -Each heme group contains an iron atom, and this is responsible for the binding of oxygen. -Has 4 polypeptide chains; 2 α chains (141aa – minus D helix); 2 β chains (146aa – shortened H helix) chains (i.e. has 4 subunits; 574 aa; M.Wt. 63,500) -Each subunit almost spherical. -Each subunit can carry 1 oxygen molecule -Thus the capacity to carry oxygen is high: Hb4 + 4O2 → Hb4(O2)4 oxy-hemoglobin -Fe2+ in the protohaem can bind to 6 atoms (like myoglobin). -The β subunits has 8 helical segments (A,B,C ….H) – just like myoglobin. The α subunits have 7 helical segments (minus the D segment).