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Biochem
first 20 slides
| Question | Answer |
|---|---|
| proteins are | biological polypeptides of amino acids joined by peptide bonds |
| what amino acid and what sugar isomers are found in biological systems? | L amino axids and D sugars |
| a molecule is chiral if: | It is non-superimposable on it's mirror image |
| amino acid side chains vary in: | Size, shape, charge, h-bond capacity, Chamical reativity |
| what amino acids are hydrophillic? | Histidine, Lysine, Cysteine, Serine, Aspartic acid. |
| what amino acids are hydrophobic? | Phenylalanine, Glycine, Alanine, Proline |
| in a zwitterion, _____ lost a proton, and ____ gained a proton | Carboxyl group lost a proton, and the amino group gained a proton. |
| the pKa is... | pH at which an ionisable group is 50% dissociated |
| ph= | pKa+log([A-]/[HA]) |
| if [A-]>[AH] then | the pH is greater than the pKa and the proton is off |
| if [AH]>[A-] then | the pH is less than the pKa and the proton is on |
| the isoelectric point is... | the pH at which there is no net charge on the molecule. |
| pI = | 1/2 (pKa1+pKa2) |
| at neutral pH whats ections are ionized? | All sections that can be ionized are. |
| condensation reaction: | monomers to dipeptide + H2O |
| Hydrolysis reaction: | dipeptide + H2O to monomers |
| peptide bond formation: -COO + H3N- | -C-N- |
| Polymers are built up by: | sequential addition of repeating units to one end |
| Why is energy needed to build a macromolecule? | Adding more order to the system with each monomer added. (increasing order = decreasing entropy) |
| why are enzymes needed to buld macromolecules? | a RX will not occur spontaneously if the free energy of the products is higher than the free energy of the reactants. |
| How does the cell get energy to the reactions? | Activated monomers, Coupled reactions. |
| What is the most common energy-releasing reaction? | ATP + H2O --> ADP +Pi |
| A protein is least soluble at what point? | The isoelectric point |
| Properties of a peptide bond: | Planar, Have partial double bond character, Almost always trans, Capable of H-bonding |
| what a.a. is sometimes cis? | proline is sometimes cis. |
| the acceptor in peptide H-bonding is _____ the donator in peptide H-bonding is______. | acceptor = -C=O donator = HN- |
| the repeating pattern of polar atoms of the peptide bonds allow for: | the formation of regular molecular structures |
| define Secondary Protein Structure: | Regular folding due to Hydrogen Bonds between atoms of the petide bonds of the protein backbone |
| What are the major secondary protein structures? | B-pleated sheets (parallel and anti-parallel), a-Helix, Loops and turns. |
| B-pleated sheets: formation, and where found | side chains of a.a. residues point up and downfrom the plane of the sheet, they are rigid, Often found in the hydrophobic interior of the protein. |
| Which a.a doesn't fit in the B-pleated sheets or a-Helix? Why? | Proline, Because it puts bends in the backbone. |
| a-Helix: formation, and where found | H-bonding between the O of one peptide bond and the H of a peptide bond 4 residues along. Often amphipathic, Found on the surface of globular proteins. turn is 3.6 residues. |
| Why do proteins form regular secondary structures? Peptide Bond atoms: a-Helices and B-sheets: | peptide bond atoms form hydrogen bonds as they're energatically favoured. a-helices and B-sheets mawimise the number of H bonds that can form between peptide atoms, are compatible with the bond lengths and angles of the covalent bonds of the backbone. |
| What determines whether the protein forms a-helix or B-sheets? | the most energetically favourable structure will form Some proteins acn adopt two different forms as there is little energy difference between the forms. |
| Protein tertiary structure: | Irregular folding in 3D Amazing diversity Shape defines function May contain non-protein components |
| Tertiary conformation is defined by: | The primary structure and its interaction with the environment |
| Tertiary conformation is maintained by: | Weak interactions between R groups. |
| Hydrogen bonds in tertiary structure form between: | side chain H bond acceptors and donators, between backbone H bonding groups(if not in secondary structures), Between one side chain and one backbone group |
| Hydrogen bonds contribution to tertiary structure: | Major determinant of conformation |
| Hydrogen bonds contribution to tertiary structure stability: | Provide relatively low stability to structure as easily broken |
| Hydrogen bonds in tertiary structure important for: | solubility of globular proteins because of interactions with water molecules. |
| Ionic interactions in tertiary structure form between: | Between charged side chains (attraction and repulsion) Between charged side chains and ions in solution. |
| Strength of ionic interactions in tertiary structure often reduced by: | Water molecules |
| Contribution of ionic interactions to tertiary structure: | Not a major determinant of structure but important eg. in some enzyme active sites. |
| Contribution of ionic interactions to tertiary structure stability: | Contribute little to stability because charged side-chains can interact with salt ions in solution or water. |
| Van der Waals Interactions are: | Transient interactions that occur between electrically neutral molecules- electron distributions produce continually fluctuating polarities. |
| Contribution of Van der Waals to tertiary structure: | Weak and too short range to affect how the protein folds. |
| Contribution of Van der Waals to tertiary stability: | Important for stability due to additive nature and the tight packing of most proteins. Important for stability of large molecules. |
| Hydrophobic Effect: | Water molecules around non-polar groups must arrange themselves to maximise H-bonding. arrange so that the hydrophobic parts are in the interior and not in contact with the water. |
| Hydrophobic effect contribution to tertiary structure: | Very important determinant of protein structure. |
| Hydrophobic effect contribution to tertiary structure stability: | No bonds but energetically favourable. |
| Disulphide Bonds form: | Between -SH groups of cysteine side chains that are close together in the tertiary structure |
| Disulphide Bonds only form | after the tertiary structure forms. |
| Disulphide bonds usually only found in proteins to be: | Secreted out of the cell. |
| Most soluble globular proteins fold with: | hydrophobic groups together and away from water. |
| Polar surface R-groups form H-bonds with: | water molecules. |
| Acidic and basic surface R-groups can form ionic interactions with | Ions in solution. |
| Polar regions of membrane proteins are arranged: | On both surfaces of the membrane extending into solution. |
| In membrane proteins,Alpha-helix has hydrophobic groups | extending out in contact with hydrophobic centre of membrane. |
| Membrane Proteins can be made: | On surface of a membrane. |
| Domains are: | Discrete sections of a single polypeptide |
| Similar Domains are used in | several different proteins |
| Different domains may have | different biological functions |
| Protein Quarternary structure: | The arrangement of 2 or more discrete polypeptide sub-units into a single, functional oligomeric protein complex. |
| Protein Quarternary Structure often held together by: | weak interactions |
| Quarternary Structure allows for: | larger sizes and more complex shapes and functions for some proteins. |
| Weak interactions can be disrupted by: | High temperatures Changes in pH Solvents hydrophobic to hydrophillic environment. |
| The a-Keratin polypeptide chain is a ...... a-helix. | Right Handed a-helix. |
| In a-keratin, ..... helical strands wrap together to form a ........ | 2 to 4 helical strands wrap together to from a superhelical coiled coil. |
| In a-keratin, there is a ..... arrangement of the two strands (.... termini at the same end). | There is a parallel arrangement of the two strands (N-termini at the same end). |
| The supercoil of a-keratin is twisted in a ....handed manner. | The supercoil of a-keratin is twisted in a left-handed manner, |
| a-keratin is rich in which hydrophobic amino acids? | Ala, Val, Leu, Ile, Met, Phe. |
| a-helix formed by: | H bonding between O at one peptide bond and the H of a peptide bond 4 residues along. |
| In a-keratin, Disulphide cross-links between helices and coiled coil sturctures..... | Add strength. |
| Structure of a-keratin: | 1. right handed a-helix. 2. left handed superhelical coiled coil. 3. protofilament. 4. protofibril. 5. intermediate filament. |
| Collagen: Dense connective tissue Tendons and Ligaments function | Connect organs and hold them together. |
| Collagen: Dense connective tissue properties related to Tendons and Ligaments function. | Long fibres (various sizes). Strong (like achoilles) Must not stretch (inelastic under repeated use) |
| Collagen: Dense connective tissue properties related to Bones, Teeth and Cartilage function. | Collagen provides a matrix for minerals. Hard, dense, sometimes hollow or honeycombed structure. |
| Collagen: Dense connective tissue Bones, Teeth and Cartilage function. | Structure and support for the body, protection for the brain. Muscles pull on bones to give movement. |
| Collagen: Loose Connective Tissue examples | Beneath eptithelial cell layers in skin, intestines, blood vessels. Important component of complex extended structures but not the only component. |
| Collagen: Loose connective Tissue properties. | Need to be flexible. Respond to body movements like bending, twisting, and stretching. Deform under pressure and return to original position (elasticity). Respond to movements in the gut, muscle movement etc. |
| How can Collagen be in both elastic and inelastic tissues? | Dense: Parallel fibrils, covelent bonds, Combined strength. Loose: Arranged perependicular to stress, Can be determined by sideways pressure, readily springs back. |
| Collagen Primary Structure have little variety in amino acids: | Every third residue is glycine. About 1 in 3 is proline or hydroxyproline. Repeating Gly-X-Pro are common. |
| Each Collagen polypeptide is.. | Wound into left-hended helices. Not found individually. NOT a-helix. |
| Difference between a-helix and collagen primary structure: | More elongated, tightly wound than a-helix. No H bonding possible within helix. Glycine and proline are incompatible with a-helix. |
| Tropocollagen: | 3 single Collagen polypeptides make it. Glycines always in centre .'. always every 3rd. Right handed. |
| Features of Tropocollagen: | Slightly staggered arrangement to allow H bonding between helices. Gly-H side chains point into centre. Pro and HydroxyPro are essential for tight helical structure. Superhelix does not stretch |
| What holds the Tropocollagen superhelix structure together? | H bonds between C=O and N-H of peptide bonds and -Oh of side-chains between different strands within the superhelix. The three chains do not need to be identical in primary structure. |
| Why are many Pro and Lys residues hydroxylated? | To allow cross-linking. |
| Degrees of structure of Collagen: | 1.Polypeptide left-handed helix. 2.Tropocollagen 3.Part of collagen fibril 4.Tendon bundles of fibrils. |
| Collagen fibril structure: | Triple helices covalently bonded via lysine cross-bridges between the strands of a triple helix and between triple helices near the N and C terminals. |
| Globular Proteins are: | Compact, roughly spherical molecules. Mostly water soluble. Hydrophobic core with hydrophillic exterior. Well defined tertiary structure. |
| Globular Protein function depends on: | weak interactions with other molecules and ligands, and other proteins. |
| Red Blood Cells last about: | 10 days. |
| RBCs deliver O2 to the body tissues via: | the blood flow in the circulatory system. |
| Myoglobin has ....... subunits. | 8 a and NO B subunits |
| Hemoglobin has...... subunits. | a and B subunits. |
| The four units of Hemoglobin: | Hemoglobin is a tetramer. has 2 identical a-subunits and two identical B subunits. Each subunit has 1 heme capable of binding O2. |
| Heme Structure: | Has a substituted porphyrine structure. |
| Myoglobin Structure: | 8 a-helices connected by turns. Heme lies between helices E and F. |
Created by:
Liarna9Joy
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