Exam #1 HBC
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| Biochemistry | Chemical composition, metabolism, nutrition, energetic, enzyme function, transfer genetic info, membrane properties, cellular organization and molecular diseases.
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| Vitalism | life and the functions of a living organism depend on a nonmaterial force or principle separate from physical and chemical processes.
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| Who disproved the theory of vitalism? | - Wohler and the urea disproved the theory. From organic to inorganic
- Watson and Crick - biological replication in DNA
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| Covalent bond | Strong force, sharing of electron pair by strong adjacent forces. Promotes large molecular diversity. C-C 85 kcal/mol
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| Electrostatic bonding (Salt bridges, salt linkage, ion pair, ionic bond) | attractive and repulsive electrical forces between atoms/ groups of atoms/molecules that are caused both by the presence of ionized species and by the electro(+) and electro(-) properties of the atoms.
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| Hydrogen Bond | weak force, hydrogen atom is covalently linked to an electronegative atom (O or N) in near proximity to another electronegative atom (O or N)
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| Hydrophobic interactions | The attractive force between nonpolar molecules or nonpolar groups which leads to the association of these groups or molecules in an aqueous environment.
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| Van der Waals interactions | 2 uncharged atoms together= electron clouds. Asymmetric/ random variations in the e- positions around one nucleus create transient/opp electric dipole in nearby atom = dipoles weakly attract each other.Closer together, e- clouds repel each other.
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| Weak bonds are? | highly reversible.
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| What is the relationship between ΔG, ΔH, and ΔS. | ΔG = ΔH – TΔS
If ΔG = 0, the reaction is at equilibrium
If ΔG = +, the reaction is not spontaneous
If ΔG = -, the reaction is spontaneous
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| Define and give examples of entropy | Entropy (measure of order)
As ΔS increases (ΔS becomes more positive), the products become less ordered (more random).
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| Predict the state of a chemical reaction from the value of ΔG. | If ΔG = 0, the reaction is at equilibrium
If ΔG = +, the reaction is not spontaneous
If ΔG = -, the reaction is spontaneous
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| Define and discuss potential energy and kinetic energy | Potential energy – The energy stored by matter as a result of its location or spatial arrangement.
Kinetic energy – The energy of motion
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| conditions for a spontaneous reaction. | the reactants must have more potential energy than the products and/or be more ordered than the products
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| Gly, Ala, Val, Leu,Ile and Pro are related by? | These aliphatic amino acids are hydrophobic. Notice that proline is the only amino acid whose central carbon atom nitrogen is in a ring. Side chains contain C and/or H
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| Phe, Tyr, Trp are related by? | contain ring structures. Have aromatic R groups and are hydrophobic. OH of tyr can be phosphorylated.
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| Met and Cys are related by? | Contain sulfur.
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| Ser and Thr are related by? | Contain hydroxyl group. The OH can be phosphorylated. Hydrophillic.
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| His, Lis and Arg are related by? | Basic and hydrophillic
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| Asp and Glu are related by? | Acidic and hydrophillic.
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| Asn and Gln are related by? | Contain Amino group and are hydrophillic.
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| Protein | polymer/chain of A.A linked by peptide bond. Protein of 50kD= molec weight 50,000 Daltons. Proteins acan be made up of 20 diff A.A
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| What is the general structure of A.A in non-ionized form? | Amino group, Side chain and carboxyl group.
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| What is the general structure of A.A in ionized form? | Amino group (+), Side chain and carboxyl group(-).
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| Amino Acids | Building block monomers of proteins. Difference in R-groups causes diff phys & chem prop to each A.A.
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| Carboxyl group | Acidic, when it donates a proton it becomes negatively charged.
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| Amino group | Basic, accepts a proton it becomes positively charged.
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| Isoelectric point | pH when molecule has 0 net charge, having a equal number of (+) & (-) charges. Molecule does not move in an electric field.
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| The central carbon in all A.A is asymmetric except for... | Glycine
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| An Amino acid can exist in 2 forms that differ in only the.... | Spatial arrangement of the 4 groups about the central carbon atom. the 2 forms are mirror image of each other and not superimposible.
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| Mirror images that are not super-imposable are | Chiral
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| Enantiomers | 2 molecules are mirror images of each other.
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| Why is Glycine not asymmetrical? | Its R-group is a hydrogen atom.
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| Proteins are made up of only which form? | Left handed form/ L-amino acids.
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| Condensation reaction. | Monomer in, water out. Removal of water.
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| Hydrolysis reation. | Monomer out, water in. Addition of water.
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| Protein macromolecules are formed by ? | Condensation reactions between A.A
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| Although 2 proteins may have the same A.A and are identical in molecular weight, they may be ... | Different molecules. Its in the sequence. Ex: Oxytocin vs. Vasopressin
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| Primary Structure(I) | Described by the type, number and sequence of A.A in the chain. The A.A seq of a protein determines its 3D structure.
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| What is responsible for maintaining the structure of a protein? | Peptide bonds of A.A
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| Secondary Structure (II) | Folding of a polypeptide chain along 1 axis of a molecule into a uniform repeating conformational pattern.
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| What causes the preferential folding of some protein domains into regions with regular, repeating, secondary motifs ? | Combo of intra-molecular H bonds and van der waals forces.
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| What are examples of secondary structural motifs? | Alpha helix and beta sheet.
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| Tertiary Structure (III) | Irregular 3D folding of the polypeptide chain UPON itself.
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| What participates in the stabilizing the tertiary structures of proteins? | Covalent bonding(disulfide bridges), noncovalent interactions( electrostatic/van deer Waals and hydrophobic interactions)
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| Homologs are _____ ? | Descended from a common ancester
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| Two proteins are homologous if they are? | Derived from a common ancestor.
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| Paralogs | Homologs, present within 1 species. DIFFER in detailes biochemical function
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| Orthologs | Homologs, present within DIFFERENT species. Have SIMILAR or IDENTICAL functions.
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| Give examples of orthologs and paralogs. | Orthologs: Bovine ribonuclease (digestive enzyme) and human ribonuclease(digestive enzyme).
Paralogs:human ribonuclease(digestive enzyme) and Angiogenin(stimulates blood vessal growth)
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| Quaternary Structure (IV) | Results from the interaction between individual polypeptide chainds to yeiled larder aggregates (multimers)
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| What can stabilize the subunit structure of the quaternary structure? | Covalent bridges and especially non-covalent interactions (electrostatic/van deer Waals and hydrophobic interactions)
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| 3D structure determines a proteins? | FUNCTION
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| Denaturation | Loss of 3D structure to cause a loss of function. The process is considered as an unfolding og the protein molecule. The can be denatured by heat, extreme pH change or chemicals.
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| Renaturation | Process by which a protein can regain its native structure and its bio activity/ function.
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