Biochemistry Gre

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catabolism

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is the set of metabolic pathways that break down molecules (lipids, polysaccharides, nucleic acids, proteins etc) into smaller units (monosaccharides, fatty acids, amino acids, nucleotides, etc.) and release energy

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anabolism

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the set of metabolic pathways that construct molecules from smaller units (requires energy)

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enthalpy

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sum of internal energy + product of pressure and volume
H=E+(p*v)

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entropy

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state of disorder or order of a system

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Gibbs free energy

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energy released for work

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second law of thermodynamics

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systems naturally tend toward a state of randomness

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law of mass action

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reactions may be driven in either direction by increasing the concentration of reactants to products

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Le Chatelier's principle

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whenever a system at equilibrium is subjected to a perturbation (change in concentration of one or more of its components), then the equilibrium will shift in a direction so as to releive the perturbation

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covalent bonding

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a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms, or between atoms and other covalent bonds (generally considered strong)

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ionic bonding

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a type of chemical bond that involves a metal and a non-metal ion (or polyatomic ions such as ammonium) through electrostatic attraction (generally considered strong; i.e. NaCl). The metal donates one or more electrons, forming a positively charged ion or cation with a stable electron configuration.

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hydrogen bond

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the attractive force between one electronegative atom and a hydrogen covalently bonded to another electronegative atom. It results from a dipole-dipole force with a hydrogen atom bonded to nitrogen, oxygen or fluorine (generally considered weak)

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van der Waals bonds

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the attractive or repulsive force between molecules (or between parts of the same molecule) other than those due to covalent bonds or to the electrostatic interaction of ions with one another or with neutral molecules (caused by correlations in the fluctuating polarizations of nearby particles)

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amphiphilic

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molecules that have portions that will dissolve in water and portions that won't (they have both hydrophilic and hydrophobic parts)

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dipole moment

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the direction and strength of a molecule's degree of polarization

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amino acid

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building blocks of proteins
20 amino acids
amino functional group and carboxyl (acid) group
H
|
NH3--C--COOH
|
R
may have 3 different forms in solution, depending on pH (acidic, isoelectric, basic)
almost always in L configuration

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aliphatic compounds

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compounds composed of carbon and hydrogen that do not contain aromatic rings (i.e. benzene rings) (G. aleiphar, fat, oil)

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aromatic compounds

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compounds composed of carbon and hydrogen that contain benzene rings or similar rings of atoms

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methyl group

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hydrophobic alkyl functional group named after methane (CH4). It has the formula -CH3

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alkyl

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univalent radical consisting of carbon and hydrogen atoms, arranged in a chain. The Alkyls form homologous series with the general formula CnH2n+1. They include methyl, CH3· (named after methane), ethyl (C2H5·), propyl (C3H7·), butyl (C4H9·), pentyl (C5H11·), etc. They are usually constituents of larger molecules, but, when occurring independently, they are known as "free radicals" and are very reactive.

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peptide bond

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chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amine group of the other molecule, thereby releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids

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secondary structure

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folding pattern of polypeptide backbone structure (i.e. helices, pleated sheets, turns)

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alpha-helix

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one of the major secondary structures found in proteins. For L-alpha-amino acids, helical structure is right-handed. 3.6 a.a. residues/turn. hydrogen boning occurs within helix so that C=O of nth residue forms hydrogen bond with (n+4)th residue. R groups point outward.

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beta-pleated sheets

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type of secondary structure--2 forms: parallel and antiparallel
parallel: backbone of p.p. chains that H-bond with each other run in same direction (both C-->N), antiparallel run in opposite directions

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beta-turns

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(the most common turn in secondary structure) is characterized by hydrogen bond(s) in which the donor and acceptor residues are separated by three residues

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tertiary structure

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3-d arrangement of complete polypeptide chain--where helices, pleated sheets, disulfide bridges all come together to form 3-d structure of protein. functional protein--important reactive groups are brought into close proximity to form appropriate active centers

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protein subunit

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individual tertiary arrangement of individual peptide chain

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quaternary structure

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interaction and arrangement of subunits of a protein

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allosteric enzyme

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(regulatory) enzymes that change their conformation upon binding of an effector. An allosteric enzyme is an oligomer whose biological activity is affected by altering the conformation(s) of its quaternary structure. Allosteric enzymes tend to have several subunits.

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dimer

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a chemical or biological entity consisting of two structurally similar subunits called monomers, which are held together by either intramolecular forces (covalent bonds) or weaker intermolecular forces.

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ribozymes

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(from ribonucleic acid enzyme) an RNA molecule that catalyzes a chemical reaction

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protease

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enzymes that cut peptide bonds in proteins

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serine protease

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an protease that has serine at the active site. used in blood coagulation and digestion primarily. (ex. trypsin, chymotrpsin, factor__, thrombin)

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holoenzyme

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active protein enzyme in combination with its coenzyme

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oxidoreductases

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enzyme beginning with 1.-
enzyme that catalyzes the transfer of electrons from one molecule (the reductant, also called the hydrogen or electron donor) to another (the oxidant, also called the hydrogen or electron acceptor).
A– + B → A + B–
i.e. oxidation of alcohol to aldehyde

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transferases

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enzyme labelled 2.-
enzyme that catalyzes the transfer of a functional group (e.g. a methyl or phosphate group) from one molecule (called the donor) to another (called the acceptor)
A–X + B → A + B–X
i.e. transfer of terminal phosphate of ATP

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hydrolases

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enzyme labeled 3.-
enzyme that catalyzes the hydrolysis of a chemical bond
A–B + H2O → A–OH + B–H
i.e. chymotrypsin and lysozyme

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electrolyte

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substances that conduct electricity in molten state or when dissolved in water--must be ionic

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alkane

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are chemical compounds that consist only of the elements carbon (C) and hydrogen (H) (i.e., hydrocarbons), wherein these atoms are linked together exclusively by single bonds (i.e., they are saturated compounds) without any cyclic structure (i.e. loops) (methane, ethane, propane, butane, pentane, etc)

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ethyl group

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C2H5 group

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methyl group

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CH3

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alkenes

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compounds that have at least one carbon to carbon double bond. CnH2n

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alkynes

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compounds that have at least one carbon to carbon triple bond. CnH2n-2

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aromatic compounds

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hydrocarbons that contain a cyclohexene type of ring system that alternates between single and double bonds. simplest is benzene

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carboxyl group

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-COOH
carboxylic acids--can be prepared by oxidation of alcohol
CH3CH2OH(I)+O2(g)-->CH3COOH(I)+H2O

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esters

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R-COOR' (similar to carboxyl group, but H is replaced by another R-group). made by reacting a carboxylic acid with an alcohol, producing an ester and water.

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aldehyde

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organic compound containing a terminal carbonyl group. This functional group, which consists of a carbon atom bonded to a hydrogen atom and double-bonded to an oxygen atom (chemical formula O=CH-), is called the aldehyde group. produced by oxidation of alcohols.
O
||
R---C---H
i.e. formaldehyde

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ketones

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compound that contains a carbonyl group (C=O) bonded to two other carbon atoms
O
||
R---C---R'

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carbonyl group

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O=C

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ether

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class of organic compounds which contain an ether group — an oxygen atom connected to two (substituted) alkyl or aryl groups
R-O-R'

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amine

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organic compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group

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amide

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In the first sense referred to above, an amide is an amine where one of the nitrogen substituents is an acyl group; it is generally represented by the formula: R1(CO)NR2R3 , where either or both R2 and R3 may be hydrogen. Specifically, an amide can also be regarded as a derivative of a carboxylic acid in which the hydroxyl group has been replaced by an amine or ammonia.