Term
| Standard Free-Energy Change |
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Definition
| delta G at standard conditions |
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Term
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Definition
| Measure of Disorder; increases with any spontaneous process |
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Term
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Definition
| measurement of energy in the form of heat |
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Term
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Definition
| amino acid in its natural state (pH=7) having a positively charged amino group and a negatively charged carboxyl group |
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Term
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Definition
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Term
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Definition
| bond between hydrogen and N, O, or F; strongest intermolecular interaction |
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Term
Charge of:
C, N, O, Na, K, Ca, Mg, Cl |
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Definition
| C=-4, N=-3, O=-2, N=+, K=+, Ca=2+, Mg=2+, Cl=- |
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Term
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Definition
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Term
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Definition
| RCONR' (b/w amino acids in proteins) |
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Term
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Definition
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Term
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Definition
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Term
| 1st law of thermodynamics |
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Definition
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Term
| 2nd law of thermodynamics |
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Definition
| entropy of any spontaneous process increases |
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Term
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Definition
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Term
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Definition
| Energy produced by one reaction drives another |
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Term
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Definition
| small molecules that carry energy in the form of covalent bonds. ie ATP, NADH |
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Term
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Definition
| Reaction that loses H20 (formation of peptide bond) |
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Term
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Definition
| Reaction that adds H20 (breaking a peptide bond) |
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Term
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Definition
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Term
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Definition
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Term
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Definition
| anaerobic energy yielding mechanism, no ATP |
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Term
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Definition
| glucose stored and released in liver & muscle |
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Term
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Definition
| aerobic energy producing mechanism |
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Term
| oxidative phosphorylation |
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Definition
| creation of ATP by electron transport chain |
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Term
| flavin adenine dinucleotide |
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Definition
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Term
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Definition
| drives ATP synthesis, passes an electron down chain to oxygen molecule. |
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Term
List by Increasing Electronegativity:
O, N, S, C, P, H. |
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Definition
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Term
| Relate pH to H+ ion concentration [H+] |
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Definition
pH is defined as the negative e logarithm of the hydrogen ion concentration in moles per liter.
pH = -log[H+]. Thus a solution of pH 3 will contain 10-3 M hydrogen ions. |
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Term
Discuss the relationship between equilibrium constant and
standard free energy change. |
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Definition
| when G = 0, a chemical equilibrium will be attained. the ration of substrate to product reaches a constant value., the equilibrium constant, K reflects the ratio of products to substrate at equilibrium pg 76, change in G0 = -1.43logK, K = [X]/[Y] when Y --> X |
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Term
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Definition
| the location on an enzyme responsible for the catalytic activity |
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Term
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Definition
| binding to an alternate location on an enzyme to regulate it |
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Term
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Definition
| secondary protein structure |
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Term
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Definition
| the magnitude of forces between two molecules |
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Term
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Definition
| a molecule or enzyme that helps a protein fold properly |
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Term
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Definition
| a non-protein molecule that is necessary for an enzyme to function properly |
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Term
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Definition
| 2 or more α helices coiled together, forms left handed helix |
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Term
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Definition
| bond between S atoms in cysteine residues |
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Term
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Definition
Linnweaver-Burke
used to determine Vmax and Km |
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Term
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Definition
| (competitive and not)- competitive competes with the active site (Vmax doesn’t change, usually reversable binding), non-competitive changes Vmax, binds to allosteric site, renders enzyme inactive, non-reversible |
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Term
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Definition
| A product later in the pathway regulating an enzyme further up the pathway |
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Term
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Definition
| protein that makes fibers |
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Term
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Definition
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Term
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Definition
| proteins that bind GTp (many have GTPase activity) |
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Term
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Definition
| proteins that are transcribed when the organism is under heat stress |
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Term
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Definition
| a hybrid cell made from fusing a specific B cell with a specific B cell with a myeloma that produces only one type of antibody |
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Term
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Definition
| enzyme that catalyses hydrolysis |
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Term
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Definition
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Term
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Definition
| enzyme that converts between isomers of a molecule |
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Term
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Definition
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Term
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Definition
| turnover number, number of enzymatic reactions per second |
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Term
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Definition
| measure of catalytic efficiency |
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Term
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Definition
| the Michaelis-Menton constant, = .5 Vmax |
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Term
| Michaelis-Menton kinetics |
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Definition
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Term
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Definition
| a big molecule that contains more than one enzyme |
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Term
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Definition
| a big molecule that contains more than one enzyme |
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Term
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Definition
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Term
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Definition
| enzyme that transfers enzymes from one molecule to another |
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Term
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Definition
| enzyme that polymerizes a molecule (ie DNA or RNA) |
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Term
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Definition
| enzyme that degrades proteins |
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Term
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Definition
| an independently folding region of a protein |
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Term
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Definition
| shows relationships between all the proteins in an organism |
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Term
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Definition
| an enzyme that phosphorylates proteins |
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Term
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Definition
| a bunch of proteins stuck together that make one thing (like lipids or DNA) |
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Term
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Definition
| enzyme that removes a phosphate from a protein |
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Term
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Definition
| adding a Pi to a protein, usually from ATP |
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Term
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Definition
| large protein complex in living organisms that degrades proteins |
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Term
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Definition
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Term
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Definition
| site to which a regulator can bind (on enzymes or DNA) |
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Term
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Definition
| domain on proteins that helps the protein find its way to other proteins |
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Term
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Definition
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Term
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Definition
| an intermediate state in a chemical reaction |
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Term
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Definition
| attaching a ubiquitin to a protein (sometimes for destruction) |
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Term
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Definition
| the maximum rate a certain amount of enzyme can catalyze a reaction. |
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Term
| 2 Unidirectional Conformational Changes in Proteins: |
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Definition
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Term
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Definition
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Term
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Definition
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Term
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Definition
| the polarity of one strand is oriented opposite to that of the other strand (base pairing) |
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Term
| "beads on a string" model |
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Definition
| dna wrapped around histones |
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Term
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Definition
| constricted region of a mitotic chromosome that holds sister chromatids together |
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Term
| chromatin remodeling complex |
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Definition
| enzyme complex that alters histone-DNA configurations, changing accessibility of DNA to other proteins |
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Term
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Definition
| small visible areas of chromosomes where the genes are being expressed. Chromatin expand to occupy increased volume when genes are expressed. |
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Term
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Definition
| DNA double helices re-form from their separate strands in a reaction that depends on the random collision of two complimentary strands. |
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Term
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Definition
| Inheritance of phenotypic changes in a cell or organism that do not result from changes in the nucleotide sequence of DNA. Can come from histone modification causing heterochromatin formation |
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Term
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Definition
| region of an interphasae chromosome that stains diffusely; "normal" |
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Term
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Definition
| gene sequence that will be present in mRNA |
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Term
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Definition
| having multiple copies of a gene on different chromosomes. |
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Term
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Definition
| turning off genes - by methylation or RNAi by example. |
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Term
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Definition
| Genes that code for proteins with a common fold (called the globin fold) ex hemoglobin, myoglobin, etc |
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Term
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Definition
| more condensed chromatin; DNA contains few genes |
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Term
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Definition
| small abundant protein rich in arginine and lysine. Core of Nucleosome. |
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Term
| Histone acetyl transferance (HAT) |
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Definition
| Adds an acetyl group to lysines of histones, increase transcription |
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Term
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Definition
| chromatin-DNA interactions are guided by combinations of histone modifications |
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Term
| Histone deacetylase complex (ADC) |
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Definition
| takes off acetyl groups, decreases transcription |
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Term
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Definition
| 'Linker' histone protein that binds to DNA where it exits from a nucleosome and helps package nucleosomes into 30nm chromatin fiber |
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Term
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Definition
| One of the core proteins involved in forming a histone. Forms a dimer with H2B and then two of these dimers join the H3-H4 tetramer. |
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Term
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Definition
| One of the core proteins involved in forming a histone. Forms a dimer with H2A and then two of these dimers join the H3-H4 Tetramer. |
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Term
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Definition
| One of the core proteins involved in forming a histone. Forms a dimer with H4. Two of these dimers come together to form a tetramer before being joined by two H2A-H2B dimers. |
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Term
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Definition
| One of the core proteins involved in forming a histone. Forms a dimer with H3. Two of these dimers come together to form a tetramer before being joined by two H2A-H2B dimers. |
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Term
| Human Accelerated Regions |
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Definition
| Regions of DNA which have changed rapidly in the evolution of humans since diverging from chimpanzees. |
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Term
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Definition
| noncoding region of a gene; excised by RNA splicing |
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Term
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Definition
| Huge paired chromosome in meiosis in immature amphibian eggs, in which the chromatin forms large stirr loops extending out from linear axis of chromosome. |
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Term
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Definition
| exposed DNA between nucleosome core particles. |
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Term
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Definition
| parts of the cell cycle - know the order. |
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Term
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Definition
| tails which protrude from the nucleosome and can be modified for various effects |
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Term
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Definition
| Mutation that doesn't change the amino acid sequence. |
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Term
| Non-histone chromosomal protein |
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Definition
| protein associated with a chromosome that's not a histone |
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Term
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Definition
| inner portion of nuclear envelope |
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Term
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Definition
| fibrous meshwork of proteins on the inner surface of the inner nuclear membrane |
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Term
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Definition
| outer portion of nuclear envelope, continuous with the ER |
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Term
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Definition
| aqueous channel through the nuclear envelope which allows selected molecules to move between nucleus and cytoplasm |
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Term
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Definition
| enzyme that splits nucleic acids by hydrolyzing bonds between nucleotides. |
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Term
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Definition
| beadlike structure in eucaryotic chromatin, composed of short length of DNA wrapped around an octameric core of histone proteins. |
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Term
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Definition
| initiated by ATP-dependant chromatin remodeling complex. Allows nucleosomal DNA to be pulled around the nucleosome core making it available to other proteins. |
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Term
| Peripheral heterochromatin |
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Definition
| condensed heterochromatin near the lamina of the nucleus, generally contains genes which are not active. |
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Term
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Definition
| giant chromosome in which DNA has undergone repeated replication and the many copies have stayed together. |
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Term
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Definition
| a measure of the total energy of a thermodynamic system. It includes the internal energy, which is the energy required to create a system, and the amount of energy required to make room for it by displacing its environment and establishing its volume and pressure. |
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Term
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Definition
| Putting the exons together to make the mRNA |
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Term
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Definition
| sequences of DNA that are repeated. duh. |
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Term
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Definition
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Term
| Single Nucleotide Polymorphism |
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Definition
| variation between individuals in a population at a specific nucleotide in DNA sequence |
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Term
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Definition
| end of a chromosome; have repeated nucleotide sequences, help protect end of chromosome from degradation. |
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Term
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Definition
| segment of DNA that can move from one genome position to another. |
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Term
| Heat treatment affecting structure of polypeptide |
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Definition
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Term
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Definition
| denatures proteins at high concentrations |
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Term
| mercaptoethanol on polypeptides |
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Definition
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Term
| 4 Mechanisms how Enzymes are Regulated |
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Definition
- cell controls how many molecules of each enzyme it makes by regulating the expression of the gene that encodes that enzyme
- cell controls enzymatic activities by confining sets of enzymes to particular subcellular compartments, enclosed by distinct membranes
- enzymes are covalently modified to control their activity
- an enzyme acting early in a reaction pathway is inhibited by a late product of that pathway (feedback inhibition) |
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Term
| Ubiquitination (detailed) |
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Definition
-monobiquitylation=histone regulation
-multiubiquitylation (multiple sites with one ubiquitin molecule per site)=endocytosis
-polyubiquitination (chain of ubiquitin molecules)=proteasomal degradation OR DNA |
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Term
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Definition
| Separates proteins by size |
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Term
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Definition
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Term
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Definition
| molecular weight, then acidity/basicity. |
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Term
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Definition
| Flourescence Resonance Energy Transfer. |
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Term
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Definition
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Term
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Definition
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Term
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Definition
| the untranslated region on the 3' end of the mRNA that follows the coding region |
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Term
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Definition
| the leader sequence beginning at the trancriptional start site of mRNA and ending one nucleotide befor ethe start codon of the coding region, usually containing a ribosome binding site. |
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Term
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Definition
| Attracts histone-modifying enzymes and binds to a component of RNA polymerase II |
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Term
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Definition
| the exons of pre-mRNA are rearranged in different ways to form different mRNAs, allowing a single gene to code for multiple proteins |
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Term
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Definition
| like in drosophila where the genes for the head are found on the top of the larvae and the genes for the bottom so it's already arranged how it should be |
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Term
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Definition
| prevents the spread of heterochromatin into genes that need to be expressed |
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Term
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Definition
| region of DNA with a greater than average density of CG sequences. These regions generally remain unmethylated. Protects house-keeping genes |
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Term
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Definition
| opposite of regulated, it is always switched on and being transcribed |
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Term
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Definition
| lytic stage. cro protein occupies a different site on the operator, blocking the synthesis of repressor but allowing its own synthesis. |
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Term
| DNA binding domain on a protein |
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Definition
| the domain of a protein that physically binds to the DNA |
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Term
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Definition
| addition of methyl groups to DNA. Extensive methylation fo the cytosine base in CG sequences is used in vertebrates to keep genes in an inactive state |
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Term
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Definition
| regulatory DNA sequence to which gene regulatory proteins bind, increasing the rate of transcription of a structural gene that can be many thousands of base pairs away. Where activator binds. |
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Term
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Definition
| Inheritence of phenotypic changes in a cell or organism that do not result from changes in the nucleotide sequence of DNA. Can be due to things such as histone modifications causing heterochromatin formation. |
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Term
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Definition
| protein that appears in 7 strips in fly larvae in response to certain protein concentration |
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Term
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Definition
| the portion of mRNA that EXITS the nucleus. This portion will get transcribed into a particular amino acid sequence by a ribosome. EXpressed |
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Term
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Definition
| the set of linked DNA sequences regulating expression of a particular gene. Includes promoter and regulatory sequences |
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Term
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Definition
| protein that binds to a specific region of DNA to prevent transcription of an adjacent gene |
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Term
| general transcription factor |
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Definition
| any of the proteins whose assembly at a promoter is required for the binding and activation of RNA polymerase and the initiation of transcription |
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Term
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Definition
| phenomenon in which a gene is either expressed or not expressed in the offspring depending on which parent it is inherited from. |
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Term
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Definition
| protein complex composed of two different polypeptide chains |
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Term
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Definition
| DNA sequence that prevents a gene regulatory protein bound to DNA in the control region of one gene from influencing the transcription of adjacent genes |
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Term
| internal ribosome entry site (IRES) |
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Definition
| specific site in eukaryotic mRNA, other than 5' end, where translation can be initiated |
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Term
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Definition
| noncoding region of a eukaryotic gene that is transcribed and then excised |
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Term
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Definition
| in the prophage stage, the lambda repressor occupies the operator, blocking synthesis of CRO and also activating its own synthesis |
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Term
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Definition
| a control region that globin genes share located far upstream from the gene cluster that is needed for proper expression f each gene in the cluster |
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Term
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Definition
| serves as an intermediate between gene regulatory proteins and RNA polymerase |
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Term
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Definition
| micro RNA - short eukaryotic RNAs that regulate gene expression through complimentary base-pairing with mRNA. Can lead either to the destruction of mRNA or block its translation |
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Term
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Definition
| method of regulating an operon by which the gene is normally active, until the control shuts it off |
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Term
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Definition
| in a bacterial chromosome, a group of contiguous genes that are transcribed into a single mRNA molecule |
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Term
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Definition
| the poly-A tail is added to the 3' end of the RNA after the poly-A signal is recognized by the RNA9 cleavage complex |
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Term
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Definition
| method of regulating an operon by which the gene is normally inactive, until the control turns it on |
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Term
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Definition
| nucleotide sequence in DNA to which RNA polymerase binds to begin transcription |
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Term
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Definition
| genetic construct in which a copy of the regulatory DNA of a gene of interest is linked to a sequence coding for an easily-detectable product |
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Term
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Definition
| part of an mRNA molecule that can directly bind a small target molecule, affecting the gene's activity |
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Term
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Definition
| Type of RNA processing that alters the nucleotide sequence of a pre-mRNA transcript by inserting, deleting, or altering individual nucleotides. |
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Term
| RNA induced silencing complex |
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Definition
| a multiprotein complex that uses either miRNA or siRNA as a template for recognizing mRNA; when it finds a complementary strand, it activated RNase, which cleaves the RNA |
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Term
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Definition
| small interfering RNA - short double-stranded RNAs that inhibit gene expression by directing destruction of complimentary mRNAs |
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Term
| integral membrane protein |
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Definition
| protein held in the bilayer by lipid groups deep in the membrane |
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Term
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Definition
| technique for monitoring the kinetic parameters of a protein by analyzing how fluorescent protein molecules move into an area of the cell bleached by a beam of laser light. |
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