Biochemistry Terms/definitions

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This polymerase synthesizes stretches of RNA on parental ssDNA

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RNA Polymerase alpha

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Enzymes differ from ordinary chemical
catalysts in four different aspects:

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Higher reaction rates
Mild reaction conditions
Great specificity
Capacity for regulation

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a small molecule that is required for the catalytic activity of an enzyme

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cofactor

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cofactors which, are permanently associated with their protein, either through covalent or noncovalent interactions.

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prosthetic group

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Term for organic molecule cofactor

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coenzyme

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A catalytically active enzyme-cofactor complex

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holoenzyme

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The enzymatically inactive protein resulting from the removal of the cofactor

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apoenzyme

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a cofactor only transiently associated with a given enzyme

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cosubstrate

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Four general mechanisms enzymes use to achieve catalytic enhancement of the rates of chemical reactions:

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catalysis by proximity
covalent catalysis
catalysis by strain
general acid base catalysis

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Five major factors affecting rate of enzyme catalyzed reaction:

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[substrate], [enzyme]
temperature
pH
denaturation

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a small molecule that binds specifically to a larger one.

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ligand

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Six major types of mechanisms to regulate enzymes

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substrate availability, covalent modification, proteoysis, alosteric effector molecule, product/feedback inhibition, protein synthesis, degradation

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Describes a groups of enzymes working together in specific metabolic pathways consisting of several steps

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multi-enzyme pathways

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The ideal enzyme for regulatory intervention is one whose quantity or activity dictates that the reaction it catalyzes is slow relative to all others in the pathway. The slowest, irreversible step in the pathway is theThe ideal enzyme for regulatory intervention is one whose quantity or activity dictates that the reaction it catalyzes is slow relative to all others in the pathway. The slowest, irreversible step in the pathway is the ___

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rate-limiting enzyme

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Three characteristics of enzyme regulation by product inhibition

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product is structurally similar to substrate, the response of the enzyme is immediate, product binds reversibly to substrate

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Four major characteristics of allosteric enzymes

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quaternary structure, effector binds to regulatory site, effector binding is reversible, sigmoid curve

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In this type of enzyme, the effector binds to regulatory site other than the active site (catalytic site, where the reaction is taking place).

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allosteric enzyme

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a form of allosteric regulation where a downstream product in the metabolic pathway inhibits the activity of the first enzyme in the pathway, thereby ensuring that the functioning of the pathway is sensitive to the intracellular concentration of the product.

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feedback inhibition

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form of enzyme inhibition where there is structural similarity between the inhibitor and the substrate and the inhibitor binds to the active site.

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product inhibition

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In allosteric enzymes, activators bind preferentially to the __ form and stabilize it, while inhibitors bind preferentially to the __ form and stabilize it.

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R-form, T-form

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This sequence of DNA connects the Nucleosome "bead" to the DNA "string" in a 10nm fiber in chromatin

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linker DNA

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The structure of the 30nm fiber in chromatin is stabilized by these features.

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Histone H1 (linker histone)
Histone N-terminal tails
Linker DNA (interspersed between histones)

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The chromatosome includes the DNA, Histone H1, and these core histone proteins.

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2 each of: H2A, H2B, H3, H4;

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Term given to stretches of amino acids at the N-terminus of each histone protein that protrude out from the nucleosome. They are subject to various covalent post-translational modifications, such as acetylation.

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histone tails

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A type of chromatin containing DNA sequences that are generally not transcribed (such as centromeres or telomeres).

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Constituitive heterochromatin

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Term for chromatin that contain genes that are not transcribed in that particular cell type, but may be transcribed in other cell types.

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Facultative heterochromatin

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a mutation involving substitutions of one purine for another (A,G) or of one pyrimdine (C,T) for another

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transition mutation

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a mutation involving a substitution that involve both a pyrimidine and a purine, which therefore involve exchanges of one-ring and two-ring structures ([A or G] to [T or C]).

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transversion mutation

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Two major ways in which the cell maintains its genomic integrity.

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High-Fidelity of DNA replication,
Repairing DNA as it occurs

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DNA polymerase possess these two functions involved in base repair

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conformational change to confirm base pairing, 3'->5' exonuclease proofreading

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In strand directed mismatch repair, this protein binds to a bulge (which indicates a mismatch) in the double-stranded DNA

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Msh protein

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In strand directed mismatch repair, this protein binds to Msh at the DNA and scans for the closest nick. Once a nick is found, it triggers the degradation of the nicked strand all the way back through the mismatch.

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Mlh protein

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This mechanism allows mistakes made by the DNA polymerase to be corrected shortly after replication.

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Strand directed mismatch repair

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In base excision repair, this protein cause each nucleotide to “flip-out” from the helix so that it can probe all faces of the nucleotide for damage. When a damaged base is found, it cleaves the bond between the damaged base and deoxyribose,

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DNA Glycosylase

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In base excision repair, after DNA glycosylase removes the damaged base, this protein removes the sugar phosphate backbone, leaving a gap.

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AP endonuclease

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A mechanism of ssDNA repair which repairs bulky DNA adducts. This method removes several nucleotides from the DNA, not just one.

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Nucleotide excision repair

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these are proteins necessary for base excision repair

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DNA glycosylase, AP endonuclease, DNA polymerase, Helicase, DNA ligase

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The repair mechanism for deamination.

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base excision repair

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The repair mechanism for base hydrolysis.

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base excision repair

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A type of mutation which may occur, if depurination occurs at the coding region of a gene.

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frameshift mutation

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This type of DNA damage can induced with UV irradiation.

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pyrimidine dimer

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The repair mechanism for pyrimidine dimer formation.

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nucleotide excision repair

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This source damages DNA, causing two adjacent thymine bases on the same strand become linked via a cyclobutane ring.

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UV irradiation

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Source of damage that induces alkylation of purines or pyrimidines

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chemical carcinogens

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Repair mechanism for purine/pyrimidine alkylation.

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O6-methyl
guanine methyltransferase enzyme

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Repair mechanism for formation of DNA adduct.

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nucleotide excision repair

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Base repair mechanism for a missing base.

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Base excision repair

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Base repair mechanism(s) for a double stranded break.

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Homologous recombination or
Nonhomologous end joining

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Base repair mechanism for link between adjacent bases (ex. thymine dimer).

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Nucleotide excision repair

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In this cell cycle phase, individual chromosomes have condensed to the point of being visible as discrete objects in the light microscope.

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prophase

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General cycle cell phase when microtubules are dispersed throughout the cell, and are used for organelle and vesicular traffic. Chromosomal DNA is loosely dispersed throughout the nucleus.

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interphase

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The cell cycle phase which is defined as the point in which the membrane of the nuclear envelope begins to break down.

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the onset of prometaphase

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Cell cycle phase when the
chromosomes, which are now maximally condensed, align at the plane equidistant between the two poles of the mitotic spindle

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metaphase

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At the beginning of this phase of the cell cycle, the two sister
chromatids begin to separate. Furrowing of the cell membrane
also begins.

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anaphase

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At the beginning of this phase, the daughter chromosomes have arrived at the poles of the spindle. The chromosomes begin to decondense, and a nuclear envelope reforms around each group of daughter chromosomes. Cytokinesis is completed during this phase.

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telophase

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Cytokinesis begins during this phase and is usually completed in this phase.

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anaphase, telephose

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a protein complex that connects each chromatid to the mitotic spindle, and acts as a “handle” by which microtubule spindle proteins can direct chromosomal movement.

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kinetochore

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This region of DNA within each chromatid joins sister chromatids together, and contains special sequences of DNA that attach to proteins of the kinetochore.

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centromere

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The cell begins Meiosis I with this many duplicated chromosomes.

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46

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This elaborate protein structure forms during meiosis and “zips” all four maternal and paternal chromatids together to hold them in place.

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synaptonemal complex

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The name given to a set of four homologous chromosomes bound together within a synaptonemal complex

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a bivalent (or tetrad).

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These are portions between chromosomes still attached to each other where homologous recombination has occurred.

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chiasmata

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Phase during cell cycle which synaptonemal complex forms and crossing over may take place.

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prophase I (of meiosis)

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In this part of the cell cycle chromosomes condense and become visible by light microscopy; microtubules begin to rearrange.

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prophase

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Part of cycle cycle when the nuclear envelope breaks down and mitotic spindles form.

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prometaphase

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Part of cell cycle when sister chromatids are pulled to opposite poles of the cell by contracting microtubules.

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anaphase

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Part of cell cycle when the chromosomes decondense, and the nuclear membrane reforms.

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telephase

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In this phase of the cell cycle, the contractile ring tightens around the cell, eventually pinching the cell in two to create two daughter cells.

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telephase

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Term used to describe the close pairing of maternal and paternal duplicated chromosomes during meiosis I.

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synapsis

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Part of cell cycle when formation of a bivalent promotes crossing over.

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prophase I of meiosis

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Around the seventh month of embryonic development, oogonia begin meiosis I and arrest at this phase, becoming primary oocytes.

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mid-prophase I

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Part of cell cycle where the cell can exist in a “resting” state, in which it is metabolizing nutrients but is not dividing.

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G0

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Stimulated by a mitogen, the cell enters this phase. It begins to replicate its non-chromosomal
contents (enzymes, metabolites, etc.) so that each daughter cell will have the appropriate supply of cellular components necessary for its survival.

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G1

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Cell cycle phase where the cell continues to grow in size so it can divide into two full-size daughter cells during mitosis.

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G2

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This chaperone uses the energy of ATP to facilitate protein folding as the
protein is being made.

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Hsp70

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A stretch of amino acids found at
the N- or C-terminus of a protein, that governs the delivery of the polypeptides to specific organelles. They are removed by by proteases after destination is reached.

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signal sequence

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Term used to describe the delivery of an elongating polypeptide chain into the lumen of the ER.

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co-translational insertion.

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This protein recognizes the signal sequence of the elongating polypeptide (in cytoplasm) and recruits to the SRP receptor.

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signal recognition particle (SRP)

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The SRP receptor uses this mechanism to ensure that the release of SRP does not occur until the ribosome has become properly engaged with the translocator.

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GTP-Hydrolysis

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These post-translation enzymes facilitate protein folding and can be found in Cytosol & ER.

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molecular chaperones (separate for each pool)

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The bulk of DNA replication is carried out by these two polymerases.

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DNA polymerases delta, and epsilon.

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These post-translation enzymes/modifications occur in the cytosol (or nucleus).

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Lipid attachment (internal lipid-anchored proteins)
Protein degradation (ubiquitination & proteasome; lysosome)
Covalent modifications of amino acid side chains
Phosphorylation, acetylation, methylation, hydroxylation (HIF1-a)

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Outline the steps of N-linked Glycosylation.

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in cytosol, two N-acetyl glucosamine binds to dolichol phosphate; mannose sugars are added, flippase inserts DP into lumen of ER; sugar array transferred to Asn of protein during translation; protein is folded modified & moves to Golgi for more modification

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Oligosaccharide addition begins this part of the cell with the addition of two
N-acetyl glucosamine sugars to the lipid carrier dolichol phosphate.

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cytosol

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In O-linked glycosylation, a flippase enzyme inverts dolichol phosphate so that its associated sugars are now in this part of the cell.

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the lumen of the ER

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In O-linked glycosylation, once in the ER, the growing oligosaccharide array is transferred from dolichol phoshpate to this residue of a protein as the protein is being translated.

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asparagine

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O-linked glycosylation begins in this part of the cell, and begins with the covalent addition of N-acetyl galactosamine to the OH groups of either serine or threonine residues within a protein.

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lumen of the Golgi,

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Post translational modification where oligosaccharides are formed by the addition of one sugar at a time and do not contain branched chains.

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O-Linked Glycosylation

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Post translational modification found on mucin proteins (the glycoproteins in
mucus secretions) and on proteolgycans of the extracellular matrix.

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O-Linked Glycosylation

(In the case of proteoglycans, the sugar attached to serine is xylose, not Nacetylgalactosamine.)

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Within the lumen of the ER, several blood clotting factors undergo this chemical modification that is critical
to their function.

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addition of gamma-Carboxyglutamate

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This enzyme complex is responsible for attaching Ubiquitin to lysine residues within a protein.

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ubiquitin ligase

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This addition of this protein can be used for normal degradation of specific proteins within the cell.

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Ubiquitin

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This enzyme binds to ubiquitin via a newly-created high energy thioester bond

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Ubiquitin-activating enzyme (E1)

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This protein accepts activated ubiquitin from E1 and catalyzes the covalent addition of ubiquitin to protein substrates

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Ubiquitin conjugating enzyme (E2):

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This protein binds to degradation signals within protein substrates, it confers specificity to ubiquitination

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Ubiquitin accessory protein (E3):

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In ubiquination, the term given to the E2-E3 complex.

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ubquitin ligase

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Under low O2 conditions, this enzyme cannot function adequately, and hydroxyproline residues are not formed. HIF-alpha is not recognized by the E3 subunit and HIF-1a is not degraded.

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proline hydroxylase (the same
enzyme that hydroxylates collagen but found in the cytoplasm)

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Under these conditions, proline hydroxylase cannot function adequately, and hydroxyproline residues are not formed.

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low O2 (Hypoxia)

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The cell division phases in which the cell components are not actively
being separated from each other (G1, S, G2) are collectively referred
to as this.

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interphase

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Lipid anchors, a post translational modification involves modification of these amino acids.

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Cysteine or glycine

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Phosphorylation (cytoplasm/nucleus), a post translational modification involves modification of these amino acids.

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serine, threonine, tyrosine

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Acetylation (nucleus), a post translational modification involves modification of this amino acid on a histone tail.

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Lysine

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This enzyme cleaves the bond between a damaged base and deoxyribose, leaving behind either an apurinic or apyrimidinic site (AP site). The sugar itself is still present, but there is no base attached to it.

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DNA glycosylase

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In base excision repair, this enzyme removes the sugar phosphate backbone, leaving a gap.

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AP endonuclease

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A steroid hormone receptor is associated with this binding domain.

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Zinc finger

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A homeodomain protein is associated with this binding domain.

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Helix turn helix

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A CREB protein is associated with this binding domain.

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Leucine zipper

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A myc protein is associated with this binding domain.

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Helix loop helix

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A sequence that binds repressor proteins in eukarotic cells.

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Silencer

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In the lac operon the repressor disassociates when this binds to it.

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Lactose

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Southern blotting uses ___ as a starting material.

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DNA

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Northern blotting uses ___ as a starting material.

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RNA

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Western blotting uses ___ as a starting material.

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Proteins

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Western blotting uses ____ as a probe.

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Antibodies

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When the albumin level is ____, the oncotic pressure is _____.

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Low, decreased

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Microarrays are used for these two purposes.

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Genotyping and gene expression

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Ultra rapid metabolizers have ___ levels of drug in their plasma, and their dosage should be _____.

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Low, increased

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Poor metabolizers have ___ levels of drug in their plasma, and their dosage should be _____.

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High, decreased

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DNA polymerase alpha is composed of two subunits, which each have distinct activities:

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DNA primase portion: synthesizes a short stand of RNA; DNA polymerase portion: synthesizes a short strand of DNA

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TFIID (with TBP) is similar to this factor in prokaryotes, in that it allows the TFIID complex to recognize and bind to the TATA box.

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Sigma

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The first protein complex to bind during eukaryotic transcription. It also contains the tata binding protein.

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TFIID

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These two transcription factors form a complex with TFIID. The first stabilizes the interaction between TBP and the DNA to which it is bound, and the second forms a bridge to RNA polymerase II, respectively.

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TFIIA & TFIIB

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The protein that stabilizes the TBP and DNA during eukaryotic transcription.

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TFIIA

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This protein that forms a bridge for RNA polymerase II and binds with TFIIF during eukaryotic transcription.

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TFIIB

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TFIIH is a multisubunit protein that has these TWO important activities:

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Two of its subunits are helicases (ATP dependent)

Another subunit has kinase activity, and phosphorylates the C-terminal domain (CTD) of RNA polymerase II

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In prokaryotes, each coding region is preceded by this short stretch of nucleotides, that serves as independent binding sites for ribosomal RNAs (for protein synthesis).

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Shine-delgarno sequence

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Term for a set of structural genes coding for a group of proteins in the SAME metabolic pathway along with the regulatory region that controls the expressions of the genes.

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operon

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This eukaryotic DNA polymerase transcribes protein coding genes.

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DNA Polymerase II

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This eukaryotic DNA polymerase transcribes tRNAs, 5S rRNA, & snRNA.

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DNA Polymerase III

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Sequence of DNA which function by binding activators that THEN regulate RNA Polymerase II through GTFs and co-activators.

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enhancers

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Regulatory proteins/transcription factors/activators enhance gene expression by this mechanism.

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stimulating the rate in which general transcription factors can assemble on the promoter.

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Enhancers can appear to act in a tissue-specific manner if __

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...DNA-binding proteins that interact with them are present only in certain tissues.

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Heterodimerization, which increases the possible number of recognition sequences is possible with these two regulatory DNA binding proteins.

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Leucine zipper, Helix-loop helix

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Pit-1 transcription factor is required for transcription of these two genes, important for development.

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growth hormone and prolactin genes

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These proteins are important in the regulation of gene expression during embryonic development

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homeodomain proteins

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This gene encodes a homeodomain-containing transcriptional factor.

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Pit-1

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General term for proteins that bind specific DNA sequences and inhibit transcription. They share the same DNA binding domains as activators.

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transcriptional repressors

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The four major mechanisms transcriptional repressors inhibit transcription:

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They compete with activators for the same DNA regulatory sequences, They bind DNA and inhibit txn by protein-protein interaction, direct & indirect repression

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The inhibition of the expression of tissue-specific genes in inappropriate cell types is accomplished by.

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transcriptional repressors

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Similarities between prokaryotic and eukaryotic mRNA's.

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5' UTR, 3' UTR, STOP & START codon

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In this type of mutation, a base substitution results in the introduction of a STOP codon

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nonsense mutation

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All tRNAs have the sequence CCA at their 3’ ends, which is the site of
___ (at the 3’ OH group of the last nucleotide).

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amino acid attachment

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anticodons in tRNA are written
in the __ direction.

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3’->5’; ex. the anticodon for the methionine codon is 3’-UAC-5’.

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This enzyme use the energy of two phosphate bonds (ATP->AMP) to catalyze the attachment of amino acids to their corresponding tRNAs via an ester linkage.

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Aminoacyl tRNA synthetases

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The catalytic activity of the ribosome is carried out by these components, not the protein component.

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rRNA components

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This part of the ribosome binds to the mRNA to ensure correct initiation, and also binds to the tRNA.

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small subunit

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Once mRNA enters the cytoplasm, the 5’ cap is bound by two translation initiation factors. These proteins will help to position the mRNA on the small ribosomal subunit.

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eIF-4G and eIF-4E

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In both prokaryotes and eukaryotic initiation, the ribosome begins elongation with the Met- tRNA (or fMet-tRNA) at the this site.

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P site.

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The time interval between binding of the tRNA
and the hydrolysis of GTP by this eukaryotic elongation factor allows inappropriately paired tRNAs to dissociate,
since the anticodon-codon H-bonding is weak.

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eEF-1a

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This binds to a termination codon at the A site and
stimulates hydrolysis of the bond between the tRNA and the
polypeptide chain at the P site. This results in the release of the
completed polypeptide from the ribosome.

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release factor/ERF (RF in prokaryotes)

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In both prokaryotes and eukaryotes, gene promoters can be located on either strand of DNA. The direction of transcription is determined by the
promoter at the beginning of each gene, which is recognized by this enzyme.

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RNA polymerase

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These are three major differences between prokaryotic and eukaryotic
transcription systems:

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mRNA coding sequences, Components of the RNA Polymerase Complex, mRNA processing (Eukaryotes Only)

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In this step of eukaryotic transcription, TFIIB forms a bridge to RNA Polymerase II. RNA Polymerase II binds to the __ complex, in association with a third factor, __, (which is bound to the Polymerase).

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TBP-TFIIB, TFIIF

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The initiation complex is composed of these transcription factors:

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TFIID, TFIIA, TFIID (with TBP), Polymerase (with TFIIF) , TFIIE and TFIIH

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This modification is found on the 5' end of eukaryotic mRNA's.

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7-methylguanosine

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After the primary transcript is cleaved. This polymerase adds, one at a time, about 200 A nucleotides to the 3’ end of sequence. This enzyme does not need an RNA or DNA template.

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poly(A) polymerase

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In mRNA, the 5’ cap provides these two features.

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stability, positioning on ribosome

Front 158

The eukaryotic primary transcript is typically cleaved 10-35 nucleotides downstream of this sequence.

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AAUAAA

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Term for not-yet-spliced mRNAs, that contain both exons and introns.

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pre-mRNAs or heterogeneous nuclear
mRNA (hnRNA),

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These conserved elements (DNA sequences) direct the removal of an intron.

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GU - 5' splice end
A - lariat formation
AG - 3' splice end

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Term for an assembly of small nuclear ribonucleoprotein particles (snRNPs) and small nuclear RNAs (snRNAs) which catalyzes intron removal.

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Spliceosome

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The addition of the poly(A) tail provides these two features to the mRNA.

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stability, signal for export of the mRNA from the nucleus to the cytoplasm

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Term used to describe the use of different patterns of splicing to give rise to different mRNA sequences (and different coding sequences).

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Alternative splicing. Alternative Splicing Provides Versatility.

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Involves the modification of a single RNA nucleotide to alter sequence. Apo-B100 and Apo- B48 are examples of proteins produced by this phenomenon.

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RNA Editing

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Type of DNA, which lacks introns normally found in the genomic version of the same gene; synthesized by reverse transcriptase.

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cDNA.

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rRNA except 5S is transcribed by this polymerase.

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RNA polymerases I

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mRNA, snRNA are transcribed by this polymerase.

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RNA polymerases II

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tRNA, 5S RNA are transcribed by this polymerase

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RNA polymerases III

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Describes the promoter sequences of prokaryotic and eukaryotic transcription respectively.

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-35 and -10 Promoter sequences, (-10 ) TATA box

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This ribosomal subunit binds to the mRNA to ensure correct initiation, and also binds to the tRNA.

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small subunit (40S)

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List the steps in eukaryotic translation initiation.

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In cytoplasm, eIF-4G & eIF-4E binds mRNA 5’ cap

Charged initiator tRNA binds to a GTPase, eIF2 (which is bound to GTP). This complex is brought to 40S.

40S binds to the 5’ end of the mRNA.

40S uses an ATP-dependent helicase activity to unwind the RNA and scan for the first AUG.

GTP is hydrolyzed by eIF2

eIF2 (now bound to GDP) dissociates, 60S binds 40S