Wk7RG
Saturday, February 16, 2019 12:40 AM
• PCR: amplification of a known DNA segment.
1. Heat to separate targeted DNA strands.
2. Add synthetic DNA oligonucleotide primers, anneal (cool).
3. Add Taq DNA polymerase to catalyze 5'-3- DNA synthesis.
Week 7 i. Polymerase will use primers as pre-existing strands.
Review on Components of Nucleic Acids
• Gene: segment of a DNA molecule that contains info on protein or RNA synthesis.
• Nucleic acids have characteristic bases and pentoses.
• Nucleotide: consists of a nitrogenous base (attached to 1' carbon), a pentose sugar, and
one or more phosphate groups (5' carbon).
○ Ribonucleotide if pentose has an -OH group on the 2' carbon.
○ Deoxyribonucleotide if pentose just has an H.
Base DNA RNA
Purines (2) A, G A,G
Pyrimidines (1) C,T C,U
• EXCEPTIONS to nucleotide structure: if nucleic acid contains a 2'-(H)deoxyribose, it is a
DNA, even if it contains a uracil. 2'-(OH)Ribose -> RNA.
○ Nucleoside: nucleic acid w/o a phosphate group.
○ Minor nitrogenous bases: altered in order to regulate/protect genes. Usually found in
tRNAs.
○ Phosphate groups of nucleotides can be in positions other than 5' carbon.
• Phosphodiester bonds link successive nucleotides in nucleic acids.
○ Phosphodiester bonds: 5'-phosphate group of one nucleotide is joined to the 3'-
hydroxyl group of the next nucleotide.
○ Sugar-phosphate backbone is hydrophilic: OH groups of sugar form hydrogen bonds
• Flux (v): rate of metabolic flow. May be high/variable during one step, but [S] will always stay w/ water.
the same. -> • Nucleotide sequence is always written in 5'->3' end.
• Homeostasis: the dynamic steady state all cells and organisms maintain. Failure of homeostatic • Oligonucleotide: <50 nucleotides, short nucleic acid.
mechanisms-> human disease. • Polynucleotide: long nucleic acid.
○ Ex. differentiation of stem cells into erythrocytes: precursor cell contain nucleus, • Nitrogenous base properties affect 3D structure of nucleic acids.
mitochondria, and little to no hemoglobin. Cell after fully-differentiating contains a lot of ○ Aromatic molecule affect structure, electron distribution, and light absorption.
hemoglobin, but no nucleus or mitochondria. -> Stem cells require regulation of cellular
protein levels.
○ "Electron delocalization in atoms of the ring gives most of the bonds a partial double-
bond character. -> pyrimidines are planar, purines are nearly planar w/ slight
• Ex. Of an extracellular signal effecting enzyme: signals generate second messengers (cyclic
pucker."
AMP, Ca2+) that mediate allosteric regulation. Can be hormonal, neuronal, growth factors, ○ All bases absorb UV light. ->Nucleic acids absorb wavelengths near 260nm.
•
cytokines.
Transcription factors (TFs): nuclear proteins that bind to specific DNA regions near a gene's
○ To minimize contact of hydrophobic base and water, hydrophobic stacking
interactions occur: where +2 bases are positioned w/ planes of their ring parallel. ->
promoter. Can activate/repress transcription of that gene-> increase/decrease protein synthesis
of an enzyme.
stabilizes nucleic acid structure
• Response elements: DNA regions that TFs bind to, controlling gene transcription. The more ○ Base pairs: hydrogen bonds form b/w A to T(or U), and C to G; responsible for
response elements a gene has, the more TFs and signals they respond to. -> double-stranded structure in DNA and RNA.
• Genes that contain the same response element can be turned on or off by a single signal.
• Protein turnover: synthesis followed by degradation; half-life of a protein. May be "energetically
expensive," but proteins w/ shorter half-lives are reaching steady state-level much faster->
quick responsiveness.
• All enzymes are sensitive to the conc of their substrates. Acts as a limiting factor to further
regulate enzyme activity. Intracellular [S] are often ≤ Km -> when [S]<< Km, rxn rate is linearly
dependent on [S]. Enzyme activity drops off at lower [S].
• Allosteric effectors: ligand that can INC or DEC enzyme activity. High hill coefficient = low [S]
needed to increase rxn rate.
• Cells cannot allow rxns (w/ large equilibrium constants) reach equilibrium.-> an INC in [S] could
produce too much product?
• Enzymes that catalyze ATP (or highly exergonic rxns) must be sensitive to regulation, to ensure
that [ATP] remains above its equilibrium level.
• Hormones can act as extracellular signals that bind to membrane receptors-> regulate
production of enzymes via protein synthesis. Glycolysis reactions
Saturday, February 16, 2019 12:40 AM
• PCR: amplification of a known DNA segment.
1. Heat to separate targeted DNA strands.
2. Add synthetic DNA oligonucleotide primers, anneal (cool).
3. Add Taq DNA polymerase to catalyze 5'-3- DNA synthesis.
Week 7 i. Polymerase will use primers as pre-existing strands.
Review on Components of Nucleic Acids
• Gene: segment of a DNA molecule that contains info on protein or RNA synthesis.
• Nucleic acids have characteristic bases and pentoses.
• Nucleotide: consists of a nitrogenous base (attached to 1' carbon), a pentose sugar, and
one or more phosphate groups (5' carbon).
○ Ribonucleotide if pentose has an -OH group on the 2' carbon.
○ Deoxyribonucleotide if pentose just has an H.
Base DNA RNA
Purines (2) A, G A,G
Pyrimidines (1) C,T C,U
• EXCEPTIONS to nucleotide structure: if nucleic acid contains a 2'-(H)deoxyribose, it is a
DNA, even if it contains a uracil. 2'-(OH)Ribose -> RNA.
○ Nucleoside: nucleic acid w/o a phosphate group.
○ Minor nitrogenous bases: altered in order to regulate/protect genes. Usually found in
tRNAs.
○ Phosphate groups of nucleotides can be in positions other than 5' carbon.
• Phosphodiester bonds link successive nucleotides in nucleic acids.
○ Phosphodiester bonds: 5'-phosphate group of one nucleotide is joined to the 3'-
hydroxyl group of the next nucleotide.
○ Sugar-phosphate backbone is hydrophilic: OH groups of sugar form hydrogen bonds
• Flux (v): rate of metabolic flow. May be high/variable during one step, but [S] will always stay w/ water.
the same. -> • Nucleotide sequence is always written in 5'->3' end.
• Homeostasis: the dynamic steady state all cells and organisms maintain. Failure of homeostatic • Oligonucleotide: <50 nucleotides, short nucleic acid.
mechanisms-> human disease. • Polynucleotide: long nucleic acid.
○ Ex. differentiation of stem cells into erythrocytes: precursor cell contain nucleus, • Nitrogenous base properties affect 3D structure of nucleic acids.
mitochondria, and little to no hemoglobin. Cell after fully-differentiating contains a lot of ○ Aromatic molecule affect structure, electron distribution, and light absorption.
hemoglobin, but no nucleus or mitochondria. -> Stem cells require regulation of cellular
protein levels.
○ "Electron delocalization in atoms of the ring gives most of the bonds a partial double-
bond character. -> pyrimidines are planar, purines are nearly planar w/ slight
• Ex. Of an extracellular signal effecting enzyme: signals generate second messengers (cyclic
pucker."
AMP, Ca2+) that mediate allosteric regulation. Can be hormonal, neuronal, growth factors, ○ All bases absorb UV light. ->Nucleic acids absorb wavelengths near 260nm.
•
cytokines.
Transcription factors (TFs): nuclear proteins that bind to specific DNA regions near a gene's
○ To minimize contact of hydrophobic base and water, hydrophobic stacking
interactions occur: where +2 bases are positioned w/ planes of their ring parallel. ->
promoter. Can activate/repress transcription of that gene-> increase/decrease protein synthesis
of an enzyme.
stabilizes nucleic acid structure
• Response elements: DNA regions that TFs bind to, controlling gene transcription. The more ○ Base pairs: hydrogen bonds form b/w A to T(or U), and C to G; responsible for
response elements a gene has, the more TFs and signals they respond to. -> double-stranded structure in DNA and RNA.
• Genes that contain the same response element can be turned on or off by a single signal.
• Protein turnover: synthesis followed by degradation; half-life of a protein. May be "energetically
expensive," but proteins w/ shorter half-lives are reaching steady state-level much faster->
quick responsiveness.
• All enzymes are sensitive to the conc of their substrates. Acts as a limiting factor to further
regulate enzyme activity. Intracellular [S] are often ≤ Km -> when [S]<< Km, rxn rate is linearly
dependent on [S]. Enzyme activity drops off at lower [S].
• Allosteric effectors: ligand that can INC or DEC enzyme activity. High hill coefficient = low [S]
needed to increase rxn rate.
• Cells cannot allow rxns (w/ large equilibrium constants) reach equilibrium.-> an INC in [S] could
produce too much product?
• Enzymes that catalyze ATP (or highly exergonic rxns) must be sensitive to regulation, to ensure
that [ATP] remains above its equilibrium level.
• Hormones can act as extracellular signals that bind to membrane receptors-> regulate
production of enzymes via protein synthesis. Glycolysis reactions
