Chemical bonds: forces of attraction between atoms that enable the formation of molecules and compounds; Hydrogen = weak bond formed that is important for
structure and function of molecules. In DNA, they form between nucleotides of opposing strands, they are weaker than covalent bonds, important for the
secondary structure of proteins, facilitate binding between the target DNA and guide RNA in the CRISPR-Cas9 system.
Central dogma of molecular biology = DNA is replicated by DNA polymerase, more DNA, DNA is then transcribed by RNA polymerase mRNA, mRNA is
then translated by the ribosome to a protein.
- DNA Replication (DNA Polymerase) = creates a permanent and inherited mutation; mistake = wrong complementary base, proofreading function fails to
correct it.
- Transcription (RNA Polymerase) = error in a single mRNA molecule but template stays correct so all others transcribed also correct, temporary and not
inherited; mistake = wrong nucleotide incorporated
- Translation (Ribosome) = mRNA template and the DNA remain correct, miscalculation or misreading by ribosome = temporary and not inherited error
X-ray Crystallography = atomic and molecular structure of a molecule, highest detail. Cryo-EM = structure of molecules in a near-native state without
crystallization, using electron beams. Fluorescence Microscopy (3D) = visible light to image cellular and sub-cellular structures that have been tagged with
fluorescent dyes (fluorophores). Limitation of light photography = The wavelength of light. Objects on the nanoscale are so small that the light aimed at them
misses. Objects <300 nm are distorted under light microscope
Sickle cell anemia = single point mutation in the beta-globin gene = abnormal hemoglobin. Under low oxygen conditions, this polymerizes into rigid, rod-like
structures = red blood cells deform = block blood flow carry less oxygen, = organ damage, shortened lifespan. CRISPRCas9 = discovered when Scientists were
studying how bacteria protect themselves from viral attacks; they used two Cas9 enzymes, making a pair of molecular scissors; guide RNA is an RNA molecule
that binds to the Cas9 protein and allows it to find the target sequence of interest., Cas9 recognizes and binds to a three-nucleotide sequence (called PAM),
throughout the genome, unwinds the DNA and binds with hydrogen bonds if the guide RNA matches the sequence; if not, the Cas9 continues on. Cas9 cleaves
the DNA strands. To edit the gene: the cell uses homology-directed repair, which fixes DNA using a template. By providing a donor DNA as a template, the gene
can be edited according to the sequence proto-oncogene = regulates cell division. If it gets mutated, it becomes an oncogene, and leads to uncontrolled cell
division, eg. Ras gene, as Ras proteins (produced by this gene) promote the transcription of proteins involved in cell division. When they become mutated to
always be “on”, gene expression increases, and they constantly signaling for cell division, leading to tumor formation; tumor suppressor gene prevents
uncontrolled cell division. If it gets mutated, the protein it produces is defective or nonfunctioning, and thus it is unable to keep cell division in control. Cancer =
certain cells grow uncontrollably and spread. Two types of genes are frequently mutated in cancer: genes that are involved in inhibition of cell growth (tumor
suppressors) and in promotion of cell growth (proto-oncogenes). DNA damage to these genes from radiation/toxin exposure= cancer. Mutations to these genes
can also be inherited unless DNA repair works properly and eliminates the mutations, then cancer would not occur
Energy balance = balance between incoming (shortwave) and outgoing (longwave) Climate (radiative) forcing = factor that drives changes in climate and
influences Earth’s energy balance, natural or anthropogenic Sunspots = Disturbances in the sun’s magnetic field can generate energetic solar events. Yearly
average number of sunspots increases during periods of high solar activity; Milankovitch cycles = systematic changes in the distance and orientation of Earth
relative to the sun that affects the amount of solar radiation (insolation) that Earth receives =Periods of glaciation and deglaciation but long timescales (26-100kyr)
so this cannot explain the rapid rise in CO2 in the last century Eccentricity = shape of earth’s orbit (100,000 year cycle). High = large seasonal discrepancy in
solar radiation (more oval orbit) Obliquity = angle that Earth’s axis is tilted relative to orbital plane (41,000 year cycle). This is why we have seasons. Greater the
tilt angle, more extreme our seasons; as it decreases, winters are warmer and summers are cooler Precession = direction Earth’s axis of pointed at (wobble)
(26,000 year cycle). Caused by tidal forces due to the sun and moon. Makes seasonal contrasts more extreme in one hemisphere and less so in the other
δ13 notation used to relate carbon isotopic values (C12 and C12) on a standardized scale
Plants preferentially take up C12 because it is lighter so there is more C13 left in the ocean and atmosphere = heavier
The CO2 in the atmosphere is becoming richer in C12 rather than C13 → CO2 is INCREASING but C13:C12 ratio is DECREASING and the δ13 is also
decreasing (becoming more negative).
structure and function of molecules. In DNA, they form between nucleotides of opposing strands, they are weaker than covalent bonds, important for the
secondary structure of proteins, facilitate binding between the target DNA and guide RNA in the CRISPR-Cas9 system.
Central dogma of molecular biology = DNA is replicated by DNA polymerase, more DNA, DNA is then transcribed by RNA polymerase mRNA, mRNA is
then translated by the ribosome to a protein.
- DNA Replication (DNA Polymerase) = creates a permanent and inherited mutation; mistake = wrong complementary base, proofreading function fails to
correct it.
- Transcription (RNA Polymerase) = error in a single mRNA molecule but template stays correct so all others transcribed also correct, temporary and not
inherited; mistake = wrong nucleotide incorporated
- Translation (Ribosome) = mRNA template and the DNA remain correct, miscalculation or misreading by ribosome = temporary and not inherited error
X-ray Crystallography = atomic and molecular structure of a molecule, highest detail. Cryo-EM = structure of molecules in a near-native state without
crystallization, using electron beams. Fluorescence Microscopy (3D) = visible light to image cellular and sub-cellular structures that have been tagged with
fluorescent dyes (fluorophores). Limitation of light photography = The wavelength of light. Objects on the nanoscale are so small that the light aimed at them
misses. Objects <300 nm are distorted under light microscope
Sickle cell anemia = single point mutation in the beta-globin gene = abnormal hemoglobin. Under low oxygen conditions, this polymerizes into rigid, rod-like
structures = red blood cells deform = block blood flow carry less oxygen, = organ damage, shortened lifespan. CRISPRCas9 = discovered when Scientists were
studying how bacteria protect themselves from viral attacks; they used two Cas9 enzymes, making a pair of molecular scissors; guide RNA is an RNA molecule
that binds to the Cas9 protein and allows it to find the target sequence of interest., Cas9 recognizes and binds to a three-nucleotide sequence (called PAM),
throughout the genome, unwinds the DNA and binds with hydrogen bonds if the guide RNA matches the sequence; if not, the Cas9 continues on. Cas9 cleaves
the DNA strands. To edit the gene: the cell uses homology-directed repair, which fixes DNA using a template. By providing a donor DNA as a template, the gene
can be edited according to the sequence proto-oncogene = regulates cell division. If it gets mutated, it becomes an oncogene, and leads to uncontrolled cell
division, eg. Ras gene, as Ras proteins (produced by this gene) promote the transcription of proteins involved in cell division. When they become mutated to
always be “on”, gene expression increases, and they constantly signaling for cell division, leading to tumor formation; tumor suppressor gene prevents
uncontrolled cell division. If it gets mutated, the protein it produces is defective or nonfunctioning, and thus it is unable to keep cell division in control. Cancer =
certain cells grow uncontrollably and spread. Two types of genes are frequently mutated in cancer: genes that are involved in inhibition of cell growth (tumor
suppressors) and in promotion of cell growth (proto-oncogenes). DNA damage to these genes from radiation/toxin exposure= cancer. Mutations to these genes
can also be inherited unless DNA repair works properly and eliminates the mutations, then cancer would not occur
Energy balance = balance between incoming (shortwave) and outgoing (longwave) Climate (radiative) forcing = factor that drives changes in climate and
influences Earth’s energy balance, natural or anthropogenic Sunspots = Disturbances in the sun’s magnetic field can generate energetic solar events. Yearly
average number of sunspots increases during periods of high solar activity; Milankovitch cycles = systematic changes in the distance and orientation of Earth
relative to the sun that affects the amount of solar radiation (insolation) that Earth receives =Periods of glaciation and deglaciation but long timescales (26-100kyr)
so this cannot explain the rapid rise in CO2 in the last century Eccentricity = shape of earth’s orbit (100,000 year cycle). High = large seasonal discrepancy in
solar radiation (more oval orbit) Obliquity = angle that Earth’s axis is tilted relative to orbital plane (41,000 year cycle). This is why we have seasons. Greater the
tilt angle, more extreme our seasons; as it decreases, winters are warmer and summers are cooler Precession = direction Earth’s axis of pointed at (wobble)
(26,000 year cycle). Caused by tidal forces due to the sun and moon. Makes seasonal contrasts more extreme in one hemisphere and less so in the other
δ13 notation used to relate carbon isotopic values (C12 and C12) on a standardized scale
Plants preferentially take up C12 because it is lighter so there is more C13 left in the ocean and atmosphere = heavier
The CO2 in the atmosphere is becoming richer in C12 rather than C13 → CO2 is INCREASING but C13:C12 ratio is DECREASING and the δ13 is also
decreasing (becoming more negative).
