BIO 130 Notes (Neumann)
Cell Theory
1. All organisms composed of one or more cells
2. Cell is structural unit of life
3. Cells arise from pre-existing cells
Two Main Types of Cells
1. Prokaryotic: (eubacteria and archaea)
-no nuclei, single-celled;
-nucleosomes twisted up and compacted in nucleoid (no membrane)
-some endomembranes present, but don’t form closed compartments
2. Eukaryotic: (plants, fungi, animals, humans)
-have nuclei, single-celled or multicellular
-sophisticated cytoskeleton, mitochondria, membrane-bound nucleus, ER, golgi complex
Did eukaryotes evolve from prokaryotes? (2 lines of evidence)
1. Fossil record - eukaryotes appear a billion years after prokaryotes do
2. Both share complicated but similar traits - similar processes of DNA synthesis, RNA production, etc
-Endosymbiont Theory:
-start with anaerobic
heterotrophic prokaryote
-increase in atmospheric oxygen,
FECA consumes anaerobic
prokaryote
-possible that the prokaryote was
able to survive protected by
FECA, and provided host energy
(ATP)
-development of more organelles
-lines of evidence for endosymbiont theory:
1. Mitochondria + chloroplasts - have circular genomes
2. Mitochondria + chloroplasts - retain their original machinery (make their own proteins and DNA)
3. Mitochondria + chloroplasts have double membrane - composition of inner and outer membranes is
different (suggests that inner one probably originated from original prokaryote that was consumed)
How do we study this diversity? -model organisms, have general attributes:
-rapid development, short life cycles, small adult size, readily available, easy to manipulate (tractable),
understandable genetics
Examples!
,The Central Dogma 𝐷𝑁𝐴 → (𝑡𝑟𝑎𝑛𝑠𝑙𝑎𝑡𝑖𝑜𝑛) → 𝑅𝑁𝐴 → (𝑡𝑟𝑎𝑛𝑠𝑐𝑟𝑖𝑝𝑡𝑖𝑜𝑛) → 𝑃𝑟𝑜𝑡𝑒𝑖𝑛
-Messenger RNA (mRNA): used for protein synthesis
-Transfer RNA (tRNA): transports AAs used for protein synthesis
-Ribosomal RNA (rRNA): part of the ribosome
(elaborated central dogma:)
1. Genome: all the DNA in a cell (including nuclear, mitochondrial, etc)
2. Transcriptome: all the RNA in a cell at a given point in time, can be changing every minute
3. Proteome: all proteins in a cell at a given point in time
4. Interactome: all protein-protein interactions
5. Metabolome: small molecules found in cell at given point in time (hormones, signalling molecules)
6. Phenome: all of the above! + more observable characteristics
Overview . (for prokaryotes and eukaryotes)
-DNA, RNA, and proteins are all linear chains of info with definite polarity
-info in nucleic acid sequence is translated into AA sequence via genetic code (universal among all species)
-(for eukaryotes only) make pre-mRNAs, mRNA has to be translated into cytoplasm for translation (in
prokaryotes translation+transcription can happen in one place)
Nucleic Acids
-genetic material in cell (organism’s blueprints)
-DNA = deoxyribonucleic acid; RNA = ribonucleic acid
1. Pentose sugar - provides scaffold for base attachment
2. Nitrogenous base - varies (ATCGU), attached to 1’ C
3. Phosphate group - negatively charged backbone, attaches to 5’ C
Bases
-purines: guanine + adenine (double ring) pyrimidines: cytosine, thymine, uracil (single ring)
Nucleic Acid Nomenclature
1. Nucleoside: sugar + base (no phosphate!!)
2. Nucleoside monophosphate (AMP): sugar + base + 1P
3. Nucleoside diphosphate (ADP): sugar + base + 2P
4. Nucleoside triphosphate (ATP): sugar + base + 3P
, Molecular Interactions -between individual molecules usually mediated by noncovalent interactions
1. Electrostatic attractions - weakened by water
2. Hydrogen bonds - strongest in a straight line !
3. van der Waals attractions
4. Hydrophobic force - nonpolar molecules pushed away from water
Nucleic Acid Chains
-DNA synthesized from deoxyribonucleoside triphosphates (dNTPs)
-RNA synthesized from ribonucleoside triphosphates (NTPs)
-nucleotides linked by phosphodiester bonds
-DNA overall has negative charge, has polarity based on 5’ and 3’ ends
Base Pairing (complementary)
-holds DNA double helix together
-A-T: 2 H bonds; C-G: 3 H bonds
Forces that keep DNA strands together
1. Hydrogen bonds -between bases
2. van der Waals attractions -bases
stacked on top of each other
3. Hydrophobic interactions -backbone is
hydrophilic+attracted to water, bases
are pushed together
4. DNA is structured antiparallel
Protein Structure
1. Primary (sequence) -AA sequence
2. Secondary (local folding) -alpha helix, beta sheet
3. Tertiary (long-range folding) -3D structure
4. Quaternary (multimeric organization) -multiple polypeptide chains
5. Multiprotein complexes -molecular machines
-proteins composed of amino acids (4 main types)
-side-chain (R group) is variable and determines type of amino acid
1. Polar charged -charged at neutral pH, act as acids/bases
2. Polar uncharged -partial charges
3. Nonpolar -primarily hydrophobic, away from water
4. Those with unique properties
Cell Theory
1. All organisms composed of one or more cells
2. Cell is structural unit of life
3. Cells arise from pre-existing cells
Two Main Types of Cells
1. Prokaryotic: (eubacteria and archaea)
-no nuclei, single-celled;
-nucleosomes twisted up and compacted in nucleoid (no membrane)
-some endomembranes present, but don’t form closed compartments
2. Eukaryotic: (plants, fungi, animals, humans)
-have nuclei, single-celled or multicellular
-sophisticated cytoskeleton, mitochondria, membrane-bound nucleus, ER, golgi complex
Did eukaryotes evolve from prokaryotes? (2 lines of evidence)
1. Fossil record - eukaryotes appear a billion years after prokaryotes do
2. Both share complicated but similar traits - similar processes of DNA synthesis, RNA production, etc
-Endosymbiont Theory:
-start with anaerobic
heterotrophic prokaryote
-increase in atmospheric oxygen,
FECA consumes anaerobic
prokaryote
-possible that the prokaryote was
able to survive protected by
FECA, and provided host energy
(ATP)
-development of more organelles
-lines of evidence for endosymbiont theory:
1. Mitochondria + chloroplasts - have circular genomes
2. Mitochondria + chloroplasts - retain their original machinery (make their own proteins and DNA)
3. Mitochondria + chloroplasts have double membrane - composition of inner and outer membranes is
different (suggests that inner one probably originated from original prokaryote that was consumed)
How do we study this diversity? -model organisms, have general attributes:
-rapid development, short life cycles, small adult size, readily available, easy to manipulate (tractable),
understandable genetics
Examples!
,The Central Dogma 𝐷𝑁𝐴 → (𝑡𝑟𝑎𝑛𝑠𝑙𝑎𝑡𝑖𝑜𝑛) → 𝑅𝑁𝐴 → (𝑡𝑟𝑎𝑛𝑠𝑐𝑟𝑖𝑝𝑡𝑖𝑜𝑛) → 𝑃𝑟𝑜𝑡𝑒𝑖𝑛
-Messenger RNA (mRNA): used for protein synthesis
-Transfer RNA (tRNA): transports AAs used for protein synthesis
-Ribosomal RNA (rRNA): part of the ribosome
(elaborated central dogma:)
1. Genome: all the DNA in a cell (including nuclear, mitochondrial, etc)
2. Transcriptome: all the RNA in a cell at a given point in time, can be changing every minute
3. Proteome: all proteins in a cell at a given point in time
4. Interactome: all protein-protein interactions
5. Metabolome: small molecules found in cell at given point in time (hormones, signalling molecules)
6. Phenome: all of the above! + more observable characteristics
Overview . (for prokaryotes and eukaryotes)
-DNA, RNA, and proteins are all linear chains of info with definite polarity
-info in nucleic acid sequence is translated into AA sequence via genetic code (universal among all species)
-(for eukaryotes only) make pre-mRNAs, mRNA has to be translated into cytoplasm for translation (in
prokaryotes translation+transcription can happen in one place)
Nucleic Acids
-genetic material in cell (organism’s blueprints)
-DNA = deoxyribonucleic acid; RNA = ribonucleic acid
1. Pentose sugar - provides scaffold for base attachment
2. Nitrogenous base - varies (ATCGU), attached to 1’ C
3. Phosphate group - negatively charged backbone, attaches to 5’ C
Bases
-purines: guanine + adenine (double ring) pyrimidines: cytosine, thymine, uracil (single ring)
Nucleic Acid Nomenclature
1. Nucleoside: sugar + base (no phosphate!!)
2. Nucleoside monophosphate (AMP): sugar + base + 1P
3. Nucleoside diphosphate (ADP): sugar + base + 2P
4. Nucleoside triphosphate (ATP): sugar + base + 3P
, Molecular Interactions -between individual molecules usually mediated by noncovalent interactions
1. Electrostatic attractions - weakened by water
2. Hydrogen bonds - strongest in a straight line !
3. van der Waals attractions
4. Hydrophobic force - nonpolar molecules pushed away from water
Nucleic Acid Chains
-DNA synthesized from deoxyribonucleoside triphosphates (dNTPs)
-RNA synthesized from ribonucleoside triphosphates (NTPs)
-nucleotides linked by phosphodiester bonds
-DNA overall has negative charge, has polarity based on 5’ and 3’ ends
Base Pairing (complementary)
-holds DNA double helix together
-A-T: 2 H bonds; C-G: 3 H bonds
Forces that keep DNA strands together
1. Hydrogen bonds -between bases
2. van der Waals attractions -bases
stacked on top of each other
3. Hydrophobic interactions -backbone is
hydrophilic+attracted to water, bases
are pushed together
4. DNA is structured antiparallel
Protein Structure
1. Primary (sequence) -AA sequence
2. Secondary (local folding) -alpha helix, beta sheet
3. Tertiary (long-range folding) -3D structure
4. Quaternary (multimeric organization) -multiple polypeptide chains
5. Multiprotein complexes -molecular machines
-proteins composed of amino acids (4 main types)
-side-chain (R group) is variable and determines type of amino acid
1. Polar charged -charged at neutral pH, act as acids/bases
2. Polar uncharged -partial charges
3. Nonpolar -primarily hydrophobic, away from water
4. Those with unique properties
