Class notes

UofT BIO130 Study Notes

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Course
Bio130 (BIO130)

Institution
University Of Toronto (U Of T )

-notes cover cellular & molecular mechanisms of DNA replication, transcription, and translation -summary of lecture slides and material discussed in class

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Uploaded on June 9, 2022
Number of pages 29
Written in 2018/2019
Type Class notes
Professor(s) Melody neumann
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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

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