1
Lecture 1 - 09/15/16
Monday, September 19, 2016
1:30 PM
Proteins: actions items of cells; regulate DNA & RNA; key regulatory molecules
Chapter 1: The Chemistry of the Cell
Approaches to Cell Biology
● Cytology → observable
○ Concerned with cellular structure, optical techniques, very visual, relies heavily on
microscopy, first identified membrane bound organelles
● Biochemistry → study of chemistry of living systems
○ Reductionist, breaks things down into constituent parts, focused on cellular functions and
cycles, separation and identification of cellular components
● Genetics
○ Information content, heredity, information flow, generations, inheritance
All of the above approaches are intertwined in modern cell biology
Importance of the Microscope in Modern Cell Theory (Cytological approach)
1665, Robert Hooke uses microscope to observe cork cells
1830s
● Compound microscope uses two lens in order to magnify specimen and later refocus light
through a second lens
● Robert Brown identified nucleus within plant cells using such
● Conclusion that all plant tissues are made of cells —> Extrapolated to say same for animals
Modern Cell Theory
Schwann, 1839
1. All organisms are comprised of cells
2. The cell is the basic unit of structure
Virchow, 1855
1. All cells arise from preexisting cells (thus being the basic unit of reproduction)
! (I want this to be an upside down exclamation sign) Facts!
● Facts are seen as tenuous and dynamic, even though what is accepted as fact today could be
wrong
● Scientific method is used to assess new information
● Experiments are designed to test hypotheses
○ Hypothesis: a model that provides a reasonable explanation for a phenomenon, may be
accepted or rejected
● Oscam’s Razor: the simplest explanation that accounts for all observed data is most likely correct
Cells
● 3 types of cells: bacteria (eubacteria), archaea (archaebacteria), ← prokaryotes; eukaryotes
○ Not a linear development; each subsequent type of cell diverged from a common ancestor
● All cells require a means to
○ Store information
○ Convert information into action
○ Make energy
, 2
○ Break things down
○ Transport substances across the membrane
● In prokaryotes (eubacteria, archaebacteria), these functions are not specialized
● Within eukaryotes, functions are specialized and compartmentalized
○ Storage —> Nucleus
○ Conversion of information —> Ribosomes, ER (synthesis machinery)
○ Energy synthesis —> Mitochondria
○ Breakdown —> lysosomes, peroxisomes (degradation machinery)
○ Transport —> membranes, vesicles, Golgi complex, ER
Evolution and Biology
● Reason why things work well, though evolution is not a linear process
● Constant competition —> most fit portion of a population, as a result of inherent variation, will
survive and reproduce
● Overproduction of offspring (in which variation exists) —> natural selection acts —> most fit
survive and pass on their genes
● Mitochondrial Evolution
○ Result of coevolution between a bacterium highly skilled in energy production and a cell
poor at producing energy
○ Cell with nucleus swallowed up bacterium, resulting in a symbiotic relationship in which
bacterium within cell became exclusively specialized for energy production
Central Dogma of Molecular Biology
Crick, 1953
● DNA —> RNA —> Proteins
○ DNA synthesized via replication
○ RNA synthesized by transcription
○ Proteins synthesized by translation (Translation because a change in language
(nucleotides —> amino acids) is involved)
■ Once information is in protein form, it cannot escape
● Crick’s original view, 1956
Chapter 2: Macromolecules of Life
Subunit Macromolecule
Sugar (monosaccharide) Sugar (polysaccharide)
Amino Acid Protein
Nucleotide Nucleic Acid (DNA,
RNA)
Hydrolysis: a molecule is broken into 2 via the addition process of a water molecule at the end
● Lyse → to split
Dehydration Synthesis / Condensation reaction: 2 molecules become 1, generating water
● Not spontaneous
● Catalyst is typically required
● Involves covalent bonding
, 3
○ Endergonic reaction, requiring an input of energy since bonds store energy
Type of Bond Key Characteristics Atoms Involved
Hydrogen relatively weak, results from partial positive H (bonded to an electronegative
Bond and partial negative charges atom) and N or O, usually
Ionic Bond fully positive and negative charges interaction bases (+) and acids (-)
Covalent strongest of the three (when aggregated), does C—C, C—O, C—N, C—H
Bond not spontaneously break (energy input
required)
Importance of Carbon
● Organic chemistry involves the study of all carbon containing compounds
● Most important atom in biological molecules —> Key molecules contain carbon backbones
● With a valence of 4 (Valence: how many bonds will form, not how many valence electrons are
present), carbon can form four chemical bonds
○ Carbon is the most important ATOM
○ Water is the most important MOLECULE
● Usually forms chemical bonds with C, H, N, S
○ These strong bonds are necessary for life
○ Bond Energy: amount of energy required to break 1 mol of bonds
■ High for C—C bonds
■ Expressed in cal/mol
● Solar radiation has inverse relationship between wavelength and energy content
○ Visible light is lower in energy than C—C bonds, thus bonds cannot be destroyed
○ UV light is higher in energy (shorter in wavelength) and thus more dangerous (can
destroy C—C bonds necessary for life)
● Hydrocarbons
○ C—H bonds exclusively
○ Insoluble in water
○ Compose interior of biological molecules (phospholipid tails)
● Long chains of C—C and C—C rings frequently present in nature
Importance of Water
● Universal, biological solvent
● Common extracellular substance
● Most abundant component of cells and organisms (75-80% of a cell’s weight)
● Polar molecule
○ Polarity allows for interactions with molecules containing partial positive or partial
negative charges
■ Uncharged as a whole
■ All O—H bonds are polar
○ Gives water its cohesive properties, temperature stability, solvent purposes
● Most of water’s properties are derived from cohesive nature
○ Electronegative oxygen at one water molecule is drawn to electropositive hydrogen
Lecture 1 - 09/15/16
Monday, September 19, 2016
1:30 PM
Proteins: actions items of cells; regulate DNA & RNA; key regulatory molecules
Chapter 1: The Chemistry of the Cell
Approaches to Cell Biology
● Cytology → observable
○ Concerned with cellular structure, optical techniques, very visual, relies heavily on
microscopy, first identified membrane bound organelles
● Biochemistry → study of chemistry of living systems
○ Reductionist, breaks things down into constituent parts, focused on cellular functions and
cycles, separation and identification of cellular components
● Genetics
○ Information content, heredity, information flow, generations, inheritance
All of the above approaches are intertwined in modern cell biology
Importance of the Microscope in Modern Cell Theory (Cytological approach)
1665, Robert Hooke uses microscope to observe cork cells
1830s
● Compound microscope uses two lens in order to magnify specimen and later refocus light
through a second lens
● Robert Brown identified nucleus within plant cells using such
● Conclusion that all plant tissues are made of cells —> Extrapolated to say same for animals
Modern Cell Theory
Schwann, 1839
1. All organisms are comprised of cells
2. The cell is the basic unit of structure
Virchow, 1855
1. All cells arise from preexisting cells (thus being the basic unit of reproduction)
! (I want this to be an upside down exclamation sign) Facts!
● Facts are seen as tenuous and dynamic, even though what is accepted as fact today could be
wrong
● Scientific method is used to assess new information
● Experiments are designed to test hypotheses
○ Hypothesis: a model that provides a reasonable explanation for a phenomenon, may be
accepted or rejected
● Oscam’s Razor: the simplest explanation that accounts for all observed data is most likely correct
Cells
● 3 types of cells: bacteria (eubacteria), archaea (archaebacteria), ← prokaryotes; eukaryotes
○ Not a linear development; each subsequent type of cell diverged from a common ancestor
● All cells require a means to
○ Store information
○ Convert information into action
○ Make energy
, 2
○ Break things down
○ Transport substances across the membrane
● In prokaryotes (eubacteria, archaebacteria), these functions are not specialized
● Within eukaryotes, functions are specialized and compartmentalized
○ Storage —> Nucleus
○ Conversion of information —> Ribosomes, ER (synthesis machinery)
○ Energy synthesis —> Mitochondria
○ Breakdown —> lysosomes, peroxisomes (degradation machinery)
○ Transport —> membranes, vesicles, Golgi complex, ER
Evolution and Biology
● Reason why things work well, though evolution is not a linear process
● Constant competition —> most fit portion of a population, as a result of inherent variation, will
survive and reproduce
● Overproduction of offspring (in which variation exists) —> natural selection acts —> most fit
survive and pass on their genes
● Mitochondrial Evolution
○ Result of coevolution between a bacterium highly skilled in energy production and a cell
poor at producing energy
○ Cell with nucleus swallowed up bacterium, resulting in a symbiotic relationship in which
bacterium within cell became exclusively specialized for energy production
Central Dogma of Molecular Biology
Crick, 1953
● DNA —> RNA —> Proteins
○ DNA synthesized via replication
○ RNA synthesized by transcription
○ Proteins synthesized by translation (Translation because a change in language
(nucleotides —> amino acids) is involved)
■ Once information is in protein form, it cannot escape
● Crick’s original view, 1956
Chapter 2: Macromolecules of Life
Subunit Macromolecule
Sugar (monosaccharide) Sugar (polysaccharide)
Amino Acid Protein
Nucleotide Nucleic Acid (DNA,
RNA)
Hydrolysis: a molecule is broken into 2 via the addition process of a water molecule at the end
● Lyse → to split
Dehydration Synthesis / Condensation reaction: 2 molecules become 1, generating water
● Not spontaneous
● Catalyst is typically required
● Involves covalent bonding
, 3
○ Endergonic reaction, requiring an input of energy since bonds store energy
Type of Bond Key Characteristics Atoms Involved
Hydrogen relatively weak, results from partial positive H (bonded to an electronegative
Bond and partial negative charges atom) and N or O, usually
Ionic Bond fully positive and negative charges interaction bases (+) and acids (-)
Covalent strongest of the three (when aggregated), does C—C, C—O, C—N, C—H
Bond not spontaneously break (energy input
required)
Importance of Carbon
● Organic chemistry involves the study of all carbon containing compounds
● Most important atom in biological molecules —> Key molecules contain carbon backbones
● With a valence of 4 (Valence: how many bonds will form, not how many valence electrons are
present), carbon can form four chemical bonds
○ Carbon is the most important ATOM
○ Water is the most important MOLECULE
● Usually forms chemical bonds with C, H, N, S
○ These strong bonds are necessary for life
○ Bond Energy: amount of energy required to break 1 mol of bonds
■ High for C—C bonds
■ Expressed in cal/mol
● Solar radiation has inverse relationship between wavelength and energy content
○ Visible light is lower in energy than C—C bonds, thus bonds cannot be destroyed
○ UV light is higher in energy (shorter in wavelength) and thus more dangerous (can
destroy C—C bonds necessary for life)
● Hydrocarbons
○ C—H bonds exclusively
○ Insoluble in water
○ Compose interior of biological molecules (phospholipid tails)
● Long chains of C—C and C—C rings frequently present in nature
Importance of Water
● Universal, biological solvent
● Common extracellular substance
● Most abundant component of cells and organisms (75-80% of a cell’s weight)
● Polar molecule
○ Polarity allows for interactions with molecules containing partial positive or partial
negative charges
■ Uncharged as a whole
■ All O—H bonds are polar
○ Gives water its cohesive properties, temperature stability, solvent purposes
● Most of water’s properties are derived from cohesive nature
○ Electronegative oxygen at one water molecule is drawn to electropositive hydrogen
