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Midterm 1
Lecture 1: Water, Weak Bonds, and Order out of Chaos
Questions:
What is biochemistry and what are some examples?
Interface science; genetics, molecular, cellular, neurobiology
What are the two rules of biochemistry?
1. No violating physics and chemistry
2. Mutation and selection - diversity of life, DNA, protein forming
What are the 4 processes that an organism must be able to carry out?
1. Acquiring food
2. Converting food to fuel for metabolic energy
3. Utilizing energy to drive processes
4. Elimination of toxic waste
What is the basic unit of life for an organism?
Cell
What is cell compartmentalization?
The way organelles in eukaryotic or prokaryotic cells live and work in separate
areas within the cell
What is important for compartmentalization for eukaryotes and prokaryotes?
Eukaryotes have many membrane enclosed compartments and organelles;
Prokaryotes have 2 membranes, non membrane internal compartmentalization
What is between the 2 membranes in a prokaryote?
Cell wall and periplasmic space
Midterm 1 1
, What is unique about the lysosomes pH?
It is low and acidic compared to the other organelles and overall cell
How do you achieve compartmentalization?
1. Membranes form enclosed space
2. Non homogenous areas in cell
3. Protein scaffolds
4. Active transport
5. Earmarking small molecules differently
What is an example of a non homogenous area in the cell?
Nucleoid
What is protein scaffolding?
Bringing different proteins together at the same time to regulate a process
What are 2 examples of earmarking?
Biosynthetic processes and catabolic degradative processes
What are the 4 classes of biomolecules?
Carbs, lipids, nucelic acids, and proteins
How is exchange of information possible with membranes?
Specialized proteins that have hydrophobic and hydrophilic sections that can
span across the lipid membrane
What is the central dogma of molecular biology?
Flow of genetic information from DNA to RNA to proteins using transcription
and translation
What goes hand in hand with DNA, RNA, and proteins respectively?
Genetic information, working copies, and enzymes/cytoskeleton
How can genetic information be carried in RNA?
Through retroviruses
What can RNA act as?
Midterm 1 2
, A catalytic or a structural factor - enzyme or ribosomal
How does an amino acid sequence form?
RNA forms a specific sequence into a certain order, which folds into a protein
What part of a protein is hydrophobic and hydrophilic?
Interior is phobic and exterior is philic
What is Rule 1 problem of a protein sequence?
How the sequence encodes its structure because of the hydrophobic
properties of the interior, leading to folding of the protein; follows laws of
thermodynamics
Why is the hydrophobic effect a problem?
Breaks laws of thermodynamics and we can’t break laws of chemistry and
physics, not entropically favored
What type of bond is not reversible?
Covalent bonds
What are the 3 fundamental non covalent bonds?
1. Hydrogen
2. Ionic/electrostatic
3. Van der Waals
What is important about a single weak interaction vs. many weak?
More non covalent(weak) bonds increases strength and structural stability
Where are conformational changes important?
Enzyme catalysis and regulation
What is important about waters structure?
Oxygen is a hydrogen bond acceptor while Hydrogen is a donor, it forms weak
hydrogen bonds with other water molecules
What do polar water molecules do in regards to ionic interactions?
Replace the ionic interactions(enthalpy) while increasing the disorder(entropy)
Midterm 1 3
, How can you relate distance between atoms with attraction?
If the distance is very large there will be little to no attraction between the
atoms, as they get closer the attraction is at its max with whatever the van der
waals contact distance is, when the atoms cross that distance they will quickly
repulse
Why do atoms repulse when they cross the van der waals distance?
The electron clouds start to interfere with one another
What is the order of strength with the 4 types of bonds?
Covalent, ionic, hydrogen, van der waals
What is the 2nd law of thermodynamics?
Entropy of a system and surroundings are always increasing in a spontaneous
process
How does water having binding sites relate to entropy?
Entropy is not maximized
What is the one exception to entropy not increasing?
When you put energy into a system
What does the hydrophobic effect drive?
Favorable nonpolar enthalpic interactions and water entropy (protein folding),
increases entropy of a system
What is the magnitude of all the bonds?
Van Der Waals(0.5 - 1 kcal, Hydrogen(1 - 5 kcal), Ionic(5 - 7 kcal), Covalent(50
- 100 kcal)
What is the significance of polymers?
Used in daily life, and made up of small units called monomers that are linked
together to form longer chains
Helpful videos/quizlets:
https://www.youtube.com/watch?v=Nwyf6G_IVXM
Midterm 1 4
Midterm 1
Lecture 1: Water, Weak Bonds, and Order out of Chaos
Questions:
What is biochemistry and what are some examples?
Interface science; genetics, molecular, cellular, neurobiology
What are the two rules of biochemistry?
1. No violating physics and chemistry
2. Mutation and selection - diversity of life, DNA, protein forming
What are the 4 processes that an organism must be able to carry out?
1. Acquiring food
2. Converting food to fuel for metabolic energy
3. Utilizing energy to drive processes
4. Elimination of toxic waste
What is the basic unit of life for an organism?
Cell
What is cell compartmentalization?
The way organelles in eukaryotic or prokaryotic cells live and work in separate
areas within the cell
What is important for compartmentalization for eukaryotes and prokaryotes?
Eukaryotes have many membrane enclosed compartments and organelles;
Prokaryotes have 2 membranes, non membrane internal compartmentalization
What is between the 2 membranes in a prokaryote?
Cell wall and periplasmic space
Midterm 1 1
, What is unique about the lysosomes pH?
It is low and acidic compared to the other organelles and overall cell
How do you achieve compartmentalization?
1. Membranes form enclosed space
2. Non homogenous areas in cell
3. Protein scaffolds
4. Active transport
5. Earmarking small molecules differently
What is an example of a non homogenous area in the cell?
Nucleoid
What is protein scaffolding?
Bringing different proteins together at the same time to regulate a process
What are 2 examples of earmarking?
Biosynthetic processes and catabolic degradative processes
What are the 4 classes of biomolecules?
Carbs, lipids, nucelic acids, and proteins
How is exchange of information possible with membranes?
Specialized proteins that have hydrophobic and hydrophilic sections that can
span across the lipid membrane
What is the central dogma of molecular biology?
Flow of genetic information from DNA to RNA to proteins using transcription
and translation
What goes hand in hand with DNA, RNA, and proteins respectively?
Genetic information, working copies, and enzymes/cytoskeleton
How can genetic information be carried in RNA?
Through retroviruses
What can RNA act as?
Midterm 1 2
, A catalytic or a structural factor - enzyme or ribosomal
How does an amino acid sequence form?
RNA forms a specific sequence into a certain order, which folds into a protein
What part of a protein is hydrophobic and hydrophilic?
Interior is phobic and exterior is philic
What is Rule 1 problem of a protein sequence?
How the sequence encodes its structure because of the hydrophobic
properties of the interior, leading to folding of the protein; follows laws of
thermodynamics
Why is the hydrophobic effect a problem?
Breaks laws of thermodynamics and we can’t break laws of chemistry and
physics, not entropically favored
What type of bond is not reversible?
Covalent bonds
What are the 3 fundamental non covalent bonds?
1. Hydrogen
2. Ionic/electrostatic
3. Van der Waals
What is important about a single weak interaction vs. many weak?
More non covalent(weak) bonds increases strength and structural stability
Where are conformational changes important?
Enzyme catalysis and regulation
What is important about waters structure?
Oxygen is a hydrogen bond acceptor while Hydrogen is a donor, it forms weak
hydrogen bonds with other water molecules
What do polar water molecules do in regards to ionic interactions?
Replace the ionic interactions(enthalpy) while increasing the disorder(entropy)
Midterm 1 3
, How can you relate distance between atoms with attraction?
If the distance is very large there will be little to no attraction between the
atoms, as they get closer the attraction is at its max with whatever the van der
waals contact distance is, when the atoms cross that distance they will quickly
repulse
Why do atoms repulse when they cross the van der waals distance?
The electron clouds start to interfere with one another
What is the order of strength with the 4 types of bonds?
Covalent, ionic, hydrogen, van der waals
What is the 2nd law of thermodynamics?
Entropy of a system and surroundings are always increasing in a spontaneous
process
How does water having binding sites relate to entropy?
Entropy is not maximized
What is the one exception to entropy not increasing?
When you put energy into a system
What does the hydrophobic effect drive?
Favorable nonpolar enthalpic interactions and water entropy (protein folding),
increases entropy of a system
What is the magnitude of all the bonds?
Van Der Waals(0.5 - 1 kcal, Hydrogen(1 - 5 kcal), Ionic(5 - 7 kcal), Covalent(50
- 100 kcal)
What is the significance of polymers?
Used in daily life, and made up of small units called monomers that are linked
together to form longer chains
Helpful videos/quizlets:
https://www.youtube.com/watch?v=Nwyf6G_IVXM
Midterm 1 4
