Exam 1 Flashcards
Know the four elements that are most abundant in living organisms.
CHON
- carbon
- hydrogen
- oxygen
- nitrogen
Be able to describe steps in chemical evolution and the types of reactions involved in making and breaking polymers.
- biologically significant monomers had to undergo condensation reactions to form polymers
- condensation - make polymers
- hydrolysis - break polymers
RNA world hypothesis
- RNA forms
- ribozyme catalyses RNA replication
- RNA catalyses protein synthesis
- RNA encodes both DNA and protein
- proteins catalyze cell activities
Why did molecules need to have the ability to self-replicate for evolution to take place?
- if molecules are complimentary, then they can potentially direct replication of themselves
- more complex molecules increase chemical versatility
- over time natural selection favored molecules that made accurate copies of themselves
Prokaryotes
- simplest cells
- a single plasma membrane
- no nucleus or organelles
- unicellular
Eukaryotes
- characterized by numerous membrane-bound organelles, including a nucleus
- much larger in size than prokaryotes
- ER, golgi, mitochondria, etc.
The phylogenetic tree of life includes three domains:
Bacteria, archaea, and eukarya
Describe the evolutionary relationship between bacteria, archaea, and eukarya.
The archaea are a group that are as distantly related to other prokaryotes as both groups are to eukaryotes.
Bacteria
Prokaryotes
Archaea
Prokaryotes, but share some features with eukaryotes
Eukarya
Eukaryotes
Evolution as a process of natural selection on mutations
Mutations - changes in an individuals genetic material
- arise at random as the result of chemical damage or inherent errors in the replication process
- a mutation that increases the chances of survival of the individual increases the likelihood that the mutation will be passed on to the next generation
Evolution as a process of natural selection on variations amongst individuals
- allows organisms to adapt to unexpected changes
- this is one reason why genetically homogenous populations are so susceptible to a single challenge
- a more heterogenous population is more likely to include individuals that can resist the adversity and recover
What is entropy?
A measure of the degree of randomness or disorder of a system
Second law of thermodynamics
The entropy of the universe is always increasing
How is the entropy of the universe always increasing and how does it take energy to decrease the energy of a system?
- all processes increase the entropy of the universe
- naturally the universe is always going to continue to have more disorder, so to reverse this process you have to use energy to restore order
What does spontaneity depend on?
Enthalpy and entropy
Equation for Gibbs free energy
Delta(G) = delta(H) - T(delta)S
How do you tell whether a process is spontaneous or non-spontaneous?
Spontaneous process occurs with a decrease in free energy
Delta(G) > 0 = non-spontaneous
Delta(G) < 0 = spontaneous
Delta(G) = 0 = equilibrium
What would teaching equilibrium mean for an organism?
Living organisms can never be at equilibrium
Equilibrium = death
How do organisms avoid reaching equilibrium while maintaining a steady state?
- exchange both matter and energy with surroundings
- living organisms achieve order by disordering the nutrients they consume
- all flows in the system are constant so that the system does not change with time
Molecular structure of water
- bent
Electronic structure of water
- the oxygen atoms sp^3 orbitals are arranged tetrahedrally
- two orbitals contain nonbonding electron pairs
Explain why ice floats in liquid water in terms of hydrogen bonds and structure.
- optimal temperature = 180
- structure of ice forms a crystal
- four hydrogen bonds per molecule
- ice is less dense than water
- latis structure and space in between water molecules
- in ice, water molecules are hydrogen bonded in a crystalline array, but in liquid water, hydrogen bonds rapidly break and re-form in irregular networks
List in order of increasing strength, the attractive forces acting on molecules.
- London dispersion forces
- dipole-dipole interaction
- hydrogen bond
- ionic interaction (noncovalent)
- covalent bonds
Van der waals interactions
- the noncovalent associations between neutral molecules
- arise from electrostatic interactions among permanent or induced dipoles
London dispersion forces
Extremely weak and fall off so rapidly that they are significant only for groups in close contact
Explain why polar and ionic molecules dissolve in water.
- solubility depends on the ability of a solvent to interact with a solute more strongly than the solute molecules interact with each other
- unfavorable to have shell
- hydrophilic substance
Hydrophilic substance
A substance whose high polarity allows it to readily interact with water molecules and thereby dissolve in water
Explain the hydrophobic effect.
- explains the exclusion of nonpolar groups as a way to maximize the entropy of water molecules
- the decrease in entropy is due mainly to increased order of the H2O
- hydrogen bond “cage” forms to maximize the number of H+ bonds
- more favorable to push all molecules together
Explain how amphiphilic molecules behave.
- form micelles or bilayers that hide their hydrophobic groups while exposing their hydrophilic groups to water
- non-polar tails
Osmosis -
- movement of water from a high solute concentration to lower solute concentration
Diffusion -
- movement of molecules from high concentration to low concentration
Hypertonic -
Water goes into tube
Value for Kw at 25C
1.00x10^-14
Relationship between pKa and strength of an acid
Acid strength is specified by its dissociation constant
Henderson-Hassalbalch equation
- relates the pH of a solution of a weak acid to the pK and the concentrations of the acid and it’s conjugate base
- useful for determining the pH of a solution containing a weak acid and for making buffer solutions
What is a buffer and how do they work?
- resist change in pH
- buffering capacity of weak acids is maximal when pH=pK
- useful range of weak acid buffers is within one pH unit of its pKa
Chemical difference between RNA and DNA
- DNA contains adenine, guanine, cytosine, and thymine deoxyribonucleotides
- RNA contains adenine, guanine, cytosine, and uracil ribonucleotides
Describe the stem-loop structure of RNA and how this could lead to higher order RNA structure, similar to that of an enzyme.
- base pairing between complementary sequences of a single RNA molecule
- RNA can bind small molecules and catalyze chemical reactions
Structural properties of DNA
- the polynucleotide chains wind around an axis to form a double helix
- the two strands are anti-parallel and form a right-handed helix
- bases occupy the core and the sugar-phosphates run the periphery
- each base is hydrogen bonded to a base in the opposite strand
Process of replication
- DNA -> genetic blueprint for cell
- Each old strand is used as a template for a new strand
Process of transcription
- Turns DNA into RNA
- mRNA -> copied message of the DNA
- make an mRNA copy or transcript from the original DNA copy
- performed by an enzyme: RNA polymerase
Process of translation
- turns RNA into protein
- occurs at the ribosome
- protein -> final product for use by the cell
- make proteins for the cell from the mRNA transcript
Central dogma of molecular biology
Replication, transcription, translation
Blunt end
- the fully base-paired ends of a DNA fragment that has been cleaved by a restriction endonuclease that cuts the DNA strands at opposing sites
- not sticky because all the nucleotides are already paired between the two strands of DNA
Sticky end
- the single-stranded extension of a DNA fragment that has been cleaved at a specific sequence in a staggered cut such that the single-stranded extension is complementary to those of similarly cleaved DNAs
- DNA fragments with complementary single-stranded extensions
Advantage of using a sticky end over a blunt end
Blunt ends
- multiple copies of gene :(
- go in backwards :(
Sticky ends
- good fidelity of cloning
- only one copy
- directionality
Steps to sequence DNA using the chain-terminator method
- first, obtain single polynucleotide strands
- complementary DNA strands can be separated by heating, which breaks the hydrogen bonds between bases
- next, polynucleotide fragments that terminate at positions corresponding to each of the four nucleotides are generated
- finally, the fragments are separated and detected
Major findings of the human genome sequencing project
- the human genome contains about 23,000 genes, corresponding to about 1.2% of its 3 billion nucleotides
- sequence differences reveal evolutionary changes
Cloning into a vector
- the cloning vector and the foreign DNA are cut by the same restriction endonuclease
- the sticky ends of the vector and the foreign DNA fragments anneal and are covalently joined by DNA ligase
- the result is a chimeric DNA containing a portion of the foreign DNA inserted into the vector
Polylinker -> has about 50 restriction enzymes in it -> where you clone your insert
- x-gal operon -> gen in PLsite disrupts operon
- ampR -> ampicillin resistance
- colony growth = plasmid
- no gene = blue colony
- gene = white colony
- white colony = gene successfully inserted
Advantages/disadvantages of cloning into a vector
- can be induced to replicate until the cell contains 2-3 thousand copies
- relatively small
- carry genes specifying resistance to one or more antibiotics
- can be used to clone DNA segments of no more than about 10-12kb
Cloning into a bacteriophage
- cleave by restriction enzyme and separate the fragments
- anneal and ligate
- in vitro packaging
- infective lambda phage now contains a foreign DNA fragment
Advantages/disadvantages of cloning into a bacteriophage
- can accommodate inserts up to 16kb
- recombinant DNA is produced in large amounts in easily purified form
Steps in a PCR reaction
- the polymerase chain reaction amplifies a DNA segment by repeatedly synthesizing complementary strands
- denaturation - separate strands by heating
- anneal
- elongation - extend primers by DNA polymerase
- two cycles
Transgenic mice
Insert human chromosome
KO mice
Remove gene from mouse
Golden rice
Has vitamin A
