Exam 1 Flashcards
(COVALENT/NONCOVALENT) bonds are strong, short, and share electrons.
Covalent
(COVALENT/NONCOVALENT) bonds are weak, long, and are by attraction only.
Noncovalent (interactions)
Covalent bonds that hold monosaccharides (carbohydrates) together to create polysaccharides are…
Glycosidic bonds
Covalent bonds that hold fatty acids plus glycerol or sphingosine derivatives together to from phospholipids or triacylglycerol are called…
Ester bonds
Covalent bonds that hold amino acids together to form polypeptides are called…
Peptide bonds
Covalent bonds that hold nucleotides together to form oligonucleotides or polynucleotides are called…
Phosphodiester bonds
The strength of a covalent or non covalent bond is measured by the _______ needed to break the bond.
Energy
Put the following bonds in order from weak to strong–
A. Salt bridges; Hydrogen bonds
B. Covalent bonds
C. Van der Waals interactions
- C
- A
- B
The strength of a bond can depend on the ________ between atoms.
Distance
How do we measure how attractive 2 ions are to each other in a vacuum?
Use Coulomb’s Law – F = k q1q2
——-
r(squared)
In Coulomb’s Law, F = Force between ions in Newtons. If F > 0 that means the ions are (ATTRACTIVE/REPULSIVE), and if F < 0 that means the ions are (ATTRACTIVE/REPULSIVE).
Repulsive
Attractive
If we want to measure how attractive the 2 ions are to each other in a biological environment, what do we need to add to Coulomb’s Law?
Relative permittivity
***Add D (dielectric constant) to the denominator (in air = 1)
What is the energy required to separate two ions?
Energy of interaction
**If E < 0 then there is an attraction
A dipole means having a ______ charge.
Partial
Dipoles can be _______ (polar) or _______ (polarizable).
Permanent
Induced
With this type of bond, an electron pair is shared.
Covalent bonds
What is the average distance of a covalent bond?
1 angstrom
What types of bonds interact through charge attraction?
Charge and/or dipole interactions
van der Waals interactions
What is the average distance of the charge and/or dipole interactions?
3 angstroms
What is the average distance of the van der Waals interactions?
3-4 angstroms
What type of bond shares a hydrogen atom/proton?
Hydrogen bonds
What is the average distance of hydrogen bonds?
2.6-3.7 angstroms (between donor and acceptor)
Water’s strange physical properties are explained by its _______ bonding ability.
Hydrogen
Ice (solid) is less dense than liquid water, and the hydrogen bond distances are (GREATER/SMALLER) in the solid than in the liquid.
Greater
This is a measure of how highly packed atoms or molecules are.
Density
This is the amount of heat needed to change the temperature of 1 g of a given substance by plus or minus 1 degree Celsius.
Specific heat capacity
This is the amount of energy needed to change 1 g of a given substance from liquid to gas.
Heat of vaporization
Hydrogen bonds _____ energy to break and ______ energy when they form.
Take
Release
The surface of water is strong. _______ is when water molecules attract each other (attraction to self). _______ is when water and other polar substances attract each other (attraction to other).
Cohesion
Adhesion
Cohesion creates what?
Surface tension
Cohesion and adhesion work together to create ______ ______.
Capillary action
Water is the _______ solvent.
Universal
Charged/Polar molecules are (HYDROPHOBIC/HYDROPHILIC) and (DISSOLVE/SEPARATE).
Hydrophilic
Dissolve
Nonpolar molecules are (HYDROPHOBIC/HYDROPHILIC) and (DISSOLVE/SEPARATE).
Hydrophobic
Separate
_______ molecules have both hydrophilic and hydrophobic parts.
Amphipathic
Chemical _______ is making and/or breaking chemical bonds.
Reactions
Most reactions are ________.
Reversible
Equilibrium (DOES NOT/DOES) mean there are equal concentrations. There is no net formation or destruction.
Does not
A weak acid is a proton (ACCEPTOR/DONOR).
Donor
A conjugate base is a proton (ACCEPTOR/DONOR).
Acceptor
What is the dissociation constant?
Ka (or Kb)
**Means acid is “falling apart”
What is the dissociation constant equation (Ka)?
Ka = [H+] [A-]
————
[HA]
**Products over reactants
Strong acids are always going to fall apart completely, so that means its Ka value will be (LARGER/SMALLER) and its pKa value will be (LARGER/SMALLER).
Larger
Smaller
Little “p” means _____, so that means Ka and pKa will always be opposites (i.e., big/small).
-log
Weak acids kind of fall apart, so that means its Ka value will be (LARGER/SMALLER) and its pKa value will be (LARGER/SMALLER).
Smaller
Larger
If it’s a strong acid it will be easier to break apart, therefore requiring less energy. This means the energy required will be (MORE/LESS) negative.
Less
If it’s a weak acid it will be more difficult to break apart, therefore requiring more energy. This means the energy required will be (MORE/LESS) negative.
More
A weak base is a proton (ACCEPTOR/DONOR).
Acceptor
A conjugate acid is a proton (ACCEPTOR/DONOR).
Donor
What is the equation for pKa?
pKa = -log Ka
** (or) pKb = -log Kb
What is the equation for the dissociation constant Kb?
***Remember for a BASE, the base itself is not dissociating, it is the WATER that is dissociating.
Kb = [BH+] [OH-]
—————–
[B]
***Products over reactants
A strong base requires more energy because it’s moving to an acid, therefore the required energy amount is (MORE/LESS) negative.
More
A weak base requires less energy moving to an acid, therefore the required energy amount is (MORE/LESS) negative.
Less
pKw = -log Kw = ????
14
pKw = pH + ????
pOH
pH = -log [???]
H+
What is the equation for Kw?
Kw = [H+] [OH-] = 10(-14) M
—————
[H2O]
What is physiological pH?
7.4
This is the term for a weak acid or weak base that can stabilize pH (absorb protons).
Buffer
What is the Henderson-Hasselbach equation?
pH = pKa + log ( [A-] )
——-
( [HA] )
What is the alternate equation we are going to use for Henderson-Hasselbach?
[A-]
—– = 10(pH-pKa)
[HA]
If pH < pKa, then our exponent is going to be negative (in modified HH equation). This means our overall value is between 0 and 1 and that most of the molecules are _______ since [HA] > [A-].
Protonated
Acid concentration is higher, that means there are more protons present (hence PROTONATED)
If pH > pKa, then our exponent is going to be positive (in modified HH equation). This means our overall value is greater than 1 and that most of the molecules are _______ since [HA] < [A-].
Deprotonated
Base concentration is higher, that means there are less protons present (hence DEPROTONATED)
If pH = pKa, then our exponent is going to be 0 (in modified HH equation). This means our overall value is 1 and that the molecules are just as likely to be _______ or _______ since [HA] = [A-].
Protonated
Deprotonated
In gel _________, the direction of migration is based on the net charge of the molecule (negative goes toward positive).
Electrophoresis
This is when the pH of ALL molecules of a given species in solution have an overall charge of 0.
Isoelectric Point (pI)
If pH < pI, that means the pH < pKa so the molecule is protonated. Thus, the molecule must have a (NEGATIVE/POSITIVE) charge.
Positive
If pH > pI, that means the pH > pKa so the molecule is deprotonated. Thus, the molecule must have a (NEGATIVE/POSITIVE) charge.
Negative
If pH = pI, then (by definition) the molecule no net ______.
Charge
The pI equations is an average of what two values?
pKa (+1) and pKa (-1)
Anything beyond pKa (+1 or -1) we DO NOT CARE. Only can use these two pKa values for pI
In this test, the pH changes over the length of the gel and proteins stop moving when they are uncharged (pH = pI).
Isoelectric focusing
If the pH > pI, then the protein is soluble (deprotonated). Most proteins are very soluble at high pH, where the molecules are (POSITIVELY/NEGATIVELY) charged and repel one another.
Negatively
If the pH < pI, then the protein is soluble (protonated). At low pH the proteins are soluble because of repulsions due to their (POSITIVE/NEGATIVE) charge.
Positive
When pH = pI then the protein has no net charge and the molecules retain regions of positive and negative charge on their surfaces. This results in an increased tendency the protein to _______ and _______ in solution.
Aggregate
Precipitate
What is the first law of thermodynamics?
Energy is neither created nor destroyed in a closed system.
This type of energy deals with motion and performing work.
Kinetic energy
This type of energy deals with the position and the potential to do work.
Potential energy
________ energy is the potential energy within chemical bonds.
Chemical
At the atomic level, atoms are always in motion (______ energy) and the electric charges of protons and electrons in atoms constantly pull and push at each other (______ energy.
Kinetic
Potential
In chemical energy and bonds, they are _______ energy to begin with but when we break the bonds they become more ______ energy because they can be used to do something else.
Potential
Kinetic
In a(n) (OPEN/CLOSED) system, energy cannot leave the system.
Closed
**i.e., the universe
In a(n) (OPEN/CLOSED) system, energy can be exchanged between the system and its surroundings.
Open
**i.e., a cell
What is the second law of thermodynamics?
Disorder is increasing
This is the term used when small molecules are assembled into large ones and energy is required.
Anabolic
This is the term used when large molecules are broken down into small ones and energy is released.
Catabolic
Which type of metabolic reactions create more disorder, catabolic or anabolic?
Catabolic – more pieces means more disorder
What is the Gibbs Free Energy Equation?
Delta G = Delta H - T (Delta S)
This is the change in available/usable energy (Gibbs free energy).
Delta G
This is the change in total energy (enthalpy) in the system.
Delta H
This is the change in disorder (entropy).
Delta S
Delta G, Delta H, and Delta S are all _____ _____, which means its value depends only on the initial and final values and not the pathway to get there.
State functions
Delta G is (POSITIVE/NEGATIVE) if free energy is released.
Negative
Delta G is (POSITIVE/NEGATIVE) if free energy is required.
Positive
If energy is released from the system, then Delta H is (POSITIVE/NEGATIVE).
Negative
In a closed system, Delta H should equal…
0
If disorder decreases, then Delta S is (POSITIVE/NEGATIVE).
Negative
If disorder increases, then Delta S is (POSITIVE/NEGATIVE).
Positive
When Delta G is negative and free energy is released, this is considered an (ENDERGONIC/EXERGONIC) reaction.
Exergonic
When Delta G is positive and free energy is required, this is considered an (ENDERGONIC/EXERGONIC) reaction.
Endergonic
When Delta G is positive and free energy is required, this is considered an unfavorable (SPONTANEOUS/DRIVEN) reaction.
Driven
When Delta G is negative and free energy is released, this is considered a favorable (SPONTANEOUS/DRIVEN) reaction.
Spontaneous
When Delta G equals 0, then the reaction is at _______.
Equilibrium
What 3 things make up a nucleotide?
Phosphate group
Sugar
Nitrogenous base
When a nucleic acid has no phosphate, it’s called a…
Nucleoside
When a nucleic acid has a phosphate, it’s called a…
Nucleotide
(DNA/RNA) has a hydrogen on the 2’ carbon.
(DNA/RNA) has a hydroxyl on the 2’ carbon.
DNA
RNA
The 1’ carbon is where the base attaches, forming a _______ bond.
Glycosidic
The 3’ and 5’ carbons are where ________ bonds form.
Phosphodiester
The 4’ carbon contains an _______ within the sugar ring.
Oxygen
In a sugar pucker, it can be either C-3’-endo or C-2’-endo. This means the _____ carbon sticks up slightly, or the _____ carbon sticks up slightly.
3’
2’
The nitrogenous bases can either be a ______ or ______.
Purine
Pyrimidine
Purines have (ONE/TWO) rings, and pyrimidines have (ONE/TWO) rings.
Two
One
Which nitrogenous bases are purines?
Adenine
Guanine
***PUre As Gold
Which nitrogenous bases are pyrimidines?
Cytosine
Thymine
Uracil
Uracil is only present in (RNA/DNA) and takes the place of (CYTOSINE/THYMINE).
RNA
Thymine
In DNA, purines ALWAYS base-pair with pyrimidines. Which nitrogenous bases pair with which?
A - T
G - C
How many hydrogen bonds are there between A - T?
How many between G - C?
2 hydrogen bonds
3 hydrogen bonds
DNA is an _______ double helix running in the 5’ to 3’ direction.
Antiparallel
In vitro oligonucleotide synthesis proceeds in what direction?
3’ to 5’
Whether a nitrogenous base is _____ or _____ means that is faces inward or outward.
Syn
Anti
This double helix structure is right-handed, has a wide and deep major groove, and narrow and shallow minor groove.
B-form
The B-from helix has a ______ sugar pucker and _____ nitrogenous base orientation.
C2’-endo
Anti
This double helix structure is right-handed, has a narrow and deep major groove, and wide and shallow minor groove.
A-form
The A-form helix has a ______ sugar pucker and ______ nitrogenous base orientation.
C3’-endo
Anti
This double helix structure is left-handed, has a flat major groove, and a narrow and deep minor groove.
Z-form
The Z-form helix has a _____ (pur) and _____ (pyr) sugar pucker and _____ (pur) and _____ (pyr) nitrogenous base orientation.
C2’-exo
C2’-endo
Syn
Anti
What helical structure is the physiological DNA form?
B-form
What helical structure is primarily seen in RNA?
***RNA can be double stranded if it folds back on itself
A-form
What are the 3 possible models for DNA replication?
Conservative
Semi-conservative
Dispersive
Hairpins and cruciforms require a ________ sequence (inverted repeat).
Palindromic
Hairpins and cruciforms are created by superhelical _____.
Strain
A triplex is a 3-stranded DNA that may or may not occur in nature. It requires a ________-_______ duplex and uses Hoogsteen hydrogen bonds.
Homopurine
Homopyrimidine
Quadriplexes are 4-stranded DNA that consist of _______ only.
Guanine
Quadriplexes occur at what 2 places?
Telomeres
Promoters
The melting temperature (Tm) = temperature at which –
- Delta G (ds – ss) = 0 (at equilibrium)
- Half of sample is ________ (ss)
Denatured
How does DNA go from 2 strands to 1?
Like a zipper
In tautomers, what is being moved?
Hydrogen
DNA has to be (SS/DS) to make tautomers/isomers.
SS
Other examples of isomers are the ______ and ______ conformation of nucleic acids.
Syn
Anti
Do we prefer syn or anti?
Anti
***We don’t like syn but it’s better than having tautomer
How many chances do we have to make a syn/anti isomer?
One (Replication fork)
How many chances do we have to make a tautomer?
Two (Replication fork and mismatch repair)
What is a transition mutation?
Swapping a purine for purine OR pyrimidine for pyrimidine (Still Pur - Pyr pairing)
In a transition mutation, what must one of the BP have?
Unfavored tautomer conformation
What is a transversion mutation?
Swapping a pyrimidine for purine OR purine for pyrimidine (Now Pur - Pur or Pyr - Pyr)
In a transversion mutation, what do the BP look like?
1 is unfavored tautomer and the other is in syn conformation
What is the mutation rate for transitions without proofreading? With proofreading?
1x10(-4)
5x10(-9)
What is the mutation rate for transversions without proofreading? With proofreading?
2.5-5x10(-6)
1-2.5x10(-10)
What base pair changes to cause sickle cell?
A to T (Glu to Val)
Sickle cell is due to _________ of the A.
Self-depurination
In the Beta-Globin gene, the self-depurination occurs in codon ______.
6
This type of induced mutation, for example, can occur when BrdU pairs with either A or G depending on its chemical state.
Base analogs
This type of induced mutation includes mustard gases.
Alkylating agents
***Carbons and hydrogens (alkyne, alkene, etc.)
This type of induced mutation is when an agent inserts itself between base pairs in DNA and can cause frameshift mutations.
Intercalating agents
This type of induced mutation is when, often a carcinogen, bonds to the DNA through covalent bonds.
Adduct-forming agents
________ are intercalating agents that upon activation with UV light form adducts with neighboring pyrimidine residues.
Psoralens
Exposure to _______ forms T-T dimers (causes cancer).
UV light
In this type of induced mutation, its mutagenic properties are actually a secondary effect: betas, gammas, and x-rays cause electrons to be ejected from an atom, leaving a free radical (free radicals are harmful to the body).
Ionizing radiation
List the hydrophobic amino acids.
Valine Alanine Glycine Leucine Isoleucine Proline Methionine Tryptophan Phenylalanine
List the polar amino acids.
Cysteine Serine Tyrosine Threonine Asparagine Glutamine
List the charged (-) amino acids.
Glutamate (Glutamic acid)
Aspartate (Aspartic acid)
List the charged (+) amino acids.
Lysine
Arginine
Histidine
What amino acids are tiny?
AGCS
What amino acids are small?
PNTD
What amino acids are medium?
HEVQ
What amino acids are large?
MILRK
What amino acids are very large?
WFY
What amino acids are very large?
WFY
What are the essential amino acids (meaning humans cannot synthesize them)?
PVT TIM HALL
(FVW TIM HRKL)
The other 10 humans can synthesize de novo (nonessential amino acids)
_________ amino acids are incorporated into proteins during translation. It includes the 20 usual amino acids, plus 2 more we have to use stop codons to get.
Proteinogenic
What is the 21st amino acid and uses the UGA/opal codon?
Selenocysteine (Sec, U)
Selenoproteins are important for good health. They reduce ______ _____ in conjunction with Vitamin E. They are required in _______ neurons (growth and coordination), and they moderate _______ responses.
Oxidative stress
Cerebellum
Inflammatory
Selenium deficiency results in myopathies, including _______ disease (cardiomyopathy) and ______ intolerance (rhabdomyolysis).
Keshan
Statin
If there is too much __________, then you can have hair and nail brittleness, “garlic breath”, gastrointestinal/neurological lesions, myopathies, renal failure, and death.
Selenocysteine
