Study guide 1 Flashcards
What is thermodynamics (TD)?
the study of energy and its effects on matter and explains exchanges between heat, energy, and work.
Heat
a form of thermal energy transferred to the system.
Energy
The capacity to do work for transfer of heat
Work
Energy given to the environment
What does TD indicate?
the direction of the process/reaction(spontaneity)
What are the 3 types of system
isolated, closed, and open
What is an isolated system
no exchange of matter or energy with surrounding
Closed system
exchange of only energy, but not matter (temperature changes)
Open system
exchange of both matters and energy
TD 1st law
energy is conserved and cannot be created or destroyed
TD 2nd law
Spontaneous processes are characterized by conversion of order to disorder.
Weak acids are-
only partially ionized in aqueous solutions
If ∆H < 0, (is negative
heat is given off and is exothermic and enthalpically favored
what is a conjugate acid of H2PO4-
H3PO4
If ∆H > 0, (is postive)
heat is absorbed, endothermic and enthalpically opposed
internal energy (U
potential energy
Enthalpy (H)
total heat content of a system
Enthalpy change
heat absorbed in a constant P
If ∆S > 0 (is positive)
disorder increases entropically favored)
If ∆S < 0
disorder decreases (entropically opposed)
If ∆G > 0: postive
nonspontaneous (endergonic)
An endergonic with a —— ∆H and a —- ∆S can be changed into exergonic reaction by decreasing the temperature
negative, negative
If ∆G < 0
spontaneous (exergonic)
If q > 0
system absorbs heat from surroundings.
A spontaneous process
occurs without the addtion of free energy, is a negative, exergonic
Free energy is
additive
∆G rxn
products - reactiants
Spontaneous reaction equation
∆G = ∆H - T∆S ≤ 0
Molecules such as methanol and ethanol are very soluble in water because
they contain O-H groups that can form multiple H-bonds with water
If q < 0
system gives off heat (exothermic)
If w > 0, positive
system does work on surroundings
if w < 0 (negative)
surroundings do work on system
An endergonic with a —— ∆H and a —- ∆S can be changed into exergonic reaction by increase the temperature
postive, postive
negative ∆H and a postive ∆S =
negative ∆G, exothermic, enthalpically favored and entropically favored, spontaneous (exergonic)
postive ∆H and a negative ∆S
enthalpically and entropically opposed, non-spontaneous
Ionic interaction bond strength
86
Keq can be determined from the change in standard free energy using the equation
Keq = -∆Ho
/RT
van’t Hoff plot
determines ∆H and ∆S using ∆G o & Keq
Slope
-∆Ho/R
Y intercept
∆So/R
Hydrophiles
polar and ionic
Hydrophobes
non polar , not dipole
Hydrophobic interactions between nonpolar molecules
require the prescene of surrounding water molecules
Hydrogen bond, bond strength
20
dipole diple interaction bond strength
9.3
covalent bond examples
o-h-460
c-h,-414
c-c -348
Ice
all 4 H bonds are satisfied, less dense, open structure
Linker DNA length
8-114 bp
O is electronegative, true or false
true
structure of water
tetrahedron- sp3 hybridization with 2 lone electron pairs
water is
polarized with a dipole moment
How many of liquid ‘s H-bonds are satisfied
about 85%
strength of H-bond is dependent on
orientation
high dielectric constant
78-water
32.6-methanol
1.9-hexame
DNA sequencing using the Sanger method requires
template, primer, DNA polymerase, dNTPs, ddNTPs
Amphiphiles
Hydrophilic heads and hydrophobic tails and can form micelles or bilayers
What are colligative propertties
properties that depend on # of solute particles
decrease freezing point.
raise boiling point.
lower vapor pressure
causes osmotic pressure.
Which Topo requires ATP hydrolysis for energy?
Topo II
non covalent interactions
-atoms are not covalently bonded to each other
-can be either attractive or repulsive
-arise from interaction between transient or stable charges on atoms
-influence the structure of biological macromolecules
acid
anything capable of donating proton
base
anything capable of accepting proton
pH=
- log10[H+ ]
What does K -acidd disassociatio constant indicate
acid strength
if K is large, pk is
small and vice versa
Henderson-Hasselbalch equation:
pH = pK + log10([A-] / [HA]
Henderson-Hasselbalch equation can determine
pH of solutiion if K and A and HA is known
N-glycosidoc bonds between
N1 (pyrimidines) or N9(purines) and C2 of deoxyribose
Phosphodiester bond between
5’ and 3’
Base Pairing of DNA
T with A – 2-H bonds
C with G—3 H-bonds
A with U —2 H-bonds
The sugar pucker is — in the – form
C2-endo; B-DNA
C3 endo; A-DNA
Knowledge about the tautomeric forms of the base of nucleic acids is needed
to understand H-bonding between complementary bases
B-DNA
Major: wide and deep
Minor: narrow and deep
C2-endo
z-dna
major: flat
minor: narrow and deep
C2 endo for pyrimidines
A-DNA
Major: narrow and deep
Minor: wide and shallow
C3 endo
The pH of cofee is 5.6. The pH of grapefruitjuice is 2.6. That means the proton concentration in coffee is
a thousand times lower than grapefruit juice
The polarity of the O-H bond is caused by the — of oxygen relative to that of hydrogen
higher electronegativity
Due to constraints on its sugar pucker, when RNA forms a double helical structure its conformation is
A-form
Nucleosome
1st level of packing
packing ratio: 6
winding of DNA around a protein core
30nm Fiver (chromatin fiber)
2nd level of packing)
coiling of beeds in a helical structure
packing ratio–40
300-700 nm fiber and chromosome -the final packaging
paking ratio 1000= interphase
10000- mitosis
Hyperchromic effect/shift
the absorbance of denatured DNA is 30-40%
Tm depends on 4 factors
GC content
salt concentration
sequence length
# gaps
Gel electrophoresis`
separating DNA by size
steps to PCR
denaturation–annealing– elongation
PCR
amplifies specific regions of dna
Sanger sequencing
limited incorporation of ddNTP results in a series of DNA fragments in various sizes
Molecular cloning
constructs a recombinant DNA molecule to generate a population of identical DNA molecules
What is packing ratio
length of dna
Histones does what with DNA
they wrap around DNA
Basic protons
have an affintiy for DNA
Core DNA has how many base pairs
146
What are some common features for cloning vector for transformation
Mutiple cloning site (polylinker
origin of replication
selection marker
What is the major grooves of dsRNA for
hydrogen bonding with external groups
