Study guide 1 Flashcards by forrest V

What is thermodynamics (TD)?

the study of energy and its effects on matter and explains exchanges between heat, energy, and work.

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Heat

a form of thermal energy transferred to the system.

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Energy

The capacity to do work for transfer of heat

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Work

Energy given to the environment

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What does TD indicate?

the direction of the process/reaction(spontaneity)

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What are the 3 types of system

isolated, closed, and open

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What is an isolated system

no exchange of matter or energy with surrounding

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Closed system

exchange of only energy, but not matter (temperature changes)

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Open system

exchange of both matters and energy

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TD 1st law

energy is conserved and cannot be created or destroyed

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TD 2nd law

Spontaneous processes are characterized by conversion of order to disorder.

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Weak acids are-

only partially ionized in aqueous solutions

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If ∆H < 0, (is negative

heat is given off and is exothermic and enthalpically favored

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what is a conjugate acid of H2PO4-

H3PO4

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If ∆H > 0, (is postive)

heat is absorbed, endothermic and enthalpically opposed

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internal energy (U

potential energy

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Enthalpy (H)

total heat content of a system

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Enthalpy change

heat absorbed in a constant P

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If ∆S > 0 (is positive)

disorder increases entropically favored)

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If ∆S < 0

disorder decreases (entropically opposed)

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If ∆G > 0: postive

nonspontaneous (endergonic)

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An endergonic with a —— ∆H and a —- ∆S can be changed into exergonic reaction by decreasing the temperature

negative, negative

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If ∆G < 0

spontaneous (exergonic)

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If q > 0

system absorbs heat from surroundings.

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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

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

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