OAT Prep: Osmotic Pressure & PCR

Conduction

direct transfer of energy from molecule to molecule via direct molecular collsions

What are the best and worst conductors?

Worst= gases

Best= metals

Convection

heat transfer by physical motion; only takes place in fluids and gases. Heat energy is transferred AWAY from the source.

Radiation

transfer of energy by electromagnetic waves. Radiation can travel through a hard vacuum.

Ex: energy from sun

specific heat

c, amount of heat energy needed to raise the temperature of 1kg by on degree K.

What is the specific heat of water?

4186 J/kg*K

Heat transfer formula

Q=mc(Tf-Ti)

Heat of transformation from solid to liquid

heat of fusion

Heat of transformation from liquid to gas

heat of vaporization

Temperature Definition

average kinetic energy of the system

Pressure definition

Force per unit surface area (F/A)

STP Conditions

273 K

1 atm

1 mole gas --> 22.4 L

Ideal Gas law

PV=nRT

n= 8.31 J/K*mol

Internal Energy of Monoatomic ideal gas

U = (3/2)nR(Tf-Ti)

*if temperature stays constant, the internal energy stays constant*

How does Q change when heat is added or removed from a system?

Heat added: Q>0

Heat removed: Q

When is work positive?

When work is done by the gas (when the gas loses energy)

When is work negative?

When work is done on the gas (when the gas gains energy)

First law of thermodynamics

Change in Internal Energy (U) = Q - W

Work in thermodynamic process

work done by a sample of gas is equal to the area enclosed by its P-V curve

When the volume of a sample of gas decreases, what is the resulting work?

Work is done on the gas, therefore the work will be negative

Cyclic processes (Pressure and Volume)

total work done by the gas is area enclosed

Final Internal energy = Initial internal energy

Isothermal process

temperature remains constant

As pressure of gas increases, the volume decreases (and vice-versa)

*if ideal gas, then Q = W

Isobaric process

Pressure remains constant

As volume increases, temperature increases

W=P(Vf-Vi)

Isovolumetric process

volume stays constant

Work = 0

U = Q

Adiabatic expansion/compression

No heat transfer into/out of the system

Q = 0

U = -W

irreversible process

all real processes; proceed in definite time order

Ex: dropping a glass onto the floor and it shatters into many pieces, this can't be undone

reversible process

system can run initial to final state or final state to initial state along the same path

Entropy Definition

degree of disorder of a system

Second Law of thermodynamics

any thermodynamic process that moves from one equilibrium state to another, the entropy of the system and its surrounding environment together will either increase or remain unchanged.

Reaction Rate

= change in concentration/time for change to occur

Rate Law

rate = k[A]^x[B]^y

overall order = x+y

Temperature & Reaction rates

rate of reaction will double every +10 degree C

Catalysts

-are not consumed or altered in reaction process

-lowers activation energy

Homogenous catalyst

catalyst is in same phase as reactants

Heterogenous Catalyst

catalyst is in different phase as reactants

Equilibrium Constant Characteristics

-Pure solids or liquids do not appear in equilibrium constant expression

-Larger Kc (>1000) --> equilibrium favors products

-Smaller Kc (

-Intermediate Kc (-1000 to 1000) --> reactants and products are present in similar amounts at equilibrium

Le Chatelier's Principle

when a stress is applied to a system at equilibrium, the system will adjust to minimize the effect of the stress

When more reactant is added, equilibrium will shift towards the products

When more product is added, equilibrium will shift towards the reactants

increase in pressure --> shift equilibrium to lower number of moles present

increase in volume --> equilibrium shift to higher moles present

principle quantum number

n

overall energy level and size of electron's path

Maximum number of electrons per shell

2n^2

Azimuthal quantum number

l

any given n, l can be any integer from 0 to (n-1)

determines the shape of the subshell

0: s (spherical)

1: p (bi lobed)

2: d (4 lobes)

3: f (6 lobes)

Magnetic Quantum number

ml

integer values ranging from -l to +l

divides subshells into individual orbitals and defines the orientation of the orbitals

Spin Quantum Number

ms

+1/2 or -1/2

magnetic properties of an atom , has no effect on the energy of the orbital

Pauli Exclusion Principle

no two electrons in an atom can have the same four quantum numbers

Aufbau principle (building-up principle)

electrons fill in the lowest energy orbital first

How to determine which subshell fills first

n + l

the lower value fills first

Hund's rule

within a given subshell p, d, or f, electrons prefer to occupy different orbitals and have parallel spins rather than pair up in the same orbital and have opposite spins.

Electrons will fill a subshell with parallel spins before pairing up.

paramagnetic

atoms, ions or molecules with unpaired electrons

diamagnetic

atoms, ions or molecules with all paired electrons

isoelectronic

atoms, ions, or molecules with an equivalent number of electrons.

one of the two will always be an ion

Planck's constant

4.15 x 10^15 Hz

Cell Theory

-all living things are made up of cells

-cells are the basic units of life

-cells come only from other cells

-cells carry genetic information in form of DNA- passed from parent cell to daughter cell

Light microscopy

light is focused on specimen by a glass lens and the image is magnified for projection on the eye or photographic film. Used to study live cells

Negative: some of the dyes/preparations may kill live specimens

Electron Microscopy

beam of electrons is used instead of light, electromagnets used instead of glass lenses.

Negative: cannot be used to study living cells because preparation kills cells

Cell fractionation

Cells whose membranes have been ruptured are centrifuged at various speeds and lengths to separate components of different sizes, densities, and shapes

Freeze fracture

used to study cell membranes and organelles, frozen specimen is fractured with a cold knife, producing a fracture plane that splits lipid bilayer membranes

What causes the fluidity of the membrane in animal cells?

Cholesterol

Cytosol

fluid component of cytoplasm

contains free proteins, nutrients, and other solutes

Eukaryotic Cell components

Membrane

Nucleus

Nucleolus

Nucleur membrane

Ribosomes

Mitochondrion

Lysosome

Cytoplasm

Endoplasmic reticulum

Golgi apparatus

Centrioles

Cytosol

Nucleolus function

site of ribosomal RNA (rRNA) synthesis

Mitochondria

site of aerobic respiration; ATP production

Double membrane

(Inner membrane --> cristae, embedded with e- carriers of ETC)

Intermembrane space: high H+

Mitochondrial matrix: site of TCA, low H+

Own circular DNA and ribosomes

Endosymbiotic hypothesis

Mitochondria developed from early prokaryotic cells and began symbiotic relationship with ancestors of eukaryotes. Mitochondria provided energy and the host cell provided nutrients and protection from exterior environment

Mitochondrial inheritance

mitochondrial DNA is identical to that of the mother

Ribosomes

protein synthesis

synthesized in nucleolus, exported to cytoplasm

contain large and small ribosomal subunits (rRNA & proteins)

Free ribosomes: cytoplasm

Bound ribosomes: outer membrane of ER

*prokaryotic ribosomes are smaller than eukaryotic ribosomes*

endoplasmic reticulum interior

lumen, some portions continuous with nuclear envelope

Smooth ER

no ribosomes, lipid synthesis and detoxification of drugs/poisons

rough ER

has ribosomes, protein synthesis.

Golgi Apparatus

stack of membrane-enclosed sacs

proteins are modified and sorted based on destination

Glycosylation

addition of sugar groups to proteins

occurs in golgi apparatus

Lysosomes

Hydrolytic enzymes involved in intracellular digestion

break down proteins, carbohydrates, nucleic acids

pH 5

important for degradation of foreign particles (bacteria) and damaged cells

Peroxisomes

Oxidative enzymes that catalyze reactions which hydrogen peroxide is produced and degraded

Break down fats into small molecules, used in liver to detoxify potentially harmful compounds such as alcohol

if enzymes released into cytoplasm, macromolecules (DNA) could be altered and would be hazardous

What cells create the most ribosomes?

Cells that produce hormones and enzymes (i.e. pancreatic cells)

Cytoskeleton

-specialized proteins that provide framework for maintenance of cell's shape

-involved in cell movement and movement of organelles within cell

Microfilaments

-component of cytoskeleton

Actin: globular protein, thin strands

Myosin: protein, thicker filaments

Intermediate filaments

component of cytoskeleton

fibrous proteins coiled into thicker cables

function in structural support of cell

Microtubules

hollow rods composed of tubulin

movement of organelles and chromosomes

maintenance of cell shape

cell motility

Centrioles

only in animal cells

microtubule-organizing centers

anchor microtubules during mitosis

"9+2 structure"

9 pairs microtubules surrounding 2 central microtubules for stability

Cilia

Flagella

Cilia

move in whip-like fashion

move fluids along cell surface or propel cell within fluid

line respiratory tract to move mucus, dead cells, dust

Flagella

move in wave-like fashion

Tight junctions

animal cells

membranes of neighboring cells attached, cells bound together tightly no material can pass between

form total barrier to transport and diffusion

Anchoring junction

animal cells

in cells subject to mechanical stress

ex: desmosomes, attach epithelial cells in skin

Gap junction

animal cells

direct connection between cytoplasm of one cell and cytoplasm of neighboring cell via channels

channels formed by connexins (proteins)

Adenine and Thymine bonds

two hydrogen bonds

Cytosine and Guanine bonds

three hydrogen bonds

DNA structure

deoxyribose, phosphate group, nitrogenous base (A, G, C, T)

RNA structure

ribose, phosphate group, nitrogenous base (A, G, C, U)

DNA helicase

breaks hydrogen bonds between nitrogenous bases

unwinds DNA helix

DNA polymerase

synthesizes new strands complimentary to original parental strands

5' to 3' beginning at origin of replication

DNA replication

replication fork formed

leading strand synthesized continuously with 1 RNA primer

lagging strand synthesized discontinuously using an RNA primer every Okazaki fragment

Transcription

DNA is copied into RNA

1. RNA polymerase binds to TATA box in promoter region

2. Nucleotides added 5' to 3'

3. hnRNA formed: introns cleaved out and exons spliced together to form mRNA, 5' end of mRNA capped, 3' polyA tail

finished mRNA leaves nucleus via nuclear pore

Translation

synthesis of amino acid chain using mRNA template

1. occurs in cytoplasm, requires GTP

2. mRNA binds to ribosome, translation begins when ribosome encounter start codon AUG

3. tRNA delivers amino acids to ribosomes

4. tRNA/amino acid temporarily binds mRNA codon, peptidy transferase creates peptide bond between adjacent amino acids

5. protein synthesis stops at stop codon (UGA, UAG, UAA)

6. post-translational modifications occur to protein product (3D folding, addition of carbohydrate/lipid/phosphate group, cleavage of signal sequences)

Pyrimidine

C, T, U

Purines

A, G

Transition

substitution of pyrimidine for another pyrimidine or purine for another purine

Transversion

substitution of pyrimidine to purine (vice versa)

Deletion

one or more nucleotides lost from sequence

Insertions

one or more nucleotides added to sequence

Transposition

sequence is inserted at incorrect location in DNA

UV Light causes...

thymine dimers

Ionizing radiation produces...

double strand breaks