ABI 102

# of Carbon bonds

4 valence/covalent bonds

Cellular Compartment Purpose

to sequester molecules for specific purposes

What do cellular compartments prevent

prevents interactions between molecules in the environment

What does Cellular Compartments Increase

Increases both local concentration and efficiency

Costs to make Compartments

• costs

• energy

• time

• substrates

System

what we are interested in (organisms)

Surroundings

everything that is not the system

What makes living organisms an open system

1. takes in nutrients

2. Releases waste

3. generates work or heat

q

heat

w

work

exothermic

system release heat

• ∆G < 0

Endothermic

System gains heat

• ∆G > 0

Entropy

measure of number of specific ways a system can be arranged

Gibbs Free Energy

change in energy for a process that combines enthalpy, entropy, and temperature

-∆H

• enthalpically favored

• ∆H < 0

• exothermic

∆H

• enthalpically opposed

• ∆H > 0

-∆S

• Entropically Opposed

• ∆S > 0

∆S

• Entropically Favored

• ∆S < 0

Spontaneous at all Temperatures

• ∆H: -

• ∆S: +

Not Spontaneous at any Temperatures

• ∆H: +

• ∆S: -

Water Physical Properties

• 104.5º angle

• tetrahedron shape

• polar

What does freezing cause

decrease in density and increase in volume

Liquid Water Components

• Reorient in picoseconds

• networks are irregular and varried

Solubility

ability of a solute to interact with the solvent more strongly than other sources

Hydrophobic Effect

water will minimize contact with hydrophobic molecules

Aggregation of Non-Polar Groups

Minimizes surface area and maximizes entropy of the entire stage

amphiphiles

Forms micelles or bilayers that hide hydrophobic groups

• polar and non-polar regions

Ice Formation

crystalline array

Liquid Formation

Irregular network

Water Dissolvable

polar and ionic substances

Dialysis

solute diffuses across a semipermeable membrane from high to low concentrations

Acidic

H⁺ > 10^-7 M

Donates Protons

Less pH

More Acidic

More Acidic

More Protons

Basic

OH^- > 10^-7

Accepts Protons

More pH

More Basic

More Basic

Less Protons

Large K_a

• Products of dissociation reactions are favored

• acid is largely dissociated/ a strong acid

Small K_a

• Undissociated acid is favored

• very little of acid is dissociated/weak acid

• K_a< 1

Features of Good’s Buffers

1. a pKa between 6 and 8

2. soluble in water

3. membrane impermeable

4. minimal salt effect

5. minimal effects from ∆T

6. know any interactions the buffer has cations with

7. chemical stability

8. biochemically inert

9. optical absorbance should never be above 230nm wavelength

10. ease of preparation

Metabolic Acidosis

Hyperventilation

pH < 7.35

High pH and High CO₂

Hyperventilation Cues

• Central chemoreceptors in the brainstem are stimulated

• peripheral chemoreceptors are stimulated by hypoxemia and acidemia

Metabolic Acidosis Causes

• Increased production of organic acids

• Decreased function = decreased renal excretion of H⁺

• Loss of HCO₃^- via alimentary or urinary system

• Reduced buffering capacity = accumulation of H⁺

Metabolic Alkalosis

Hypoventilation

pH > 7.45

Low pH and Low CO₂

Metabolic Alkalosis Causes

• H⁺ lost via gastric secretion or renal excretion

• HCO₃^- accumulates in plasma (vomiting)

• excess HCO₃^- from renal impairment

Respiratory Acidosis

Hypoventilation

pH < 7.35

Low pH and High CO₂

Respiratory Acidosis Causes

• narcotics

• obstructive sleep apnea

Fixing Respiratory Acidosis

increased ventilation or retain HCO₃^-

Respiratory Alkalosis

Hyperventilation

pH < 7.35

High pH and Low CO₂

Respiratory Alkalosis Causes

Hypoventilation

Acidemia

decreased pH in blood

Alkalemia

Increased pH in blood

Acidosis

Condition in which there is too much acid in the body’s fluids

Alkalosis

Condition in which there is too much base/alkali in the body’s fluids

Hypercapnia

excess of CO₂ in the blood

Hypocapnia

Deficiency of CO₂ in the blood

Nucleotides

• nitrogenous base

• ribose/deoxyribose sugar

• one or more phosphate groups

Purine

2 rings

Pyrimidine

1 ring

X=H

Base

X=Ribose

Base

X=Ribose Phosphate

Nucleotide

Base

Adenine

Ade

A

Nucleoside

Adenosine

Ado

A

Nucleotide

Adenylic Acid

Adenosine Monophosphate

AMP

Amino Acid

• building blocks of protein

• ⍺-COOH pKa~2.2

• ⍺-NH₂ pKa~9.4

Peptide Bond Polymerization

Condensation

Peptide Bond

resulting CO-NH linkage