Chapter 1: Introduction to the Chemistry of Life

carnosine

beta-alanine + histidine

found in heart, muscle, and brain

antioxidant, helps stop cell damage

anserine

Beta alanine + 3-methyl-L-histidine

found in skeletal muscle and brain

antioxidant, pH buffer

capsaicin

lipophilic, odorless

triggers burning sensation by binding to the TRPV1 ion channel in sensory neurons

carnitine

quaternary ammonium ion needed for cell energy production

essential shuttle for long-chain fatty acids into mitochondrial matrix — so they can be beta-oxidized into ATP

Biochemist’s periodic table

necessary for all life

CHNOPS

Cl^-, Na⁺, K⁺

Mg²⁺, Ca²⁺

B, F, Si, As, Se, Br, I, Sn

V, Cr, Mn, Mo, Fe, Co, Ni, Cu, Zn

What defines a living organism?

complex and organized

has metabolism, replicates/reproduces, acclimates to environment

take up nutrients, release waste products, generate work and heat, are open systems (never @ equilibrium)

4 main classes of biomolecules

1. proteins

2. lipids

3. nucleic acids

4. carbohydrates

Eukaryotes

have a nucleus

E.R.: site of cell component synthesis

aerobic metabolism in mitochondria

Central Dogma of Molecular Bio

DNA —> RNA —> protein

compartmentalization

division of cell into smaller, functionally discrete systems

• energy transduction

• helps regulate transport

• helps organize (localization) —> stores DNA

• allows efficiency

• protection

size of e.coli vs size of normal animal cell

e.coli ~4 micrometers

animal cell ~10-100micrometers

3 domains

1. Bacteria 16s RNA

2. Archaea = 16s RNA

3. Eukarya = 18s RNA

endosymbiosis

horizontal gene transfer

usually prokaryotes

contributes to antibiotic resistance and is a quick evolution

1. transformation of loose pieces of DNA

2. conjugation - pieces of dna exchanged during physical contact (plasmid)

3. transduction - virus that infects bacteria (bacteriophage) accidentally carries genetic material from one host cell and injects it into a new on

Biological evolution

variation in heritable traits of populations over successive generations

1. Natural selection mechanism

   1. random variation — mutations in heritable traits

   2. not random selection of traits that confer reproductive advantage

2. genetic drift: random mutations

outcomes of biological evolution

adaptation, speciation, biodiversity, extinction, coevolution, convergence, artificial selection

unit of heat, energy, work

Joule

kg*m²/s²

or C*V

electric potential

volt (V)

J/C

angstrom

10^-10 m

0.1 nm

100pm

Thermodynamics

study of energy and its effects on matter

1st law of thermodynamics

energy is conserved

total energy of universe is constant and can neither by created nor destroyed during any physical or chemical process

enthalpy is ΔH

ΔE = q+w

q= sum of heat transferred

w=work done

2nd law of thermodynamics

entropy (S) of the universe must increase for any spontaneous process

entropy = degree of randomness in a system

entropy increases in bottom picture as their are more possible arrangements

Gibbs (free) energy

indicative of spontaneity

ΔG<0 —> spontaneous

ΔG>0 —> not spontaneous

ΔG=equilibrium

ΔG = ΔH - TΔS

ΔG depends on the concentration of substrates and products

aA + bB —> cC + dD

ΔG’ = ΔG^*’ + RTln (([C]^c[D]^d)/([A]^a[B]^b))

enthalpically favored: exothermic or endothermic?

exothermic

living systems are characterized by being in _________ steady state

non-equilibrium steady state

in homeostasis, flex is constant but concentrations are far from equilibrium

Carboxylic Acid-Amine Reactions: Hydrolysis

water is added to cleave the peptide bond

Endopeptidases break peptide bonds (amides) inside protein chains — use water to split the bond between a carboxylic acid carbonyl carbon and an amine nitrogen, turning the amide back into separate carboxylic acid and amine groups

Carboxylic Acid-Amine Reactions: Condensation

Water is removed to create a peptide bond

R—COOH + NH₂—R’ —> R—COO—NH—R’

Cat. by ribosomes — ribosome facilitates linking peptides to build proteins, bypassing the high energy barriers of direct thermal reactions

lipid formation — esterification

Carboxylic Acid + Alcohol ⇌ Ester + Water

• Catalyst: Requires an acid catalyst, such as concentrated sulfuric acid (H₂SO₄) or p-toluenesulfonic acid, to speed up the reaction.

• Equilibrium: The reaction is reversible, meaning it reaches a balance point between reactants and products.

• Driving the Reaction: To get more ester, scientists use extra alcohol or remove the water as it forms (LeChatelier’s)

Carb formation

Protonation: The acid protonates the hemiacetal hydroxyl group (-OH).

Leaving Group Loss: Water (-H₂O) departs from the molecule.

Carbocation Formation: A resonance-stabilized oxonium ion (carbon-oxygen π bond with a positive charge on oxygen) forms.

Nucleophilic Attack: An alcohol molecule attacks the electrophilic carbon.

Deprotonation: Loss of a proton yields the neutral acetal.

Amine

alcohol

ROH

-OH hydroxyl group

Thiol

RSH

-SH sulfhydryl group

ether

ROR

—O— (ether linkage)

aldehyde

ketone

Carboxylic acid

ester

thioester

Amide

Imine (Schiff base)

disulfide

R—S—S—R

features disulfide linkage

phosphate ester

diphosphate ester

phosphoanhydride group

phosphate diester