CHE 4341 Ch.1 & 2

What is biochemistry?

The study of how the remarkable properties of living organisms arise from chemistry

"What is true of E. coli is true of the elephant." – who said this and what does it mean?

Jacques Monod, 1954; refers to the biochemical unity of life

Name the 5 foundational principles of Chapter 1

1) Cells are the fundamental unit of life 2) Cells use a small set of carbon-based molecules 3) Living organisms exist in dynamic steady state 4) Cells self-replicate via DNA 5) Organisms evolve over time

What three things do all cells share?

A plasma membrane, cytoplasm, and genetic material (DNA) in a nucleoid or nucleus

What does cytosol contain?

Enzymes, RNA molecules, metabolites/cofactors, and inorganic ions (K+, Na+, Mg2+, Ca2+)

What sets the lower limit of cell size?

The minimum number of biomolecules required to function

What is the smallest known cell type and its size?

Mycoplasmas, ~300 nm diameter

What sets the upper limit of cell size?

Surface area to volume ratio (surface area grows as r², volume grows as r³)

How do cells solve the surface area/volume problem as they grow?

Highly folded/convoluted cell surfaces

What are the three domains of life?

Bacteria, Archaea, Eukarya

How are the three domains classified?

Based on ribosomal RNA sequence comparisons

Which two domains are more closely related to each other?

Archaea and Eukarya

What are phototrophs?

Organisms that use sunlight as an energy source

What are chemotrophs?

Organisms that use chemical fuels as an energy source

What are autotrophs?

Organisms that fix CO2 directly as a carbon source

What are heterotrophs?

Organisms that require organic compounds from other organisms as a carbon source

Cyanobacteria are classified as what?

Photoautotrophs

Humans are classified as what?

Chemoheterotrophs

Approximate size of E. coli

~2 µm long, <1 µm diameter

How many ribosomes and enzymes does E. coli have?

~15,000 ribosomes; ~1,000 different enzymes

What are plasmids?

Small circular DNA segments in bacteria

Gram-positive vs gram-negative bacteria differ in what two features?

Number of membranes; presence/thickness of peptidoglycan layer

Function of the nucleus

DNA storage; transcription

Function of mitochondria

ATP production; aerobic respiration

Function of the endoplasmic reticulum

Protein and lipid synthesis (rough/smooth)

Function of the Golgi complex

Protein processing and sorting

Function of lysosomes

Intracellular digestion

Function of peroxisomes

Fatty acid oxidation; ROS detoxification

Function of chloroplasts

Photosynthesis (in plants)

Typical eukaryotic cell size

5–100 µm diameter (1,000–1,000,000x larger than bacteria)

Who developed subcellular/cell fractionation?

Albert Claude, Christian de Duve, George Palade

What does low-speed centrifugation isolate?

Nuclei, plasma membranes

What does medium-speed centrifugation isolate?

Mitochondria, lysosomes, peroxisomes

What does high-speed centrifugation isolate?

ER fragments, vesicles

What does very high-speed centrifugation isolate?

Ribosomes, large macromolecules

What remains in the supernatant after fractionation?

Soluble cytosolic proteins

What are the three types of cytoskeletal filaments and their widths?

Actin filaments (~6 nm), microtubules (~22 nm), intermediate filaments (~10 nm)

Function of actin filaments

Shape, movement, cell division

Function of microtubules

Organelle transport, mitosis

Function of intermediate filaments

Structural support

What is the hierarchy of cellular organization?

Monomeric units → Macromolecules → Supramolecular complexes → Organelles → Cells

What noncovalent interactions hold supramolecular complexes together?

Hydrogen bonds, ionic interactions, van der Waals forces, hydrophobic effect

Why is carbon ideal for building biomolecules?

Forms stable bonds with up to 4 other atoms, can form chains/branches/rings, bonds with C, H, O, N, S, P

Length and flexibility of a carbon single bond

~0.154 nm, free rotation

Length and flexibility of a carbon double bond

~0.134 nm, rigid, no free rotation

What percent of a cell's dry weight is carbon?

More than 50%

Hydroxyl functional group properties

-OH; polar, hydrogen-bonding

Amino functional group properties

-NH2; basic, charged at low pH

Carboxyl functional group properties

-COOH; acidic, charged at high pH

Phosphate functional group properties

-OPO3(2-); negatively charged

Sulfhydryl functional group properties

-SH; forms disulfide bonds

The four major classes of macromolecules and their monomers

Proteins (amino acids), Nucleic acids (nucleotides), Polysaccharides (sugars), Lipids (fatty acids, etc.)

Composition of E. coli by weight

Water 70%, Proteins 15%, RNA 6%, Polysaccharides 3%, Lipids 2%, DNA 1%

What are stereoisomers?

Molecules with the same bonds/formula but different spatial arrangement

What are geometric (cis-trans) isomers?

Stereoisomers arising from restricted rotation around double bonds

Example of cis-trans isomers with different biological roles

Maleic acid (cis) vs. fumaric acid (trans)

What are enantiomers?

Mirror-image stereoisomers arising from chiral centers

What defines a chiral center?

A carbon bonded to 4 different substituents

Do enantiomers have the same chemical properties?

Yes, but they can have different biological activity

Which enantiomer form do amino acids in proteins use?

L form only

Which enantiomer form does glucose use?

D form only

Why do biological molecules exist as only one stereoisomer?

The enzymes that synthesize them are themselves chiral and produce only one form

Aspartame stereochemistry example

L,L form is sweet; its stereoisomer is bitter

Citalopram stereochemistry example

(S)-Citalopram is active (antidepressant); (R)-Citalopram is inactive

What is molecular configuration?

Fixed spatial arrangement that requires breaking covalent bonds to change (e.g., L vs D amino acid)

What is molecular conformation?

Spatial arrangement from rotation around single bonds; interconverts rapidly without bond breaking

Open vs. closed vs. isolated system

Open exchanges matter and energy; closed exchanges energy only; isolated exchanges neither

What thermodynamic state do living organisms exist in?

Dynamic steady state (not equilibrium)

Gibbs free energy equation

ΔG = ΔH − TΔS

What does a negative ΔG mean?

Exergonic, spontaneous reaction

What does a positive ΔG mean?

Endergonic, non-spontaneous reaction (requires energy input)

What does ΔG = 0 mean?

The reaction is at equilibrium

Does ΔG tell you the rate of a reaction?

No, only whether it proceeds (thermodynamics, not kinetics)

Equation relating standard free energy to equilibrium constant

ΔG° = −RT ln Keq

Large Keq corresponds to what kind of ΔG°?

Large negative ΔG° (favors products)

What is the ΔG° of ATP hydrolysis?

−30.5 kJ/mol (approximately −50 kJ/mol under cellular conditions)

Why is ATP hydrolysis so exergonic in cells?

Cells maintain [ATP]/[ADP] far above equilibrium, creating disequilibrium

How does ATP power cellular reactions?

Couples exergonic to endergonic reactions via shared intermediates

Are free energy changes additive when reactions are coupled?

Yes, ΔG values sum when reactions are combined

By how much do enzymes increase reaction rates?

10^6 or more

Are enzymes consumed in reactions?

No

Do enzymes change the equilibrium of a reaction?

No, only the rate

How do enzymes speed up reactions?

Lower activation energy, stabilize transition state, provide stereospecific binding, orient reactants

What is catabolism?

Degradation of molecules that releases energy, generating ATP and NAD(P)H

What is anabolism?

Synthesis of complex molecules that requires energy, consuming ATP and NAD(P)H

What is feedback inhibition?

End product of a pathway inhibits an early enzyme in that pathway, shutting it down when the product accumulates

What are the base pairing rules in DNA?

A pairs with T; G pairs with C

What does DNA complementarity enable?

Replication and repair

Size of the E. coli genome

4.64 million base pairs (one circular chromosome)

Size of the human genome

~3 billion base pairs, ~20,000 genes

What is the central dogma of molecular biology?

DNA → RNA → Protein

What happens during transcription?

DNA sequence is copied into complementary mRNA (occurs in nucleus in eukaryotes)

What happens during translation?

mRNA sequence is converted into an amino acid sequence at ribosomes

What determines a protein's function?

Its 3D shape (native conformation)

"Nothing in biology makes sense except in the light of evolution" – who said this?

Theodosius Dobzhansky, 1973

What evidence supports common ancestry of all life?

Universal genetic code, universal use of ATP, conserved central metabolic pathways, shared gene sequences

What is the source of most mutations?

Rare errors during DNA replication

What role does gene duplication play in evolution?

Allows one copy to mutate freely and evolve new functions while the other retains the original function

What was the Miller-Urey experiment (1953)?

Simulated early atmosphere (NH3, CH4, H2O, H2) with electrical sparks; produced amino acids and organic compounds abiotically

What is the RNA World Hypothesis?

RNA came first in evolution because it can both store information and catalyze reactions (ribozymes)