Chemical Reactions and Properties of Water

Chemical Reactions and Energy

• Chemical reactions, like Cl2 + H2 -> 2HCl, proceed from higher to lower energy states, similar to Val the waitress transferring from a busy to a less demanding job. Electrons seek stability, driving the reaction.

• Energetic differences between broken and formed bonds are channeled rather than lost, essential for biological pathways requiring precise molecular positioning in cells, such as specific organelles/compartments and timing tied to energy availability (ATP).

• Methane (CH4 + 2O2 -> CO2 + 2H2O) combustion requires activation energy (spark) due to its high combustion temperature compared to ambient conditions.

Water's Properties

• Water's polarity and cohesiveness permit attraction to other molecules, aiding in bodily functions.

• Water's high heat capacity (melting/boiling points) helps regulate internal temperature for living organisms.

• Water's effective solvent properties enable dissolving various substances, facilitating nutrient uptake.

Molecular Assembly and Energy Flow

• Larger molecules formation from smaller molecules is energetically favorable, with energy flow from higher to lower energy.

Cellular Macromolecules

• Alpha-D-glucose contributes to carbohydrates/polysaccharides.

• Glycosidic bonds link carbohydrate units to form macromolecules.

• Cellulose (polysaccharide) provides structural support and energy storage.

• DNA (nucleic acid) stores genetic information.

• Triglyceride (lipid) acts as energy storage and membrane component.

• Hemoglobin (protein) serves as a transporter.

• Glycogen (polysaccharide) acts as a storage form of carbohydrate.

Starch vs. Cellulose Digestion

• Starch contains digestible alpha-glycosidic bonds, while cellulose contains indigestible beta-glycosidic bonds.

• Humans lack the cellulase enzyme required for cellulose digestion.

Fats and Structure

• Saturated fats (e.g., butter) are solid because their straight chains allow close packing.

• Unsaturated fats (e.g., olive oil) are liquid because their bent structures prevent close packing.

Amino Acids and Bonds

• Amino acids are linked by peptide bonds to form polypeptide chains.

• Polypeptide chains fold into functional proteins.

Amino Acid Abbreviations

• Glycine (Gly, G)
• Alanine (Ala, A)
• Valine (Val, V)
• Leucine (Leu, L)
• Isoleucine (Ile, I)
• Methionine (Met, M)
• Phenylalanine (Phe, F)
• Tryptophan (Trp, W)
• Proline (Pro, P)
• Serine (Ser, S)
• Threonine (Thr, T)
• Cysteine (Cys, C)
• Tyrosine (Tyr, Y)
• Asparagine (Asn, N)
• Glutamine (Gln, Q)
• Aspartate (Asp, D)
• Glutamate (Glu, E)
• Lysine (Lys, K)
• Arginine (Arg, R)
• Histidine (His, H)

Protein Structure Models

• Atomic-bond model: Shows covalent bonds.

• Space-filling model: Demonstrates relative atomic sizes, allows viewing of interactions.

• Ribbon model: Highlights protein secondary structures (alpha-helices and beta-sheets), useful for comparisons and evolutionary analysis.

Nucleic Acid Bases

• Adenine (Purine) pairs with Thymine (Pyrimidine) in DNA.

• Guanine (Purine) pairs with Cytosine (Pyrimidine) in DNA and RNA.

• Uracil (Pyrimidine) pairs with Adenine in RNA.

ATP and Deoxynucleotides

• ATP is a ribonucleotide.
• DNA polymerase uses deoxynucleotide triphosphates for energy.

Chromatin Structure

• Chromatin is composed of DNA and proteins (histones).

• Chromatin functions in packaging DNA and regulating transcription.

• Nucleosomes are the structural units of chromatin comprised of histone proteins.

DNA Replication

• DNA replication is semi-conservative, each new double helix contains one original and one new strand.

Origins of Replication and A-T Rich Regions

• Origins of replication often occur in A-T rich regions due to the weaker double bonds between A and T.

DNA Replication: Leading vs. Lagging Strands

• DNA polymerase III adds nucleotides to the 3' end, leading strand replicates continuously; lagging strand replicates in Okazaki fragments.

Okazaki Fragments and DNA Ligase

• DNA ligase joins Okazaki fragments into a continuous lagging strand.

PCR

• PCR uses DNA's denaturation and annealing properties for amplification.

• Taq polymerase is used for its heat stability in PCR.

Central Dogma: Processes in Image

Mitosis, transcription, translation, locations of ribosomes, DNA polymerase, disulfide bond formation, RNA polymerase, Okazaki fragments, polypeptide chain formation, primary transcript result.

RNA Types

• mRNA: Carries genetic code from DNA to ribosomes.

• tRNA: Carries amino acids to ribosome during translation.

• rRNA: Structural component of ribosomes.

Transcription

• Transcription factors initiate transcription.
• Base pair sequences are crucial.
• RNA polymerase II produces RNA.

Coding Vs. Template Strands

• RNA polymerase uses the template strand.
• We report the coding strand because it has the same sequence as the mRNA transcript.

Wobble Hypothesis

• Wobble allows for flexibility in the 3rd base of a tRNA codon, reducing the number of tRNA types required.

mRNA Processing (Splicing)

• The process of removing introns and joining exons forms mature mRNA.

• The 5' cap and poly(A) tail protect and aid in mRNA function, not translation.

• Splicing occurs, followed by ribosomal activity.

Ribosomal Sites

• A site: Incoming aminoacyl-tRNA attaches.

• P site: Growing polypeptide chain binds.

• E site: Exit site for tRNA.

Smallest Cellular Component

• Protein.

Biological Molecules' Backbone

• Carbon.

Covalent Bonds of Carbon

• Carbon can form single, double, and triple covalent bonds.

Cell Membrane Importance

• Selectively permeable membranes provide a barrier between the inside and outside of a cell.

Amphipathic Molecules

• Amphipathic molecules have charged and uncharged regions.

Cellular Structural Hierarchy

• Organic Molecules → Macromolecules → Supramolecular structures → Organelles→ Cells

Water's Polarity

• Water's polarity stems from unequal electron sharing.

Selectively Permeable Membrane

• A selectively permeable membrane allows some molecules through, not others.

Non-Polymer Macromolecule

• Lipids.

Fatty Acid Structure and Function

• Fatty acids are long hydrocarbon chains with a carboxyl group.

• They serve as building blocks for other lipids.

Amino Acid Chemical Nature

• The amino acid's R group determines its chemical nature.

Cholesterol Function

• Cholesterol is a steroid component in eukaryotic membranes and a basis for hormones.

Trans Fats

• Trans fats are unsaturated fats mimicking saturated fats in shape and are associated with health risks.

DNA Information Flow

• Transcription occurs first, followed by translation.

DNA Polymerase Reaction Direction

• DNA polymerase reaction occurs in the 5' to 3' direction, adding to the 3' end.

Histone Modifications

• Histone modifications affect DNA packing and gene regulation.

PCR Enzyme Error

• Human DNA polymerase cannot function at high temperatures, failing the extension step of PCR.

Explore the fundamentals of chemical reactions and the unique properties of water that make it essential for life. Understand energy transitions during reactions and how water's characteristics contribute to biological functions. This quiz covers key concepts essential for biology and chemistry students.