Unit 1: Biochemistry Flashcards

Elements of Life

• Six main elements compose all living organisms:

  • S - Sulfur

  • P - Phosphorus

  • O - Oxygen

  • N - Nitrogen

  • C - Carbon

  • H - Hydrogen

Organic Chemistry and Carbon

• Organic Chemistry: The chemistry of carbon compounds.

• Atomic Structure and Bonding Capacity:

  • Carbon (atomic number 6) has four valence electrons in its outer shell.

  • Having four valence electrons allows carbon to bind with four atoms simultaneously, forming diverse, stable, and complex molecular structures.

Biological Organization and Macromolecules

• Four Main Classes of Biological Macromolecules:

  • Carbohydrates

  • Lipids

  • Nucleic Acids

  • Proteins

• Four Levels of Biological Organization:

  • Level 1: Monomers: Basic chemical building blocks, such as nucleotides, amino acids, and simple sugars (monosaccharides).

  • Level 2: Macromolecules: Polymeric chains created from connected monomers, including DNA, proteins, and cellulose.

  • Level 3: Supramolecular Complexes: High-order molecular assemblies, such as chromosomes, plasma membranes, and cell walls.

  • Level 4: The Cell and Its Organelles: Complete functional units containing membrane-bound organelles.

Questions & Discussion

• Question: Why do we study macromolecules?

  • Answer: Macromolecules are studied because they are essential components of a cell, forming its cellular structure and driving its biochemical processes.

Macromolecule Sizes and Polymerization

• Monomers: Single, individual repeating units of macromolecules.

• Polymers: Groups of monomers connected together into larger molecular structures.

• Polymerization: The chemical process of forming polymers from individual monomer units.

Macromolecules Metabolism: Anabolism and Catabolism

• Dehydration Synthesis (Anabolism):

  • Monomers are joined together to form polymers.

  • Occurs when a catalyst removes water ($H_2O$) by extracting a hydroxyl group ($-OH$) from one monomer and a hydrogen atom ($-H$) from another, creating a new covalent bond between the units.

• Hydrolysis (Catabolism / Digestion):

  • Water acts like a catalyst to break the bonds between two subunits of a macromolecule.

  • Cleaves polymers back into individual monomer components by reinserting water components ($-OH$ and $-H$).

Carbohydrates

• Monomer: Monosaccharides (simple single-ring sugars).

  • Monosaccharide Examples: Glucose, Fructose, and Galactose.

• Polymer: Polysaccharide.

  • Polysaccharide Examples: Cellulose and Starch.

• Elemental Composition: Carbon, Hydrogen, and Oxygen.

  • Elemental Ratio: Strictly $1 : 2 : 1$ ($C : H : O$).

• General Structure: Ring structures.

• Primary Function: Main source of rapid energy for biological activity.

Lipids

• Monomer Building Blocks: Glycerol and Fatty acids.

• Elemental Composition: Carbon, Hydrogen, and Oxygen.

  • Elemental Ratio: Not in a fixed $1 : 2 : 1$ ratio (contains far less oxygen relative to carbon and hydrogen).

• General Structure: Long hydrocarbon chains.

• Primary Function: Long-term energy storage, insulation, and membrane components.

• Types of Fatty Acids:

  • Saturated Fatty Acids:

  • Made up entirely of single carbon-carbon ($C-C$) bonds.

  • Allows the straight fatty acid tails to stack compactly on top of each other, making them solid at room temperature.

  • Derived from animal sources.

  • Considered nutritionally bad.

  • Unsaturated Fatty Acids:

  • Contains at least one double carbon-carbon ($C=C$) bond.

  • The double bond introduces a physical bend in the fatty acid tail, preventing stacking and keeping them liquid at room temperature.

  • Derived from plant sources.

  • Considered nutritionally good.

Proteins

• Monomer: Amino Acid.

• Elemental Composition: Carbon, Hydrogen, Oxygen, and Nitrogen.

  • Elemental Ratio: Not in a fixed ratio.

• General Structure of an Amino Acid:

  • Centered around a central carbon atom connected to:

  • Amine Group ($-NH_2$)

  • Carboxyl Group ($-COOH$)

  • Spare Group / Variable Side Chain (R-Group): Varies among different amino acids.

  • Examples of Amino Acids:

  • Alanine: R-group is a methyl group ($-CH_3$).

  • Serine: R-group is a hydroxymethyl group ($-CH_2OH$).

• Functions and Examples:

  • Transports substances in and out of cells.

  • Fights diseases (e.g., antibodies).

  • Produces enzymes that catalyze cellular reactions.

  • Forms structural components like muscles and bones.

Nucleic Acids

• Monomer: Nucleotide.

• Examples: RNA and DNA.

• Elemental Composition: Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus.

  • Elemental Ratio: Not in a fixed ratio.

• Primary Function: Stores and transmits genetic information.

• Three-Part Structure of a Nucleotide:

  • 5-Carbon Sugar (Pentose sugar)

  • Phosphate Group

  • Nitrogenous Base

Nucleic Acid Base Pairing and Structural Bonding

• Hydrogen Bonds Between Nucleotides: Hydrogen bonds form between complementary nitrogenous bases on opposite strands of DNA.

• Base Pairing Bonding Strengths:

  • Cytosine ($C$) and Guanine ($G$): Form a triple bond.

  • Adenine ($A$) and Thymine ($T$): Form a double bond.

• Backbone: The phosphate group forms the continuous structural backbone of DNA.

Macromolecule Elements Summary

• Carbohydrates: CHO (Carbon, Hydrogen, Oxygen in $1 : 2 : 1$ ratio).

• Lipids: CHO (Carbon, Hydrogen, Oxygen without a fixed ratio).

• Proteins: CHON (Carbon, Hydrogen, Oxygen, Nitrogen).

• Nucleic Acids: CHONP (Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus).