Basic Biochemistry - Vocabulary Flashcards

States of Matter

  • Anything that occupies space and has mass.
  • States: Solid – definite volume and shape; Liquid – definite volume but shape determined by container; Gas – no definite shape or volume.

Elements and Compounds

  • Elements: fundamental substances that make up all matter (e.g., H, He, O, C).
  • Compound: substance composed of two or more elements joined by chemical bonds (e.g., Glucose C$6$H${12}$O$6$, Methane CH$4$, Carbon dioxide CO$_2$).
  • Distinction:
    • Elements
    • Compounds
    • Elements & Compounds as basic categories of matter

Major Elements of the Human Body

  • Major elements by approximate percentage:
    • Oxygen (O): ~65.0%
    • Carbon (C): ~18.5%
    • Hydrogen (H): ~9.5%
    • Nitrogen (N): ~3.2%
    • Calcium (Ca): ~1.5%
    • Phosphorus (P): ~1.0%
    • Potassium (K): ~0.4%
    • Sulfur (S): ~0.3%
    • Sodium (Na): ~0.2%
    • Chlorine (Cl): ~0.2%
    • Magnesium (Mg): ~0.1%
  • Trace elements include boron (B), chromium (Cr), cobalt (Co), copper (Cu), fluorine (F), iodine (I), iron (Fe), manganese (Mn), molybdenum (Mo), selenium (Se), silicon (Si), tin (Sn), vanadium (V), and zinc (Zn).
  • Note: Percentages reflect typical adult human body composition; values are approximate and vary by individual and measurement method.

Atomic Structure and Subatomic Particles

  • Atomic mass unit (amu): Located in the nucleus; protons have +1 amu; neutrons have ~1 amu; electrons have ~1/2000 amu.
  • Protons: positive charge, mass ~1 amu.
  • Neutrons: neutral, mass ~1 amu.
  • Electrons: negative charge, mass ~1/2000 amu; orbit nucleus in electron shells.
  • In neutral atoms: number of protons = number of electrons.

Isotopes

  • Isotopes: same number of protons and electrons but different number of neutrons.
  • Isotopes with more neutrons are heavier and often unstable/radioactive.
  • Some radioactive isotopes are used in medical imaging.

Energy Concepts

  • Forms of energy include:
    • Kinetic Energy (movement): KE=12mv2KE = \tfrac{1}{2} mv^2
    • Potential Energy (stored): energy due to position
    • Chemical Energy (stored in chemical bonds)
    • Thermal Energy (random motion of particles)
    • Mechanical Energy (motion of macroscopic objects)
    • Electrical Energy (movement of charges in a conductor)
    • Magnetic Energy, Sound Energy, Light Energy, Elastic Energy, Nuclear Energy, Gravitational Energy
  • Total energy in any process is conserved (Law of Conservation of Energy):
    • For a system: KE<em>i+PE</em>i+W<em>nc+OE</em>i=KE<em>f+PE</em>f+OEfKE<em>i + PE</em>i + W<em>{nc} + OE</em>i = KE<em>f + PE</em>f + OE_f
    • KE: kinetic energy; PE: potential energy; W
      wnc: work done by non-conservative forces; OE: other energy terms (as defined in the source).
  • Note: Energy can change form or transfer between systems, but the total remains constant.

The Periodic Table: Basics

  • Elements arranged by increasing atomic number Z (number of protons).
  • Key terms:
    • Atomic number (Z): number of protons (and electrons in neutral atoms).
    • Atomic symbol: one- to three-letter designation (e.g., H, He, C, Na).
    • Atomic mass/Atomic weight: average mass of all isotopes of an element.
    • Elements organized into groups (alkali metals, alkaline earth metals, transition metals, halogens, noble gases, lanthanides, actinides, etc.).
  • Note: The table in the transcript shows a broad snapshot including group classifications and sample entries (e.g., H, He, Li, Na, K, Mg, Ca, etc.).

Electron Orbitals and Shells

  • Electrons occupy orbitals arranged in shells around the nucleus.
  • First shell (1s) capacity: 2 electrons.
  • Second shell (2s, 2p) capacity: 8 electrons total (2 in 2s, 6 in 2p across three 2p orbitals).
  • Neon example: 2 electrons in first shell + 8 in second shell = 10 electrons (two shells filled).
  • Outer shell: valence shell. Full valence shells render atoms stable and unreactive; incomplete valence shells make atoms reactive and capable of forming bonds.

Electron Orbitals and Valence with Visual Models

  • Shell model (simplified for learning):
    • 1st shell: max 2 e⁻
    • 2nd shell: max 8 e⁻
  • Valence electrons determine bonding behavior and chemical reactivity.

Ions, Molecules, and Bonding

  • Ionic bonding: Electrostatic attraction between cations (+) and anions (−); in large groups, ions form crystalline salts.
  • Water can dissolve salts by dissociating ionic bonds and releasing charged particles (ions).
  • Anions: negatively charged ions (formed when atoms gain electrons).
  • Cations: positively charged ions (formed when atoms lose electrons).
  • Example: Sodium (Na) tends to donate an electron to chlorine (Cl) to form Na⁺ and Cl⁻, producing ionic bonds.

Ionic Bonds and Salts

  • Water as solvent of salts allows dissociation into ions.
  • Ions in solution participate in electrical signaling, osmosis, and other physiological processes.

Covalent Bonding and Molecules

  • Covalent bonds involve sharing electrons between atoms.
  • Types:
    • Single covalent bond: H–H
    • Double covalent bond: O=O
    • Triple covalent bond: N≡N
  • Non-polar covalent bonds: electrons shared equally (e.g., O–O in O₂).
  • Polar covalent bonds: electrons shared unequally, creating partial charges (e.g., H–O in H₂O).
  • Polar covalent bonds lead to molecular polarity and hydrogen bonding.

Hydrogen Bonds

  • Hydrogen bonds (H-bonds) form between a slightly positive hydrogen atom and an electronegative atom (e.g., O, N).
  • Example: Water molecules strongly hydrogen-bond with each other, producing cohesion, surface tension, and high boiling point.
  • Hydrogen bonds contribute to properties like water surface tension and the ability of certain structures to float or stay intact in aqueous environments.

Water: Properties and Roles in Biology

  • Water as universal solvent; participates as reactant/product; critical in transport and temperature regulation.
  • Roles in the body:
    • Lubrication of joints
    • Lung fluids aid respiration
    • Digestion and cardiovascular transit
    • Temperature regulation via heat absorption/release
    • CSF cushions brain and protects against injury
  • Water participates in many reactions (e.g., hydrolysis and dehydration synthesis).

Water-Based Solutions: Types of Mixtures

  • Solution: homogeneous and clear (e.g., seawater, seawater).
  • Colloid: homogeneous but scatters light; particles do not settle (e.g., milk, jelly).
  • Suspension: heterogeneous with suspended particles that settle (e.g., mud, blood).

Acids, Bases, and pH

  • Acid: substance that releases H⁺ in solution.
  • Base: substance that releases OH⁻ or accepts H⁺ in solution.
  • pH: measure of relative acidity/alkalinity; pH = $-\log_{10}([H^+])$.
  • Pure water: pH ≈ 7.
  • Strong acids like HCl can have pH ≈ 0; 0 is 10⁷ times more acidic than pH 7.
  • Buffers: solutions of weak acids and their conjugate bases that neutralize added acids/bases, helping maintain stable pH.
  • Example buffer system: H₂O + CO₂ ⇌ H₂CO₃ ⇌ H⁺ + HCO₃⁻ (carbonic acid-bicarbonate buffer system in blood).

Functional Groups and Carbon Chemistry

  • Key functional groups in organic molecules:
    • Hydroxyl: –OH
    • Carboxyl: –COOH
    • Amino: –NH₂
    • Methyl: –CH₃
    • Phosphate: –PO₄^{2-}
  • Carbon-based chemistry forms the backbone of organic compounds; carbon can form diverse bonding patterns with H, O, N, and other elements.

Carbohydrates: Structure and Storage

  • Basic units: monosaccharides (e.g., glucose, fructose, galactose).
  • Hexoses: glucose, fructose, galactose (C₆H₁₂O₆ family).
  • Pentoses: ribose, deoxyribose.
  • Disaccharides: sucrose (glucose + fructose), lactose (galactose + glucose), maltose (glucose + glucose).
  • Polysaccharides: glycogen (animal storage of glucose); structural polysaccharides like cellulose (not discussed in depth here) play roles in support and energy storage.
  • Functions: energy source and storage; components of ATP, RNA, DNA, glycoproteins, and glycolipids.

Lipids: Structure and Types

  • General class: hydrophobic or amphipathic molecules; include triglycerides, phospholipids, sterols, and glycolipids.
  • Triglycerides (neutral fats): glycerol backbone with three fatty acid chains attached via dehydration synthesis; a major energy reserve.
    • Saturated fatty acids: no double bonds; typically solid at room temperature.
    • Unsaturated fatty acids: one or more cis double bonds; typically liquid at room temperature.
  • Phospholipids: polar head (hydrophilic) and non-polar tail (hydrophobic); major component of cell membranes.
  • Steroids (sterols): four-ring hydrocarbon structure; include cholesterol and steroid hormones; roles in membranes and signaling.
  • Prostaglandins: lipid-derived signaling molecules; regulate blood pressure and pain sensation among other functions.

Proteins: Building Blocks and Structures

  • Building blocks: amino acids (20 standard types) with a common structure and variable R group (side chain).
  • Peptide bonds: covalent bonds linking amino acids via dehydration synthesis.
  • Protein structure levels:
    • Primary: amino acid sequence.
    • Secondary: local folding patterns such as alpha-helix and beta-pleated sheets.
    • Tertiary: three-dimensional folding of a single polypeptide.
    • Quaternary: assembly of multiple polypeptide chains.
  • Globular vs. fibrous proteins: functional vs structural roles.
  • If the order of amino acids in the primary structure changes, it can alter folding and function drastically (structure determines function).

Enzymes

  • Enzymes catalyze chemical reactions and increase reaction rates by lowering activation energy.
  • The reaction can proceed with or without the enzyme, but the enzyme provides an alternative pathway with a lower activation energy.
  • Enzymes are typically not consumed in the reaction (they are catalysts).

Nucleic Acids: Nucleotides, DNA, RNA, and ATP

  • Nucleotides: basic units containing a pentose sugar, a phosphate group, and a nitrogenous base (Purines: Adenine A, Guanine G; Pyrimidines: Cytosine C, Thymine T, Uracil U).
  • DNA (Deoxyribonucleic Acid): nucleotide storage of genetic information; double-stranded helix; base pairing: A with T (two hydrogen bonds) and C with G (three hydrogen bonds).
  • RNA (Ribonucleic Acid): ribose-containing nucleotide; usually single-stranded; base pairing: A with U; C with G.
  • ATP (Adenosine Triphosphate): adenine nucleotide with ribose and three phosphate groups; functions as the primary energy currency of the cell; energy is released when terminal phosphate is removed.
  • Nucleotides serve as monomers for nucleic acids and as energy carriers (ATP) and signaling molecules.

Summary of Core Concepts and Connections

  • Matter and energy: matter exists in states; energy transforms but total energy is conserved.
  • Atoms, isotopes, and bonding: protons/electrons determine charge; neutrons alter mass; bonding governs molecular structure and reactivity (ionic, covalent, polar/nonpolar, hydrogen bonds).
  • Water and pH: water enables biochemistry and buffering maintains homeostasis; pH is a log-scale measure of H⁺; buffers mitigate pH changes.
  • Macromolecules and metabolism: carbohydrates, lipids, proteins, and nucleic acids form the basis of energy and genetic information; enzymes regulate metabolic pathways; ATP provides usable energy.
  • Real-world relevance: bond types and interactions underlie physiology (neural signaling via ions, muscle contraction, enzyme kinetics, pH balance, nutrient storage and mobilization).

Practice and Review Questions (Key Concepts to Recall)

  • What are the three states of matter and how are they defined?
  • List the four major elements in the human body and their approximate percentages.
  • How do kinetic and potential energy relate during a chemical reaction?
  • What is a valence shell and why are full valence shells stable?
  • Distinguish ionic and covalent bonds; give examples.
  • What is an exchange reaction? (identify factors that influence reaction rates.)
  • Name three important functions of water in the human body.
  • Differentiate hydrolysis and dehydration synthesis.
  • Is a substance with pH 4 stronger or weaker than pH 5? By how much?
  • What is a carboxyl group and where is it found?
  • Name three types of polysaccharides and their roles.
  • Are saturated fats solids or liquids at room temperature?
  • How many amino acids are found in the human body?
  • What are the two types of secondary structure in proteins?
  • What are the key differences between DNA and RNA?
  • What is the structure and function of ATP?