The Chemical Basis of Life I: Atoms, Molecules and Water
Biology for Science Majors I (BIOL 1306)
Instructor: Dr. Romina Dimarco
Subject: The Chemical Basis of Life I: Atoms, Molecules, and Water
In-class Activities (ALAs) & Attendance
Attendance Record
Only one per group
Student name: Write your first and last name exactly as it appears in Canvas
Clear handwriting is required
In-class Activities (ALAs)
Should be completed individually in Canvas
Discussion of answers with partner allowed
Must submit the activity before leaving class; cannot be completed outside class time
Attendance Issues for ALA #1
Some students completed the attendance sheet but did not submit the assignment on Canvas.
Others submitted the assignment but did not provide the attendance sheet.
If an assignment has not been graded, or you have a zero but can prove attendance and participation (by bringing the partner worked with), please consult with the instructor after class.
Recitations
Students are taking the Diagnostic Exam.
Two additional days added in CASA for this exam (September 4 is the last day).
Average score will be calculated after receiving all scores, and cutoff score will be communicated via email.
Detailed discussions regarding Recitations will occur Monday; Recitations to begin next week.
Homework Assignments
Start Date: Homework assignments for Week 2 commence this week
Assignments include:
One SmartBook assignment
One Homework assignment
Deadline: Due Sunday of the assigned week at 9:00 PM.
Example: For this week, due date is Sunday, September 7th at 9:00 PM.
Policy: No extensions on homework assignments as per the syllabus.
Chemistry and the Evolution of Life
Chemistry is inherently linked to the evolution of life.
Natural processes allow simple inorganic molecules (water, methane, ammonia, hydrogen) to react spontaneously, creating complex organic molecules (amino acids, nucleotides, lipids) that serve as the foundational building blocks of life.
Basic Atomic Structure
Atoms Composed of:
Protons: Positively charged particles
Neutrons: Neutral particles
Electrons: Negatively charged particles
Arrangement:
Protons and neutrons are found in the nucleus.
Electrons found in orbitals surrounding the nucleus.
Total protons = total electrons, ensuring the atom is electrically neutral.
A visual analogy: If an atom occupied the same volume as a stadium, the nucleus would size comparison equate to that of a pea.
Atomic Numbers and Isotopes
Mass Number: Total of protons + neutrons
Atomic Number: Characteristic number of protons in an atom’s nucleus, defining the element.
Isotopes: Variants of an element with differing neutron counts (e.g., ^{12}C and ^{14}C).
Atomic Mass Measurement: Expressed in Daltons.
Electron Arrangement Around Nucleus
Electrons circulate atomic nuclei in specific regions termed orbitals.
Each orbital accommodates up to two electrons.
Orbitals are organized into electron shells:
Electron shells are numbered (1, 2, 3, …) indicating distance from the nucleus; smaller numbers signify closeness.
Electron Fill Order
Each electron shell has a specific number of orbitals:
A shell having one orbital can accommodate two electrons, and four orbitals can hold up to eight electrons.
Electrons fill inner shells first before outer shells.
Examples of abundant elements found in organisms alongside their valence:
Hydrogen: Valence = 1
Carbon: Valence = 4
Oxygen: Valence = 2, etc.
Chemical Bonds
Basic Concepts
Chemical Bonds: Formed through unfilled electron orbitals allowing the combination of atoms.
Stability of Atoms: Atoms achieve stability by filling their electron orbitals
Types of Bonds
Covalent Bonds
Formed through shared unpaired valence electrons by connecting the nuclei of the bonded atoms, thus filling orbitals.
Ionic Bonds
Established when electrons transfer from one atom to another, resulting in oppositely charged ions that attract one another.
Covalent Bonds
Example: Hydrogen atoms with one unpaired electron form covalent bonds (e.g., H_2) by sharing two electrons.
Nonpolar Covalent Bond: Electrons shared equally between atoms, executing a symmetrical distribution.
Polar Covalent Bonds
In water (H₂O), electrons are shared unevenly due to electronegativity differences -- oxygen being more electronegative leads to partial charges:
Oxygen: Partial negative charge (δ–)
Hydrogen: Partial positive charge (δ+)
Ions and Ionic Bonds
Ion: Charged atom or molecule.
Cation: Positively charged ion (e.g., Na^+).
Anion: Negatively charged ion (e.g., Cl^-).
Ionic Bonds: Attraction between oppositely charged ions that leads to a full valence shell.
The Electron-Sharing Continuum
Electrons can be shared in bonds on a continuum: ranging from nonpolar covalent (equal sharing) to polar covalent (unequal sharing) to ionic (complete transfer).
Chemical Reactions
Occur when substances combine, rearranging atoms within molecules, forming larger molecules or splitting compounds into smaller entities.
New bonds are created and existing bonds are broken in these processes.
Bond Formation and Capacity
The number of unpaired electrons determines bonding capability:
Atoms with multiple unpaired electrons can create various single, double, and even triple bonds (for instance, N_2 contains a triple bond).
Molecular Geometry and Representation
The geometry of bonds dictates molecular shape.
Molecular Formulas: Display the number and type of atoms within a molecule (e.g., H2O, CH4).
3-D Models: Ball-and-stick and space-filling models visualize molecular geometry.
Structural Formulas: Show bonding arrangements and the types of bonds present (single, double, or triple).
The Importance of Carbon
Carbon is notably versatile due to its four valence electrons, enabling the formation of various covalent bonds and creating diverse molecular shapes.
Significant in chemical evolution, it forms the backbone of organic molecules and various structures (e.g., C8H{18} - Octane, C6H{12}O_6 - Glucose).
Understanding Acids, Bases, and pH
pH Scale: Measures hydrogen ion concentration in solutions.
Pure water: pH 7 (neutral)
Acids: pH < 7 (higher H+ concentration)
Bases: pH > 7 (lower H+ concentration)
Buffers: Substances that minimize pH changes in a solution.
Functional Groups: Determinants of Chemical Behavior
Functional Groups such as amino, carboxyl, hydroxyl, carbonyl, phosphate, and sulfhydryl impact a molecule’s reactivity and interactions due to their specific properties.
Water: The Universal Solvent
Water constitutes approximately 75% of a typical cell and is fundamental for life processes due to its role as an excellent solvent.
Properties of Water and Hydrogen Bonds
Water’s polar covalent nature leads to the formation of hydrogen bonds, resulting in numerous unique properties:
Cohesion, adhesion, less density as a solid than in liquid form, and strong heat absorption capacity.
Cohesion: Likes bind together leading to high surface tension.
Adhesion: Differs with binding to unlike molecules.
Dissociation of Water and Acid-Base Reactions
Water frequently dissociates into hydrogen ions (H+) and hydroxide ions (OH-), causing it to act as both a weak acid and a weak base.
Study Guide Questions – Chapter 2
What are the three subatomic particles of an atom, and where are they located?
How do atomic number and mass number differ?
What is the difference between covalent and ionic bonds?
What determines whether a covalent bond is polar or nonpolar?
What is a hydrogen bond, and why is it weaker than covalent bonds?
Why is water considered the "solvent of life"?
What properties of water result from hydrogen bonding (e.g., cohesion, adhesion, surface tension, high heat capacity)?
What is an acid? What is a base?
What is the pH scale, and what does each unit represent?
Which four elements make up most of living matter, and why are they so abundant?