ch 2
Atomic Structure
Basic Composition of Atoms
Composed of:
Protons
Neutrons
Electrons
Charge of Subatomic Particles
Protons: Positive charge
Neutrons: Neutral (no charge)
Electrons: Negative charge
Determining Atomic Numbers and Neutron Counts
Atomic Number
Defines the number of protons in an element.
Example: Cobalt has an atomic number of 27, indicating it has 27 protons.
Calculating Neutrons
Neutrons = Atomic Weight (mass number) - Atomic Number
The number of neutrons can be calculated by subtracting the atomic number from the atomic weight.
Elements and Their Common Forms
Common Elements in Biology
Carbon (C): Core element in organic chemistry, forms long chains and rings.
Hydrogen (H)
Oxygen (O)
Nitrogen (N)
Trace Elements: Sodium (Na), Potassium (K), and others.
Isotopes and Their Concepts
Definition of Isotope
Variants of the same element with different numbers of neutrons.
All isotopes have the same number of protons but differ in neutron count.
Examples of Carbon Isotopes
Carbon-12: 6 protons, 6 neutrons (most abundant form).
Carbon-13: 6 protons, 7 neutrons.
Carbon-14: 6 protons, 8 neutrons; this isotope is radioactive and decays over time.
Used in carbon dating to estimate the age of fossils.
Electron Configuration and Atomic Shells
Electron Arrangement
Electrons orbit around the nucleus in shells or orbitals.
The first shell can hold 2 electrons, subsequent shells can hold up to 8.
Electrons occupy shells sequentially: 2 in the first shell and 8 in the second.
Valence Electrons
Electrons in the outermost shell that determine reactivity and bonding behavior of elements.
Chemical Bonds
Elements seek to achieve full outer shells, typically 8 electrons.
Types of bonds:
Ionic Bonds: Transfer of electrons (e.g., sodium and chlorine form NaCl).
Covalent Bonds: Sharing of electrons remains between atoms (polar and nonpolar covalent bonds).
Electronegativity and Bonding Types
Electronegativity
Measure of an atom's ability to attract electrons.
Generally increases across a period in the periodic table (e.g., left to right).
High Electronegativity: Elements like fluorine tend to attract electrons strongly.
Bonding Types
Nonpolar Covalent Bond: Equal sharing of electrons (e.g., H₂, O₂).
Polar Covalent Bond: Unequal sharing of electrons (e.g., H₂O).
In water, oxygen is more electronegative than hydrogen, resulting in a partial negative charge on the oxygen and partial positive charges on the hydrogens.
Properties of Water and Its Importance
Water as a Universal Solvent
Water dissolves many substances due to its polar nature, creating hydrogen bonds with various ionic and polar compounds.
Unique Properties of Water
High surface tension due to hydrogen bonding (e.g., water strider bugs).
Retains heat well; takes considerable energy to change temperature significantly.
Exists as a liquid over a broad temperature range (0-100 °C).
Chemical Reactions
Types of Reactions
Synthesis Reaction: Combines two or more reactants to create a larger molecule (e.g., dehydration synthesis).
Hydrolysis Reaction: Breaks down a larger molecule into smaller units, requiring water (e.g., splitting starch).
Metabolism
Involves both catabolic (breaking down) and anabolic (building up) reactions.
Macromolecules in Biology
Four Major Types of Macromolecules
Lipids: Fat molecules, triglycerides (saturated and unsaturated), phospholipids, and steroids.
Carbohydrates: Sugars and starches, important for energy storage.
Proteins: Made from amino acids, crucial for structural and functional roles in cells.
Nucleic Acids: DNA and RNA, responsible for genetic information storage and transfer.
Acids, Bases, and pH Scale
Acidic vs. Basic
Acids release H⁺ ions in solution; bases release OH⁻ ions.
Water's pH is about 7, making it neutral.
pH Scale
Range from 0 (acidic) to 14 (basic); important in biological processes.
Ion concentration changes affect biological functions and enzyme activity.
Electrolytes
Importance of Electrolytes
Essential for various biochemical pathways; e.g., sodium and calcium are crucial for neuronal signaling and maintaining the electrolyte balance.
Example of Salts
Sodium chloride (NaCl): essential for cellular functions and hydration status.
Atomic Structure - Basic Composition of Atoms
Composed of:
Protons
Positively charged subatomic particles found in the nucleus.
The number of protons determines the identity of an element (atomic number).
Neutrons
Neutral particles that also reside in the nucleus.
Contribute to the atomic mass but not the charge.
Electrons
Negatively charged particles that orbit the nucleus in electron shells.
Participate in chemical bonding and reactions.
Charge of Subatomic Particles
Protons: Positive charge +1
Neutrons: Neutral (no charge)
Electrons: Negative charge -1
Determining Atomic Numbers and Neutron Counts
Atomic Number
Defines the number of protons in an element.
Example: Cobalt has an atomic number of 27, indicating it has 27 protons.
Calculating Neutrons
Neutrons = Atomic Weight (mass number) - Atomic Number
The number of neutrons can be calculated by subtracting the atomic number from the atomic weight.
For example, if Carbon has an atomic weight of 12, it has 6 neutrons (12 - 6 = 6).
Elements and Their Common Forms
Common Elements in Biology
Carbon (C): Core element in organic chemistry, forms long chains and rings, essential for life.
Hydrogen (H): The simplest and most abundant element; a key component of water and organic molecules.
Oxygen (O): Vital for cellular respiration and as a part of water.
Nitrogen (N): Crucial for the formation of amino acids and nucleic acids.
Trace Elements: Sodium (Na), Potassium (K), Calcium (Ca), and others play essential biological roles.
Isotopes and Their Concepts
Definition of Isotope
Variants of the same element with different numbers of neutrons, affecting atomic mass.
All isotopes have the same number of protons but differ in neutron count.
Examples of Carbon Isotopes
Carbon-12: 6 protons, 6 neutrons (most abundant form for life).
Carbon-13: 6 protons, 7 neutrons; stable isotope used in scientific studies.
Carbon-14: 6 protons, 8 neutrons; this isotope is radioactive, decays over time, and is used in carbon dating to estimate the age of organic materials.
Electron Configuration and Atomic Shells
Electron Arrangement
Electrons orbit around the nucleus in shells or orbitals with distinct energy levels.
The first shell can hold 2 electrons, subsequent shells can hold up to 8 electrons (octet rule).
Electrons occupy shells sequentially: 2 in the first shell and 8 in the second.
Valence Electrons
Electrons in the outermost shell that determine reactivity and bonding behavior of elements.
Elements strive to achieve full outer shells, typically 8 electrons, for stability.
Chemical Bonds
Types of bonds formed to achieve stable electron configurations:
Ionic Bonds: Transfer of electrons where one atom donates an electron to another (e.g., sodium and chlorine form NaCl).
Covalent Bonds: Sharing of electrons between atoms.
Can be polar (unequal sharing, e.g., in H₂O) or nonpolar (equal sharing, e.g., in O₂).
Electronegativity and Bonding Types
Electronegativity
Measure of an atom's ability to attract electrons in a chemical bond.
Generally increases across a period in the periodic table (e.g., from left to right).
High Electronegativity: Elements like fluorine (F) exhibit strong electron attraction capabilities.
Bonding Types
Nonpolar Covalent Bond: Equal sharing of electrons (e.g., H₂, O₂).
Polar Covalent Bond: Unequal sharing of electrons (e.g., H₂O).
In water, oxygen is more electronegative than hydrogen, leading to a partial negative charge on the oxygen and partial positive charges on the hydrogens.
Properties of Water and Its Importance
Water as a Universal Solvent
Water dissolves many substances due to its polar nature, facilitating biochemical reactions.
Forms hydrogen bonds with various ionic and polar compounds.
Unique Properties of Water
High surface tension due to hydrogen bonding allows objects, like water strider bugs, to walk on its surface.
Retains heat well; it requires considerable energy to change temperature significantly, which helps regulate climate.
Exists as a liquid over a broad temperature range (0-100 °C), crucial for life.
Chemical Reactions
Types of Reactions
Synthesis Reaction: Combines two or more reactants to create a larger molecule (e.g., dehydration synthesis occurs when forming complex carbohydrates from simple sugars).
Hydrolysis Reaction: Breaks down a larger molecule into smaller units with the addition of water (e.g., the split of starch into glucose units).
Metabolism
Involves both catabolic (breaking down nutrients) and anabolic (building up structures) reactions that sustain life.
Macromolecules in Biology
Four Major Types of Macromolecules
Lipids: Fat molecules (triglycerides - includes saturated and unsaturated fats), phospholipids, and steroids serve various functions including energy storage and making up cellular membranes.
Carbohydrates: Includes sugars and starches, significant for energy storage and quick energy release for cellular functions.
Proteins: Composed of amino acids, perform structural and functional roles, including enzymes that facilitate biochemical reactions.
Nucleic Acids: DNA and RNA, responsible for the storage and transfer of genetic information that dictates cellular functions.
Acids, Bases, and pH Scale
Acidic vs. Basic
Acids release H⁺ ions in solution; bases release OH⁻ ions, which can neutralize acids.
Water has a pH of about 7, making it neutral, the midpoint of the scale.
pH Scale
Ranges from 0 (strongly acidic) to 14 (strongly basic); significant in biological processes influencing enzyme activity and chemical reactions.
Changes in ion concentration can severely affect cellular processes.
Electrolytes
Importance of Electrolytes
Essential for various biochemical pathways; e.g., sodium (Na⁺) and calcium (Ca²⁺) are crucial for neuronal signaling and maintaining cell membrane potential.
Example of Salts
Sodium chloride (NaCl): An essential electrolyte for cellular functions and important for maintaining hydration and osmotic balance in the body.
1. Waxes
Definition: Waxes are hydrophobic substances that do not easily dissolve in water.
Examples of Waxes:
Ear Wax: Protective covering in human ears.
Beeswax: Produced by bees for various purposes including building honeycombs.
Mycobacterium: Some bacteria are covered in wax, aiding in preventing desiccation (drying out).
Desiccation: The process of dehydration or removal of moisture from an object.
Example: During drought conditions, bacteria with a protective waxy coating can survive longer due to moisture retention.
2. Steroids
Definition: Steroids are a type of hormone characterized by a specific four-ring structure made primarily of carbon atoms.
Example Steroids:
Testosterone and Androgens: Examples of steroid hormones related to muscle development and growth.
Cholesterol: A common and important steroid in biological systems.
Structure of Cholesterol: Typically exhibits a four carbon ring structure, with variations in carbon atoms.
Role of Cholesterol:
Stabilizes plasma membranes by fitting between phospholipids, reducing their movement and enhancing membrane integrity.
Two common forms of steroid structural organization:
Six carbon rings.
Five carbon rings.
R groups and chains can be added to produce various hormones (e.g., testosterone, estrogen).
3. Adenosine Triphosphate (ATP)
Definition: ATP is the primary energy carrier in cells.
Importance:
Supplies energy for biochemical reactions including muscle contraction and cellular processes.
Formed from glucose, the preferred carbohydrate source, which can be derived from various starches and sugars.
Related Concepts:
Glycoproteins: Proteins with sugar molecules attached that act as receptors on cell surfaces, turning cellular processes on and off.
Carbohydrate Structure:
General formula: (CnH{2n}O_n)
Where n refers to the number of carbon atoms and suggests that for carbohydrates, the amount of hydrogen is typically double that of carbon, and the amount of oxygen is equal to the number of carbons.
Importance of Carbohydrates:
Serve as energy sources, structural components in cell walls, and participate in intercellular communication.
4. Proteins
Backbone Structure: The basic structure of proteins is referred to as an NCC backbone, indicating the arrangement of nitrogen, carbon, and another carbon atom.
Functions of Proteins:
Building block of muscle.
Stabilize phospholipid bilayers when incorporated into membranes.
Enzymatic functions:
All enzymes are proteins, but not all proteins are enzymes; some proteins serve other functions such as signaling or structural roles.
Chemical Process of Synthesis:
Dehydration Synthesis: The formation of a peptide bond between amino acids by the removal of water.
The bonding process involves the terminal carbon and nitrogen atoms of adjacent amino acids.
Thus, the fundamental structure is a linear chain of amino acids (the primary structure).
Higher Order Protein Structures:
Primary Structure: Sequence of amino acids.
Secondary Structure: Formation of local structures such as alpha helices or beta sheets, stabilized by hydrogen bonds.
Example:
Alpha Helix: Resembles a spiral staircase.
Beta Sheet: Resembles crinkled paper.
Tertiary Structure: Further protein folding resulting in a greater degree of molecular complexity; stability can also include covalent bonding such as disulfide bridges (between cysteine residues).
Quaternary Structure: Multiple protein subunits coming together to form a functional protein.
5. Nucleic Acids
Nucleotide: The monomer of nucleic acids, consisting of a sugar, phosphate group, and nitrogenous base.
Composition: Phosphates are added to the five-prime carbon of the sugar, while nitrogenous bases attach to the one-prime carbon.
Types of Bases:
Purines: Adenine and Guanine.
Pyrimidines: Cytosine, Thymine, and Uracil.
Structure:
DNA is antiparallel, meaning one strand runs in a 5'-3' direction while the complementary strand runs in a 3'-5' direction.
Hydrogen Bonds: Stabilize the DNA helix; between complementary nucleotide pairs A-T (2 hydrogen bonds) and G-C (3 hydrogen bonds).
Adenosine Triphosphate (ATP)
General Information
ATP is the primary energy currency in biological systems, essential for cellular processes.
Cellular activities requiring energy, such as lifting and movement, rely on ATP.
ATP is primarily derived from glucose, a type of carbohydrate.
Carbohydrates
Functions of Carbohydrates
Carbohydrates play several roles in biological systems, including:
Energy storage and supply
Structural components of cell walls
Components of glycoproteins (proteins with carbohydrates attached that act as receptors).
Recognizing Carbohydrates
Typically, carbohydrates follow the empirical formula of CnH{2n}O_n.
Where:
C = number of Carbon atoms
H = number of Hydrogen atoms (twice that of Carbon)
O = Oxygen atoms (equal to the number of Carbon)
Examples of carbohydrates include glucose and lactose.
Proteins
Protein Structure
Proteins have a classic backbone described as NCC (N, C, C).
Functions of proteins include:
Building muscle
Stabilizing the phospholipid bilayer
Serving as enzymes and receptors
Enzymatic Activity
All enzymes are proteins, but not all proteins serve as enzymes.
Enzymes function by lowering the activation energy of reactions, thereby allowing reactions to occur more quickly.
Peptide Bonds
Peptide bonds are formed between amino acids via dehydration synthesis, resulting in the loss of a water molecule.
This bond formation occurs specifically between the terminal carbon of one amino acid and the nitrogen of the next amino acid.
Structural Levels of Proteins
Primary Structure
The linear sequence of amino acids forms the primary structure of a protein.
It is not functional at this stage.
Secondary Structure
Proteins can fold into specific shapes, such as:
Alpha helices, resembling a spiral staircase
Beta sheets, comparable to a crinkled piece of paper
This folding is stabilized by hydrogen bonds.
The protein remains non-functional at this level.
Tertiary Structure
Involves further folding and bonding (including hydrogen and disulfide bonds).
At this stage, the protein may achieve functionality.
Quaternary Structure
Some proteins comprise multiple polypeptide chains, known as quaternary structure.
This structure allows for more complex functions.
Nucleotides
Structure of Nucleotides
Nucleotides serve as monomers for nucleic acids (DNA and RNA).
A nucleotide contains:
A phosphate group
A five-carbon sugar (ribose or deoxyribose)
A nitrogenous base (purines or pyrimidines)
Families of Bases
Two main families of nitrogenous bases:
Purines: Adenine (A), Guanine (G)
Pyrimidines: Cytosine (C), Thymine (T) (in DNA), and Uracil (U) (in RNA)
Complementary base pairing occurs, with A pairing with T (or U) and G pairing with C.