Biochemistry and Molecular Biology Review

Test Preparation Overview

• To effectively prepare for the test, focus on the objectives and key topics outlined in the material.

I. Biochemistry

• Anatomy of the Atom

  • Basic unit of matter, consists of protons, neutrons, and electrons.

• Subatomic Particles

  • Protons: positively charged, in nucleus.

  • Neutrons: neutral, in nucleus.

  • Electrons: negatively charged, orbit nucleus.

• Isotopes

  • Atoms of the same element with different neutron counts.

    Ions: Atoms that have gained or lost electrons, resulting in a net charge.

• Atom Characteristics

  • Valence Electrons: Electrons in the outermost shell, determine bonding.

  • Elements categorized as Metal, Non-Metal, Metalloid.

• Molecule: A group of atoms bonded together.

• Compound: A molecule comprised of different elements.

• Organic: Molecules containing carbon, typically associated with living organisms.

• Scientific Method

  • Inductive Reasoning: Specific observations to broader generalizations.

  • Deductive Reasoning: Applying general principles to specific cases.

  • Independent Variable: The variable that is changed.

  • Dependent Variable: The variable that is measured.

II. Periodic Table

• Reading the Periodic Table

  • Understand elements, atomic number, atomic mass, and symbol.

• Trends in the Periodic Table

  • Learn about atomic size, ionization energy, and electronegativity.

• Charge is an important concept that refers to the electrical property of atoms and ions, which affects their interactions and bonding behavior. This understanding is essential for predicting how different elements will combine to form compounds, as well as their reactivity in biological systems.

• Determine the charge of an atom when it ionizes based on electron transfer.

III. Mass and Weight

• Mass: Measure of the amount of matter.

• Weight: Gravitational force acting on mass.

IV. Isotopes Naming and Calculating

I. Isotopes
A. Common Isotopes
1. Carbon-12 (C-12)
2. Carbon-14 (C-14)
B. Naming Isotopes
1. Based on mass number
- Example: Carbon-14 (C-14)
C. Calculating Isotopic Abundance and Averages
1. Use relative abundances of isotopes
2. Apply mass numbers for calculation

V. Electron Orbital Properties

• Learn to name isotopes based on mass number (e.g., Carbon-14).

• Calculate isotopic abundance and averages.

V. Electron Orbital Properties

• Electron Configuration: Distribution of electrons in an atom's orbitals.

• Octet Rule: Atoms tend to bond in such a way that they have eight electrons in their valence shell.

VI. Bonding

• Types of Bonds:

  • Non-polar Covalent: Equal sharing of electrons between atoms.

  • Polar Covalent: Unequal sharing of electrons, creating partial charges.

  • Ionic Bonds: Transfer of electrons from one atom to another, leading to positive and negative ions.

• Examples include metal with non-metal and non-metal with non-metal bonding.

VII. Properties of Water

• Water's unique properties, including cohesion, adhesion, high specific heat, and solvent capabilities, essential for life.

VIII. States of Matter

• Solid, Liquid, Gas: Properties and behaviors of different states.

• Mixtures: Composed of two or more substances that retain their individual characteristics.

IX. pH Scale

• Measure of hydrogen ion concentration, indicating acidity or alkalinity.

• Dehydration Synthesis and Hydrolysis

  • Dehydration Synthesis: Joining molecules by removing water.

  • Hydrolysis: Breaking down compounds by adding water.

X. Anatomy of Biomolecules

• Carbohydrates:

  • General characteristics, structures (monosaccharides, disaccharides, polysaccharides), sources in the body.

• Proteins:

  • Structure identification, general characteristics, body roles.

• Nucleic Acids:

  • Structure of DNA and RNA, functions in heredity and protein synthesis.

• ATP: Energy currency of the cell, composed of adenine, ribose, and phosphate groups.

XI. Cellular Biology

• Anatomy of Lipids: Structure and functions in membranes and energy storage.

• Metabolism:

  • Catabolism: Breakdown processes.

  • Anabolism: Building processes.

I. Prokaryotic Cells
A. Characteristics
1. Smaller and simpler in structure
2. Lack a defined nucleus
3. Genetic material in a single circular chromosome
4. Usually unicellular
5. Reproduce asexually through binary fission

II. Eukaryotic Cells
A. Characteristics
1. Larger and more complex in structure
2. Contain a defined nucleus
3. Genetic material in multiple linear chromosomes with histone proteins
4. Can be unicellular or multicellular
5. Reproduce both asexually and sexually

III. Key Differences
A. Nucleus
- Prokaryotic cells: lack a true nucleus
- Eukaryotic cells: have a well-defined nucleus
B. Organelles
- Prokaryotic cells: lack membrane-bound organelles
- Eukaryotic cells: contain various membrane-bound organelles (e.g., mitochondria, endoplasmic reticulum)
C. DNA Structure
- Prokaryotic cells: circular DNA
- Eukaryotic cells: linear DNA
D. Cell Size
- Prokaryotic cells: generally smaller
- Eukaryotic cells: generally larger
E. Reproduction
- Prokaryotic cells: asexual reproduction (binary fission)
- Eukaryotic cells: both asexual and sexual reproduction

XII. Scientific Data Types

• Quantitative Data: Numerical data that can be measured.

• Qualitative Data: Descriptive data that can be observed but not measured.

XIII. Exponents and Scientific Notation

• Understand how to manipulate bases and calculate using scientific notation.

XIV. Cell Biology

Functions of various cell components include:

• Nucleus: Acts as the control center of the cell, containing genetic material (DNA) and regulating gene expression.

• Mitochondria: Known as the powerhouse of the cell, they produce energy (ATP) through cellular respiration.

• Ribosomes: Sites of protein synthesis, translating messenger RNA (mRNA) into proteins.

• Endoplasmic Reticulum (ER):

  • Rough ER: Studded with ribosomes, involved in protein synthesis and processing.

  • Smooth ER: Lacks ribosomes, involved in lipid synthesis and detoxification.

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

• Lysosomes: Contain digestive enzymes for breaking down waste materials and cellular debris.

• Peroxisomes: Enzymes that detoxify harmful substances and metabolize fatty acids.

• Cell Membrane: Composed of phospholipids and proteins; regulates what enters and exits the cell, maintaining homeostasis.

• Cell Theory: Fundamental concepts about the characteristics of cells.

• Cell Membrane Anatomy and Function:

  • Composed of phospholipids, proteins, carbohydrates, cholesterol.

  • Functions involve concentration gradients, passive and active transport mechanisms.

XV. Transport Mechanisms

• Passive Transport:

  • Diffusion: Movement from high to low concentration.

  • Osmosis: Special case of diffusion involving water.

• Active Transport: Requires energy to move substances against concentration gradients (e.g., ion pumps).

Endocytosis and exocytosis are essential cellular processes that facilitate the transport of large molecules and particles across the plasma membrane, which is crucial for maintaining cellular homeostasis and facilitating communication between cells.

• Endocytosis: This is the process by which cells internalize substances from their external environment. It involves the invagination of the cell membrane to form a pocket that engulfs extracellular material. This pocket eventually pinches off to form a vesicle containing the ingested material.

  • Types of Endocytosis:

  • Phagocytosis: Often referred to as 'cell eating,' this mechanism is primarily used by immune cells to engulf large particles such as pathogens or dead cells. The vesicle formed is called a phagosome.

  • Pinocytosis: Known as 'cell drinking,' pinocytosis involves the uptake of small droplets of extracellular fluid along with dissolved solutes. The vesicles formed are smaller than those in phagocytosis.

  • Receptor-Mediated Endocytosis: This specific form of endocytosis involves receptors on the cell surface binding to specific ligands, followed by engulfment and internalization. This process ensures that cells efficiently internalize biomolecules like hormones or nutrients that bind to these receptors.

• Exocytosis: This process is the opposite of endocytosis. It involves the fusion of vesicles containing intracellular substances with the plasma membrane, resulting in the release of their contents into the extracellular space. Exocytosis is crucial for the secretion of hormones, neurotransmitters, and enzymes.

  • Stages of Exocytosis:

  • Vesicle Transport: Membrane-bound vesicles transport materials from the Golgi apparatus to the plasma membrane.

  • Vesicle Fusion: The vesicle fuses with the cell membrane, which requires the presence of specific proteins known as SNAREs that facilitate the fusion process.

  • Release of Contents: Upon fusion, the vesicle opens, and its contents are released into the extracellular environment.

  • Significance: Exocytosis not only allows for the secretion of molecules but also plays a role in adding components to the cell membrane, which is vital for growth and repair.

Understanding the mechanisms of endocytosis and exocytosis is critical for comprehending how cells interact with their environment and maintain homeostasis, as well as their implications in processes like immune responses, nutrient uptake, and neurotransmission.

XVI. Molecular Biology

I. Central Dogma
A. Definition: Flow of genetic information from DNA to RNA to Protein

II. DNA Structure
A. Shape: Double helix
B. Components:
1. Nucleotides
2. Bases:
- Adenine (A) pairs with Thymine (T)
- Guanine (G) pairs with Cytosine (C)

III. RNA Structure
A. Shape: Single strand
B. Components:
1. Nucleotides
2. Bases:
- Uracil (U) replaces Thymine (T)

IV. Protein Synthesis
A. Steps involved:
1. Transcription ( translation produces proteins
a. From DNA to RNA
2. Translation
a. From RNA to Protein

Transcription:

• Purpose: To create RNA copies of genes from DNA. 

• Where it happens: In the nucleus of eukaryotic cells, and in the cytoplasm of prokaryotic cells. 

• Key players: DNA, RNA polymerase, and various other enzymes. 

• Steps:

  1. Initiation: RNA polymerase binds to the DNA sequence near a gene. 

  2. Elongation: RNA polymerase moves along the DNA, creating a complementary RNA molecule. 

  3. Termination: The RNA polymerase encounters a signal to stop transcription, and the RNA molecule is released. 

Translation:

• Purpose: To synthesize proteins using the information encoded in RNA. 

• Where it happens: In the cytoplasm of eukaryotic cells, and in the cytoplasm of prokaryotic cells. 

• Key players: mRNA (messenger RNA), tRNA (transfer RNA), ribosomes, and amino acids. 

• Steps:

  1. Initiation: The ribosome binds to the mRNA and an initiator tRNA carrying the first amino acid. 

  2. Elongation: The ribosome moves along the mRNA, codon by codon, with tRNA molecules bringing the corresponding amino acids. 

  3. Termination: The ribosome encounters a stop codon, and the completed polypeptide chain is released. 

• Cell Cycle: Phases include Interphase, PMAT (Prophase, Metaphase, Anaphase, Telophase), and Cytokinesis.

XVII. Math in Science (MIS)

• Metric System: Understand prefixes and convert units using scientific notation.

• Temperature Scales: Be able to read and calculate temperature conversions.

• Significant Figures: Understand rules for precision in measurements.

• Graphing:

  • Read graphs and understand variables (independent and dependent).

  • Know how to set up a working table for data representation.

• Slope of a Line:

  • Calculate using the formula $ ext{slope} = \frac{\Delta y}{\Delta x}$

  • Understand how to find intercepts and equations of lines for graphing.