Honors Biology Midterm

Unit 1: Scientific Method

Part I: Experimental Design

Element of Good Experimental Design:

  1. Measurable Results:

    • Explanation: Quantifying the data allows for objective analysis versus relying on subjective obser\

    • vations (qualitative data).

  2. Isolated Experimental Variable:

    • Explanation: To determine the impact of one variable on the results, only one variable should be tested and all other variables must remain constant. For example, if both sugar concentration and temperature vary across tests, it is impossible to identify which factor influences the results.

  3. Large Sample Size:

    • Explanation: A larger sample size enables a more accurate representation of results by reducing the influence of outliers on data accuracy.

  4. Multiple Trials:

    • Explanation: Conducting more trials serves the same purpose as increasing sample size by diluting the effect of any outliers and enhancing data reliability.

  5. Control Group:

    • This group is essential in experiments as it establishes a baseline for comparison, allowing researchers to determine the effect of the independent variable by assessing any changes observed in experimental groups.

Part II: Abstract

Elements of a Well-Written Abstract:

  • What was done in the experiment.

  • How the experiment was done.

  • The results of the experiment.

Part III: Elements of a Experiment

  • Hypothesis: If ___, then ___, because ____.

    • Declarative statement – no I’s or We’s

    • Both a dependent and independent variable

    • Predict specific trend/direction

    • Concise and logical rationale provided

    • Ex. The amount of enzymatic hydrolysis will increase as temperature increases because higher temperatures typically enhance enzyme activity until denaturation occurs.

  • Dependent Variable: Outcome being measured in a scientific experiment, affected by changes to the independent variable.

    • Ex. Amount of enzymatic hydrolysis (loss of protein).

  • Independent Variable: The factor that is changed or controlled in a scientific experiment.

    • Ex. Temperature (°C).

  • Control Group: A group that has not received the experimental treatment or is kept under standard, controlled conditions. It serves as a necessary benchmark to measure how experimental groups perform in comparison.

    • Purpose: It allows researchers to eliminate and isolate variables, ensuring that results are due to the independent variable and not external factors.

  • Graph Setup:

    • Y-Axis: Independent Variable

    • X-Axis: Dependent Variable

  • Best Graph for Data Type:

    • Scatter plot graph with linear trendline: Continuous data with a linear trend.

    • Line graph: Continuous data with no single or clear linear trend.

    • Bar graph/Column graph: Discrete data.

    • Pie chart: Discrete data, displays percentages and parts of a whole.

  • Quantitative Data: Objective information that expresses a quantity and can be measured numerically, allowing for statistical analysis and comparison of results.

  • Qualitative Data: Descriptive, subjective information like characteristics or qualities, which can not be measured numerically.

IV: Correlation Coefficient

  • Experiment: Studying effects of caffeine on fish heart rate.

  • Data Collected:

    • Caffeine in mg: (0, 1, 2, 3, 4, 5)

    • Heart Rate in bpm: (59, 48, 39, 29, 18)

  • Best Graph Type: A scatterplot with a linear trendline because it effectively shows individual data points and their relationship.

  • Relationship Type: Inverse relationship, indicated by an increase in caffeine leading to a decrease in heart rate.

  • Correlation Strength: This relationship exhibits a strong negative correlation.

  • Estimated Correlation Coefficient: A negative value suggesting strong correlation, possibly around -0.9.

IV: How To Write Conclusions

  •  Claim:

    • Describe what was learned from the experiment

    • Identify patterns in data and relationships between variables

    • Was the hypothesis supported or not?

  • Evidence:

    • Describe quantitative information provided in tables and graphs

    • unusual data points are indicated and discussed

  • Reasoning:

    • Reasons to support or reject hypothesis are included

    • How does the evidence support the claim?

  • Methods

    • Logical, specific sources of errors and possible effects of errors are

    • Addressed (where necessary)

    • suggestions for improvements to the current experiment design

    • suggestions for further study

Unit 2: Characteristics of Life

Part I: Characteristics of Life

Part II: Metabolism and Energy Pathways

  • Energy Transformation:

    • Process by which organic molecules are converted into usable energy (ATP) via digestion and cellular respiration.

    • Photosynthesis Equation: Sunlight + H₂O + CO₂ → Glucose + O₂.

    • Cellular Respiration: Reactants are glucose and oxygen, that yield ATP, CO₂, and water.

Part III: Homeostasis and Human Body Systems

I. Respiratory System

  • Key Structures:

    • Diaphragm: Muscle aiding in breathing.

    • Alveoli: Air sacs for gas exchange.

II. Digestive System

  • Key Functions:

    • Mechanical Digestion: Physical breakdown of food.

    • Chemical Digestion: Breakdown using enzymes (e.g. amylase).

I. Cellular Organization

  • Levels of Organization:

    • Cell

    • Tissue

    • Organ

    • Organ System

    • Organism

II. Metabolism

  • Definition: Metabolism encompasses all chemical processes within a living organism.

  • Law of Conservation of Energy: Energy cannot be created or destroyed, rather transformed.

  • Types:

    • Aerobic: Requires oxygen; yields 38 ATP.

    • Anaerobic: No oxygen required; yields 2 ATP.

III. Responsiveness

  • Homeostasis: The body’s ability to maintain stable internal conditions.

    • Stimulus: A change in the environment that triggers a response.

    • Response: The detectable action taken in reaction to the stimulus.

IV. Growth and Development

  • Definition: Growth in unicellular organisms refers to an increase in size, while in multicellular organisms, it implies an increase in cell number.

V. Reproduction

  • Reproduction Types:

    • Asexual: Single parent; no genetic variation.

    • Sexual: Two parents; genetic variation provided.

  • DNA: Molecule that carries genetic information, dictating organism traits.

VI. Forms of Reproduction

  • Asexual Reproduction:

    • Binary Fission: Equal division (

    • Budding: Unequal division

  • Sexual Reproduction involves genetic contributions from both parents.

Part VII: Metabolism and Energy Pathways

  • Energy Transformation:

    • Process by which organic molecules are converted into usable energy (ATP) via digestion and cellular respiration.

    • Photosynthesis Equation: Sunlight + H₂O + CO₂ → Glucose + O₂.

    • Cellular Respiration: Reactants are glucose and oxygen, that yield ATP, CO₂, and water.

Part VIII: Homeostasis and Human Body Systems

I. Respiratory System

  • Key Structures:

    • Diaphragm: Muscle aiding in breathing.

    • Alveoli: Air sacs for gas exchange.

II. Digestive System

  • Key Functions:

    • Mechanical Digestion: Physical breakdown of food.

    • Chemical Digestion: Breakdown using enzymes (e.g. amylase).

Other Polymer Lipids

Other Lipids

  • Waxes:

    • Examples include beeswax and ear wax (cerumen).

  • Steroids:

    • Characteristics:

    • Extremely hydrophobic.

    • Structural lipid, not a triglyceride.

    • Structure consists of 4 fused rings of carbon to which various groups of elements are attached.

    • Examples include cholesterol and testosterone.

Phospholipid

  • A special type of triglyceride found within cell membranes.

    • Characteristics:

    • Amphipathic: Contains both polar and nonpolar regions.

    • Contains a phosphate group, which is charged and polar (hydrophilic).

    • Structure of a phospholipid:

      • The phosphate group is attached to the glycerol backbone.

Diagram: 
  Phosphate group -[O-] 
    |  
  H2C-O-C-C-C-C-H  
         | 
         H

D. Nucleic Acids

Monomer of Nucleic Acids - Nucleotide

  • Composed of:

    1. 5-carbon sugar.

    2. Phosphate group.

    3. Nitrogen base.

  • Structure of a nucleotide:

   O-P= O 
   | 
   N-Base

Nucleotide Structure Example

  • DNA Nucleotide:

    • Contains deoxyribose sugar.

    • Possible bases include:

    • Thymine

    • Guanine

    • Cytosine

    • Adenine

  • RNA Nucleotide:

    • Contains ribose sugar.

    • Possible bases include:

    • Uracil

    • Guanine

    • Cytosine

    • Adenine

Polymers of Nucleotides

  • Polymers:

    • DNA (Deoxyribonucleic Acid)

    • RNA (Ribonucleic Acid)

Structures and Functions

  • DNA Structure: Contains deoxyribose sugar, phosphate group, and nitrogen bases (A, G, C, T).

  • RNA Structure: Contains ribose sugar, phosphate group, and nitrogen bases (A, G, C, U).

DNA Function:

  • Copied during cell division.

  • Found only in the nucleus.

  • Stores the genetic code and determines protein structure.

RNA Function:

  • Acts as a temporary copy of genetic code.

  • Found in nucleus, ribosomes, and cytoplasm.

  • Directly involved in protein synthesis.

Base Pairing:

  • DNA Base Pairing:

    • Thymine = Adenine

    • Cytosine = Guanine

  • RNA Base Pairing:

    • Uracil = Adenine

    • Cytosine = Guanine

II. Properties of Water

  • Water is a polar covalent molecule.

  • Polar Molecule: A molecule with two oppositely charged regions.

Hydrogen Bonding:

  • Attraction between the oppositely charged regions of polar molecules.

Properties of Water Include:

  1. Temperature Stabilization:

    • Water resists dramatic temperature changes, helping maintain homeostasis in cells.

  2. Capillarity:

    • Rise of water in narrow tubes due to:

      • Cohesion: Attraction between water molecules.

      • Adhesion: Attraction between water molecules and tube molecules.

  3. Density:

    • Ice is less dense than water, allowing it to float.

    • Water freezes from the top down.

  4. Solubility:

    • Water dissolves polar or ionic substances easily but does not mix well with nonpolar substances.

    • Hydrophobic Substances: Nonpolar and do not dissolve in water (e.g. lipids).

    • Hydrophilic Substances: Polar and dissolve easily in water (e.g. alcohol).

  5. Solutions:

    • A homogeneous mixture of two or more substances; one (solute) is dissolved in another (solvent).

    • Example: Air, soda, vinegar.

    • Aqueous solution: Solvent is water.

Acids and Bases:

  • Acids:

    • Form when hydrogen ions mix with water and have a low pH (lower pH = stronger acid).

    • Example:

HCl -> H⁺ + Cl⁻

  • Bases:

    • Form when hydroxide ions mix with water and have a high pH (higher pH = stronger base).

    • Example:

NaOH -> Na⁺ + OH¯ + H₂O
pH Scale:

  • Measures acidity or alkalinity of solutions.

  • Indicator substances change color based on pH level (e.g. Litmus Paper, phenolphthalein).

Neutralization Reaction:

  • Acid + Base → Salt + Water

  • Example:

HCl + NaOH → NaCl + H₂O

Unit 4 - Cell Biology

I. Introduction to Cell Biology

  • Robert Hooke (1665): First to use the term "cell"; observed cork cells (dead).

  • Anton van Leeuwenhoek (1670's): Father of modern microbiology; first to observe living cells.

  • Cell Theory:

    1. All organisms are composed of one or more cells.

    2. Cells are the basic units of structure and function for all living things.

    3. Cells arise only from pre-existing cells.

II. Cell Diversity - Two Main Types

  1. Prokaryotic Cells:

    • Simplest, oldest cell types; found only in bacteria.

    • No nucleus and no membrane-bound organelles.

    • DNA located in the nucleoid region.

    • Always unicellular.

  2. Eukaryotic Cells:

    • More modern, complex cells; contain a nucleus and membrane-bound organelles.

    • Found in plants, animals, fungi, and protists.

    • DNA enclosed in the nucleus; may be unicellular or multicellular.

Comparison of Cell Types

  • Prokaryotic Cells:

    • Structure: Capsule, cell wall, plasma membrane, ribosomes, nucleoid.

    • Characteristics: Smaller, simpler, less complex, always unicellular.

  • Eukaryotic Cells:

    • Structure: Nucleus, nucleolus, rough/smooth endoplasmic reticulum, Golgi apparatus, mitochondria, lysosomes, etc.

    • Characteristics: Larger, more complex, membrane-bound organelles, multicellular.

Plant vs Animal Cells

  • Plant Cell Structure:

    • Chloroplasts, cell wall, large central vacuole.

  • Animal Cell Structure:

    • Lysosomes, multiple small vacuoles.

III. General Cell Organelles/Structures

  • Cell Membrane (Plasma Membrane):

    • Outer boundary; regulates what enters/leaves the cell.

  • Cytosol (Cytoplasm):

    • Clear fluid filling the cell containing organelles.

  • Nucleus:

    • Contains genetic material, controls cell activities.

  • Endoplasmic Reticulum (ER):

    • Smooth ER: No ribosomes.

    • Rough ER: Contains ribosomes; site of protein synthesis.

  • Golgi Apparatus:

    • Packaging and processing organelle; modifies proteins for export.

  • Lysosome:

    • Contains digestive enzymes; breaks down waste.

  • Mitochondria:

    • Powerhouse of the cell; site of ATP production during aerobic respiration.

  • Cytoskeleton:

    • Provides shape and support to the cell; made of microtubules and microfilaments.

  • Vacuole:

    • Storage organelle, typically large in plant cells for storing water and nutrients.

IV. Cell Specialization

  • Cells vary in appearance and function depending on their roles within an organism:

    • Examples: Sex cell, muscle cell, fat cell, immune cell, stem cell, bone cell, epithelial cell, nervous cell, blood cell.

Unit 5 - Cell Membrane and Cellular Transport

I. Plasma Membrane

  • Controls movement of materials in/out of the cell; crucial for homeostasis.

  • Phospholipid Bilayer:

    • Comprises most of the membrane; hydrophilic heads and hydrophobic tails.

II. Protein Structures in Plasma Membrane

  • Integral Proteins: Embedded within the membrane.

    • Channel Proteins: Pass substances across the membrane.

      • Non-Gated (always open)

      • Aquaporins (for water molecules)

      • Gated (only open when stimulated)

    • Carrier Proteins: Facilitate transport across the membrane.

    • Marker Proteins: Involved in cell recognition.

    • Receptor Proteins: Bind substances and trigger cellular responses.

  • Peripheral Proteins: Attached to the membrane surface.

  • Glycolipids: Carbohydrates attached to lipids.

  • Glycoproteins: Carbohydrates attached to proteins.

III. Cellular Transport Mechanisms

Passive Transport

  • Movement of materials without energy.

  1. Simple Diffusion: Movement from high to low concentration.

  2. Facilitated Diffusion: Assisted by membrane proteins for larger or charged molecules.

  3. Osmosis: Diffusion of water across a membrane.

Active Transport

  • Requires ATP energy; moves substances against their concentration gradient.

  • Ion Pumps: Carrier proteins moving ions.

    • Example: Sodium-Potassium pump.

  • Endocytosis: Cell takes in large particles.

    • Receptor-mediated endocytosis:

      • Acquiring specific materials from the environment through use of receptor proteins found at specific sites (coated pits) on the outer surface of the cell membrane

    • Phagocytosis:

      • What: Engulfing whole cells or one-celled organisms

      • How: Formation of vacuoles, broken down by digestive enzymes of lysosome

      • Simple Terms: “cell eating”

    • Pinocytosis:

      • What: Taking in liquids or dissolved solutes by a cell

      • How: Formation of vacuoles, broken down by digestive enzymes of lysosome

      • Simple Terms: “cell drinking”

  • Exocytosis:

    • What: Passage of large molecules to the outside of the cell without going through pores of cell membrane

    • How: Vesicles fuse with the cell membrane as the molecule is released outside the cell

    • Simple Terms: Release of substances outside the cell.

  • Interconnected membrane structures working together for transport processes.

Unit 6a - ATP and Photosynthesis

Cellular Energy: ATP

  • ATP (Adenosine Triphosphate): The energy currency of the cell; has three phosphate groups.

  • ADP (Adenosine Diphosphate): Has two phosphate groups.

ATP Cycle

  1. Energy stored in ATP by cellular respiration.

  2. Energy released by breaking the phosphate bond; converting ATP to ADP.

  3. Energy from food recharges ATP.

Photosynthesis Overview

  • Takes place in chloroplasts; converts sunlight into chemical energy.

  • Has two main reactions: Light-dependent and Light-independent (Calvin Cycle).

Chloroplast Structure

  • Thylakoids: Membrane-bound structures where light-dependent reactions occur.

  • Stroma: Liquid matrix where the Calvin Cycle occurs.

Photosynthetic Reactions

  1. Light-dependent Reactions:

    • Require water and sunlight.

    • Produce oxygen and energy carriers (ATP and NADPH).

    • Equation:

H2O + light -> O2 + ATP + NADPH

  1. Light Independent Reactions (Calvin Cycle):

    • Use CO₂ to produce glucose.

    • RuBisCO catalyzes carbon fixation.

    • Overall Equation:

CO₂ + ATP + NADPH -> C6H12O6 + ADP + P + NADP
Alternative Pathways for Photosynthesis

  • Plants in arid environments use adaptations like CAM and C₄ pathways for water conservation.

Unit 6b - Cellular Respiration

Overview of Cellular Respiration

  • Process of breaking down glucose to produce ATP.

  • Two types: Anaerobic and Aerobic.

Anaerobic Respiration (Fermentation)

  1. Lactic Acid Fermentation:

    • Glycolysis:

C6H12O6 -> 2 C3H6O3 + 2 ATP

  1. Alcoholic Fermentation:

    • Glycolysis:

C6H12O6 -> 2 C2H5OH + 2 CO2 + 2 ATP
Aerobic Respiration

  • Requires oxygen.

  • Divided into stages that occur in the mitochondria, yielding up to 38 ATP from glucose.

Stages of Aerobic Respiration

  1. Glycolysis: Occurs in the cytoplasm; splits glucose.

  2. Krebs Cycle: Takes place in mitochondrial matrix.

  3. Electron Transport Chain: Occurs in the inner mitochondrial membrane, utilizing ATP Synthase.

Summary Reaction for Cellular Respiration
Glucose + O2 -> CO2 + H2O + 38 ATP