AP BIOLOGY MIDTERM

Outline: Cumulative Midterm AP

( Phylogenetic Tree Concepts, Study of Life, Ecology, Biochemistry, Cell Organelles, and

Bioenergetics)

The midterm will exclude any mathematical questions.

I. Phylogenies Concepts:

You should be able to read and interpret a Phylogenetic tree and a Cladogram.

Phylogenetic tree is a diagram showing the evolutionary relationships among biological species

based on similarities and differences in genetic or physical traits or both.

Parts of a phylogenetic tree:

Composed of nodes and branches

Internal nodes represent ancestors, points in evolution, when the ancestor diverged to form two

new species.

The length of each branch is proportional to the time elapsed since the split.

Sis taxa represents closely related shared common ancestor.

Cladograms- constructed by shared derived traits to analyze the difference among groups of

species from one another.

 Phylogenetic Tree

II. Study of Life:

- Differences between Eukaryotes and Prokaryotes

- Domains of life ( Bacteria, Archaea, Eukarya)

- Kingdoms ( Protista, Fungi, Plantae (plants), Animals)

III. Ecology:

Ecology is the study of how living things interact with each other, and with their environment.

Biotic factors — which are the living aspects of the environment

Abiotic factors- which are the nonliving aspects of the environment

A. Levels of this hierarchy in Ecology:

1. Population

2. Community

3. Ecosystem

4. Biome

5. Biosphere

B. Population

- Pattern Distribution – Clump, Scattered, Uniform

-Population Strategies K and R

- Survivorship curves I, II, III- How do the curves relate to specific populations?

C. Understanding concepts - Exponential and Logistic growth models

 Population Strategies K and R

 Predator and Prey Relationship Model

D. Categories of a community relationships:

 Symbiosis

 Predation

 Competition

E. Symbiosis- Types of Relationships: ( be able to identify the relationships)

 Mutualism

 Commensalism

 Parasitism

IV. Biochemistry

A. You should know the following bonds (Ionic, Covalent, Hydrogen)

B. Water Properties:

You should be able to identify all the properties of water

Polar molecule, allowing for the formation of hydrogen bonds.

Hydrogen bonds allow ions and other polar molecules to dissolve in water.

Notes on Properties of Water:

Therefore, water is an excellent solvent. Due to its ability to form Hydrogen bonds and being

polar.

The hydrogen bonds between water molecules cause the water to have a high heat capacity,

meaning it takes a lot of added heat to raise its temperature. As the temperature rises, the

hydrogen bonds between water continually break and form anew. This allows for the overall

temperature to remain stable, although energy is added to the system.

Water also exhibits a high heat of vaporization, which is key to how organisms cool

themselves by the evaporation of sweat.

Water’s cohesive forces allow for the property of surface tension, whereas its adhesive

properties are seen as water rises inside capillary tubes.

Ice less dense than water

The extra hydrogen bonds that occur when water freezes increase the space between molecules,

causing a decrease in overall density.

C. Macromolecules Notes:

Four types of organic compounds: Proteins, Carbohydrates, Nucleic Acids, and Lipids

You should the function, monomers, and examples for each macromolecule

Macromolecules are made up of single units known as monomers that are joined by covalent

bonds to form larger polymers.

o Carbohydrates

Carbohydrates are a group of macromolecules that are a vital energy source for the cell and

provide structural support

Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides depending

on the number of monomers in the molecule

You should know the types of classes of sugars and types of examples: Monosaccharide

example is glucose, Disaccharide

o Lipids

Lipids are a class of macromolecules that are nonpolar and hydrophobic

Types of lipids include fats and oils, waxes, phospholipids, and steroids.

Phospholipids – Hydrophilic vs Hydrophobic

You should be able to know the structure of a phospholipids

Fats are a stored form of energy

Fats are made up of fatty acids and either glycerol

Fatty acids may be unsaturated or saturated, depending on the presence or absence of double

bonds in the hydrocarbon chain. If only single bonds are present, they are known as saturated

fatty acids. Unsaturated fatty acids may have one or more double bonds in the hydrocarbon

chain. Phospholipids make up the matrix of membranes.

Their basic structure has four fused carbon rings. Cholesterol is a type of steroid and is an

important constituent of the plasma membrane, where it helps to maintain the fluid nature of the

membrane.

o Proteins

They help in metabolism by providing structural support and by acting as enzymes, carriers, or

The building blocks of proteins (monomers) are amino acids.

Please know all four levels of the protein structure:

Proteins are organized at four levels: primary, secondary, tertiary, quaternary:

The primary structure is the unique sequence of amino acids.

The secondary structure: local folding of the polypeptide to form structures such as the α helix

and β-pleated sheet

The tertiary structure: three-dimensional structure

The quaternary structure: occurs with two or more polypeptides combine to form the complete

protein structure

Protein shape and function linked; any change in shape caused by changes in temperature or pH

may lead to protein denaturation and a loss in function.

Nucleic Acids:

Nucleic acids are molecules made up of nucleotides that direct cellular activities such as cell

division and protein synthesis.

Each nucleotide is made up of a pentose sugar ( either ribose or deoxyribose), a nitrogenous

base, and a phosphate group.

There are two types of nucleic acids: DNA and RNA.

-Understand the Nitrogenous bases that makeup DNA and RNA

- Understand the structure of DNA and RNA strands

DNA:

double-helical structure with the two strands running in opposite directions, connected by

hydrogen bonds, and complementary to each other.

Sugar- deoxyribose

RNA:

single-stranded and is made of a pentose sugar (ribose), a nitrogenous base, and a phosphate

group.

RNA is involved in protein synthesis and its regulation:

Enzyme:

Understand how enzymes work

V. Cells:

Cells are the basic units of the structure and function of living things

Know the Functions of the various organelles found in Prokaryotic and Eukaryotic cells

See slides for organelles ( you are responsible for all organelles seen on slides)

A. Eukaryotic and Prokaryotic Cells: Know the difference between each

 The differences between eukaryotic cells (such as those in humans and other animals)

and prokaryotic cells (such as bacteria)

 The structures and functions of cell parts, including mitochondria, the plasma

membrane, cytoplasm, cytoskeleton, nucleus, ribosomes, Golgi apparatus,

endoplasmic reticulum, vesicles, and vacuoles

 Prokaryotic cells do not have a nucleus. Eukaryotic cells do have a nucleus, along

with other organelles.

B. Cytoplasm and Cytoskeleton

 Cytoplasm is a thick solution that fills a cell and is enclosed by the cell membrane. It

has many functions. It helps give the cell shape, holds organelles, and provides a site

for many of the biochemical reactions inside the cell.

 cytoplasm of a eukaryotic cell also contains a membrane-enclosed nucleus and other

organelles.

 The cytoskeleton is a highly organized framework of protein filaments and tubules

that criss-cross the cytoplasm of a cell. It gives the cell structure and helps hold cell

structures (such as organelles) in place within the cytoplasm.

 Be familiar with: Microtubules, microfilaments, intermediate filament.

C. Cell Organelles: You will be required to know ALL the organelles and their functions,

as discussed in class. (Below are some organelles we touch upon).

 An organelle is a structure within the cytoplasm of a eukaryotic cell that is enclosed

within a membrane and performs a specific job. Although ribosomes are not enclosed

within a membrane, they are still commonly referred to as organelles in eukaryotic

cells.

 The nucleus is the largest organelle in a eukaryotic cell, and it is considered to be the

cell's control center. It controls gene expression, including controlling which proteins

the cell makes.

 The mitochondria (is an organelle that makes energy available to the cells. It is like

the power plant of the cell.

 The endoplasmic reticulum (ER) is an organelle that helps make and transport

proteins and lipids. Rough endoplasmic reticulum (RER) is studded with ribosomes.

Smooth endoplasmic reticulum (SER) has no ribosomes.

 The Golgi apparatus is a large organelle that processes proteins and prepares them

for use both inside and outside the cell. It is also involved in the transport of lipids

around the cell.

 Both vesicles and vacuoles are sac-like organelles that may be used to store and

transport materials in the cell or as chambers for biochemical reactions. Lysosomes

and peroxisomes are vesicles that break down foreign matter, dead cells, or poisons.

 Centrioles are organelles located near the nucleus that help organize the

chromosomes before cell division, so each daughter cell receives the correct number

of chromosomes.

 Ribosomes are small structures where proteins are made. They are found in both

prokaryotic and eukaryotic cells. They may be found alone or in groups within the

cytoplasm or on the RER.

D. Plasma Membrane

Structure of a Plasma Membrane: Arrangements of a Phospholipids

E. Active Transport vs. Passive Transport:

Active Transport- Na K Pump and vesicle transport

Passive Transport- Osmosis and Diffusion

VI. Bioenergetics:

Energy and Metabolism

Metabolism – is the sum of all the chemical reactions that take place in cells.

 Catabolic - breaking down the reaction

 Anabolic – building the reaction

Energy – capable of doing work.

 All reactions require an input of energy called activation energy in order to reach the

transition state at which they will proceed. E A is the amount of energy needed to begin a

reaction.

ATP: Adenosine Triphosphate

 ATP- consist of adenosine ( the nucleotide adenine plus ribose) and three phosphates

 ATP unstable due to the three phosphate in ATP are all negatively charged and repel one

another.

 Thus, when one phosphate (PO 4 -3 ) group is removed from ATP by hydrolysis, therefore

forming a stable molecule called ADP ( adenosine diphosphate ) results. This process

releases energy.

Key Terms:

Reduction – the gain of electrons or protons

Oxidation – the loss of electrons or protons

 Chemiosmosis - process by which a proton gradient powers the production of ATP as

protons flow down the gradient through the ATP synthase channel.

Enzymes:

 Acts as catalyst, by lowering the activation energy, and therefore, increasing the rate of

the reaction.

 Enzymes are specific and act only on certain substrates.

 Shape of an enzyme determines which substrate an enzyme will act upon.

 Enzymes fold in a certain way, there is one or more active sites where a substrate can

bind.

 Shape of an enzyme can be altered or denatured and the enzyme will no longer function

as the normal condition.

 High temperatures and extreme pH levels can denature an enzyme

 Induced fit refers to the way in which an enzyme and a substrate forms an enzyme –

substrate

Cellular Respiration:

glucose + 6 oxygen  6 water + 6 carbon dioxide + energy ( ATP)

Glycolysis:

You should be able to explain the following:

What is the overall result, in terms of molecules produced, in the breakdown of glucose by

glycolysis?

o Occurs in the cytoplasm

Glycolysis is the first phase of cellular respiration. It does not use oxygen to break down 1

glucose molecule into 2 molecules of pyruvate with the release of 4 ATP or two net ATP. This

ATP is produced by a substrate level phosphorylation, which is carried out with the help of an

allosteric kinase.

 Glycolysis starts with glucose and ends with two pyruvate molecules, a total of four ATP

molecules and two molecules of NADH.

Summary:

Glycolysis is the first pathway used in the breakdown of glucose to extract energy. Glycolysis

consists of two parts: The first part prepares the six-carbon ring of glucose for cleavage into two

three-carbon sugars. ATP is invested in the process during this half to energize the separation.

The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and

attaches them to NAD + . Two ATP molecules are invested in the first half and four ATP molecules

are formed by substrate phosphorylation during the second half. This produces a net gain of two

ATP and two NADH molecules for the cell.

Summary Oxidation of Pyruvate and the Citric Acid Cycle (Krebs Cycle)

Oxidation of Pyruvate:

 In the presence of oxygen, pyruvate is transformed into an acetyl group attached to a

carrier molecule of coenzyme A. The resulting acetyl CoA can enter several pathways,

but most often, the acetyl group is delivered to the citric acid cycle for further catabolism.

During the conversion of pyruvate into the acetyl group, a molecule of carbon dioxide

and two high-energy electrons are removed. The carbon dioxide accounts for two

(conversion of two pyruvate molecules) of the six carbons of the original glucose

molecule. The electrons are picked up by NAD + , and the NADH carries the electrons to a

later pathway for ATP production. At this point, the glucose molecule that originally

entered cellular respiration has been completely oxidized. Chemical potential energy

stored within the glucose molecule has been transferred to electron carriers or has been

used to synthesize a few ATPs.

Krebs Cycle ( Citric Cycle)

- Occurs in the mitochondrial matrix

- Initiated by the pyruvate ( product from glycolysis)

- Utilizes the pyruvate from glycolysis . Thus, by doing so releases small amount of

ATP and the waste product of carbon dioxide.

- Outcome/Products – NADH and FADH 2, which carry protons and electrons to the

electron transport chain ( ETC) in the cristae membrane where oxidative

phosphorylation occurs.

The Electron Transport Chain:

Produces most ATP ( roughly 30 – 38)

The ETC pumps protons and electrons through the cristae membrane gradient through a series of

REDOX reaction to create a proton gradient.

o Couples two reactions, within the cristae membrane- one exergonic (electrons are pulled

toward oxygen) and the other endergonic ( pumps protons against a gradient to create a

proton gradient ).

o Outcomes: CO 2 + H 2 0

Redox reactions – means one substance is reduced while other is oxidized

OIL RIG:

Reduction is the gain of electrons

Oxidation is the loss of electrons or protons

Chemiosmosis:

The process in which a proton gradient powers the production of ATP as protons flow down the

gradient through the ATP synthase channel.

Summary of ( ETC, also know as the Oxidation Phosphorylation:

The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final

electron acceptor of the electrons removed from the intermediate compounds in glucose

catabolism. The electron transport chain is composed of four large, multiprotein complexes

embedded in the inner mitochondrial membrane and two small diffusible electron carriers

shuttling electrons between them. The electrons are passed through a series of redox reactions,

with a small amount of free energy used at three points to transport hydrogen ions across a

membrane. This process contributes to the gradient used in chemiosmosis. The electrons passing

through the electron transport chain gradually lose energy, High-energy electrons donated to the

chain by either NADH or FADH 2 complete the chain, as low-energy electrons reduce oxygen

molecules and forms water. The end products of the electron transport chain are water and ATP.

The catabolism (breakdown) of glucose under aerobic conditions occurs in three pathways:

o Glycolysis –

o Pyruvate Oxidation-

o Citric Acid Cycle/ Krebs Cycle

o ETC – inner membrane mitochondria ( cristae)

Which produces the reduced enzymes NADH and FADH 2 . There coenzymes are then

oxidized by the ETC and ATP is produced by oxidative phosphorylation.

Fermentation: Know examples of where they are found

First step is Glycolysis

 Fermentation makes ATP without oxygen ( anaerobic), which involves glycolysis

only.



I. lactic acid fermentation:

pyruvate from glycolysis changes to 2 lactic acid and 2 NAD .

This type of fermentation is carried out by the bacteria in yogurt, and by your own muscle cells.

II. Alcoholic fermentation:

pyruvate changes to 2 alcohol, 2 NAD, 2 carbon dioxide.

This type of fermentation is carried out by yeasts and some bacteria.

Photosynthesis

6co2 + 6 water + energy ( sun)  glucose + 6 oxygen

Chloroplast

Light Dependent Reactions:

- Thylakoid

Photosystem:

- PS II ( photolysis – use light breaks water makes oxygen ( waste product) ) / PS I (

makes ATP, by the flow of Hydrogen protons thorough ATP Synthase Complex)

- Products- NADPH, Oxygen, ATP

Light Independent Reactions:

- Stroma

- Clavin Cycle

( Breaks down carbon dioxide or fixation of carbon dioxide to produce sugar,

glucose)

- Produces- ATP, NADPH, Glucose

Cumulative Midterm AP Biology Outline

I. Phylogenetic Tree Concepts

Phylogenetic Tree

• Definition: A diagram showing evolutionary relationships among biological species based on genetic and/or physical trait similarities and differences.

• Components:

  • Nodes: Represent common ancestors.

    • Internal nodes indicate divergence points where a species split into two.

  • Branches: Represent evolutionary pathways and relationships.

    • Length of branches often correlates with the time elapsed since divergence.

  • Sister Taxa: Groups sharing a most recent common ancestor.

Cladogram

• Definition: A diagram that organizes species based on shared derived traits, highlighting differences among groups.

• Purpose: Useful for analyzing relationships without indicating time or genetic distance.

II. Study of Life

Eukaryotes vs. Prokaryotes

• Eukaryotes: Have membrane-bound organelles and a nucleus (e.g., plants, animals, fungi, protists).

• Prokaryotes: Lack membrane-bound organelles; no nucleus (e.g., bacteria, archaea).

Domains of Life

1. Bacteria: Prokaryotic organisms; found in diverse environments.

2. Archaea: Prokaryotic; often live in extreme conditions.

3. Eukarya: Includes all eukaryotic organisms.

Kingdoms

• Protista: Diverse group including algae and protozoa.

• Fungi: Decomposers; includes yeasts, molds, and mushrooms.

• Plantae: Multicellular, photosynthetic organisms.

• Animalia: Multicellular, heterotrophic organisms.

III. Ecology

Overview

• Definition: Study of interactions between living organisms and their environment.

• Factors:

  • Biotic: Living components (e.g., plants, animals).

  • Abiotic: Nonliving components (e.g., temperature, water).

Levels of Organization

1. Population: Group of the same species in an area.

2. Community: Different populations interacting.

3. Ecosystem: Community plus abiotic factors.

4. Biome: Large ecosystems characterized by climate (e.g., desert, tundra).

5. Biosphere: All ecosystems on Earth.

Population Dynamics

• Patterns of Distribution:

  • Clumped: Grouped in clusters.

  • Uniform: Evenly spaced.

  • Random: No specific pattern.

• Population Strategies:

  • K-strategists: Fewer offspring, high parental care.

  • R-strategists: Many offspring, low parental care.

• Survivorship Curves:

  • Type I: High survival in early/midlife, decline later (e.g., humans).

  • Type II: Constant survival rate (e.g., birds).

  • Type III: Low early survival, but those that survive live long (e.g., fish).

Growth Models

• Exponential Growth: Rapid increase without limits.

• Logistic Growth: Growth slows as population reaches carrying capacity.

Community Relationships

1. Symbiosis:

   • Mutualism: Both benefit (e.g., bees and flowers).

   • Commensalism: One benefits, other unaffected (e.g., barnacles on whales).

   • Parasitism: One benefits, other is harmed (e.g., ticks on animals).

2. Predation: Predator-prey interactions.

3. Competition: Organisms compete for resources.

IV. Biochemistry

Types of Bonds

1. Ionic: Transfer of electrons.

2. Covalent: Sharing of electrons.

3. Hydrogen: Weak bonds between polar molecules.

Properties of Water

• Polarity: Allows hydrogen bonding.

• Key Properties:

  • Excellent solvent.

  • High heat capacity.

  • High heat of vaporization.

  • Cohesion (surface tension).

  • Adhesion (capillary action).

  • Ice less dense than liquid water.

Macromolecules

1. Carbohydrates:

   • Function: Energy source, structural support.

   • Monomer: Monosaccharides (e.g., glucose).

   • Examples: Starch, glycogen, cellulose.

2. Lipids:

   • Function: Energy storage, membrane structure.

   • Types: Fats, oils, phospholipids, steroids.

   • Structure: Hydrophilic head, hydrophobic tail (phospholipids).

3. Proteins:

   • Function: Enzymes, structural components.

   • Monomer: Amino acids.

   • Structure: Primary, secondary, tertiary, quaternary levels.

4. Nucleic Acids:

   • Function: Genetic information storage and transfer.

   • Monomer: Nucleotides.

   • Examples: DNA (double-stranded), RNA (single-stranded).

Enzymes

• Function: Catalysts that lower activation energy.

• Specificity: Enzyme-substrate binding.

• Factors Affecting Activity: Temperature, pH, denaturation.

V. Cells

Prokaryotic vs. Eukaryotic Cells

• Prokaryotes: Smaller, no nucleus, fewer organelles.

• Eukaryotes: Larger, nucleus, complex organelles.

Key Organelles

• Nucleus: Control center; houses DNA.

• Mitochondria: Powerhouse; produces ATP.

• Endoplasmic Reticulum (ER):

  • Rough ER: Protein synthesis.

  • Smooth ER: Lipid synthesis.

• Golgi Apparatus: Processes and packages proteins.

• Lysosomes: Digestive enzymes.

• Cytoskeleton: Provides structure (microtubules, microfilaments).

• Plasma Membrane: Phospholipid bilayer; controls transport.

Transport Mechanisms

• Passive Transport: Diffusion, osmosis (no energy required).

• Active Transport: Uses energy (e.g., sodium-potassium pump).

VI. Bioenergetics

Metabolism

• Catabolism: Breakdown of molecules (releases energy).

• Anabolism: Synthesis of molecules (requires energy).

ATP (Adenosine Triphosphate)

• Structure: Adenine, ribose, three phosphates.

• Function: Primary energy carrier.

• Conversion: ATP → ADP + Pi (releases energy).

Cellular Respiration

1. Glycolysis:

   • Occurs in cytoplasm.

   • Breaks glucose into two pyruvate molecules.

   • Produces 2 ATP (net) and 2 NADH.

2. Citric Acid Cycle (Krebs Cycle):

   • Occurs in mitochondria.

   • Produces NADH, FADH2, and ATP.

3. Electron Transport Chain:

   • Uses NADH and FADH2 to create a proton gradient.

   • Drives ATP production via ATP synthase.

Key Processes

• Chemiosmosis: Proton gradient powers ATP synthesis.

• Oxidation-Reduction Reactions:

  • Oxidation: Loss of electrons.

  • Reduction: Gain of electrons.