Cumulative Midterm AP Biology Outline

Phylogenetic Tree

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

Nodes

Represent common ancestors in a phylogenetic tree.

Cladogram

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

Eukaryotes

Organisms that have membrane-bound organelles and a nucleus (e.g., plants, animals, fungi, protists).

Prokaryotes

Organisms that lack membrane-bound organelles; no nucleus (e.g., bacteria, archaea).

Domains of Life

Categories in biology including Bacteria, Archaea, and Eukarya.

Symbiosis

Interactions between different species, including mutualism, commensalism, and parasitism.

Mutualism

A type of symbiosis where both species benefit (e.g., bees and flowers).

Exponential Growth

A rapid increase in population without limits.

Logistic Growth

Growth that slows as population reaches carrying capacity.

Ionic Bond

A type of bond formed through the transfer of electrons.

Covalent Bond

A type of bond formed by the sharing of electrons between atoms.

Hydrogen Bond

Weak bonds between polar molecules, important for properties of water.

Macromolecules

Large molecules necessary for life, including carbohydrates, lipids, proteins, and nucleic acids.

Catabolism

The breakdown of molecules that releases energy.

Anabolism

The synthesis of molecules that requires energy.

ATP

Adenosine Triphosphate, the primary energy carrier in cells.

Glycolysis

The metabolic pathway that breaks glucose into two pyruvate molecules, producing 2 ATP and 2 NADH.

Citric Acid Cycle

Also known as the Krebs Cycle, it occurs in mitochondria and produces NADH, FADH2, and ATP.

Chemiosmosis

Process where a proton gradient powers ATP synthesis.

Oxidation

The loss of electrons during a chemical reaction.

Reduction

The gain of electrons during a chemical reaction.

Photosynthesis

=

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

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

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)

Fermentation: Know examples of where they are found

lactic acid fermentation and Alcoholic fermentation

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.

OIL RIG:

Reduction is the gain of electrons

Oxidation is the loss of electrons or protons

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

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

glycolysis?

• Breaks down 1 glucose molecule into 2 pyruvate molecules.

• Produces 2 net ATP and 2 NADH.

Where does glycolysis occur?

• Glycolysis occurs in the cytoplasm of the cell.

what is glycolysis?

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 a net gain of 2 ATP. This ATP is produced by substrate-level phosphorylation, which is carried out with the help of an allosteric kinase.

What are the end products of glycolysis?

• Glycolysis starts with glucose and ends with two pyruvate molecules, four ATP molecules (net gain of 2 ATP), and two NADH molecules.

Halves of Glycolysis

Preparatory Half: The six-carbon glucose ring is prepared for cleavage into two three-carbon sugars. Two ATP molecules are invested to energize the process.

Halves of Glycolysis

Payoff Half: ATP and high-energy electrons are extracted. Four ATP molecules are generated by substrate-level phosphorylation, resulting in a net gain of two ATP, along with two NADH molecules.

Enzyme function

Enzymes act as catalysts by lowering activation energy and increasing reaction rates.

Enzyme Specificity

Enzymes are specific and only work on certain substrates.

Enzyme Shape and Substrate

The shape of an enzyme determines which substrate it can act on.

Enzyme Active Site

Enzymes fold in a way that creates one or more active sites where substrates can bind.

Enzyme Denaturation

If an enzyme's shape is altered or denatured, it can no longer function properly.

Factors that Denature Enzymes

High temperatures and extreme pH levels can denature enzymes.

Enzyme Induced Fit

The induced fit model describes how an enzyme and a substrate interact to form an enzyme-substrate complex.

organelle

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.

nucleus

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

cells control center. It controls gene expression, including controlling which proteins

the cell makes.

mitochondria

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

the power plant of the cell.

endoplasmic reticulum (ER)

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.

Golgi apparatus

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.

vesicles

A vesicle is a small, membrane-bound structure that transports materials within or outside of a cell. It is used by cells to store and move substances like proteins, lipids, and other molecules.

vacuole

A vacuole is a membrane-bound organelle found in cells, especially plant cells. It is used for storage and maintains the cell's internal environment. like a storgae unit

Lysosomes

Lysosomes are membrane-bound organelles in cells that contain enzymes responsible for breaking down waste materials, cellular debris, and foreign substances. They act like the cell’s "garbage disposal" system, tyoe of vesicle.

peroxisomes

Peroxisomes are small, membrane-bound organelles found in most eukaryotic cells. They contain enzymes that help break down toxic substances and fatty acids. The primary function of peroxisomes is to detoxify harmful byproducts of metabolism and assist in the breakdown of fatty acids, type of vesicle

Centrioles

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

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.

You will be required to know ALL the organelles and their functions,

as discussed in class.

Nucleus, Mitochondria,Ribosomes, Endoplasmic Reticulum (ER), Golgi Apparatus, Lysosomes, Peroxisomes, Vacuoles,Plasma Membrane, Cytoskeleton, Centrioles ,Chloroplasts (in plant cells), Cell Wall (in plant cells, fungi, bacteria), Cilia and Flagella, and Nucleolus

Plasma

This is the outer membrane that surrounds the entire cell, controlling what enters and leaves, it's essential for maintaining homeostasis and communication between cells.

Structure of a Plasma Membrane:

Arrangements of a Phospholipids.

Nuclear Membrane (Nuclear Envelope):

The membrane surrounding the nucleus. It has pores that control the movement of materials (like RNA and ribosomal subunits) between the nucleus and the cytoplasm.

Mitochondria

Mitochondria have two membranes. The outer membrane is smooth, while the inner membrane is folded into cristae, where ATP is produced.

Chloroplast Membranes

In plant cells, chloroplasts have a double membrane. The inner membrane surrounds the stroma, and the thylakoid membrane contains chlorophyll for photosynthesis.

Active Transport:

Definition: Movement of substances across a cell membrane against their concentration gradient (from low to high concentration).

• Energy Requirement (ATP)

Na K Pump and vesicle transport

Active Transport Examples:

• Moving glucose into cells for energy production.

• Moving ions to maintain proper cellular function.

Passive Transport:

Definition: Movement of substances across a cell membrane without the use of energy, following the concentration gradient (from high to low concentration). Does NOT require energy. Osmosis and Diffusion

Passive Transport Examples:

• Oxygen and carbon dioxide moving in and out of cells.

• Water moving in and out of cells through osmosis.

activation energy

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.

Catabolic

breaking down the reaction

Anabolic

building the reaction

DNA (Deoxyribonucleic Acid): Bases

• Adenine (A): Pairs with Thymine (T).

• Thymine (T): Pairs with Adenine (A).

• Cytosine (C): Pairs with Guanine (G).

• Guanine (G): Pairs with Cytosine (C).

RNA (Ribonucleic Acid): Bases

• Adenine (A): Pairs with Uracil (U) (not Thymine as in DNA).

• Uracil (U): Pairs with Adenine (A).

• Cytosine (C): Pairs with Guanine (G).

• Guanine (G): Pairs with Cytosine (C).

DNA Structure:

• Double Helix: DNA is composed of two strands twisted around each other to form a double helix.

• Backbone: The backbone of each strand is made of deoxyribose sugar (a 5-carbon sugar) and phosphate groups. These are connected by covalent bonds.

• Base Pairing: The nitrogenous bases (A, T, C, G) from each strand pair up through hydrogen bonds: A with T and C with G, forming the "steps" of the helix.

• Antiparallel Strands: The two strands run in opposite directions, meaning one runs 5' to 3' (five prime to three prime), and the other runs 3' to 5'.

RNA Structure:

• Single Strand: RNA is usually a single-stranded molecule, although it can form secondary structures in certain regions.

• Backbone: The backbone of RNA is made of ribose sugar (which has an extra oxygen compared to deoxyribose in DNA) and phosphate groups.

• Base Pairing: Similar to DNA, RNA has A, C, and G, but Uracil (U) replaces Thymine. A pairs with U, and C pairs with G.

Key Differences in Structure:

• DNA: Double-stranded, contains deoxyribose, and uses Thymine (T).

• RNA: Single-stranded, contains ribose, and uses Uracil (U) instead of Thymine.

primary structure

The primary structure is the unique sequence of amino acids.

secondary structure:

local folding of the polypeptide to form structures such as the α helix

and β-pleated sheet

tertiary structure:

three-dimensional structure

quaternary structure: The tertiary structure: three-dimensional structure

occurs when two or more polypeptides combine to form the complete protein structure

Kingdoms

The major classifications of life within the domain Eukarya: Protista, Fungi, Plantae, and Animalia.

Ecology

The study of how living organisms interact with each other and their environment.

Biotic factors

Living components of an environment that affect ecosystems.

Abiotic factors

Non-living chemical and physical components of the environment.

Population

A group of individuals of the same species living in a specific area.

Community

An assemblage of different populations that inhabit a common environment.

Ecosystem

A biological community of interacting organisms and their physical environment.

Biome

A large geographical biotic unit, a major community of plants and animals with similar life forms.

Biosphere

The global sum of all ecosystems, where life exists.

Clump distribution

A pattern where individuals are grouped together in patches.

Scattered distribution

A pattern where individuals are spread out randomly over an area.

Uniform distribution

A pattern where individuals are evenly spaced within an area.

K-strategy

Population strategy characterized by low growth rates and high parental investment.

R-strategy

Population strategy characterized by high growth rates and low parental investment.

Survivorship curves

Graphical representations of the number of individuals in a population that survive at different ages.

Predator and Prey relationship model

An ecological relationship where one organism (the predator) feeds on another (the prey).

Commensalism

A type of symbiosis where one organism benefits while the other is unaffected.

Parasitism

A type of symbiosis where one organism benefits at the expense of the other.

Polar molecule

A molecule with a distribution of charge leading to positive and negative ends.

Hydrogen bonds in water

Responsible for the unique properties of water, including its solvency and heat capacity.

High heat capacity of water

refers to its ability to absorb and store a large amount of heat energy without experiencing a significant change in temperature. This property is due to the hydrogen bonding between water molecules, which requires substantial energy to break.