Key Concepts in Biology: Structure, Function, and Processes

Subatomic particles

Protons, neutrons, and electrons that make up an atom.

Protons

Positively charged particles located in the nucleus of an atom.

Neutrons

Neutral particles located in the nucleus of an atom.

Electrons

Negatively charged particles that orbit the nucleus in specific energy levels or shells.

Atomic number

Determined by the number of protons in the nucleus of an atom.

Atomic mass

Equal to the number of protons and neutrons in the nucleus.

Isotopes

Atoms of the same element that have different numbers of neutrons and different atomic masses.

pH

A measure of the hydrogen ion concentration in a solution, calculated using pH = -log[H+].

pOH

A measure of the hydroxide ion concentration in a solution, calculated using pOH = -log[OH-].

Relationship between pH and pOH

pH + pOH = 14.

Carbohydrates

Organic compounds made of monosaccharides, serving functions such as energy storage and structural support.

Monosaccharides

Simple sugars like glucose, fructose, and galactose that are the monomers of carbohydrates.

Lipids

Fats and oils composed of fatty acids and glycerol, serving functions like energy storage and cell membrane structure.

Proteins

Polymers made of amino acids that perform various functions including catalyzing reactions and providing structural support.

Amino acids

The monomers that make up proteins.

Nucleic Acids

Polymers made of nucleotides that store and transmit genetic information.

Nucleotides

The monomers that make up nucleic acids like DNA and RNA.

Plasma Membrane

The membrane surrounding the cell that regulates the movement of substances in and out.

Cytoplasm

The jelly-like substance within the cell membrane that contains organelles.

Nucleus

The organelle that contains the cell's genetic material.

Endoplasmic Reticulum (ER)

An organelle involved in the synthesis of proteins and lipids.

Osmosis

The passive movement of water across a semi-permeable membrane, like the cell membrane, from a region of high water concentration to a region of low water concentration.

Solutes

Substances dissolved in a solvent (like water).

Concentration

The amount of solute dissolved in a given volume of solvent.

Intracellular Fluid (ICF)

The fluid inside the cell.

Extracellular Fluid (ECF)

The fluid outside the cell.

Hypotonic Solution

If the ECF has a lower solute concentration than the ICF, water will move into the cell, causing it to swell.

Hypertonic Solution

If the ECF has a higher solute concentration than the ICF, water will move out of the cell, causing it to shrink.

Isotonic Solution

If the ECF and ICF have the same solute concentration, there will be no net movement of water.

Dehydration

When you lose water, the solute concentration in your extracellular fluid increases, drawing water out of your cells and causing them to shrink.

Rehydration

When you drink water, you dilute the extracellular fluid, causing water to move back into your cells and restoring them to their normal volume.

Fluid overload

When you drink too much water too quickly, the solute concentration in your extracellular fluid decreases, potentially leading to a dangerous condition called hyponatremia.

Potential Energy Diagram

A graph that shows the energy changes that occur during a chemical reaction as it progresses from reactants to products.

Reactants and Products

The starting materials are on the left side of the diagram and the final materials are on the right side.

Energy Levels

The vertical axis (y-axis) represents the energy of the reactants and products, with higher energy values at the top of the diagram.

Enthalpy Change (ΔH)

The difference in energy between the reactants and products, indicating whether energy is absorbed or released.

Exothermic Reaction

A reaction where the products have lower energy than the reactants, meaning energy is released (ΔH is negative).

Endothermic Reaction

A reaction where the products have higher energy than the reactants, meaning energy is absorbed (ΔH is positive).

Activation Energy (Ea)

The difference in energy between the reactants and the transition state, representing the energy required for the reaction to proceed.

Activation Energy and Reaction Rate

A higher activation energy means a slower reaction rate because more energy is required for the reaction to proceed.

Catalysts

Substances that lower the activation energy by providing an alternate reaction pathway, leading to a faster reaction rate.

Reverse Reaction

The activation energy for the reverse reaction (products to reactants) is also indicated on the diagram.

Reaction Progress

The horizontal axis (x-axis) represents the reaction coordinate, which indicates the progress of the reaction from reactants to products.

Cellular Respiration

A process that generates energy for cells, involving 3 main stages: glycolysis, the citric acid cycle, and oxidative phosphorylation.

Glycolysis

The input is glucose, the location is the cytoplasm. Glucose is broken down into two pyruvate molecules, producing a small amount of ATP (2 net ATP) and NADH (2 NADH). The output is Pyruvate, ATP, and NADH.

Citric Acid Cycle

The input is pyruvate (converted to acetyl-CoA) and the location is the Mitochondrial Matrix. Acetyl-CoA enters the cycle, undergoing a series of reactions that release carbon dioxide, produce ATP, and generate NADH and FADH2. The output is carbon dioxide, ATP, NADH, FADH2.

Oxidative Phosphorylation

The input is NADH, FADH2, and oxygen, and the location is the mitochondrial inner membrane. Electrons from NADH and FADH2 are passed along the electron transport chain to create a proton gradient, which then drives the synthesis of ATP.

Light Dependent Reactions

Occur in the Thylakoid Membrane, where chlorophyll and other pigments absorb light energy.

Electron Transport Chain

Electrons are passed along an electron transport chain, releasing energy that is used to pump protons across the thylakoid membrane, creating a proton gradient.

Generation Of ATP and NADPH

The energy from the light is used to convert ADP and NADP+ into ATP and NADPH respectively, storing energy.

Light Independent Reactions

Also known as the Calvin Cycle, occur in the Stroma.

Carbon Fixation

Carbon dioxide from the atmosphere is taken up and converted into organic molecules, primarily glucose.

Sugar Synthesis

The ATP and NADPH produced during the light dependent reactions are used to power the Calvin cycle and fix carbon dioxide.

Glucose Synthesis

Through a series of reactions, carbon dioxide is converted into glucose, which is then used by the plant for energy and other processes.

Regeneration

The cycle regenerates its starting molecules to continue the cycle.

Cell Cycle

Describes how the number of chromosomes, the number of homologous pairs, and amount of DNA varies in different stages.

G1 Phase

The cell grows and prepares for DNA replication. DNA content is 2c (2 copies of each chromosome) and chromosome number is 2n (diploid).

S Phase

DNA replication occurs, doubling the DNA content. DNA content becomes 4C but the chromosome number remains 2n.

G2 Phase

The cell continues to grow and prepare for mitosis. DNA content is still 4C, and the chromosome number is 2n.

M Phase

DNA is separated into two identical daughter cells. DNA content returns to 2C, and the chromosome number remains 2n in each daughter cell.

Meiosis 1

Homologous chromosomes (1 from each parent) pair up and may exchange genetic material through crossing over.

Prophase 1

Homologous chromosomes pair up and may exchange genetic material through crossing over.

Metaphase 1

Homologous pairs line up at the cell's equator.

Anaphase 1

Homologous chromosomes separate, moving to opposite poles of the cell. The number of homologous chromosomes pairs is halved.

Telophase 1 & Cytokinesis

The cell divides resulting in two daughter cells, each with half the original numbers of chromosomes (haploid, 1n).

Meiosis II

Sister chromatids (identical copies of a chromosome) line up at the cell's equator.

Prophase II

The chromosomes condense.

Metaphase II

Sister chromatids line up at the cell's equator.

Anaphase II

Sister chromatids separate, moving to opposite poles.

Telophase II & Cytokinesis

The cell divides, resulting in four daughter cells, each with a haploid number of chromosomes (1n) and a single copy of each chromosome.

DNA Content

Replication in S phase doubles DNA content, but it is halved during meiosis I and II.

Chromosome Number

The number of chromosomes remains the same during the cell cycle (2n) except when DNA replication occurs (S phase) and when the cell undergoes meiosis. Meiosis I and II reduce the chromosome number by half (2n to 1n).

Homologous Pairs

The number of homologous pairs is halved during meiosis I when homologous chromosomes separate.

Homozygous

RR or rr.

Heterozygous

Rr.

Phenotype

The observable traits or characteristics of an organism, resulting from genotype and interactions with the environment.

Genotype

The genetic makeup of an organism, referring to specific alleles it possesses for a specific gene.

Gene

A unit of heredity, a sequence of DNA that codes for a specific protein or trait.

Allele

A specific variation of a gene; different alleles can result in different traits.

Identifying Genotypes

If a plant has purple flowers (dominant trait) and you know the dominant allele is 'P', the plant's genotype could be PP (homozygous dominant) or Pp (heterozygous).

Predicting Phenotypes

Knowing the genotypes of individuals, you can predict the phenotypes of the offspring using tools like Punnett squares.

Understanding Dominant and Recessive Alleles

Dominant alleles mask the expression of recessive alleles.

Complete Dominance

Example: Tall pea plants (T) are dominant to short pea plants (t). Cross: If you cross two heterozygous tall pea plants (Tt x Tt), you'll get 1 TT (homozygous dominant, tall), 2 Tt (heterozygous, tall), 1 tt (homozygous recessive, short). Genotypic Ratio: 1:2:1 (TT:Tt:tt). Phenotypic Ratio: 3:1 (tall:short).

Incomplete Dominance

Example: Red and white snapdragons produce pink offspring when crossed (Rr). Cross: If you cross two heterozygous pink snapdragons (Rr x Rr), you'll get 1 RR (homozygous dominant, red), 2 Rr (heterozygous, pink), 1 rr (homozygous recessive, white). Genotypic Ratio: 1:2:1 (RR:Rr:rr). Phenotypic Ratio: 1:2:1 (red:pink:white).

Co-dominance

Example: ABO blood groups (IA, IB, i) in humans. Cross: If you cross a person with type AB blood (IAIB) with someone with type O blood (ii), you'll get 1 IAi (type A blood), 1 IBi (type B blood). Both are heterozygous and express both A and B antigens. Genotypic Ratio: 1:1 (IAi:IBi). Phenotypic Ratio: 1:1 (type A: type B).

Sex Linkage

Example: X-linked recessive. Female (XX): Can be homozygous normal (XX), heterozygous carrier (XNXn), or homozygous affected (XnXn). Male (XY): Has only one X chromosome, so if he inherits an X-linked recessive allele, he will express the trait.

Cross

If a female carrier (XNXn) is crossed with a male who is unaffected (XNY), their offspring will be: Females: 50% carrier (XNXn), 50% normal (XNXN); Males: 50% unaffected (XNY), 50% affected (XnX).

Phenotypic and Genotypic ratios

Will be different for males and females.

Punnett square

A helpful tool to visualize all possible combinations of alleles from parents to offspring, used to determine both genotypic and phenotypic ratios for any monohybrid cross.

Double Helix

DNA's structure is a double helix, meaning two strands intertwine to form a spiral staircase shape.

Sugar-Phosphate Backbone

Each strand has a repeating sequence of sugar (deoxyribose) and phosphate groups, forming a backbone.

Antiparallel Strands

The two strands are antiparallel, meaning they run in opposite directions, with one strand having a 5' phosphate end and the other a 3' hydroxyl end.

Base Pairing

The two strands are held together by complementary nitrogenous bases (adenine, thymine, guanine, and cytosine), forming base pairs (A-T and G-C) within the helix.

Directionality

The 5' and 3' ends of the DNA strands define their directionality, with DNA replication and synthesis always proceeding from the 5' end to the 3' end of the new strand.

Transcription Process Step 1

Identify the template strand: Determine which DNA strand will be used as the template for transcription.

Transcription Process Step 2

RNA polymerase binding: The enzyme RNA polymerase binds to a specific region on the DNA, known as the promoter.

Transcription Process Step 3

DNA unwinding: The DNA double helix unwinds near the transcription initiation site, creating a transcription bubble.

Transcription Process Step 4

RNA synthesis (elongation): RNA polymerase reads the template DNA strand in the 3' to 5' direction and synthesizes a complementary RNA molecule in the 5' to 3' direction.

Transcription Process Step 5

Termination: The RNA polymerase reaches a terminator sequence on the DNA, and the newly synthesized RNA molecule is released.

Base Pairing Rules for RNA

A (DNA) pairs with U (RNA); T (DNA) pairs with A (RNA); G (DNA) pairs with C (RNA); C (DNA) pairs with G (RNA).