AP Bio Vocab (Units 1-3)

Ionic Bonds

Bonds formed from transfer of electrons between atoms, produce positive and negative ions and formed from differences in electronegativities.

Covalent Bond

Bonds formed when electrons are shared between atoms because of similar electronegativities. Bonds can be polar (eg oxygen-water bonds)

Hydrogen Bond

Strongest intermolecular force, created between hydrogen and one of nitrogen, oxygen, or fluorine.

Occurs between water, DNA strands, protein folding

Properties of Water

1. Universal solvent - can dissolve polar and ionic substances

2. Ability to form hydrogen bonds (strong adhesion/cohesion) - capilliary action of water, transpiration

3. High specific heat capacity - moderation of temperature, evaporative cooling

4. Liquid form is most dense (ice floats) - seasonal overturn, insulation for lakes during winter

pH

Lower than 7 = acidic, Greater than 7 = basic, 7 = neutral

Changes in pH can reduce biodiversity, buffers are used to stabilize pH. Indicator species can reflect changes in pH of an environment

Properties of Carbon

All organic compounds have carbon

1. Able to create large molecules

2. Can create chains (straight, branched, or ringed compounds)

3. 4 valence electrons → 4 covalent bonds

Isomer

A difference in the structure of a molecule with the same molecular formula. Form = function → isomers cannot perform the same function

1. Structural - Different arrangement of molecules (glucose vs fructose)

2. Enantiomers - Different orientation of molecules (mirroring)

3. cis-trans - Different spatial arrangement around a double bond

Functional Groups

Specific arrangements of atoms that change the properties of molecules, often involved in reactions or interactions

1. Hydroxy l (-OH)

2. Carboxyl (-COOH)

3. Carbonyl (C=O)

4. Amino (-NH2)

5. Sulfhydryl (-SH)

6. Phosphate (-OPO3 2-)

7. Methyl (-CH3)

Classes of Macromolecules

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic Acids

Dehydration Synthesis

Process by which polymers are created where water is produced by combining monomers/ends of a pre-existing polymer. Uses hydroxyl and carboxyl functional groups

Hydrolysis

Breaking down a polymer by re-introducing water. Turns polymers back into monomers/less complex molecules.

Carbohydrates

Monomer: Monosaccharide (glucose, fructose, galactose - all isomers)

Polymer: Disaccharide (2 monomers), polysaccharide (starch, chitin, cellulose, glycogen)

Function: Energy storage (short term) and support

Lipids

Composed of C, H, O, and P in phospholipids. Nearly insoluble in water

Monomer: Fatty acids/glycerol

DO NOT form polymers, form hydrocarbon chains: Saturated fats, unsaturated fats, trans fat, steroids, phospholipids

Function: Energy storage (long term), protection of vital organs, insulation

Saturated Fats

Each carbon in the chain, with the exception of the carboxyl group, has only single bonds (saturated with hydrogens). Allows tight packing → leads to cardiovascular disease when saturated fats build up in blood vessels. Primarily produced by animals

Unsaturated Fats

The chain has at least one double bond between carbon atoms, causing a bent shape. Does not pack tightly → can melt at lower temperatures than saturated fats. Primarily produced by plants

Trans Fats

Unsaturated fats that are changed to become saturated (shape changes from kinked to straight). Produced by hydrogenating repeatedly heating or unsaturated fats. Now acts as saturated fat, increases risk of cardiovascular disease.

Phospholipid

Composed of phosphate (hydrophilic) head and fatty acid (hydrophobic) tails. Creates phospholipid bilayer in cell membranes

Steroids

Made of 4 fused carbon rings that function as hormones in the body. Eg Cholesterol, estrogen, testosterone

Proteins

Monomer: Amino acid

Polymer: Polypeptide (amino acids linked by peptide bonds). Differ in structure due to number/arrangement of amino acids

Function: Structure, transport, storage, defense, enzymes

Amino Acid Structure

1. Central carbon atom

2. Amino group (-NH2)

3. Carboxyl group (-COOH)

4. Hydrogen atom (-H)

5. R group

R group determines which amino acid and its properties (hydrophobic, hydrophilic, acidic, basic, etc). Influences protein structure → function of end protein

Protein Folding/Structure

1. Primary - Order of amino acids

2. Secondary - 3D shape caused by hydrogen bonding between amino acids to form helix or folded plane

3. Tertiary - 3D shape caused by interactions between R groups (H-bonds, disulfide bonds, hydrophobic interactions etc). Disulfide bonds “lock” shape

4. Quaternary - Assembly of 2+ separate peptide chains

Denaturation

Breakdown/changes to protein structure caused by changes to pH environment, ions, high temperature, etc. Prevents protein from functioning properly, possibly reversible but can be permanent as well. IMFs of 2nd-4th structure are broken

Nucleic Acids

Monomer: Nucleotide

Polymer: Nucleic polymer

Function: Store genetic material/information, transfer of genetic information via DNA/RNA

DNA Structure

Composed of 2 strands of deoxyribose, phosphate, and nucleotide bases in a double helix structure. Strands held together by hydrogen bonds between bases and run anti-parallel to each other. Grows in 5’ → 3’ direction

Bases: Adenine, thymine, guanine, cytosine

RNA Structure

Composed of ribose, phosphate, and nucleotide bases in a single strand structure

Bases: Adenine, uracil, guanine, cytosine

Purine

Adenine and guanine bases composed of 2 rings. Must match with a pyrimidine base to stabilize nucleic acid structure

Pyrimidine

Cytosine, uracil, and thymine bases composed of 1 ring. Must match with a purine base to stabilize nucleic acid structure

Adenine-Thymine/Uracil bond

2 hydrogen-bonds, easier to separate than Cytosine-Guanine bonds

Cytosine-Guanine bond

3 hydrogen-bonds → separate at higher temperatures, harder to separate than Adenine-Thymine/Uracil bonds

Cell Theory

1. All living things are made of cells

2. All cells came from pre-existing cells

3. Cells are the basic unit of life

Cells

1. Prokaryotic

2. Eukaryotic

All cells are enclosed by a selective barrier (plasma membrane) and have ribosomes, cytosol, and contain genetic material (RNA or DNA)

Theory of Endosymbiosis

Eukaryotic cells emerged after mitochondria and chloroplasts were engulfed by a pre-existing cell. Supported by mitochondria and chloroplasts having their own DNA which is circular like in prokaryotes

Eukaryotic Cells

Have internal membranes → distinct organelles, DNA is wrapped with histone proteins in chromosomes, has cytoskeleton, metabolism is aerobic, cells are typically larger. Ribosomes are also typically larger

Prokaryotic Cells

No internal membranes → no distinct organelles other than ribosomes, DNA is naked and circular in nucleoid region (no nuclear membrane), metabolism can be aerobic or anerobic, ribosomes tend to be smaller, cells overall are quite small

Surface area/Volume in regards to the cell

Cells are small to maximize surface area to volume ratio → diffusion is slow so to transport enough stuff into the cell, cell can’t be too big or not enough will diffuse in

For cells to cover long distances, they must be very thin to maximize surface area (eg neurons)

Organelles - Nucleolus

Synthesis of rRNA (ribosomal RNA) and assembly of ribosomes. Not membrane bound, found in eukaryotic cells around the nucleus.

Organelles - Ribosomes

Found freely in cytoplasm (prokaryotic and eukaryotic) or bound to the rough endoplasmic reticulum (RER) in eukaryotic cells. Free ribosomes = proteins for cell use, bound ribosomes = proteins for export/part of membrane

Organelles - Endomembrane System

Composed of nuclear envelope, ER, Golgi Apparatus, lysosomes, vesicles/vacuoles, and plasma membrane. Regulates protein traffic and performs metabolic cell functions

Organelles - Nucleus

Contains genetic information (chromosomes, DNA, etc). Has nuclear membrane, selectively permeable to regulate transport of mRNA. Site of transcription (DNA → RNA)

Organelles - Endoplasmic Reticulum (ER)

System of channels and sacs for synthesis of proteins (Rough ER, has ribosomes) and lipids (Smooth ER, no ribosomes).

Organelles - Golgi Apparatus

Flattened membrane sacs that process and package proteins produced by the RER into vesicles for transport. Vesicles can then be used for transport within or outside of the cell

Organelles - Lysosome

Sacs of digestive enzymes, allows for intracellular digestion, apoptosis, autophagy. Enzymes only effective at low pHs found inside the lysosome, if lysosome breaks open enzymes will denature. Generally not found in plant cells.

Organelles - Mitochondria

Site of cellular respiration (ATP production), found in eukaryotic cells (both animal and plant). Double-membrane bound organelle, contains its own DNA. Made of outer membrane, intermembrane space, inner membrane, cristae, and matrix.

Organelles - Vacuoles

Membrane bound structures used for storage. Derived from ER and Golgi Apparatus. In plant cells, central vacuole is responsible for turgor pressure.

Organelles - Chloroplasts

Only found in plant cells, hold chlorophyll and are site of photosynthesis. Double membrane bound organelle, absorbs light energy and synthesizes sugars. Composed of thylakoid (stacks = grana), stroma, and lumen. Has its own DNA independent of the cell

Organelles - Cell Wall

Only found in plant cells, made of cellulose to provide structure and protection to cell.

Organelles - Cell Membrane

Selectively permeable structure that engulfs the whole cell. Typically made of phospholipid bilayer with integrated sugars, proteins, and other molecules. Regulates what enters/exits by polarity and size. Larger or polar molecules can enter through active transport through the membrane or facilitated diffusion. Represented by the fluid mosaic model

Fluid Mosaic Model

Representation of the phospholipid bilayer and its embedded proteins/sugars. Held together by weak interactions → allows mobility in layers.

• Integral Protein - fully embedded proteins, pass through the whole membrane

• Peripheral Protein - partially embedded proteins, only pass through some of the membrane

• Glycoproteins - proteins with carbohydrates bonded to them, acts as a signaling molecule

Membrane Protein functions

1. Transport - Channel, pumps, carriers, and ETC proteins move molecules across the membrane

2. Signaling - Protein receptors bind to chemical messengers (hormones) to initiate signal transduction pathway

3. Cell-to-cell recognition - Glycoproteins participate in autocrine, paracrine, and juxtracrine

4. Enzymatic Activity - Membrane holds protein in place

5. Attachment to cytoskeleton (stabilize location and maintain cell shape)

Active Transport

Transport that requires ATP and tends to move substances against their concentration gradients.

• Endocytosis/Exocytosis

• Pumps (eg Na+,K+ pump)

• Contractile vacuole

• Cotransport

• ETC

Passive Transport

Movement of molecules with their concentration gradients. Can be facilitated by proteins as long as no ATP required.

• Diffusion

• Osmosis

• Facilitated Diffusion

Hypertonic

Solution A has a greater concentration of solute than Solution B. Water would travel into solution A

Hypotonic

Solution A has a lower concentration of solute than Solution B. Water would travel into solution B

Isotonic

Solution A has the same concentration of solute as Solution B. There is no net movement of water, they are in dynamic equilibrium

Osmotic Potential

Tendency of water to move across a permeable membrane into a solution

Osmolarity

Concentration of all solutes in a solution. Water will move from lower osmolarity solutions to higher osmolarity solutions

Water Potential

Water moves from high water potential to low water potential. Calculated by adding solute potential and pressure potential. Open systems have NO pressure potential (eg animal cells). Plant cells have cell walls → have pressure potential.

Ψw = Ψs + Ψp

Aquaporins

Specialized pores that allow water to move through a cell membrane easier

Cotransport

A concentration gradient is created by ATP and then movement of the species with the concentration gradient pulls another substance through a membrane (eg H+ and sucrose, H+ gradient created with proton pump (ATP) and the subsequent of H+ with the new gradient pulls sucrose against its concentration gradient)

Enzymes

Molecules that can speed up a chemical reaction that are not consumed in the process. Lower the activation energy of a reaction. Are substrate specific (only bind to a specific substrate) and may denature due to temperature, pH, and salinity

Enzyme Regulation

Ways to increase/decrease enzymatic activity

• Competitive inhibition (active site) - A molecule that resembles the substrate binds to the active site, preventing the enzyme from activating

• Allosteric control (non-competitive inhibition) - A molecule binds to the allosteric site, either allowing the enzyme to bind to its substrate or inhibiting it

Energy

Ability to do work. Living systems need constant supply of energy for maintenance of homeostasis/order → no energy = death. Most common form of energy for systems is ATP, produced by cellular respiration

Photosynthesis

6 H2O + 6CO2 → C6H12O6 + 6O2

Production of glucose, light energy converted into chemical and carbon is fixed into usable sources. Chlorophyll = pigment responsible for photosynthesis

• Light Reactions

• Light-Independent Reactions/Calvin Cycle

Photosynthesis Light Dependent Reactions

Using light energy directly to produce ATP and NADPH. O2 produced as a byproduct of photolysis (H2O → 2H+ + 2e- + 1⁄2O2). Occurs in the thylakoid membranes, specifically in photosystems 2 and 1

Photosynthesis Light-Independent Reactions (Calvin cycle)

Using energy stored in NADPH and FADH2 to produce sugars. Occurs in the stroma, fixes atmospheric CO2 into G3P (glucose pre-cursor)

Autotroph

Organisms that can produce their own energy (self-feeders)

• Producers

• Phototrophs - use solar energy to produce organic compounds

• Chemoautotrophs - use inorganic energy (eg heat) to create organic compounds

Absorption Spectrum

Graph that shows wavelengths of light that are absorbed by a specific pigment. Absorbed light energy excites electrons to higher energy levels

Action Spectrum

Graph that shows wavelengths of light that are effective in driving photosynthesis (sum of all pigments)

Photosystem 2

First protein complex in light dependent reactions (photosynthesis). Located in thylakoid membranes. Uses solar energy to split water into oxygen, protons (H+) and electrons. Initiates the ETC for photosynthesis

Photosystem 1

Comes after Photosystem 2. Protein complex that produces NADPH for Calvin Cycle’s carbon fixation.

Chemiosmosis/Photophosphorylation

Making ATP from ADP and Pi from light energy. Done by ATP synthase, H+ flows with concentration gradient (thylakoid membrane → stroma)

H2O + ADP + Pi + NADP+ + light → ATP + NADPH + O2 + H+

H+ Gradient

Formed by ETC of Photosystem 2 pumping H+ into lumen, photolysis producing H+ in lumen and NADPH formation reducing H+ concentration in the stroma