AP Biology Vocab

all the small lil things you should know that are not incredibly easy

Heat of Vaporization

• The amount of energy(joules/calories) needed to vaporize one gram or mole of a substance from a liquid to a gas at constant temp and pressure.

Evaporative Cooling

• Occurs when the highest kinetic energy molecules of a liquid evaporate, reducing the average kinetic energy(temperature) of the remaining liquid

Hydration shell

• A sphere of water(H2O molecules) that surrounds dissolved ions, orienting themselves to match the ions charge(+ or -)

Hydrophilic/Hydrophobic

• Hydrophilic refers to a molecules affinity for water as a polar molecule, and is therefore attracted to water

• Hydrophobic is the opposite, as a non polar molecule, it is repelled by water

Cohesion

• The ability for like molecules(not just water) to stick together due to intermolecular forces(like hydrogen bonding for water)

Adhesion

• The ability for molecules to stick to different surfaces like water’s ability to stick to other polar surfaces due to its already polar nature.

Specific Heat Capacity

• Specific heat capacity is the amount of energy (in joules or calories) required to raise the temperature of 1 gram of a substance by 1 degree Celsius.

Solvent

• Substance that is being dissolved in the solute

• For example: NaCl(salt) is the solvent when placed in water

Solute

• Substance dissolving the solvent

• For example: Water is the solute when NaCl is placed in water

Dalton

• The approximate weight of 1 proton or 1 neutron(unit of mass)

Hydrocarbons

• Carbon atoms bonded with Hydrogen

Isomers

• Molecules with the same chemical formulas but with different atomic orientations, resulting in multiple distinct molecules

• For example: Glucose & Fructose are both written as C6H12O6 but are different 

Trans-isomers

Cis-isomers

Both are variations of the same molecule

• atoms/groups are on opposite sides of each other on a ring structure

• Differentiating factor = atoms/groups are adjacent to each other

These occur around a rigid structure, typically a double bond or a ring

Enantiomers

• Molecules with the same molecular formula but are structurally mirror images of each other

Polymers

• LONG Molecular chains made up of repeating monomers(smaller units) which can be composed of multiple kinds of monomers

Monomers

• A single molecular unit that has the ability to covalently bond with other monomers(not just its own type of monomer) to form a larger chain called a polymer

Macromolecules

• Massive molecules(usually polymers) made from other organic molecules that are fundamental to life

• These include: Carbohydrates, Proteins and Nucleic Acids

Monosaccharides

• A single simple carbohydrate that is usually some form of CH2O

• Serve as monomers for other more complex carbs

• Examples include Fructose and Glucose

Disaccharides

• A more complex carbohydrate that is formed through 2 monosaccharides bonding through a glycosidic linkage(a covalent bond) through a dehydration reaction

• For example: Maltose is formed through two molecules of glucose

Polysaccharides

• The most complex form of carbohydrate, formed through hundreds to thousands of monosaccharides joined by glycosidic linkages

• Often used as fuel storage, and are hydrolyzed when needed or are used as structural protections

Enzymes

• Specialized large protein molecules(a macromolecule) that speed up chemical processes by catalyzing the process

Dehydration Reaction

• A reaction that bonds two monomers together through the loss of a -OH from one and a -H from another in order to create a polymer and a H2O

• A “build” mechanism

• Forms macromolecules

Hydrolysis Reaction

• The process of H2O pushing apart two bonded monomers apart, one gaining a hydroxyl group and the other gaining a H

• A “break” mechanism

• Digestion that breaks complex carbs into simpler sugars

Ester Linkage

• A covalent bond formed between a glycerol and fatty acids through a dehydration reaction, creating a triglycerol

Carbohydrates

• One of the 4 main biological macromolecules and ranges from small simple sugars (monosaccharides) to big complex carbohydrates(polysaccharides)

• Functions: Providing sugar(energy) to cells and serving as structural components

Lipids

• Composed of mostly hydrocarbons, is characterized by its Hydrophobic nature allowing them to group up together in water

• Includes: Fats, Phospholipids, Waxes and Steroids

Fats

• Is a lipid

• Formed through an ester linkage with glycerol and fatty acids, the resulting triglycerides are able to store tons of energy

Saturated Fat

• Refers to when the fatty acid lacks double bonds, allowing them to pack tightly to each other. Is seen in animal fat and stores lots of energy

Unsaturated Fat

• Refers to when the structure of the hydrocarbon chains in a fatty acid contains double bonds(altering their typically straight structure), preventing them from packing tight. Most commonly seen in oils

Phospholipids

• A type of lipid, is typically seen as the cellular bilayer(membrane) since its dual(ampipathic) hydrophobic & hydrophilic nature forms a natural shield 

Waxes

• A type of lipid characterized by an alcohol group bonded(via ester linkages) to a long fatty acid chain

• Super duper hydrophobic and is therefore seen in waterproofing!(like ducks put it on their feathers so they stay waterproof)

Steroids

• A type of lipid characterized by its 4 carbon skeleton rings

• They differ through the varying positions of their functional groups(Ex. hydroxyl)

• Cholesterol and the sex hormones are common examples

Trioses

• a monosaccharide with 3 carbons formed in a straight line

Hexoses

• a monosaccharide with 6 carbons formed MOST likely in a ring but occasionally in a straight line as well

• Most common

Glycosidic Linkage

• A covalent bond formed through a dehydration reaction between two monosachharides to form disaccharides or polysaccharides

• Have 2 forms: α(alpha) and β(beta)

  • Alpha linkages are all the same

  • Beta linkages alternate

• Enzymes that hydrolyze(break down) these linkages are unable to do both(alpha and beta). This is why we poop, our enzymes can only deal with one, and the other goes out as waste

Aldoses & Ketoses

• Aldoses= monosaccharides with an aldehyde group (-CHO)

• Ketoses= monosaccharides with a ketone group (C=O)

Glycerol

• An alcohol molecule with a 3 carbon backbone with a -OH group on every Carbon

• This structure allows it to form ester linkages to other molecules like fatty acids

Fatty Acids

• Long hydrocarbon chains with a carboxyl group (-COOH) at one end.

• This carboxyl group allows them to form ester linkages with glycerol (or other alcohols) through a dehydration reaction, creating lipids such as triglycerides and phospholipids.

Bilayer

• Also called the cellular membrane, is a layer around the cell made of phospholipids that controls what comes in and out of the cell while providing protection.

Polypeptide

• A molecule formed through the formation of amino acids bonded via peptide bonds

• Polypeptides are linear chains of amino acids and are only called proteins when folded into 3 dimensional shapes

Peptide bond

• A bond formed between amino acids

• Is a dehydration reaction

To be more specific: a covalent bond formed between the carboxyl group of one amino acid and the amino group of another amino acid.

Proteins

• Incredibly specialized and complex molecules made up of one or more polypeptides

• Is 3-D in shape(polypeptides are only linear)

• Have tons of diversity in their workplace, with some of their functions:

  • Enzymes

  • Structural

  • Transport

  • Signaling

  • Defense

  • Movement

  • Storage

Amino Acids

(Hydrophobic)

(Hydrophilic)

(Acids and Bases)

• Amino acids are the building blocks of proteins.

• Each amino acid consists of one central(alpha) carbon surrounded by:

  • An amino group(like NH2),

  • A Carboxyl group

  • A H

  • A R side group(molecular groups bonded to the amino acid that determine its properties)

• An amino acid can be acidic, basic polar(hydrophilic), or hydrophobic based on the properties of the R side group

Disulfide Bridges

• Covalent bond formed in polypeptides(can be the same polypeptide or in different ones) between the sulfhydryl groups within the polypeptide.

• These sulfhydryl groups are only existent in the amino acid cysteine

Most importantly, these bonds fold the polypeptide into a protein with a 3-D structure

Denaturation

• The unfolding of a protein's three dimensional shape through stress placed on the protein.

• This leads to the complete destruction of that proteins function

Chaperonins

• Chaperonins- Cylindrical tubes that house a protein and provides it with optimal conditions to form

• They are also a type of protein themselves

Proteins: Primary Structure

• The primary structure of a protein consists of a linear chain of its amino acids

• Only peptide bonds between the amino acids are prevalent at this stage

• Act as the blueprint for the rest of the protein to follow as it forms

Proteins: Secondary Structure

• The secondary structure is where the initial folding of the polypeptide occurs

• This folding occurs between the carboxyl O of one and the H of the other(not R groups) and is formed/stabilized by hydrogen bonds(H and O = hydrogen bonding!)

• There are two commonly seen structures as a result of this folding:

  • Alpha-helix (α-helix) as a spiral or a coil

  • Beta-pleated sheet (β-pleated sheet) as a sheet like structure

Proteins: Tertiary Structure

• The tertiary structure is when a singular polypeptide chain attains its complex 3-D form

• It does so through the folds that occur via many interactions and attractions such as:

  • H-bonding

  • Disulfide Bridges

  • Hydrophobic interactions(non-polar parts are pushed into the core of the molecule)

  • Van Der Waals(IMFS)

  • Ionic Bonds(between the negatively and positively charged parts of the R groups)

• These interactions are often a driven by the R side groups of the amino acids

• Tertiary structures can be proteins on their own

Proteins: Quaternary Structure

• Quaternary structures emerge when 2 or more polypeptides come together to form an even more complex protein

• The attractions between these polypeptides are the same forces as the ones within tertiary structures

• Examples are collagen and hemoglobin

Polynucleotides

• A long chain of many nucleotides(polymer) linked together through phosphodiester bonds

• Make up the nucleic acids like DNA & RNA

Antiparallel

• When two molecular strands are running side by side but in opposite directions

• The most famous example is DNA, with its two strands going in opposite directions

  • This is critical for the replication process of DNA as the two strands are complementary

Nucleotides

• A monomer consisting of three parts:

  • A nitrogenous base(adenine, guanine, thymine, cytosine, uracil)

  • A five-carbon sugar (ribose in RNA, deoxyribose in DNA)

  • One or more phosphate groups

• These monomers are linked via phosphodiester bonds to form polynucleotides, the polymer that makes up nucleic acids

DNA

• Is a nucleic acid

• Found in the nucleus of Eukaryotic cells, DNA(or deoxyribonucleic acid) holds the genetic code for life

• It exists as a double helix and its main function is to allow cells to duplicate accurately as well as transcribing RNA, which drives protein synthesis

RNA

• Is a nucleic acid

• Is transcribed from DNA(meaning it is based on DNA’s language into its own RNA language)

• Main function is the synthesis of proteins(is quite complicated)

• Exists as a single strand

Nitrogenous base

• A slightly basic molecule and consist of Adenine, Guanince, Thymine, Cytosine and Uracil(in RNA instead of T)

• Are rings containing Carbon and Nitrogen

• Their specific sequence within Nucleotides determines the genetic code

• Complement each other(crucial in DNA’s replication)

  • Guanine and Cytosine

  • Adenine and Thymine/Uracil

Pentose

• A 5 carbon sugar

  anything with -ose is usually a sugar

• Another part of nucleotides

• a monosaccharide with 5 carbons formed in either a ring or in a straight line (linear)

Phosphate Group

• A functional group: phosphorus atom bonding with 4 oxygen atoms

• In a nucleotide, this group is bonded to the 5’ carbon

• Important for ATP(adenosine triphosphate)

Purines

• Nitrogenous bases characterized by a double-ring structure

• Include Adenine and Guanine(complementary)

Pyrimidines

• Nitrogenous bases characterized by a single ring structure. Includes Cytosine, Thymine and Uracil in RNA

Functional groups: Hydroxyl

• -OH

• Is polar

Functional groups: Carbonyl

• Determines whether a sugar is a ketone or an aldose

Functional groups: Carboxyl

• -COOH

• acts like an acid

Functional groups: Amine

• -NH2

• Acts like a base

Functional groups: Sulfhydryl

• -SH

• Can react with itself to stabilize proteins

Functional groups: Phosphate

• -PO3

• Contributes negative charge allowing molecules to react with H2O

Functional groups: Methyl

• -CH3

• Impacts gene expression

Phosphodiester Bonds

• Dehydration reaction created between nucleotides to form polynucleotides(like Dna and Rna)

Nucleus:

Made out of what parts?

What do each of these parts do?

Nucleus is the general statement of these parts:

1. Nuclear Envelope, a double membrane structure perforated with nuclear pores that decide what comes in and out the nucleus

2. Chromatin, DNA strands(uncoiled form) wrapped around stabilizing proteins called histones. When preparing to replicate, the chromatin condenses into chromosones

3. Nucleolus, the dense middle section of the nucleus, is where RNA is synthesized and is also where the initial structures of ribosomes are formed

Ribosomes:

Initially formation where?

Have what role based on where they are?

• Ribosomes have their initial(and partial) formation within the nucleolus

• Free Ribosomes in the cytoplasm synthesize ALL the proteins required to operate within the cytoplasm, such as enzymatic proteins(these proteins will stay within the cell indefinitely)

• Bound Ribosomes in the rough ER will produce proteins that will either be destined for the bloodstream(secretion), cell membrane, or various organelles of the cell like the Golgi Apparatus or Lysosomes. 

Endoplasmic Reticulum?

What are the different types and what differentiates them?

The Endoplasmic reticulum is a wide network of membranes with various functions:

• The rough ER has ribosomes in it, giving it a rough appearance. 

  • Is responsible for the synthesis of proteins, which are then secreted into the bloodstream or into other organelles

  • Makes a whole bunch of membrane for all the other organelles

• The smooth ER with 0 ribosomes drives metabolic processes

  • Is responsible for detoxifying toxic materials within the cell

  • Synthesis of lipids(like steroids)

  • Metabolizes carbs

  • Stores Calcium Ions

Golgi Apparatus

Two faces?

Also produces ___________

• The Golgi Apparatus is like the warehouse shipper of the cell, it receives membranes(called vesicles) from other organelles. For example, the Golgi Apparatus receives proteins from the ER and after modifying and packaging them, it is sent out to a specific destination.

• The Golgi Apparatus looks like a bunch of membranous sacs(called cisternae)

• When “receiving” something, it goes to its cis face, where the vesicle fuses with the cis face

• The trans face then packages them and sends them out

• The Golgi is also responsible for the production of macromolecules like polysaccharides

Lysosomes

Two processes?

• Lysosomes are membranous sacs that contain powerful enzymatic proteins

• When something comes into the cell, it is encapsulated in a membrane called a food vacuole. The Lysosome then fuses with the food vacuole, releasing all its enzymatic proteins within, breaking the substance down(hydrolysis). This process is called phagocytosis

• The Lysosome also has the ability to recycle materials within a cell, allowing a cell to continuously renew itself. This process is called autophagy

• Inside the Lysosome is a very acidic environment

• An example is the macrophage, a human white blood cell that helps destroy foreign things in our bloodstream

Vacuoles

What are they?

What are the different types?

• A vacuole is a large, membrane-bound sac found in the cytoplasm of a cell. Its function is to hold various materials, including water, food, and waste products.

Large central Vacuole

• Large Central Vacuole (in plants): This is a prominent vacuole that stores water, nutrients, and waste products. It is crucial for maintaining turgor pressure, which is the internal pressure that keeps a plant cell rigid and helps the plant stand upright.

Contractile vacuole

• Contractile Vacuole (in some protists): These vacuoles are found in freshwater protists like Paramecium. They expand as water flows into them and then contract to pump excess water out of the cell. Their primary role is osmoregulation (maintaining water balance) to prevent the cell from bursting.

Food Vacuole

What process is it associated with?

• Food Vacuoles (in some protists and animals): These temporary vacuoles are formed during phagocytosis to store food particles. They fuse with lysosomes, which release digestive enzymes to break down the food for the cell to use.

Cytoskeleton

• A network of fibers that functions as both structural support and communication within the cell

  • Is made of microtubules and microfilaments

Microtubules

• Shape the cell, guide organelle movement, and separate chromosones. Cilia & Flagella have microtubules within them

Microfilaments

• Super thin part of the cytoskeleton

• Structure: They provide structural support for the cell, particularly in maintaining its shape and resisting tension.

  Movement: Microfilaments are involved in many forms of cell movement, including muscle contraction, amoeboid movement, and the formation of pseudopods.

  Cytoplasmic Streaming: In plant and animal cells, they are responsible for the circular flow of the cytoplasm, which helps distribute nutrients and organelles.

Endosymbiont Theory

• A proven scientific theory that states that both the mitochondria and chloroplasts(good for producing energy) originated from bacteria with the similar function

Mitochondrian

creates what byproduct?

cellular _______

• Is responsible for cellular respiration, generating most of a cells ATP which is used as a source of energy 

Chloroplast

creates what byproduct?

• Found in plant cells(green) and are present in all photosynthetic cells.

• Creates glucose as a product of photosynthesis

Extracellular Matrix

• Is a complex network of macromolecules secreted by cells(like glycoproteins & proteoglycans) and provides stability in tissues while also holding and influencing cells within the tissues. 

Amphipathic

• Means to be both hydrophobic and hydrophilic, most likely because of their two different ends(like a phospholipid)

Fluid Mosaic Model

This model describes the membrane as a fluid structure with its parts like phospholipids or proteins moving about.

These proteins are depicted as floating within the bilayer

Membrane fluidity

Is caused by what?

How do external stressors affect it?

Role of cholestrol?

• Membrane fluidity describes the fluid nature of the membrane as loose hydrogen bonds hold it together, allowing its lipids and proteins to have some degree of freedom in their movements.

• Stressors like an increase in temperature will increase the fluidity of the membrane

• Cholestrol acts as a fluidity buffer within the membrane

Membrane proteins overview:

Two major groups?

• While phospholipids make up the main form of the cellular bilayer, its proteins are what dictate much of the membrane’s functions.

• For example, there are over 50 kinds of different membranous proteins within a red blood cell 

• The two main groups are: Integral Proteins & Peripheral Proteins

• These membrane proteins can be connected to various structural supports such as the cytoskeleton within the cell or the extracellular matrix outside the cell, allowing the cells themselves to have a stronger framework

• However they have A LOT of functions(and there is another flashcard about that)

Integral Proteins

• Are embedded within the bilayer. They either span the full width of the bilayer with either end poking out from each side, or are partially embedded, but still in the bilayer.

  • Most span the full width and are called: Transmembrane proteins

Peripheral Proteins

• Are under the bilayer(within the cell), and are loosely bounded there

Membrane Proteins Functions:

(6 major kinds)

1. Transport- Some transmembrane proteins can have Hydrophilic channels within them to shuttle a specific kind of solute while others use ATP energy to actively transport substances

2. Enzymatic Activity- Allows the membrane to carry out metabolic processes(sometimes these proteins group up as well to perform sequenced processes)

3. Signal Transduction- Proteins exposed to the outside can have receptors to receive signaling molecules to relay the message

4. Cell-Cell recognition- Some Glycoproteins serve as identifiers and are recognized by other proteins in other cell membranes

5. Intercellular binding- Membrane proteins can hook themselves to various lengths and are more long lasting than the process in cell-cell recognition

6. Attachment to structural supports- Membrane proteins can attach to the cytoskeleton or the extracellular matrix to stabilize the cell and overall strucure of the area

Role of Glycoproteins within the cell membrane

• Since glycoproteins(proteins with carbs) are so diverse, they act as identifiers - markers to distinguish one cell from one another

Selective permeability

• Defines the cell membrane’s ability to “choose” or allow certain substances through the membrane while keeping undesirable ones out/in

• Non-polar substances like CO2 and O2 cross the lipid bilayer more easily while polar molecules like glucose and even water have a harder time crossing. 

• The membrane is only one gateway though, and molecules can pass through via membrane transport proteins

Transport Proteins

• Since the cell membrane itself is made of lipids, which are non-polar & therefore don’t allow polar molecules to pass easily, transport proteins like aquaporins aid in the transport of substances into the cell. 

• Furthermore, there are two kinds of transport proteins: Channel proteins and Carrier proteins

  • Channel proteins provide a Hydrophilic channels within their membrane spanning structure to essentially bypass the membrane(all passive transport)

  • Carrier proteins hold on to their “passengers” and modify their own shape to pass release their passengers into the cell(passive & active Transport)

• Aquaporins(channel), specifically, are incredibly important to bring water into the cell and are responsible for most of the supply a cell gets 

Passive Transport(diffusion)

• Diffusion is essentially transport of a substance with no energy investment

• They go down to what is called the concentration gradient(a substance will diffuse from where its most concentrated to least concentrated)

Osmosis definition:

• Water moves from an area of higher to lower free water concentration(lower to higher solute concentration)

• This is essentially because solutes(like NaCl) are polar as ions broken down in water, and the H2O forms hydration shells around them, compacting into a smaller space, leaving more space for more water to fill. 

Isotonic

• A state of a cell where there is no net movement of water across the plasma membrane(like equilibrium)

Hypertonic

• A state of the cell where more water is expelled rather than brought in, causing the cell to shrivel and shrink.

• And this will happen due to more solute outside the cell causing osmosis to occur

Hypotonic

• A state of the cell where more water is brought in rather than expelled, causing cells to either expand, or in serious cases lyse which is essentially the cell exploding due to severe bloating(like my stomach)

Osmoregulation

• Evolutionary adaptations within cells living in hypertonic or hypotonic conditions to survive(such as a contractile vacuole to expel water in a hypotonic environment)