Biology Khanacademy

Cohesion

The attraction of molecules to other molecules of the same kind

Adhesion

The attraction of molecules of one kind to molecules of a different kind

Meniscus

The shape made by a liquid substance at the top of it’s surface.

An adhesive liquid will make a concave up ______ whereas a cohesive liquid will make a concave down/convex ______.

Hydrophilic

A charged or polar substance that interacts with and dissolves in water

Hydrophobic

A nonpolar neutral substance that does not interact well with water. Seperates from it unlike hydrophilic substances.

Evaporative Cooling

The notion that, due to convection and cooler molecules being pushed to the bottom as well as hotter molecules being pushed to the top, water molecules with higher KE evaporate first and as they do so the surface from which they escape cools i.e. its average KE goes down.

Polar molecule

A neutral, or uncharged molecule that has an asymmetric internal distribution of charge, leading to partially positive and partially negative regions.

Organic Molecule

Any molecule that has carbon in it. (Some exceptions such as CO2 and CO exist)

Hydrocarbon

Any molecule that has exclusively hydrogen and carbon atoms.

The Aufbau Principle

The principle that states electrons first fill subshells of the lowest available energy. This principle is the reason for atoms having 1s 2s 2p 3s 3p 4s filled and then beginning to fill 3d. (3d has higher available energy and 4s has a lower energy level)

Hydroxyl Functional Group

Follows the form R-O-H

Polar with partial negative on oxygen atom and partial positive on hydrogen

Methyl Functional Group

Follows the form R-C^-H_-H-H

Non polar and hydrophobic

Carbonyl Functional Group

Follows the form C=O

Polar with partial negative charge on oxygen atom and partial positive on carbon

Carboxyl Functional Group

Follows the form R-C^=O_-(O-H)

Polar with partial positive on H and C atoms and partial negative on O atoms. Additionally due to the high polarity the oxygen can hog electrons and release an H+ cation => this functional group is acidic.

Amino Functional Group

Follows the form R-N^-H_-H

Polar/Charged. Has one lone pair of electrons => Works well as a base as it is likely to attract H+ cations and thus to neutralise acids.

Phosphate Functional Group

Follows the form R-O-P^=O-O-H_-(O-H)

Charged/Polar. Due to the electronegativity of Oxygen it can hog the electrons and thus this functional group can act as an acid by releasing H+ cations into a substance. Note that this functional group can also be drawn as already having lost its H+ ions due to it being so acidic. Additionally it can further be drawn as its O anion having already bonded to other molecules after it has lost its H+ ion. It is drawn like this in DNA.

Sulfhydryl Functional Group

Follows the form R-S-H

Polar because sulfur is more electronegative than hydrogen but less polar than hydroxyl due to sulfur being less electronegative than oxygen.

Ionic bonds

Bonds created by the donation or receiving of electrons thus creating oppositely charged ions that bond to each other. These bonds occur when the difference in electronegativity between two molecules is so large that one molecule actually takes electrons.

Covalent bonds

Bonds created by the sharing of one or more electrons between 2 atoms

Cations

Positive ions formed by losing electrons.

Anions

Negative ions formed by gaining electrons.

London dispersion force

A force that occurs as a result of the random constant motion of electrons. This force occurs in a special moment within which the electrons of a molecule are all in a certain region resulting in a partially positive charge in the opposite region and a partially negative charge in the region containing the electrons.

This partial charge in both region can then induce an opposing partial charge in nearby molecules by pushing electrons away or attracting them and thus attracting the whole molecule resulting in a temporary bond.

Hydrogen bond

A bond that occurs due to polar molecules specifically ones containing hydrogen. Certain partially positive or negatively charged areas will be attracted to other molecule’s partially negative or positively charged areas respectively.

Van der waals force

Any intermolecular force of attraction not involving covalent bonds or ionic ones. Basically hydrogen bonds or london dispersion forces

Dehydration Synthesis

The process by which monomers combine together in order to build polymers. In this process a hydroxyl group and hydrogen atom is lost from each monomer thus creating an H2O molecule (hence the name _________ ________). The leftover missing bonds that were removed from the monomers to create the H2O molecule are then replaced by a bond between the monomers binding them together creating a polymer.

Hydrolysis

The opposite of dehydration synthesis. The process by which polymers are broken down into monomers (fundamental building blocks) in this process an H2O molecule is absorbed and the bond between sub-polymers is broken and replaced by a hydroxyl group on one sub-polymer and by an H atom on the other one.

Polymer

A molecule made up of multiple consecutively bound monomers. The way in which these are bound can be in different ways thus forming different macromolecules.

Monomer

A molecule that can be bonded to other identical molecules in order to form a polymer.

Monosaccharide

The fundamental units of carbohydrates. Serve as primary energy and often referred to as “simple sugars”. One of the most popular examples of one is glucose. These are essentially sugar monomers.

Polysaccharide

Long chains of carbohydrate molecules composed of monosaccharides. Essentially long chains of monosaccharides. _____________ and monosaccharides are the same as polymers and monomers. (I.e. the former is a conjunction of the latter and the latter is the building block for the former). This term is essentially an esoteric specific word for sugar polymers.

Ester bond

A covalent bond formed between a hydroxyl group from a carboxylic acid and a hydrogen atom from an alcohol. This bond is characterized by a carbonyl group and an oxygen atom single bonded to a carbon. During the creation of this bond the carboxylic acid always loses donates the OH group and the alcohol the H atom.

This bond follows the form

R-C=O_O-R’

Esterification

The process of creating an ester bond. During this process dehydration synthesis occurs to make the bond. These bonds occur between carboxylic acids and alcohols. Note that during _____ the carboxylic acid always provides a hydroxyl group and the alcohol always provides the H atom.

Ester

Any molecule with a carbonyl group and an oxygen that forms a single bond with the same carbon responsible for the carbonyl group (i.e. the carbon also double bonded to another Oxygen). These organic compounds react with water to produce alcohol through hydrolysis and can, in the backwards reaction, undergo esterification/dehydration synthesis.

Purines

Nitrogenous bases with 2 rings. This group of nitrogenous bases includes Adenine and Guanine which are both found in DNA.

Pyrimidines

Nitrogenous bases with 1 ring. This group of nitrogenous bases includes Thymine which is found in DNA, Uracil which is found in RNA and Cytosine which is found in both.

Amino Acids

The building blocks of protein. Generally follow the form (H-^H-_N)-R-_C^-H-(C^=O_-O-H)

Alpha Carbon

The carbon that is next to a functional group in an organic compound.

Polypeptide

A chain of more than one amino acid.

Monopeptide

A chain of one amino acid, the building block of a protein.

Peptide bond

The bond created between amino acids that form polypeptides. These bonds are created through dehydration synthesis between the amino acids. In this type of bond a covalent bond is created between a nitrogen and carbon atom.

Zwitterions

Molecules with parts that are charged i.e. parts that have excess electrons or a lack of but regardless still overall neutrally charged due to the charged parts being opposite and cancelling out. One example of __________ are amino acids at physiological PH as they donate H+ cations on one side but attract H+ cations using lone pair electrons on another.

Aldehyde group

A group of functional molecules following the form R-C^=O-H. Basically ketones but with a hydrogen atom attached instead of another molecule.

Ketone group

A group of functional molecules following the form R-C^=O-R’. This group contains the smaller sub-group: aldehydes.

Isomer

A name for a distinct configuration of an element. Molecules can have the same formula but some molecules arrange themselves and bond in distinct ways and orders and thus can give the molecule specific properties depending on the arrangement. A specific configuration/arrangement of a molecule is called an ________. For example an _____ of glucose is fructose.

Stereoisomers

An isomer of an element that only differs in the way in which atoms arrange themselves around one or more atoms. An ______ of an element will have atoms bonded in the same order but when viewed in 3d the seperation between certain atoms and the direction in which they point may differ among ________.

Glycerol

A molecule involved in the formation of fats/triacylglycerol. Also an alcohol. Has 3 carbons and 3 hydroxyl groups. Forms an ester bond through dehydration synthesis in order to create fat.

Acyl group

A functional group that envelops ester groups. This group follows the form R-C^=O-R’. This group generally refers to the carbon groups derived from carboxylic acids and differ from carbonyl groups due to carbonyl groups being a more general functional group.

Cis configuration

Configuration of an isomer in which a sub-molecule on one side will have the same position if the whole molecule is mirrored.

Trans configuration

Configuration of an isomer in which a sub-molecule on one side will have the same position if the whole molecule is mirrored and flipped upside down.

Fats/Triacylglycerol

The building block of lipids.

Nucleus

Powerhouse of the cell. Only found in eukaryotes.

Cells

The most basic unit of life. All living organisms are made up of one or more of these things.

Rough endoplasmic reticulum/ER

Parts of the endoplasmic reticulum with ribosomes attached. mRNA which attaches to a ribosome on this part translates a protein into the E.R Lumen. This protein then travels to the smooth E.R and buds off creating a vesicle.

Smooth endoplasmic reticulum/ER

Parts of the endoplasmic reticulum with no ribosomes attached. Also responsible for certain functions such as: Synthesis of carbohydrates, lipids, and steroid hormones, detoxification of medications and poisons, and storage of calcium ions.

Free Ribosomes

Ribosomes not connected to the surface of the endoplasmic reticulum. If an mRNA binds to one of these translation is paused and the ______ becomes bound to the endoplasmic reticulum.

Golgi Bodies/Golgi Apparatus

Parts of cells that look like the endoplasmic reticulum but are detached from the nuclear membrane. These are responsible for maturing vesicles that bud off the transitional E.R. allowing these vesicles, which contain proteins, to either embed into the cell membrane or to be transported outside of it and hence outside the cell. This part of the cell is mainly responsible for sorting packaging and tagging proteins and lipids found in transport vesicles in order to ensure they end up in the right place. When maturing vesicles, the vesicles travel to the cis face of the ____ ____. Fuse with it; after which they drop off their contents into the lumen of the ____ _____. The contents dropped then mature and finally bud off in transport vesicles through the trans face.

Mitochrondria

Powerhouse of the cell. Where ATP, a protein that drives many processes, is produced. Evolutionary biologists suggest these may have been independent cells and started living in eukaryotic cells. These have their own DNA which all come from the biological organisms mother/parent.

Chloroplasts

The section of an eukaryotic cell in which photosynthesis takes place. Only found in plants/algae.

Vacuoles

Part of cells that contains water and enzymes. Usually a storage compartment. In plants they can be significant and play a role in shaping the plant.

Lysosome

A compartment in a cell containing a whole series of enzymes that help break down things i.e. lysing. These are basically organelles that contain digestive enzymes and act as organelle-recycling faculties of animal cells. These don’t digest themselves due to the proteins inside containing a large amount of carbohydrate-sugar-groups attached to them. The inside of these are typically more acidic than cytosol due to needing to break down things using enzymes.

Process transcription

Translating DNA into mRNA. This process occurs in the nucleus.

Process translation

Decoding mRNA in order to produce a protein. This process occurs at a ribosome.

Cytosol

Fluid between organelles outside the nucleus that are not enclosed by an additional membrane other than the cells.

Cytoplasm

Most often everything (including organelles and cytosol) outside the nucleus and mitochondria of a cell but inside the cell. More specifically everything enclosed in the cell membrane of a cell but not inside an additional membrane (the mitochondria and the nucleus both have their own double lipid bilayer hence they are not part of this component)

Vesicle

Anything in a cell transported around the cell in its own mini membrane. An example would be a protein formed in the rough E.R. that has “budded off”.

Endoplasmic Reticulum Lumen

The space inside the endoplasmic reticulum that proteins and other things travel through.

Transitional Endoplasmic Reticulum

A tiny specialized patch of smooth E.R designed to allow the creation of vesicles that contain proteins. This patch allows proteins to bud off the E.R.

Endomembrane System

The system of all membranes that interact with each other in cells. A group of membranes and organelles in eukaryotic cells that work together to modify, package, and transport lipids and proteins. Any organelle that receives proteins from the golgi apparatus’ can be considered a part of this system however receiving proteins from the golgi apparatus is not a necessary condition to be part of this system.

Structural Protein

A protein that helps provide shape and form to tissues and cells.

Functional Protein

A protein that carries out specific biological tasks such as catalyzing reactions or transporting molecules. Enzymes are a type of __________ _________.

Golgi apparatus lumen

The space inside the golgi apparatus within which transport vesicles drop off proteins or lipids in order for them to be matured and then placed into transport vesicles finally budding off the trans face of the golgi apparatus.

Phagocytosis

A process in which white blood cell (macrophages) lysosomes fuse into a phagocyte in order to digest it and nullify a pathogen. This process occurs when macrophages nullify a virus. In this much larger process a pathogen is absorbed into the plasma membrane of a macrophage creating a phagosome. This phagosome then encounters a lysosome and _____ occurs creating a shared compartment. The enzymes in the lysosome then break down the pathogen and finally undigested material is released through a vesicle out of the cell.

Phagosome

The state of a pathogen when it is inside of a macrophage but has not yet undergone phagocytosis with a lysosome. In this state the pathogen is inside the plasma membrane and is contained in a vesicle but has not yet been broken down.

Macrophage

Another term for white blood cells.

Peroxisomes

An organelle that houses enzymes involved in oxidation reactions that produce hydrogen peroxide (hence the name ______). This type of organelle is not part of the endomembrane system.

Cristae

The folds inside the inner membrane of a mitochondrion. More specifically the area inbetween the folds located inside the inter membrane space. Look like long caverns.

Inter membrane space

The space inbetween the inner and outer phospholipid bilayer within a mitochondrion

Porins

Spots on the outer phospholipid bilayer of a mitochondrion. These allow small molecules such as monosaccharides to pass through but prevent larger molecules from entering.

Matrix

In reference to a mitochondrion the place inside the inner phospholipid bilayer.