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5 main properties that emerge due to hydrogen bonding

1. cohesion
2. high specific heat
3. high heat of vaporization
4. low density of ice
5. solubility



- water is cohesive which allows water to stick to water
- there are so many hydrogen bonds that water is a liquid at room temperature due to cohesion
- also responsible for surface tension since water is repelled by air, there is a tensile force of attraction at the surface of water



- water is adhesive which means it attracts other molecules as well because of its polarity
- water adheres to polar substances which is why things get wet when you put them in water
- non-polar compounds cannot form hydrogen bonds so water cannot interact with it


example of cohesion and adhesion

- example: capillary action. narrower tubes have higher surface area which means that water can attach itself to the sides of the tubes more. this makes water “go up” the sides of tubes. see meniscus

ALLOWS: water to move up roots and seeds to swell with water to germinate


Specific Heat capacity

high specific heat= more energy to change and raise temperature= easier way to maintain internal temperature of body


high Heat of Vapourization

high heat of vaporization= when it is hot outside, body heats up and water starts to evaporate. evaporation cools the skin as it allows some of the heat that went into the body to go into breaking the hydrogen bonds of water to turn to gas.

- a fan just accelerates the cooling process because it blows away the water vapour collected on your skin allowing more water to evaporate therefore more cooling


Low density of ice (see picture)

- In water's liquid form, hydrogen bonding pulls water molecules together.
- As a result, liquid water has a relatively compact, dense structure.
- As water freezes, the dipole ends with like charges repel each other, forcing the molecules into a fixed lattice in which they are farther from each other than they are in liquid water.
- As water freezes into ice, the molecules become frozen in place and begin to arrange themselves in a rigid lattice structure that actually places the molecules farther apart due to the hydrogen bonding pulling them together before.
- since the molecules are actually farther apart when frozen, it is less dense than water allowing it to float

lakes do not freeze solid allowing fish to survive winter


Solubility (see picture)

- water molecules gather loosely around polar/ionic sunstances due to the hydrogen bonding or simply just dipole attractions.
- water surrounds the ions/polar substances which separates the substance into individual ions/particles
- since you cannot see these particles, it appears that the substance has “dissolved” in water while water has simply surrounded the substance not allowing it to interact with another particle of the same substance
- this is called a hydration shell when water surrounds the particle

ALLOWS: molecules that are polar to move inside cell membranes more easily which allows more chemical reactions to take place inside cells



any substance that dissociates in water to increase the concentration of H+ in a solution or any PROTON DONOR (gives H+).



a tiny fraction of water molecules will ionize into Hydrogen and OH ions due to collisions between water molecules. you can call the ionized/dissociated hydrogen ion a “proton”.



any substance that removes H+ from a solution of any PROTON ACCEPTOR



A buffer acts as a proton donor as a solution becomes basic, but as a 
proton acceptor as a solution becomes acidic. It thus moderates the change 
in pH when other processes are releasing or removing protons. Carbonic 
acid is a common buffer in living systems.

CO2 + H2O (equilibrium arrow) H2CO3 (equilibrium arrow H+ + HCO3-

If excess acid is added to a solution, the equilibrium shifts to the left and 
CO2 is released as a gas. If a base is added, it 
removes H+, and CO2 reacts with water to form bicarbonate and replace most of the "missing" H+. Carbonic acid maintains a pH of about 7.4, while other buffers will hold pH near other values.


pH scale facts

the absolute value of the exponent of the molarity of H+ (ex. concentration of H+ is 10^-7 means that pH is 7)

pH times pOH ALWAYS equals 10^-14 M ^2

logarithmic which means each increase is by a power of ten. 9-7 = 100 times stronger


What is the relationship between electrons and energy levels?

more electrons= more energy levels= more energy


What are hydrogen bonds? How do they form?

hydrogen bonds: bonds that form between highly electronegative atoms like F (rare),O,N and Hydrogen. They are the strongest types of bonds that form other than ionic which also means that it increases the boiling point of the atom that has it.


basic elements of life

hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P) and sulfur (S)


polarity and bonds scale

- electronegativity is greater than 1.7 is ionic
- from 0.5 to 1.7 is a polar covalent bond
- from 0 to 0.5 is non-polar covalent bond


most common elements in biological molecules



biological molecules

proteins, carbohydrate, nucleic acid, lipids


molecular formula

- useful to find number of atoms of each type
- useful for stoichiometry


empirical formula

- shows simplified ratio
- useful to find a “formula” for a type of molecule
- ex. all monosaccarides have a certain ratio of molecules


order for writing names

- for organic molecules only (contain both carbon and hydrogen)


skeletal formula

- condensed form of structural formula
- at every “joint” there is a carbon bonded but that is omitted
- the bond must be against the carbon so if there are 3 H bonded to it, you must write it as H3C and then the bond!


carbon special features

- makes lots of bonds (4) which makes a greater variety of molecules
- relatively stable (more closer to top, less atomic radius)
- can form large, stable molecule chains (carbon can also attach to itself)
- forms moderate energy bonds that can be broken and reformed easily


• o – is assumed to

also have a hydrogen attached to it originally but then it dissociated


• when molecules are basic or acidic, they can be written as

ions with either hydrogen attached or hydrogen dissociated


in molecules that form polymers

you must have one H and one OH bond


condensation synthesis reaction

- two separate items condensing into one
- monomer H is removed from one and combined with the OH from another monomer to create a dimer. The bond that H and OH came from connects the two monomers together
- trimer, tetramer etc.
- circles represent one monomer


- hydrolysis

used for breaking polymers. you break a molecule of water and the H and OH are used to replace the bond between monomers
- starch breaking into maltose is example of hydrolysis reaction
- lysis: breaking
- hydro: water


r in skeletal formula

- “R” is the variable region meaning that the end that the r is attached to is standard for a type of molecule with “R” being the part that is changed
- can also show variable region by a blank box


ring in skeletal formula

- sometimes there is a hexagonal shape thing which is a isomer structure with alternating double bonds in different possible formations. the electrons in the bond move around and are called “delocalized electrons” since they move around. benzene ring


organic chemistry

- organic chemistry consists of carbon and hydrogen containing molecules


a lower pH

indicates a higher concentration 
of H+,


structural formula

shows every carbon (no bends, its super messy lol)


hydrocarbons make good



theoretically, the carbon chain can be



cc and ch bonds are very

nonpolar so hydrocarbons are always nonpolar


functional groups create

diversity in carbon chains and also allow them to sometimes be polar and can also form hydrogen bonds


structural isomers

differences in structure of carbon skeleton



same carbon skeleton but differ in how the groups attached to the skeleton are arranged in spae (alpha, beta glucose)


stereoisimer chirals

mirror image versions of the same molecule (ir reffering to the right verion, say dextro, if left, levo abbreviated as D-sugars and L-amino acids)


condensation synthesis

- produces water



breaks water


hydrocarbon chain special features

- basic carbon structures can be called hydrocarbon chains
- they are nonpolar and don’t dissolve in water
- how they are made useful is through functional groups, where you can take a bond and replace it with some other elements
- With a small amount of energy, carbon bonds can be broken and reformed but they will rarely have enough kinetic energy to break spontaneously



one carbon attached



more than 3 carbon chains



3-20 monomers


what types of molecules go through condensation and hydrolysis?

- carbohydrates
- all proteins
- nucleic acids


lipids identifying features

- all extremely non polar
- all are fat soluble

Carbohydrates and lipids contain carbon, hydrogen and oxygen but lipids especially have tons of CH bonds


lipids features

- hydrophobic so good for waterproofing
- used to keep either water out or water in
- strong insulators against heat and electricity
- very rich in C-H bonds therefore an excellent reserve of stored energy (more than carbohydrates)
Slow to heat and cool


lipids structure

in form of triglycerides (a glycerol and 3 fatty acids)
- this is made using an ester bond and condensation synthesis


how can triglycerides vary

- fatty acids may be various lengths (4-18 carbons)
- may have double or single bonds
- different fatty acids may be mixed in various combinations in the same triglyceride


saturated lipids

- have no double bonds
- form solids at room temp
- animal fats


unsaturated fats

- some double bonds
- can be hydrogenated to make them more saturated (then called trans fats)
- plant oils


amphiphilic molecule

- glycerol with two fatty acids
- used for membrane because it has one soluble and one insoluble end



Made using a saturated fatty acid combined with a long-chain alcohol using a condensation synthesis reaction
Tend to be solid
Looks like a crocodile thing
Can not be unsaturated


carbohydrates structure

- usually follow (CH2O)n pattern


carbohydrates features

- lots of CH bonds therefore good for energy storage



- small, water soluble, and fairly rich in chemical 
- functional groups make it polar
- rich in energy which can be captured in form of ATP
- transported easily over membranes


monosaccarides as structural isomers

Monosaccharides also exist at structural isomers, which 
have the same chemical formula, but a different 
structure. Glucose and fructose are structural isomers.


monosaccharides are mostly ___ (symmetry)

Most monosaccharides are asymmetrical, and thus exist as two 
stereoisomers or enantiomers - left handed or "levo-" and right handed or 
"dextro-". The stereoisomers of glucose are called L-glucose and D-
glucose or (dextrose). L-glucose is not used by most organisms.



- two monosaccharides bonded together (only bonds in aq solutions)
- will be in ring form in water
- store twice as 
much energy per molecule, and thus produce less osmotic 
potential in a cell
- a glycosidic linkage forms between the two glucose



- Long-
term storage works best with an insoluble molecule, which cannot diffuse or 
interfere with reactions that occur in solution. Most organisms make some kind of 
starch for this purpose.

Starches can be broken down fairly easily to maltose, when energy demands 
require it.



- made up of polysaccarides
- which is a polymer of beta glucosamine (glucose with an added amino and a carbonyl, which makes it more polar. this makes even MORE hydrogen bonds which makes it even stronger!


aldose monosaccaride

has an aldehyde functional group which builds a hexagonal ring


a ketose monosaccharide

has a keytone functional group. this forms a pentagonal ring


glycosidic linkage

between a carbon-oxygen- carbon

an alpha 1-4 bond is called a alpha 1-4 glycosidic bond.


large molecule solubility

Polymers become less and less soluble even if the monomers that make it up are super polar


lipids and energy

Not an immediate source of energy (like carbohydrates since they go directly into energy reactions)
Fat attracts less water than glycogen and stores more energy per area than glycogen


types of lipids

- triglycerides
- saturated and unsaturated
- trans



- formed using condensation synthesis
- To form them, molecules just clump together, there is no chaining like carbohydrates
- To bond the glycerol and fatty acids together, the H and OH creates water. This creates THREE water molecules
- forms an esther bond


esther bond

- This is between oxygen and the carbon on the fatty acid and the carbon from the fatty acid. It is different from glycosidic bond since it has a double bonded oxygen on one of the carbons
- This is an ester bond, which is a characteristic feature of combining lipids


Saturated and unsaturated lipids

Referring to the saturation of the triglycerides
When forming a double bond between two carbons, you have to take two hydrogens away
This is unsaturated since it has a double bond now
Double bonds create more kinks so they can’t stack as well together. This creates less bonds between the molecules therefore liquid at room temperature if made by unsaturated fats


trans fats

Cis isomer is when the fatty acid goes out from the double bond from the same side
Trans isomer is when the fatty acid goes out from double bond from opposite sides. These are not natural. The carbon chain creates a line going across the molecule
Cis and trans fat are both unsaturated
Hydrogenation is the process where you add hydrogen to unsaturated fats



Steroids are hormones derived from cholesterol that play important roles in maturation, sexual function, stress, mineral balance (especially sodium) and, in other animals, molting and metamorphosis.

3 hexagonal carbon rings with one pentagonal carbon ring


carbohydrate features

Many hydroxyl groups
Moderate number of C-C and C-H bonds
Oscillate between ring and chain form
Keto- and aldo- groups in chain form


Many hydroxyl groups feature

Strongly hydrophilic, and therefore small carbs are very water soluble and easy to diffuse


Moderate number of C-C and C-H bonds

Moderate amount of potential energy that can be released in oxidation reactions


Oscillate between ring and chain form

Relatively easy to convert from one form to another in solution (α / β)
- get your to make different kinds of polymers with same monomers


Keto- and aldo- groups in chain form

Interact with taste buds to produce sensation of sweetness (indicates ripeness of fruit)


name for a simple sugar (monomer)



name for a double sugar



a short chain of linked sugars



a long chain of linked glucose molecules



Why are starches called storage polysaccharides?

α- glucose.Starches can easily be hydrolyzed to yield glucose again when energy is required. amylopectin and amylose make starch and amylopectin is insoluble and for granules in plants


Properties of lipids

Primarily hydrocarbon chains and rings (few functional groups)
Many C-C and C-H bonds
Low electrical conductivity
Slow to heat and cool


Primarily hydrocarbon chains and rings (few functional groups) feature lipids

Strongly hydrophobic – useful for waterproofing (cells, leaves, fur and feathers)


Many C-C and C-H bonds

High potential energy when oxidized – good low mass storage molecule


Low electrical conductivity

Good insulator for nerves (myelin sheaths)


Slow to heat and cool

Good thermal insulation – subcutaneous fats in whales, seals, waterbirds, humans


Identify four categories of lipid.

Triglycerides (or triacylglycerols) = fats and oils
Steroids Waxes


What are the two most important categories of lipids?

Triglycerides (or triacylglycerols) = fats and oils


Why are trigycerides considered macromolecules but not technically polymers?

While polymers can be extended ad infintum with the addition of more monomers, fats have only three fatty acid residues.


What is a steroid? What molecule are all other steroids derived from?

A lipid soluble hormone derived from cholesterol


monosaccarides have

2-6 carbons

6 carbons: hexose
5: pentose
4: tetrose
3: triose


alpha glucose

alpha is carbon pointing down
always alpha glucose monomers attached would create a ring shape (alpha helix, creates only carbon 1 bonded to carbon 4. alpha 1-6 brances two alpha 1-4 bonds together (glycosidic bond) to create amylopectin. amylopectin plus amylose is plant starch??).


beta glucose

always beta glucose creates more (beta pleated sheets) chain forms. this is because beta linkages form alternating up and down. this is good for keeping these chains together. the hydroxyls create hydrogen bonds which mean that those chains are held ridgedly close together. these bundles bundle with other chains and more hydrogen bonding occurs. this makes this bundle very strong which can be used in plants to make the cell wall.


The main component of a membrane is a type of lipid called a



lipids are good for membranes since they

Non polar
Hydrophobic nature makes them good waterproofing molecules
Membranes allow for separation of cell from environment
Cell usually has a water based environment


phospholipid structure

Derived from triglycerides
The third fatty acid is replace is replaced with a polar compound with a phosphate and another polar group



Amphiphilic is both hydrophobic and hydrophilic in nature.

This causes phospholipids to spontaneously make bilayers due to hydrogen bonding of polar heads and then attraction to opposite charges from water molecules and then in between, the fatty acid tails will be oriented inside. These forces keep this layer balanced and should a force press on it, it will “bounce” back


Fluid mosaic model

Has proteins suspended it in

Things that can’t get across naturally are polar and large.


Phospholipids (in membrane)

Provides a permeable barrier as well as a matrix for proteins.


Transmembrane proteins (in membrane)

Goes from one side of membrane to another (lets charged ions go through.

carriers, receptors


carrier protein (in membrane)

Molecule fits in and the protein changes shape and then carrier molecule through


Protein receptor (in membrane)

Binds to a molecule and gives a change to the protein structure which may release a signal on the inside the cell


Interior proteins (in membrane)

Interior to the cell membrane
Determines the shape of the cell as well as acting as anchor sites for proteins


Glycoproteins (in membrane)

Have oligosaccarides attached to protein or lipid
They are invovled in recognition which helps to identify cells of your own body. AKA red blood cell recognize each other in your body and reject others


Glycolipids (in membrane)

Used for tissue recognition (blood type)


Cholesterol (in membrane)

Has to do with membrance fluidity
More cholesterol means less fluidity of cell membrane since it pushes the proteins together


Passive transport

Facilitated diffusion


Osmosis (Passive transport)

High water potential has more solute
Low water potential has less solute
Water moves from high to low water potential
Hypotonic has low concentration (this creates bursting in cell since water rushes into cell)
Isotonic is balanced
Hypertonic is when water is drawn out and cell shrivels up


facilitated diffusion (Passive transport)

Carrier protein has a shape of the ion it wants to bring in. when the protein binds to it, it changes shape (confirmational change)
Channel protein recognize certain ions and let them through


diffusion (Passive transport)

(net movement from areas of high concentration to low concentration)
Helps with small and non-polar (oxygen, co2,


Active transport

All require energy
Depends on where molecules are going


Active transport in membranes using proteins

- They will be different but they will use ATP to change the protein shape since the active transport is moving stuff outside cell against concentration gradient
(facilitated diffusion moves things inside cell so with the concentration gradients)


symporter (Active transport in membranes using proteins)

This is a symporter protein (transports things in the same direction)


Antiporter (Active transport in membranes using proteins)

(opposite directions)


Uniporter (Active transport in membranes using proteins)

(only one molecule being transporter)


Bulk transport

Endocytosis (Phagocytosis, Pinocytosis, Receptor mediated endocytosis)


Phagocytosis (Bulk transport)

Solid particles, cell eating


Pinocytosis (Bulk transport)

Cell drinking, large fluid


Receptor mediated endocytosis (Bulk transport)

Selective material transport by having receptors bind to certain cells


Exocytosis (Bulk transport)

Out of cell
Waste has a membrane around it which then attaches to membrane of cell and then opens up and releases to environment



- amylose is helix (most common plant starch)



- amylopectin is helix with branching (most common plant starch)



- glycogen is helix with tons of branching (found in humans)
- insoluble

glycogen is more frequently attached since that makes it easier and FASTER for the RELEASE of energy since animals move around and muscles need a ton of energy.



has low concentration (this creates bursting in cell since water rushes into cell)



is balanced



is when water is drawn out and cell shrivels up


diffusion is good for

small non polar things


Keto- and aldo- groups in chain form (functional for primates)

Interact with taste buds to produce sensation of sweetness (indicates ripeness of fruit)


Why can’t animals with starch digesting enzymes break down cellulose

- Enzymes bind to their substrates based on shape.
- starch evolved earlier Cellulose cell walls evolved much later, and most lines of eukaryotes do not seem to have come up with an enzyme that can bind to and hydrolyze cellulose.

(Note that cellulose fibres tend to cross bond with each other forming a network that is very difficult to attack.)


how do animals get energy from cellulose

A few bacteria, the great master chemists of the living world, along with some fungi, have evolved enzymes that will hydrolyze cellulose. All cellulose digesting animals depend on symbiotic bacteria (or protists that themselves have probably borrowed bacterial functions in the case of termites.)


carbon chains (identify)

just carbon


hydrocarbon chain (identify)

c and h


carbohydrates (identify)

C and OH (ketose, aldose, pentose, triose ___(mono, di, poly) saccharide


- fatty acid is (identify)

carboxyl group and hydrocarbon chain (cis/trans ___ poly, mono saturated fatty acid)


- triglycerides (identify)

glycerol and 3 fatty acids


- phospholipids (identify)

glycerol, 2 fatty acids and phosphate


- waxes (identify)

a saturated fatty acid combined with a long-chain alcohol


- steroid (identify)

3 hexagonal carbon rings with one pentagonal carbon ring


Compare and contrast passive and active membrane transport

- energy not required
- goes with gradient
- useful for small and dissolveable molecules to get through
- not selective

- requires ATP molecules for energy to change shape of proteins
- can be selective
- can bring in large amounts of material
- membrane changes shape to allow material to come through
- can transport proteins, ions, large cells and complex sugars in