AP Biology Review For Organic Molecules and Functional Groups

organic molecules

basis is carbon (can form four covalent bonds), carbon likes to bond likes to bond with other carbon and hydrogen atoms. it also will bind oxygen, nitrogen, phosphate, and sulfur

isomers

compounds that have the same elements,m same number of each atom, but have different structures and thus different properties

cis-trans isomers

different arrangement around a double bond (cis-same, trans-different)

enantiomers

differ in spatial arrangement around an asymmetric carbon - result is 2 molecules that are mirror images of each other (ex. ibuprofen has two enantiomers, s-ibuprofen and r-ibuprofen, s is effective, r isn’t)

functional groups

chemical groups attached to the “skeleton” of an organic molecule, directly involved in chemical reactions, and thus the function of the molecule

hydroxyl group

chemical formula - OH

structure - R-O-H (R being the other part of the molecule)

properties - polar

commonly found in - carbs, nucleic acids, r-groups of amino acids

carbonyl group

chemical formula - CO

structure - O=C with two single bonds to R (R being the other part of the molecule)

properties - polar

commonly found in - fatty acids, phospholipids, triglycerides

carboxyl group

chemical formula - COOH

structure - O=C with a single bond to R and and single bond to OH (R being the other part of the molecule)

properties - polar

commonly found in - amino acids and fatty acids

amino group

chemical formula -RNH2, RNH3+

structure - R-N with two single bonds to H or R-N with three single bonds to H (R being the other part of the molecule)

properties - polar

commonly found in - proteins

sulfhydryl

chemical formula - R-SH

structure - R-S-H (R being the other part of the molecule)

properties - polar

commonly found in - proteins

phosphate group

chemical formula - PO4 3-

structure - one double bonded O and three single bonded O all bonded to P

properties - polar

commonly found in - genetic material (DNA + RNA)

methyl group

chemical formula - CH3

structure - C with 3 single bonds to H and a single bond to R (R being the other part of the molecule)

properties - non-polar

commonly found in - proteins, amino acids, and lipids

cells are built from 4 main classes

DNA, carbs, lipids, proteins

construction of polymers

there are two types of reaction, dehydration synthesis or condensation reaction and hydrolysis

what is a dehydration/condensation reaction?

a chemical process where two smaller molecules join together to form a larger molecule (polymer), directly resulting in the loss of a water molecule (H2O)

what is a hydrolysis reaction?

a chemical process where a polymer is broken down with the addition of a water molecule (H2O)

what is made when carbohydrates in the form of simple sugars are converted into energy

ATP (by the process of cellular respiration)

what is the ATP-ADP cycle?

ATP loses a phosphate group (through hydrolysis) to make energy for the cells, creating ADP, and when an ADP molecule gets a phosphate group (phosphorylation) and energy form a food source is added it forms ATP again

what is the general information about carbohydrates that should be known?

carbohydrates are also often referred to as sugars, they can be converted into ATP or stored for future use, some organisms use them for structure (cell walls in plants), and there are three main groups

what are the three main groups of carbohydrates

1) monosaccharides

2) disaccharides

3) polysaccharides

what are monosaccharides?

single molecule with carbon skeletons that range from 3 to 7 carbons (the most common one being glucose, C6H12O6)

what is it called when there are 5 carbons (and what are two examples)

a pentose (ex. deoxyribose and ribose, deoxyribose being found in DNA and ribose being found in RNA)

a pentose will always have the chemical formula C5H10O5

what is it called when there are 6 carbons (and what are three examples)

a hexose (ex. glucose, fructose, galactose)

a hexose will always have the chemical formula C6H12O6

what is the typical ratio of carbon to hydrogen to oxygen?

1:2:1

what are disaccharides?

2 monosaccharides joined together formed by a dehydration reaction with a glycosidic bond

what is a glycosidic bond?

a glycosidic bond is a covalent bond that forms during a dehydration reaction between a carbohydrate (sugar) and another molecule, breaking down through hydrolysis

what are three common examples of disaccharides?

maltose, lactose, and sucrose (-ose ending meaning sugar/carbohydrates which would be broken down by an enzyme ending in -ase, an example being lactose and lactase)

what are polysaccharides?

hundreds to thousands of monosaccharides joined together, each monosaccharide being joined by a glycosidic bond, there are two groups

what are the two groups of polysaccharides?

1) storage (ex. starch and glycogen)

2) structural (ex. cellulose and chitin)

what is going on with storage polysaccharides?

these molecules are used for energy storage for future use by both plants AND animals, plants take excess glucose and store it as starch which is stored in organelles called plastids

ex. amylose is a straight chain, but amylopectin branches off, and stored as starch

what is important to know about the storage polysaccharide glycogen?

it is the storage polysaccharide in animals, and there are two main tissues this is found in (which are your liver and your muscles)

what is the difference between starch and glycogen vs. cellulose?

starch and glycogen have a lot of branches whereas cellulose (fiber) is very uniform

what is up with the structural polysaccharide cellulose?

cellulose composes the cell wall and its structure is very uniform comparative to storage polysaccharides and cellulose is made up of glucose

can humans digest cellulose?

humans cannot digest cellulose (some animals can, like cows and termites) thus in humans our digestive tract uses it to rough our insides and use as fiber to regulate stool

what is up with the structural polysaccharide chitin (kai-tin)?

chitin has a different structure and is the exoskeleton of many insects

what are the general properties of lipids?

they can be used as energy storage or structural purposes, they are very effective at storing energy, more efficient than carbs, they are nonpolar thus highly hydrophobic, and there are three general families

what are the three general families of lipids?

1) triglycerides

2) phospholipids

3) steroids

what is going on with fatty acids?

main structural component of triglycerides and phospholipids

two types - saturated (tail structure completely covered in hydrogens) and unsaturated (two double bonded carbons in tail structure)

what is going on with the formation of triglycerides?

triglycerides form when three fatty acid molecules bond to one glycerol molecule through a dehydration reaction that releases three H2O molecules, and when the dehydration reaction occurs, an ester linkage is formed binding each fatty acid to the glycerol backbone, and three water molecules are released during the whole process during the dehydration reaction, and the final triglyceride is hydrophobic because of its long, nonpolar, hydrocarbon chains of fatty acids

what are the difference between saturated and unsaturated triglycerides?

saturated - “bad”, solids at room temp, found in animals, no double bond

unsaturated - “good”, liquid at room temp, found in plants, double bond (allowing for liquid state)

what are trans fats and why are they bad?

trans fats are unsaturated fatty acids that contain a trans-configuration double bond, meaning the carbon chains lie on opposite sides of the carbon-carbon double bond, allowing the molecule to pack tightly (like a saturated fat)

how are trans fats formed?

adding hydrogen and enzymes to convert unsaturated fats to saturated fats (think margarine)

what is a phospholipid and what are its properties?

phospholipids are vital date molecules that form the structural backbone of all living cell membranes

main properties: major components of cell membrane, only 2 fatty acids but also includes a phosphate group

what is the structure of phospholipids?

the structure of phospholipids is amphipathic, meaning it is a molecule that is both polar and non-polar (polar head, non-polar tail)

what are steroids?

steroids are a type of lipids and characterized by 4 fused rings (ex. cholesterol)

what is cholesterol made of? what does it do?

cholesterol consist of vitamin D, bile acids, steroid hormones, and cell membrane

cholesterol is one of many steroid hormones used for long-distance communication

how are peptide bonds formed?

peptide bonds are formed by amino acids bonding together by a dehydration reaction

what is important to know about polypeptides and genes?

genes (sections of DNA) code for polypeptide chains, amino acids link together, creating a protein (when the chain partakes in protein folding)

what is important to know about different kinds of proteins?

they all have their own 3D shape

what do you need to know about protein folding?

-most proteins fold spontaneously based on the amino acid sequence

-reinforced by the interactions between side chains of amino acids

what are the two main types of proteins?

-fibrous (looks like twizzlers)

-globular (looks like a glob)

what to know about protein structure and function?

structure leads to function

especially true because of the majority of proteins rely on recognizing and binding to another molecule

what is denaturation of proteins?

the proteins loses it 3D shape and function due to changes in pH, temp, ionic strength, solubility

what is important to know about hydrophobic interactions?

-amino acids = non-polar

-they concentrate towards the inner portion

what is important to know about hydrogen bonds?

-occur between amino acids that have polar side chains

what is important to know about ionic bonds?

they happen between acidic and basic amino acids because of the positive and negative charge

what is important to know about disulfide bridges?

-only between cystine and cysteine

-covalent bonds between cysteine amino acids

what is the central dogma of molecular biology

DNA to RNA to Proteins

what is a gene?

segment of DNA that codes for a polypeptide that fold into a protein

what makes up the monomers (or nucleotides) of DNA and RNA?

a phosphate group, sugar, and a nitrogenous base (this is usually just represented by the first letter of the nitrogenous base)

what are the 4 nitrogenous bases for DNA, and what gets replaced in RNA?

adenine (A), guanine (G), cystine (C) and thymine (T), and thymine is replaced by uracil (U) in RNA

what are A and G classified as between the two types of nitrogenous bases?

purines

what are C, U, and T classified as between the two types of nitrogenous bases?

pyrimidines

what is the rule about the two types of nitrogenous bases and pairing?

one purine MUST pair with one pyrimidine (they cannot pair with a base of the same type)

what does adenine (A) always pair with?

in DNA - thymine (T)

in RNA - uracil (U)

what does guanine always pair with?

cystonsine (C)

what is the mnemonic device to remember the pairings between nitrogenous bases?

AT GC (at grove city)

what is the backbone of DNA?

sugar and phosphate (think what makes up a WHOLE nucleotide)

what is meant by antiparallel orientation and what is important to know about it?

antiparallel - running in opposite directions (thus the way the sugars are running are different)

one strand of DNA will run 5’ to 3’ and one will run 3’ to 5’

RNA can run either but will only run ONE way because it only has ONE strand (depending on which way you look at it because RNA should always start with a phosphate group)

the way you can tell instantly is by looking at if the strand starts with a phosphate group or not

because carbon always attaches to the nitrogenous base, this is why the orientation can flip

what is the difference in structure between DNA and RNA?

DNA is double stranded, whereas RNA is single stranded

DNA has deoxyribose (which has one less sugar), and RNA has ribose

DNA is antiparallel in orientation, RNA will only run one way because of it’s one strand

DNA has ATGC, RNA has AUGC

what is the difference in function between DNA and RNA?

DNA stores genetic material/information (genes code for polypeptides which code for proteins)

RNA is used for transcription or carrying messages from DNA to ribose where proteins are made (mRNA specifically)

what is the first FRQ on the test about?

water

why is a water molecule polar?

oxygen is electronegative, and hydrogen has a partial positive charge

what is cohesion and what does it causer?

H2O are attracted to other H2O molecules, causing surface tension

what is adhesion and what does it cause?

water is attracted to other substances (such as glass) causing attraction to any other polar molecule

is water a solvent? why?

water is a great solvent (or great at dissolving things) due to its polarity (other molecules will bond with either hydrogen or oxygen, think salt (NaCl))

is ice more or less dense than water?

ice is less dense because when the temperature lowers, the hydrogen bonds become more stable, making ice less dense than water

does water have a high or low heat of vaporization?

high heat of vaporization, because water carries a lot of heat

why does ice cool water (think thermal energy)

thermal energy is the total kinetic energy of the atoms or molecules in a substance due to their random motion, and heat is the transfer of thermal energy between substances of different temperatures, thermal energy naturally moves spontaneously from a warmer object (higher temperature) to a cooler object (lower temperature), when ice is added to water, the cooling process occurs through thermal energy transfer, and ice it cools water by absorbing thermal energy from the warmer water

what is important to know about water’s high specific heat?

specific heat is the amount of energy that needs to be absorbed or lost for the substance to change its temp by one degree celsius, meaning that since water has a high specific heat, water’s temp will change less than other liquids when it absorbs or loses heat