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Organic Chemistry Flashcards

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1
Q

4 groups of molecules that make organic compounds

A

Carbohydrates
Lipids
Proteins
Nucleic acids

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2
Q

Why is carbon everywhere in organic chemistry?

A

it has 4 valence e- and wants to form 4 covalent bonds to stabilize -> it can form all kinds of shapes (chains, rings, branches)

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3
Q

Macromolecule

A

long, complex, often repeating units

eg. glycoprotein (carb + protein)

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4
Q

Carbohydrate

A

energy, storage of energy, cellular structures

‘hydrated carbon’ (water containing)

CH2O

3 types: mono, di, polysaccharides

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5
Q

monosaccharide

A

simplest carb, simple sugar
water soluble, hydrophilic

3-7 C in a ring
- hexose sugar: 6 C
eg. glucose, fructose (found in fruit then converted into glucose in the body)

  • pentose sugar: 5 C
    eg. deoxyribose, ribose
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6
Q

disaccharide

A

simple
2 monosaccharides joined by dehydration synthesis reaction (anabolism)

  • water gets extracted (created) during ‘dehydration synthesis’
  • hydrolysis (catabolims): when disaccharide decomposes into its monosaccharide components

eg. glucose + fructose = sucrose (table sugar)

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7
Q

anabolism

A

cells using synthesis reactions to build molecules they need for functioning

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8
Q

hydrolysis

A

type of catabolism. sucrose is decomposed into glucose and fructose using water

  • releases the energy held in bonds and generates the molecular building blocks a cell needs
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9
Q

catabolism

A

opposite of anabolism, decomposition of nutrients

eg. hydrolysis

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10
Q

polysaccharides

A

combo of many monosaccharides joined by dehydration synthesis

not soluble

structure or energy storage function

eg. glycogen (stores fuel in body), starch (stores fuel in plants), cellulose (plant structure, digested into monosaccharides by herbivores and used for fuel)

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11
Q

most abundant organic molecule in biosphere

A

cellulose

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12
Q

glycoprotein

A

macromolecule of carbohydrate attached to a protein

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13
Q

lipids

A

energy stored in fat, structure, some hormones (chemical messengers)

generally hydrophobic

C, O, H (like carbs, but lower O)
- sometimes P

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14
Q

5 lipid classes

A

neutral fats (triglycerides)
waxes
phospholipids
steroids
eicosanoids

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15
Q

neutral fats (triglycerides)

A

3 fatty acids + 1 glycerol (3 C simple sugar) molecule
- function: energy. body gets energy by breaking down (hydrolysis) bonds, then stores excess in adipose
- hydrophobic
- nonpolar

  • form an ‘E’ shape with glycerol as the backbone.
  • formed through dehydration synthesis (3 waters produced)
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16
Q

fatty acid

A

building block of lipids
carboxylic acid chain (usually straight)
- chain of C with 1-2 H attached (single or double bond) to each carbon
- nonpolar tails

  • saturated: all single bonds, as many H attached to C as possible (animal fat, solid at room temp)
  • unsaturated: 1+ double bonds, not all C filled with H (plant fat, liquid)
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17
Q

lipoprotein

A

macromolecule of proteins + lipids
- transport of fat
- hydrophilic proteins allow the fat to be shielded from blood plasma as it travels

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18
Q

phospholipids

A

glycerol backbone + 2 fatty acids in one direction
+ 1 phosphate group (PO4) attached to N compound in other direction
- main component of cellular membranes, myelin sheath

P attached to N side (head):
- hydrophilic (soluble)
- polar

2 fatty acid side (tail):
- hydrophobic (insoluble)
- nonpolar

-> makes phospholipids have 2 layers (‘lipid bilayer’) when placed in water (heads attach to water, tails repel)

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19
Q

steroids

A

4 interlocking HC rings
- hydrophobic
- nonpolar
- very little O
- different types form by attaching functional groups

eg. cholesterol (forms bile salts to help fat digestion, used to create hormones [steroid precursor])
- cortisol: glucocorticoid produced in adrenal, increases glucose and glycogen in body, anti-inflammatory
- aldosterone: mineralcorticoid made in adrenal, influences absorption of Na and Cl in kidney, water balance in body
- estrogen
- sodium glycocholate: principle bile salt (fat digestion: emulsify lipids and break up large fat globules so there’s more surface area for hydrolysis. secreted by liver)

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20
Q

eicosanoids

A

20 (‘eicosa’) C fatty acid + ring structure
- important for mediating complex chemical processes

  • prostaglandins (PGs): mediate inflammation
  • thromboxane: mediate platelet function (vasoconstriction and clumping)
  • leukotrienes: mediate bronchoconstriction + increase mucus
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21
Q

most abundant organic molecule inside body

A

protein

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22
Q

proteins

A

C, O, H, N (sometimes P, S, Fe)
- amino acids linked (sequence makes them unique and defines function)

think ‘worker’ molecules that organize and facilitate all metabolic processes:
- catalyze (speed up) reactions in body
- transport ions in and out of cells
- cell and tissue structure
- growth
- defense against invaders

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23
Q

amino acids

A

20 that share same basic structure
- central C attached to H, amino group (NH2), carboxyl group (COOH), and a unique side chain designated with ‘R’

  • R group defines each amino acid
  • link together to form proteins (building blocks)
  • DNA determines arrangement (shape) of amino acids (which determines the function of resulting proteins)
  • R group can be: a) neutral/nonpolar b) neutral/polar c) basic d) acidic

aminos linked by dehydration synthesis (COOH of one links to NH2 of another)
= peptide bond, dipeptide (2 NH2), tripeptide (3 NH2), polypeptide (10+ NH2), ‘protein’ (100+ NH2)

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24
Q

protein structures

A

shape (2 kinds) directly determines function
- fibrous: long and firm
- globular: puzzle piece shape that connects to invaders, ‘antibodies’

4 levels:
1. primary structure: sequence of NH2s that form peptide chain
2. secondary: bend of the peptide chain (results from H bonds)
3. tertiary: overall shape of single protein molecule from folding in (H and covalent bonds)
4. quaternary: 2+ protein chains join to form macromolecule, stabilized by H and covalent bonds

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25
Q

amino acid shapes (secondary)

A

most common: alpha helix (slinky) and beta-pleated (accordion)

can both occur within the same protein at different spots along the chain

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26
Q

formation of tertiary structure

A

protein molecule folds in on itself so hydrophobic amino acids are shielded from watery environment, outer hydrophilic amino acids allow the protein to be water soluble

  • held by:
    1. hydrophobic regions inside
    2. H bonds (3+)
    3. salt bridges between acidic and basic amino acids
    4. disulfide bonds (S in part of protein covalently bonded to S in another part) eg. found in vasopressin and oxytocin
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27
Q

structural proteins (fibrous)

A

stable, rigid, water-insoluble
- add strength to tissue or cells
- long stringy shape
eg. collagen (main protein in CT), fibrin (CT in blood clots), keratin

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28
Q

functional proteins (globular)

A

water soluble, flexible, 3D shape that can change
- highly chemically active molecules
eg. enzymes (catalysts for reactions), hormones, antibodies

29
Q

enzymes

A

speed up a chemical reaction without being destroyed/altered
- specific to the reaction they catalyze and to their substrates (the substances they act upon)
- specificity determined by shape, charge, and hydrophobic/philic properties of enzyme AND substrates
- specificity referred to as ‘lock and key’ properties of the enzyme (enzyme perfectly fit substrates)
- often a series of reactions with the products of a first acting as substrates for the next
- often react along lipid membranes
eg. electron transport system

30
Q

nucleic acids

A

C, O, H, N, P
- largest molecule in the body

2 classes:
1. DNA (deoxyribonucleic): instructions in nucleus on how to build proteins - ultimately determining shape and function of every tissue -> shape and function of a living organism
2. RNA (ribonucleic): transfers instructions out of nucleus into cytoplasm for proteins to be built

31
Q

nucleotides

A

molecular building blocks of nucleic acids
- 5 types, all have same basic structure (N base + pentose sugar + phosphate group)
- types named for their N base
- deoxyribose: the pentose in DNA
- ribose: the pentose in RNA

  1. adenine (A) - RNA/DNA
  2. guanine (G) - RNA/DNA
  3. cytosine (C) - RNA/DNA
  4. uracil (U) - only in RNA
  5. thymine (T) - only in DNA
  • code for a specific animo acid determined by grouping of 3 nucleotides (eg. C-G-T is code for alanine)
32
Q

gene

A

sequence of nucelotides that make one long peptide chain
- combined with protein to form CHROMOSOMES
- chromosomes replicate during cell division and make identical copies in ‘offspring’ cells

33
Q

DNA structure

A

2 parallel strands of A G C T (nitrogenous bases)
- connected by H bonds, twisted into double helix
- sugar-phosphate sides (sugar of one nucleotide links to sugar of adjacent)
- A -> T
- G -> C
- specific order of nucleotides unique to every individual

34
Q

RNA sturcture

A

1 strand of nucleotides (A G C U)

3 types based on role in protein synthesis:
1. transfer (copies info in DNA)
2. messenger (carries info out of nucleus)
3. ribosomal (uses info to create proteins)

35
Q

ATP (adenosine triphosphate)

A
  • an RNA nucleotide with N base (‘adenine’) + 2 extra phosphate groups
  • glucose from food broken down into monosaccharides, resulting energy stored in ATP
  • ATP = ‘energy currency’ of cells
  • nutrients added to the body -> cells use nutrients up in cellular respiration -> creates ATP
  • energy stored in phosphate bonds of ATP (‘high energy bonds’)
  • breaking of these bonds -> release of energy
  • bonds are broken by enzymes moving phosphate group to another molecule (the receiving molecule = ‘phosphorylated’, has some temporary energy to do some work)
  • ATP that lost a phosphate group = ‘ADP’ (adenosine diphosphate). if it loses another phosphate group = ‘AMP’ (adenosine monophosphate)
  • As more glucose is metabolized, phosphate groups can be added back to revert to ATP again
36
Q

ATP functions

A

muscle cell contraction
enzymatic reation
molecule transport across cell membranes

37
Q

what bonds do organic compounds contain?

A

C-C or C-H covalent

38
Q

carbon traits

A

small
neutral charge
shares e- with other atoms (enables chains/rings to form)
functional groups can attach to these ^

39
Q

what is a functional group?

A

unique combo of atoms that differentiates organic compounds from another
- determine the chemical properties of the compound (metabolically active portion of molecule)
- many organic molecules have more than one

40
Q

alkane

A

hydrocarbon with only single bonds
- simplest

nonpolar
insolube
less dense than water
least reactive

eg. methane, propane, butane, mineral oil, petroleum jelly

41
Q

alkene

A

hydrocarbon with at least one double bond

nonpolar
insoluble
less dense than water
reactive

eg. lycopene (antioxidant that prevents cells from oxidizing), ethylene (makes polyethylene - plastic used in hospital equipment)

42
Q

alcohol

A

hydroxyl group attached to C

hydrogen bonding can occur
solubility depends on number of C per hydroxyl (lower molecular weight = high solubility)

eg. methanol (simplest alcohol, makes formaldehyde), ethanol (drinks), isopropyl alcohol (causes tissues to contact and limits secretions ‘astringent’), glycerol (nontoxic, moisturizer, treats constipation)

43
Q

phenol

A

hydroxyl connected to benzene ring

weak acids
damage skin by denaturing proteins

eg. phenol (antispetic and disinfectant), lysol, polyphenols (antioxidant, prevents another substance from oxidizing)

44
Q

ether

A

2 C bonded to O

unreactive
less polar than alcohols
slightly soluble due to oxygen forming H bonds
flammable

eg. diethyl ether (anesthetic - makes brain unconscious), divinyl ether (anesthetic)

45
Q

adelhyde

A

carbonyl group (carbon double bonded to O) bonded to one H

polar
lower molecular weight adelhydes are soluble

eg. formaldehyde (simplest, usually used in solution called ‘formalin’ which embalms)

46
Q

ketone

A

carbonyl group (C double bonded to O) bonded to 2 C

carbonyl group is polar
lower molecular weight ketones are soluble
ketones = partially broken down fats

eg. acetone (simplest, solvent), progesterone (hormone, helps uterus wall accept fertilized eggs), testosterone

47
Q

carboxylic acid

A

carboxyl group (COOH)

low molecular weights very soluble (8+ C = insoluble)
weak acids
balance of carboxylic acid and carboxylate ion depending on pH (7.4 - cellular fluids, carboxylate ion predominates)
fatty acids are carboxylic w/long hydrocarbon chains (12-20 C)
first found in natural fats

eg. lactic acid (found in muscle cells after exercise), citric acid (cellular energy), pyurvic acid (energy-conversion)

48
Q

ester

A

compound with ester group
key structural feature in lipids

eg. PET (thread used for sutures), nitroglycerin (dilates veins when heart is failing)

49
Q

amine

A

derivative of ammonia where 1+ H replaced by organic (R) group

fever than 6 C = soluble
weak bases (react w/water to release hydroxide ions)
amine drugs given in form of salts bc they dissolve in body (eg. benzalkonium chloride - quaternary ammonium salt, kills pathogens on contact, detergent action destroys membranes that coat and protect microorganisms, used to wash hands before surgery).

  • neurotransmitters (carry nerve impulses from one neuron to another)
  • epinephrine (adrenaline), hormone that increases blood glucose and raises blood pressure
  • eg. alkaloids, atropine (preoperative drug to relax muscles), morphine (central nervous system depressant), codeine (central nervous system depressant)
50
Q

amide

A

carbonyl group attached to N

less than 6 C = soluble
neutral
eg. nylon, wool, thiopental (intravenous anesthesia), diazepam (tranquilizer), ampicillin (antibiotic)

51
Q

detergents and soaps

A

cleaning comes through emulsifying agents (coating around substance that separates)
soaps and detergent dissociate to form ions when in water
nonpolar substances such as oils/grease, attracted to uncharged ends of soap ions

52
Q

antiseptic vs disinfectant

A

antispetic = used on living tissue
disinfectant = used on objects

53
Q

oxidizing antiseptics

A

destroy compounds essential to bacterial function, may damage skin (hydrogen peroxide, iodine)

54
Q

oxidizing disinfectants

A

sodium hypochlorite (bleach)
calcium hypochlorite (bleaching powder)

55
Q

glucose

A

the most nutritionally important monosaccharide

AKA ‘dextrose’/’blood sugar’

other sugars must be converted into this in the liver

56
Q

galactose

A

hexose monosaccharide
similar structure to glucose

component of lactose, component of nerve tissue

57
Q

fructose

A

the sweetest monosaccharide

AKA levulose/fruit sugar

58
Q

sucrose

A

disaccharide of glucose + fructose.

common household sugar
found in plants

59
Q

maltose

A

disaccharide of 2 glucose
formed during digestion of starch

60
Q

lactose

A

disaccharide of 1 galactose and 1 glucose

milk sugar

61
Q

starch

A

polysaccharide of glucose units
STORAGE form of glucose in plants
- 2 forms in plants: amylose (unbranched), amylopectin (branched, more common)

can be used for ENERGY function when hydrolyzed into mono or di

62
Q

glycogen

A

polysaccharide of glucose units
used by animals to STORE glucose (in liver and muscles)

used for ENERGY on hydrolysis (glucose gets released. helps maintain blood sugar levels)

similar structure to amylopectin but more branched

63
Q

cellulose

A

polysaccharide of glucose units
most important STRUCTURAL polysaccharide (plant cell walls)
most abundant organic compound on earth

FIBER: not easily digested, stimulates contraction of intestines (except for in herbivores who have bacteria in digestive system that hydrolyzes)

64
Q

essential fatty acids

A

needed by body but not synthesized in adequate amounts inside the body (eg fish oil supplements)

linoleic and linolenic acids: produce hormone-like substances that regulate blood pressure, clotting, blood lipid levels, immune response, inflammation response bnr45v

65
Q

waxes

A

long chain fatty acid + long chain alcohol
insoluble
protective coating on feathers, fur, skin (eg sebum)

66
Q

simple vs conjugated proteins

A

simple: only amino acids
conjugated: amino acids + prosthetic groups

prosthetic groups: lipids, carbs, metal ions, phosphate groups

67
Q

protein size

A

too large to pass through cell membranes
contained inside cells they were formed in
leak out if cell is damaged (eg. protein in urine = kidney issues)

68
Q

protein denaturation

A

protein unfolds, loses shape thus loses function
- hyperthermia (40 degrees -> death at 30 min at 41.7 degrees)
H bonds break (tertiary structure breaks)

69
Q

protein types (functions)

A
  1. catalytic (enzymes)
  2. structural
  3. storage - for molecules/ions
    eg. ovalbumin (stored form of aminos in embryos of bird eggs), casein (storage protein in milk)
  4. protective
    eg. antibodies, blood clotting
  5. regulative - of hormones
    eg. growth, gastrin (stimulates stomach to secrete acid), glucagon (stimulates glycogen metabolism in liver), insulin (regulates glucose metabolism)
  6. nerve impulse transmission - receptors of molecules that pass b/w gaps of nerve cells
    eg. rhodopsin (retina), acetylcholine receptor
  7. movement - muscle
  8. transport - molecules and ions throughout body
    eg. serum albumin (transports fatty acids from adipose), hemoglobin (carries O from lungs to tissues)

Chemistry (5 decks)

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