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Organic Chemistry Flashcards

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1
Q

What is organic chemistry

A

organic - has carbon in molecules - involved reactions of organic compounds

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2
Q

What is valence in organic chemistry

A

number of bonds to an atom in a stable (uncharged) molecule.

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3
Q

How many bonds do C, O, H, F, Br, N, Cl, I

A

C = 4
O = 2
F = 1
Br = 1
H = 1
N = 3
I = 1

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4
Q

Alkanes

A

They are a type of hydrocarbon

  1. simplest organic molecules
  2. Only contain C and H atoms,
  3. Simplest alkane is methane, CH4
  4. The bond angles in alkanes are 109.5 degrees (tetrahedral bond angle)
  5. alkanes can be linear, branched or cyclic
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5
Q

first 10 branched alkanes

A
  1. methane
  2. Ethane
  3. Propane
  4. Butane
  5. Pentane
  6. Hexane
  7. Heptane
  8. Octane
  9. nonane
  10. Decane
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5
Q

What is the principal of carbon chain

A

The backbone with the longest sequence of continuous carbon atoms

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6
Q

When naming the branches of alkanes
2C

4C

A

2 carbon atoms = ethyl

4 carbon atoms = Butyl

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7
Q

When is a molecule determined to be saturated or unsaturated?

A

When a Carbon has a single bond = saturated
when a carbon has a double bond = unsaturated

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8
Q

do alkenes contain single or double bonds?

A

contain at least one double bond between the carbon atoms

double bond = saturated

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9
Q

How do you name molecule?

A
  1. parent = the main chain (longest stretch of C-atoms containing certain groups)
    - identify the longest chain present which includes anu double bonds or triple bonds
  2. Unsaturation = double or triple bonds that are present
  3. substituents = groups coming off main group
  4. Functional group = ending to indicate the group after which the molecule is named.
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10
Q

What is the nomenclature for Alkenes ‘ene’ and ‘yne’

A

ene = double bond
yne = triple bond

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11
Q

what is a functional group?

A

are specific group of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules.

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12
Q

Where are hydroxyl OH groups found?

A

alcohols
single bond between oxygen and hydrogen
R group attaches to a Carbon atom

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13
Q

where are carbonyl groups found?

A

Found in aldehydes (-CHO) and ketones (-CO)

Double bond between the carbon and oxygen

aldehydes (end of the chain): r group attaches to either carbon or hydrogen

Ketones (in the middle): R group is attached to carbons of molecule (can attach both sides)

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14
Q

Where are carboxyl groups found?

A

In carboxyl acids

Double bond between the carbon and oxygen

r group attaches to either carbon or hydrogen

Has a OH group attached. - COOH means an acid

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15
Q

What is the priority of alcohols, aldehydes, ketones and carboxylic acids?

A
  1. carboxylic acids - COOH
  2. aldehydes - CHO
  3. ketones -CO-
  4. alcohols - OH
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16
Q

what is an aromatic compound?

A

Display resonance (circle), which gives them extra stability. All of C-C bonds

hydrocarbon ring - such as benzene

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17
Q

What is esterification?

A

Made from a carboxylic acid and an alcohol -
Esterification is the process of combining an organic acid (RCOOH) with an alcohol (ROH) to form an ester (RCOOR) and water;

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18
Q

what are prefixes for the following compounds?
Alcohol
Ether
aldehyde
ketone
acid
ester
amine
amide

A

Alcohol - + ol
Ether + oxy
aldehyde + al
ketone +one
acid +oic acid
ester +oate
amine +amine
amide +amide

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19
Q

What are structural isomers?

A

compounds with the same molecular formula, but atoms are connected in different ways. They will have different physically properties.

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20
Q

What are stereoisomers?

A

are compounds with the same connections between atoms but different 3D geometry

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21
Q

What are two types of stereoisomers?

A
  1. Optical isomers (enantiomers)
  2. Cis-trans isomers (arrangements around double bonds)
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22
Q

Describe what a enantiomer is?

A

a molecule that contains a carbon atom bonded to four different groups is non-superimposable on its mirror images.

Tetrahedral carbon atoms with four different groups attached can results in enantiomers- called chiral carbon.

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23
Q

Describe what a cis-trans isomerism or geometric isomerism is?

A

Formed because of restricted roatation around a double bond

cis isomer - two similar groups on the SAME side of the double bond

Trans isomer - two similar groups of the OPPOSITE side of the double bond

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24
Q

What are carbohydrates?

A

polyhydroxyaldehydes or polyhydroketones

based of hydroxyl (-OH) and carbonyl (C double bond O) groups

Storage of chemical energy (glucose, startch, glycogen)

Structural carbohydrates - cellulose, chitin, connective tissues

other biological roles - DNA and RNd

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25
Q

What are monosaccharides and common example of a monosaccharides?

suffix?

A

contains one carbon chains
contains one carbonyl (C double bond O) group

Aldoses contain aldehyde group = glucose
Ketoses contain ketone group = fructose
depending on carbonyl group found on structure of carbohydrate

“ose” identifies carbos
tri- tetr, pent- = carbon atoms in the main chain

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26
Q

do carbohydrates contain chiral carbons? and what is the 2D depiction called?

A

yes, and 2D depiction is called fischer projection (indicated with * )

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27
Q

D- and L- monosaccharides are considered enantiomers, what does this mean?

A

they are mirror images of each other
when hydroxyl group is on right is D-sugars
and when on the left L-sugars

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28
Q

What is the compound called when aldehydes and/or ketones react with alcohols?

A

Hemiacetals associated with cyclic monosaccharides

when aldehyde group reacts with hydroxyl group - forms a links (hemiacetals)

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29
Q

What is a anomeric carbon?

A

a new stereocenter upon cyclisation - if the hydroxyl group is;

beta L-“sugar” - above
alpha D”sugar”- below

only worry about Carbon 1

30
Q

6 membered hemiacetal rings
5 membered hemiacetal rings

A

Pyranoses
Furanoses

31
Q

How are glycosides formed?

A

Hemiacetals react with excess alcohol in the presence of an acid catalyst to form acetals.

The cyclic acetal derived from monosaccharide is called glycoside - and formed with bonds called glycosidic bond.

32
Q

formation of N-glycosides and what structure are they well known to form

A

N- indicates nitrogen link

Hemiacetals reacting with amines to form N-glycosides

formed from D-ribose and aromatic bases such as pyrimidine bases and purine bases. They are structural units of nucleic acids DNA, RNA and nucleosides.

base and ribose - connects to sugar with nitrogen - glycosidic bond. N-glycosides.

33
Q

What are disaccharides?

A

consists of two monosaccharide units linked by glycosidic bond between the anomeric carbon of one and an -OH group.

34
Q

what are polysaccarides?

A

are polymers of monosaccharides units joined by glycosidic bonds

such as starch and glycogen

35
Q

does starch have both a-1,4- and b-1,6 glycosidic bonds?

A

No, starch hasa-1,4 and -1,6- glycosidic bonds
24-30 glucose units per branch
carbohydrate storage for plants

36
Q

does glycogen have both a-1,4- and b-1,6 glycosidic bonds?

A

no, glycogen has a-1,4 - and a-1,4 glycosidic bond

12-14 glucose
carboydrate reserve in animals (liver and muscle)

37
Q

What is the difference between the structure of starch and cellulose? and what is the major reasoning for this

A

The glycosidic bonds are different, cellulose has B-1,4-glycosidic bonds and there are no branches in cellulose.

forms a rod like insoluble fibres due to strong hydrogen bonding between -OH groups from parallel chains. Gives plants the ability to grow.

38
Q

what are amino acids and what protein roles do they have

A

building blocks of proteins, containing basic (amine) and acidic (carboxylic acid) functional groups.

structure (keratin collagen)
catalysis (enzymes)
movement (muscle actin and myosin)
transport (haemoglobin, albumin)
protection (immune system, antibodies)

39
Q

What are the main structural points of an amino acid?

A

r group on bottom
Carboxyl group on top
enantiomeric formation = Hydrogen atom and Amino group —> if left = D-configuration and if right = L-configuration

Most commonly nature configuration is L-amino acid

40
Q

What are the four categories of amino acids?

A
  1. non-polar sides chains (hydrophobic)
  2. Polar, un-ionised side chains (hydrophilic)
  3. acidic side chains (hydrophilic)
  4. basic side chains (hydrophilic)
41
Q

What is amphoteric?

A

able to react as acid or as base

42
Q

What is isoelectric point?

A

pH at which amino acid is neutral or exist primarily as zwitterion (dipolar ion). Isoelectric point for each amino acid is different depending on its structure.

43
Q

What charge do amino acids have below the isoelectric point?

A

at pH below the isoelectric point, amino acids are still positively charged

44
Q

What charge do amino acids have above the isoelectric point?

A

At ph above the isoelectric point, amino acids become neutral and the O becomes negative

45
Q

Do each amino acid have the same isoelectric point?

A

no, they all have different isoelectric points,

46
Q

what happens when two amino acids react with each other?

A

for an amide bond called a peptide bond. The product of this reaction is called dipeptide ( 2 units), tripeptide (3 units)

47
Q

What types of hierarchy structures do proteins have?

A

Primary

secondary

tertiary

quaternary.

48
Q

What are characteristics of primary structure in amino acids?

A

Primary - Simple sequence of amino acids in a polypeptide chain (joined with peptide bonds) has two sides

  1. C-terminal
  2. N-terminal

extend chain and grow,

Amino acids with free -NH3+ group is first (n-terminal_
Amino acid with free - COO- group is last (c-terminal)

49
Q

What are the characteristics of a secondary structure?

A

3D dimensional arrangement - ordered arrangement of amino acid residues in localised regions (based on hydrogen bonding)

Contain two common motifs alpha helix and beta-sheet

50
Q

What structure assisting in forming a secondary structure together?

A

Hydrogen bonds hold the structure in place - formed between oxygen amino acid, and hydrogen atom of another.

  1. alpha helix - right hand helix shape
    > C=O hydrogen bonds to N-H within chain
    > R groups point out from helix
  2. B-pleated sheet - 2 main types parallel and antiparallel.

> Contains C = O and N-H groups lie in plane street

> C=O groups of one chain hydrogen bonds to N-H groups of neighbouring chain
R groups in a given chain alternate between above and below the plane of the sheet.

consist of two or multiple proteins together.

51
Q

How are tertiary structures held together?

A

overall folding pattern and arrangement in space (3D) of atoms in a single polypeptide chain.

included alpha helix and beta sheet - forms tertiary structure.

Disulfide bonds (-S-S-)
hydrophobic interactions
hydrogen bonding
ionic linkages

52
Q

What is a quaternary structure?`

A

Only proteins with more than one chain. when two proteins are linked together through hydrophobic sites = dimer (2), trimer (3), tetramer (4)

example - haemoglobin

53
Q

What is denaturation? and what causes denaturatisation

A

major change in secondary, tertiary or quaternary structure. loss of order in structure.

Caused by;
1. pH change
2. increase in temperature
3. salts,
4. agitation
5. solvent composition

54
Q

Is there peptide bond cleavage in denaturation?

A

no

55
Q

What are enzymes?

A

biological catalysts that speed up the chemical reactions

protein with catalytic activity

they are not used up during the reaction, in the same form when the reaction is complete.

56
Q

What is the mechanism of enzymes

A

enzyme, active site and substrate

The active site on the enzyme attaches to the substrate via temporary bonds. Called lock and key analogy

they are very specific “lock” is substate, active site is “key’ carrying out specific reaction

57
Q

What types of enzymes are there?

A

simple enzymes - composed solely of protein, single or multiple subunits

Complex enzymes = co-enzyme

protein plus organic molecule or metal ion (co factor = non protein portion)

58
Q

What is a holoenzyme?

A

Complex enzymes that was once a apoenzyme, with the cofactor. forming a holoenzyme.

59
Q

Why do we need co-factors?

A

Lock and key - never perfect fit in reality
the substrates never has a perfect fit, needed an ‘adaptor’

helping enzymes conclude the reaction.

60
Q

What are endo and exo acting enzymes?

A

important for enzymes that hydrolyse protein or polysaccharides. A combination of both may lead to complete hydrolysis of the macromolecule.

exo enzyme will release single amino acid and the endo enzyme with release peptids

61
Q

What is the difference between nucleosides and nucleotides?

A

Nucleosides is composed of pentose and a bonded through C1 (anomeric carbon) of the sugar to a heterocyclic base (purine or pyrimidine) by a B-N0 glycosidic bond.

“dine”

Pentose: monosaccharide with 5 carbons.

Nucleotide - is a nucleoside in which a single phosphate group has been esterified with a hydroxyl group (commonly 3’ or 5’) on monosaccharide ring.

62
Q

In regards to the primary structure, where do the bonds occur?

A

3’ hydroxyl of one deoxyribose unit is joined by phosphodiester bond to the 5’ hydroxyl of the next deoxyribose unit

reads from 5’end to 3’end

63
Q

What are the differences between DNA and RNA?

A

RNA is similar but found in higher quantities and with multiple copies

RNA
- single stranded
- Ribose sugar (OH group)
- 3 types of RNA (ribosomal RNA, transfer RNa and messenger RNA)
- uracil used

DNA
- double stranded
- thymine
- Deoxyribose as the sugar (H+)

64
Q

What is a lipid?

A

generic term that describes components in organic solvents, but are in-soluble in wate

65
Q

What are types of lipids

A

Triacylglycerols
phospholipids
sphingolipids
Steroids
Waxes
Fat soluble vitamins
carotenoids

66
Q

Where are lipids found?

A

1 storage lipids (fats and oils) - to carry out metabolic reactions (energy storage, thermal insulation and globules stored in cells)
2. structural lipids - found in cell membrane
3. Hormones and defence

67
Q

Fatty acids structures, what are two ways they differ?

A

fatty acids differ in two ways

COOH - carboxyl group

  1. length - determined by the number of carbons
  2. degree of saturation - which is determined by the number of double bonds between carbon atoms.

no carbon - carbon double bonds = saturated
one carbon - carbon double bonds = unsaturated
two of more carbon-carbon double bonds - polysaturated

68
Q

What defines a cis, trans - isomers?

A

Cis - hydrogens are attached to carbon atoms are on the same side of the double bond

Trans - hydrogens attached to carbon atoms are on either side of the double bond

69
Q

How is triacylglycerol formed?

A

Fatty acids are components of triacylglycerol

firstl, carboxylic acid and alcohol undergo esterification, joining esters and water.

Thus forming a glycerol that will form with a fatty acid and =
triacylglycerol is formed from fatty acid and glycerol.

its an esterification - is the reaction of an alcohol with carboxylic acid to give ester and water

70
Q

how do you break the ester bond in a triacylglycerol?

A

completed through hydrolysis = saponification.

71
Q

What are phospholipids?

A

diesters of glycerol and long chain carboxylic acids (fatty acids)

formed with phospholipid (head group) is attached to C-3 through phosphodiester bond.
and fatty acid tails with

importance can form and arrange a polar phospholipid bilayer in animals and plant cells. Polar head groups orientated into the aqueous environment whilst the hydrophobic chain for a non-polar domain inner.

72
Q

What are sterols?

A

male and female hormones
cholestrol

consist of interconnected rings of carbon atoms = Gonane.

73
Q

What are surfactants?

A

Amphiphilic molecules - contain both hydrophobic and hydrophilic domains

can form foam. arrangement of surfactants at the air-water interface - emulsion

Chemistry (9 decks)

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