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Semester 1 Revision > Chemistry Clinical Sciences 11-13 > Flashcards

Chemistry Clinical Sciences 11-13 Flashcards

1
Q

Why did scientists previously considered that organic molecules were special?

What experiment proved that living systems are not special?

A

Previously scientists considered organic molecules produced by LIVING SYSTEMS to be SPECIAL because organic molecules could not be synthesized in a lab.
The WOHLER’S EXPERIMENT proved that living systems were not special by the creation of UREA in the lab.

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2
Q

What is Organic Chemistry?

A

ORGANIC CHEMISTRY is the STUDY and SYNTHESIS of CARBON- based molecules which contain C-H bonds.

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3
Q

List compounds which contain carbon but are NOT organic molecules.

A 
Oxides of Carbon (CO2 and CO). 
Carbonates (Na2CO3).
Bicarbonates (NaHCO3)
Metal Carbides (CaC2)
Metal Cyanides (KCN)
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4
Q

Give an example to show that Organic Chemistry obeys the same fundamental laws of chemistry.

A

COVALENT BONDING is the SAME in organic molecules as in simple molecules.

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5
Q

Why is organic chemistry a separate discipline?

A

There are LARGE numbers of compounds, UNIQUE chemical and physical PROPERTIES and UNIQUE CARBON character.

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6
Q 
Comparison between Organic and Inorganic Compounds:
Composed of what elements?
Bonding?
Solubility?
Flammable?
Isomerism?
Chemical Reactions?
Classifications?
A

O- Composed of C, H and a few other elements.
I- Composed of all known elements.
O- Covalent bonding.
I- Often Ionic bonding.
O- Variable- Depends on structure and bonding (often generalised as reverse of inorganic).
I- Highly soluble in water; low solubility in non- polar solvent.
O- Mostly flammable
I- Mostly non- flammable.
O- Isomerism common.
I- Isomerism less common (only transition metal complexes).
O- Chemical reactions occur between molecules- can be slower.
I- Chemical reactions occur between ions- usually fast and quantitative.
O- Classifications include functional groups; skeletal structures and homologous series.
I- Classifications include acids; bases; salts.

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7
Q

Rules for drawing skeletal formula.

A

If no bonds are shown then presume the CARBON is bonded to HYDROGEN atoms.
When there is a BEND in the CHAIN a CARBON is present.
Atoms which are not carbon/ hydrogen atoms must be SHOWN. Even HYDROGEN atoms which are attached to other ELEMENTS, MUST be shown.

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8
Q

Importance of Organic Compounds in the Body

A

Aspirin= Commonly used painkiller- Carboxylic acids, esters and aryl functional groups.
Adrenaline- Secreted by adrenal glads in response to stress. Alcohol, amine and phenol functional groups.
Cis- 11- Retinal is in the human eye and has the ability to detect light by changing its conformation to absorb light which sends a signal regarding vision. Alkene and Aldehyde Functional Groups.
Soaps are produced by reaction of a base with fats and oils contain ester functional groups.

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9
Q

What are naturally derived compounds?

Give some examples of naturally deprived compounds.

A

Compounds which occur in a natural state.

Fuels- Wood, coal, oil and alcohol.
Building Blocks- Proteins, liquids, sugars, nucleic acids and vitamins.
Drugs- Penicillin, quinine, morphine, erythromycin, vincristine, thyroxine.
Flavours- Vanillin
Dyes- Indigo and Woad.

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10
Q

What are synthetic compounds?

Give some examples of synthetic compounds.

A

SYNTHETIC compounds are developed from NATURALLY deprived structures which MIMIC some of their functions.
SALBUTAMOL is a treatment for ASHMA and has a similar structure to ADRENALINE.
Textiles- Nylon
Material- Rubber + Plastic.
Drugs- Parcetamol, Salbutamol, Statins, Anti- depressants.
Ingredients- Soaps, Detergents, Shampoos ect.

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11
Q 
CARBON
Group?
Metal/ Non- Metal?
Electronic structure? 
Isotopes?
Who does carbon form strong bonds with?
Types of bonds carbon forms?
A 
Group 4
Non- Metal 
1s22s22p2 
Two stable isotopes- 12C and 13C. 
Carbon forms STRONG bonds with itself in CHAINS and RINGS as well as with other elements such as HYDROGEN, NITROGEN, SULFUR and OXYGEN. 
Forms Single, Double and Triple bonds.
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12
Q

What are hydrocarbons?

A

HYDROCARBONS are molecules made of HYDROGEN and CARBON molecules ONLY.

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13
Q

What are saturated hydrocarbons? Examples.

A

Only contain Carbon- Carbon single bonds. For example alkanes.

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14
Q

What are unsaturated hydrocarbons? Examples.

A

Contain at least one Carbon- Carbon double bond. For example Alkenes, aromatics and alkynes.

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15
Q

What type of molecule are alkanes? What is there general formula?

A

Linear molecules.

CnH2n+2

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16
Q

What type of molecule are cycloalkanes? What is there general formula?

A

Cyclic molecules.

CnH2n

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17
Q

What do mono- alkenes contain? What is there general formula?

A

1 Carbon- Carbon DOUBLE bond with a general formula C2H2n.

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18
Q

What do mono- alkynes contain? What is there general formula?

A

1 Carbon- Carbon TRIPLE bond with a general formula CnH2n-2.

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19
Q

What do aromatics contain? What is there general formula?

A

1 or more rings of 6 Carbon atoms called BEZENE RINGS.

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20
Q

What are the rules for naming alkanes?

A
  1. NAME the LONGEST CONTINOUS chain of carbons, known as the PARENT CHAIN.
  2. NUMBER the chain starting at the end nearest an attached group.
  3. IDENTIFY and NAME attached groups.
  4. NAME the LOCATION of the attached group depending on the carbon number it is attached to.
  5. Groups such as di, tri, tech, SHOULD NOT be included in the alphabetical order. Place a comma between multiple numbers.
  6. Assemble in ALPHABETICAL order.
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21
Q

Naming attached alkyl groups:

A

Methyl (CH3)
Ethyl (CH3CH2)
Propyl (CH3CH2CH2)

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22
Q

How can structural isomers of organic compounds be distinguished?

A

By using prefixes indicating the type of branching present in the Carbon chain.

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23
Q

Non- systematic names for organic molecules include:

A

N- Alkane= Unbranched.
Iso- alkane= 2 methyl groups and no other branches.
Neo- alkane= 3 methyl groups and no other branches.

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24
Q 
Classification of Carbons:
Primary Carbon
Secondary Carbon 
Tertiary Carbon
Quaternary Carbon
A

Primary Carbon- A carbon which is bonded to one other carbon atom.
Secondary Carbon- A carbon bonded to two other carbon atoms.
Tertiary Carbon- A carbon bonded to three other carbon atoms.
Quaternary Carbon- A carbon bonded to four other carbon atoms.

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25
Q

How can you classify organic compounds?

A

Carbon Chain/ Ring

Functional Group

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26
Q

What are Aliphatic compounds?

A

Compounds containing an OPEN CHAIN of carbon atoms.

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27
Q

What sub groups can aliphatic compounds be divided into?

A

Alicyclic compounds

Saturated hydrocarbons Unsaturated hydrocarbons

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28
Q

What are alicyclic compounds? Give an example.

A

ALICYCLIC compounds are RINGS of saturated carbon atoms such as cyclo-butane.

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29
Q

What are Saturated hydrocarbons?

A

SATURATED hydrocarbons have NO carbon- carbon DOUBLE BOND.

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30
Q

What are unsaturated hydrocarbons?

A

UNSATURATED hydrocarbons have at least ONE Carbon- Carbon DOUBLE BOND.

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31
Q

What are aromatic compounds. Give an example.

A

Compounds which contains a RING where ALL of the atoms are UNSATURATED are known as AROMATIC compounds such as BENZENE or ANILINE.

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32
Q

What are heterocyclic compounds?

A

HETEROCYCLIC compounds contain a RING made up of carbon and at least ONE OTHER ELEMENT such as nitrogen, oxygen or sulfur.

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33
Q

What are Acyclic molecules?

A

Acyclic molecules DO NOT contain a ring system and include unsaturated/ saturated alicyclic compounds

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34
Q

What are cyclic molecules?

A

Cyclic molecules CONTAIN a ring system and include alicyclic, aromatic or heterocyclic molecules.

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35
Q

What does a functional group in a molecule do?

A

gives it characteristic chemical properties (how the molecule reacts).
acts as a site of chemical reactivity.
serves as the basis of nomenclature.
classifies its family.

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36
Q

What is a polyfunctional compound?

A

Have MORE than one FUNCTIONAL GROUP.

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37
Q

What does the principal functional determine?

What happens with the second functional group?

A

Determines the class.

The second functional group is treated as a substituent.

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38
Q

List the principal functional group order.

A

CARBOXYLIC ACID > ESTER > ACID HALIDE > AMIDE > NITRILE > ALDEHYDES > KETONES > ALCOHOLS > AMINES > DOUBLE BOND > TRIPLE BOND > HALOGEN > NITRO

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39
Q

What is the homologous series?

A

A GROUP of ORGANIC compounds with similar CHEMICAL properties in which members contain the SAME FUNCTIONAL GROUP but different lengths of carbon chains. They different by CH2 unit.

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40
Q

What are successive members of a homologous series called?

A

HOMOLOGUES

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41
Q

What is the same about members in the same homologous series?

A

SAME general formula.
PREPARED by similar methods.
SIMILAR chemical properties.
GRADUAL variation in physical properties with increasing molecule weight.

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42
Q

What two types of orbitals can be created from linear combination of atomic orbitals?

A 
Hybrid Atomic Orbitals (sp, sp2 and sp3). 
Molecular Orbitals  (σ, σ*, π, π*).
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43
Q

What are hybrid orbitals?

A

COMBINATION of atomic orbitals from the SAME atom.

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44
Q

What are molecular orbitals?

A

COMBINATION of atomic or hybrid atom orbitals from DIFFERENT atoms.

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45
Q

What orbitals to second row elements like Carbon, Oxygen and Nitrogen use to hybridise to form sp, sp2 and sp3?

A

Their 2s and 2p orbitals.

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46
Q

Describe the s orbital.

A

Spherical

Lower in energy than the other orbitals in the same shell.

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47
Q

Describe the p orbital.

A

Dumb-bell shape.
Nodal plane passes through nucleus.
Higher in energy than s orbital.
Three p orbitals in the same shell.

48
Q

What is hybridisation?

A

The idea that atomic orbitals fuse to form NEWLY hybridized orbitals which influences a molecules GEOMETRY and BONDING PROPERTIES.

49
Q

Because of Carbon’s electron configuration (1s22s22p2)

i) how many unpaired electrons does carbon have?
ii) how many bonds should carbon be theoretically able to make?
iii) How many bonds does carbon form?

A

2 Unpaired electrons
2 bonds
Makes 4 bonds.

50
Q

How does Carbon make 4 bonds?

A

To make 4 bonds one of the 2s electrons is PROMOTED into the VACANT orbital which supports the idea that the s orbital and the 3 p orbitals are being combined to form HYBRID ORBITALS.

51
Q

Hybridisation requires energy but why is it favourable?

A

Hybridisation REQUIRES energy but it is FAVOURABLE because of decreased electron- electron repulsion

52
Q

What compounds does sp3 hybridisation occur in?

Describe what occurs in sp3 hybridisation?

A

Sp3 hybridisation is used in SATURATED compounds. ALL 4 atomic orbitals combine to give 4 HYBRID orbitals. All the hybrid orbitals have the SAME energy.

53
Q

What shape do the sp3 orbitals point towards?

The overlap of the sp3 orbital produces what bond?

A

Tetrahedron

Sigma Bond

54
Q

What is a sigma bond?

A

A sigma bond is a bond formed by the overlap of orbitals in an END- TO- END fashion with the electron density concentrated BETWEEN the nuclei of the bonding atoms.

55
Q

Describe what occurs in sp2 hybridisation?

A

In Sp2 hybridisation the s orbital and TWO p orbitals combine to give 3 hybrid orbitals, with the third p orbital remaining UNCHARGED.

56
Q

What shape do the sp2 orbitals point towards?

The overlap of the sp3 orbital produces what bond?

A

Triangle

Sigma Bonding.

57
Q

In sp2 hybridisation, describes what happens with the p orbital.

A

The p orbital is PERPENDICULAR to them which is known as PI BONDING.

58
Q

What is pi bonding?

A

Pi bonding is a bond formed by the overlap of orbitals in a SIDE- BY- SIDE fashion with the electron density concentrated ABOVE AND BELOW the plane of the nuclei of the bonding atoms.

59
Q

In what compounds is sp2 hybridisation used?

A

ALKENES, CARBONYLS and AROMTATIC RINGS, which all have DOUBLE BONDS (all double bonds).

60
Q

Describe what occurs in sp hybridisation?

A

The s orbital and ONE p orbital combine to give 2 hybrid orbitals and two p orbitals which are UNCHARGED.

61
Q

What shape do the sp orbitals give? Bond angle?

A

180 and a linear molecule.

62
Q

In sp hybridisation, describes what happens with the p orbital

A

P orbitals are PERPENDICULAR to them which is used are used in pi bonding.

63
Q

In what compounds is sp hybridisation used?

A

ALKYNES and NITRILES which all have TRIPLE BONDS.

64
Q

Properties of hybrid orbitals.

A

Hold ELECTRONS CLOSER to the nucleus.
The bond becomes SHORTER therefore STRONGER.
More DIRECTIONAL, so they have more effective bonding interactions.
The more s-character in an orbital, the LOWER the energy- INCREASED stability of an electron in that orbital.

65
Q

How are sigma bonds formed?

What rotation is involved in sigma bonding?

A

Sigma bonds are formed by “DIRECT” overlap and ELECTRON DENSITY is along the LINE of the bond. SYMMETRIC WRT ROTATION, object looks the same after some rotation of a partial turn, round the bond.

66
Q 
What orbitals can a sigma bond be formed between?
Which orbital (bonding/ original atomic orbital) has a lower energy?
A

A bond may be formed between s-s, p-p, s-p or hybridized orbitals.
The bonding molecular orbital is LOWER in energy than the original atomic orbital.

67
Q

Describe the bonding in Methane.

A

Sigma Bonding
Carbon need to get hybridised. Four sp3 hybrid orbitals forms a tetrahedron. Add 4 Hydrogens. Combination of 1s and 3p. Sigma bonds between H and 4 sp3.

68
Q

Describe the bonding in Ethane.

A

Sigma Bonding

Each carbon uses 3 sp3 orbitals to bond to HYDROGEN and remaining sp3 orbital on each CARBON overlaps.

69
Q

How are pi bonds formed?

A

Pi bonds are formed by “PARALLEL” overlap of p orbitals. Electron density is ABOVE and BELOW the plane of the bond, which forms AFTER sigma bonds.

70
Q

Which has a higher energy sigma bonds or pi bonds.

A

Pi bonds are Higher in energy than sigma bonds, therefore weaker and more easily broken.

71
Q

Describe the bonding in ethene.

A

A double bond (2 pairs of shared electrons) consists of a sigma bond and a pi bond.

72
Q

Describe the bonding ethyne.

A

A triple bond (3 pairs of shared electrons) consist of a sigma bond and two pi bonds.

73
Q

Describe the bonding in Benzene.

A

Pi electrons DELOCALISED around the ring, above and below and plane.

74
Q

Describe the bond length and strength in a single, double and triple bond.

A

BOND LENGTH- Longest- Single, Double, Triple.

BOND STRENGTH- Highest, Triple, Double, Single.

75
Q

What are isomers?

A

ISOMERS are molecules which have the SAME molecular formula but differ in the arrangement of their atoms.

76
Q

What are structural isomers?

A

STRUCTURAL isomers (aka constitutional) differ in their BONDING sequence (bonding sequence)/ molecular skeleton.

77
Q

What are stereoisomers?

A

STEREOISOMERS differ only in the ARRANGEMENT of ATOMS in space.

78
Q

Are structural isomers the same/ different compounds? What properties do they have?

A

Structural isomers are usually DIFFERENT compounds with DIFFERENT PHYSICAL and CHEMICAL properties.

79
Q

List the different types of structural isomerism and describe what they are.

A

Chain or Skeletal isomerism- Difference in the CARBON SKELETON.
Position isomerism- Difference in POSITION of Functional Group.
Functional isomerism- Difference in IDENTITIY of the Functional Group.
Tautomerism- MOVEMENT of BONDS and a PROTON.

80
Q

What is tautomerism?

A

STRUCTUAL isomers of CHEMICAL compounds are readily interconverted (cause two things to be converted into each other).

81
Q

Give an examples of Chain/ Skeletal Isomerism.

A

Butane

2- methyl propane

82
Q

Give an examples of Positional Isomerism.

A

Butan-1-ol

Butan-2-ol

83
Q

Give an examples of Functional Group Isomerism.

A

Diethyl ether
Propanal
Propanone

84
Q

Give an examples of Tautomerism.

A

Cyclohexanone

Cyclohex-1-enol.

85
Q

Name the two types of stereoisomerism.

A

Geometric (cis-trans; E/Z) Isomerism

Optical Isomerism

86
Q

What is geometric isomerism a result of?

A

RESTRICTED ROTATION around a bond.

87
Q

What bonds (single, double, triple) does geometric isomerism occur in?

A

Geometric Isomerism occurs in molecules with a DOUBLE bond because there is limited rotation around the double bond. Full rotation would breaking the double bond and is not allowed without input of ENERGY. There is free rotation around Single (sigma) bonds.

88
Q

What are the requirements for geometric isomerism to occur?

A

Double bond.
DIFFERENT GROUPS at each end of the bond
DIFFERENT PHYSICAL and CHEMICAL PROPERTIES.

89
Q

How are geometric isomers distinguished from each other?

A

CIS and TRANS

90
Q

What is the cis isomer?

A

(Z) Two alkyl groups are on the SAME side of the double bond.

91
Q

What is the trans isomer?

A

(E) Two alkyl groups are on the OPPOSITE side of the double bond.

92
Q

What is an alykl group?

A

Group is when an alkane is missing 1 HYDROGEN.

93
Q

What ability do optical isomers have?

A

OPTICAL ISOMERS have the ability to rotate plane- polarised light in opposite directions.

94
Q

What does Plane- polarised light describe?
What is polarised light?
What is a polariser?

A

Plane- polarised light describes the STATE of POLARISATION of a light source. Polarised light is light that VIBRATES in a SINGLE direction due to its passage through a polariser. A POLARISER is an OPTICAL filter that lets light waves of a specific polarization pass through while BLOCKING light waves of other polarisations.

95
Q

Compound that ROTATES the plane of polarised light to the RIGHT (CLOCKWISE) is known as?

A

DEXTROROTATORY or d- isomer or (+) isomer.

96
Q

Compound that ROTATES the plane of polarised light to the LEFT (ANTICLOCKWISE) is known as?

A

LAEVOROTATORY or l- isomer or (-) isomer.

97
Q

What is another way to describe how an optical isomer rotates the plane of polarised light.

A

(+) (-)

98
Q

When is a molecule describe as Chiral? By?

A

A molecule is described as CHIRAL if it has NO PLANE of SYMMETRY. A carbon atom bonded to FOUR DIFFERENT substituents lacks a plane of symmetry so it is called a CHIRAL CENTRE or ASYMMETRIC carbon atom.

99
Q

Optical isomers are non- superimposable mirror images. Give an example in the body of non- superimposable mirror images.

A

The lungs.

100
Q

What is a mess compound?

A

A MESO COMPOUND is a compound which contains TWO or MORE IDENTICAL substituted sterocentres. It has an INTERAL SYMMETRY PLANE that dives the compound in half. Meso compounds are OPTICALLY INACTIVE but may have CHIRAL CARBONS.

101
Q

How to classify a Meso Compound?

A
  1. TWO or MORE IDENTICAL substituted sterocentres.
  2. INTERAL SYMMETRY PLANE.
  3. STEROCHEMISTRY should CANCEL out  R or S should cancel out.
102
Q

For a meso compound how would you label a chiral compound s and r?

A

Number groups in order of priority and then draw an arrow from the highest priority group the lowest priority group.
If the arrow is ANTICLOCKWISE= S.
If the arrow is CLOCKWISE= R.

103
Q

How do you draw optical isomers?

What do normal lines, wedges and dashed lines mean?

A

Using a perspective view. Normal lines are in PLANE of the page.
WEDGES come OUT of the page.
DAHSED lines go INTO the page.

104
Q

How do you name Chiral Centres? How are these letters assigned.

A

S and R

R and S are assigned by looking at arrangement of groups around the chiral centre.

105
Q

Chirality of an amino acid and sugars are often described by?
How are these letters assigned?

A

D and L
Assigned by their configuration to GLYCERALDEHYDE. Also can be assigned by studying structure, but generally complicated to apply.

106
Q

What are Fischer Projections?

A

FLAT drawings that represent a 3D molecule and are commonly used for SUGARS.

107
Q

Describe the rules for Fischer Projection:

A
  1. Carbon chain is on the VERTICAL line.
  2. ROTATION of 180o in plane DOES NOT CHANGE molecule.
  3. DO NOT rotate 90o.
  4. DO NOT turn over out of plane.
108
Q

What are Fischer projections used to show mirror images?

A
  • Easy to draw.
  • Easy to identify enantiomers.
  • Easy to find internal mirror planes.
109
Q

What is an enantiomer?

What does an enantiomer represent? Why are they different?

A

An ENANTIOMER is an OPTICAL ISOMER which is a ON-SUPERIMPOSABLE MIRROR IMAGES of a chiral carbon.
Represent 2 optical isomers.
OPPOSITE rotatory powers are from the opposite ARRANGEMENT of GROUPS around each asymmetric carbon atom.

110
Q

Enantiomers have identical physical properties, except?

A

Their interaction with plane of polarised light.

111
Q

What are diasteromers?

A

STEROISOMERS that are not MIRROR IMAGES of each other.

112
Q

If a structure has n chiral centres, how many possible isomers does it have?

A

n

2

113
Q

What are Epimers?

A

diastereomers which differ at only one carbon atom.

114
Q

What is the most common example of disasteromers?

A

Most common examples of diastereomers is a molecule with 2 or more chiral carbons where at LEAST ONE but NOT ALL DIFFER.

115
Q

What compounds can be disasteromers?

A

Diastereomers include cis- trans isomers and other examples involving rotation.

116
Q

Are the properties of disasteromers similar?

A

Two diastereomers will have DIFFERENT PHYSCIAL properties, for example melting and boiling point and stability. They have different CHEMICAL REACTIVITY with both achiral and chiral reagents.

117
Q 
Comparison between Diastereomers and Enantiomers: 
Rotate Plane of polarised light? 
Physical and Chemical Properties?
NMR spectroscopy?
Seperation by physical methods?
Interactions with chiral molecules?
Taste and Smell?
A

E- Rotate Plane of polarised light by equal amounts in opposite directions.
D- Mat rotate plane of polarised light but by different amounts.
E- Identical physical and chemical properties. Identical by NMR spectroscopy.
D- Different physical and chemical properties. NMR spectra visibly different.
E- Impossible to separate by normal physical methods.
D- Possible to separate by normal physical methods.
E- Interact differently with chiral molecules- this allows separation techniques.
D- Interact differently with both chiral and chiral molecules.
E- Differ in taste and smell.
D- Differ in taste and smell.

Semester 1 Revision (9 decks)

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