Chemistry- applied stuff

what is a monosarccharide

The chemical building block of a sugar, consisting of carbon, hydrogen, and oxygen, that links together via a glycosidic linkage to make larger saccharides

• 1:2:1 ratio of C, H, O

what are the 3 main structures of carbohydrates

3-carbon sugars (glyceraldehyde) are intermediate forms of sugar

5-carbon sugars ( ribose, deoxyribose ) used in DNA and RNA

6-carbon suagrs (fructose or glucose) used for energy

how to draw a Fischer projection

can be used to draw carbohydrates, with each vertical bond being a dash bond and each horizontal bond being a wedge bond

• if draw with solid bonds it is referred to a straight chain nomenclature

stereochemistry of carbohydrates

Carbohydrates are chiral molecules that use D and L to label enantiomers and not R and S

• Are assigned D or L based on the placement of the OH group on the carbon before the CH2OH

• If OH is on the right = D ( more common in nature)

• If OH is on the left = L

what are the two types of monosaccharides

Monosaccharides can either be aldose or ketose sugars

• aldose if it has an aldehyde at the end

• ketose if it has a ketone at the end

what is the prefered structure of a carbohydrate

Sugars are mostly cyclic, especially when they are 6-carbon carbohydrates, but can convert between straight and cyclic structures in an equilibrium reaction

• straight chain structures are drawn as Fischer projections

• Cyclic structures are drawn as chair structures or hawthorn projections

What is a hemiacetal

a functional group that forms when you create a cyclic structure of a simple carbohydrate

• is a carbon bound to an ether and an alcohol found where the two ends of the straight chain meet to become cyclic

which way do different OH’s point when creating a cyclic structure

Exception for the last chiral carbon that determines D and L, as that is used to form the cyclic link

• OH groups on the right side face down

• OH groups on the left side face up

how do straight chains bind to create cyclic forms

• If the molecule is a pyranose (6 carbons), then it will form a hexagon

• If the molecule is a furanose ( 5 carbons), then it will form a pentagon

• Regardless of the type of monosaccharide, the isomer-determining carbon binds the carbon of the carbonyl group on either the aldehyde or the ketone

anomeric carbons

When a cyclic form is created, it also leads to the creation of new chiral centres allow the molecules to form isomers called anomers

• they also have different names if a cyclic structure

what is pyranose vs fructose

Pyranose: the cyclic form of glucose (6 carbons) - the isomer-determining portion is a hydrogen and an OH

Furanose: the cyclic form of fructose (5 carbons) - the isomer-determining portion is CH2OH and H

How to differentiate anomers

• if the OH group on C1 id facing up add beta symbol in front of name

• if the OH group on C1 is facing down add the alpha symbol infront of the name

What are complex carbohydrates

includes disaccharides, oligosaccharides and polysaccharides bound by glycosidic linkages

what is a glycosidic linkage

A glycosidic linkage forms, creating a functional group called an acetal, which is a Carbon bound to two ethers

• Named based on the carbons of attachment between molecules , with the carbon that determines alpha and beta being 1 and going clockwise + alpha or beta

how does the orientation of the OH groups effect molecules

Can affect the molecules' purpose and stability

• If one OH is pointing up in one molecule and pointing down in another, then those are two different molecules with different functions

• too many electron-dense groups in one area can cause steric hinderance

How to name a carbohydrate

1. Add aldose or ketose in front, depending on whether it has an aldehyde or a ketone

2. Count the number of carbons in the cycle

3. add the number word + ose at the end instead of ane

4. can also add D or L or alpha or beta

what is a chair structure

A structure used to draw cyclohexanes/hexapyranose

• First, draw two parallel lines and connect the ends either upwards or downwards, depending on the direction of the parallel lines

• can start counting from anywhere on the carbon

what is an equatorial vs axial

Every carbon will have bonds in a tetrahedral shape, with bonds either being equatorial or axial ( one each per carbon)

• if they are equatorial, they point left or right

• if they are axial, they point up or down

• each has an up position (line point up) or a down position (line points down)

what is ring flipping

Chair structures have two different conformations, with each folded portion of the main structure switching

• Any bonds in the axial position will switch to the equatorial position, and vice versa

• can effect the stability of a molecule

how can axial verse equaltorial bond effect stability

• when bonds to bulky groups are in the equatorial position, they form a staggered formation, reducing electron repulsion and making it more stable (require less energy to remian stable so it is more common in nature)

• when bonds to bulky groups are in the axial position they form an eclipsed formation causing electron repulsion and making it less stable

what is a 1,3-diaxial interaction

An interaction between bulky groups on the first and 3rd carbon atoms in a chair structure that causes a lot of electron repulsion

• eclipsed interaction

cis or trans in chair structures

The CIS chair structure shows two bulky groups pointing in the same direction on either side of a molecule ( regardless of equatorial or axial)

The trans chair structure shows two bulky groups pointing in different directions

how do Cis and trans effect stability of a molecule

Cis and trans structures can differ in the position of their bonds as either up or down

• The up position on one carbon could be axial, making the molecule less stable

• difference between cis and trans can introduced axial bonds to the molecule effect stability

what can effect the pH of blood

• Intense exercise can lower pH due to excess H+ (more acidic) as it is removed from muscle by blood due to glucose metabolism alongside CO2

• severe anxiety can also increase the pH of blood due to excess OH ( more basic)

what maintains the pH of blood

Buffers are components made of weak acids and their conjugate bases (salts) that prevent OH- and H+ from affecting the pH of blood

• work best when their concentration well exceeds that of H+ or OH ions

• can be carbonic acid(H2CO3), phosphate and protein buffers in blood

what do buffers do if proton levels increase

The conjugate base form of the buffer binds to the H+ to convert to its acidic form

• aka become protonated

• H3O + base —> H2O + acid

what do buffers do if hydroxyl level increase

the acid component binds with the OH and converts to its conjugate base form

• become deprotonated

• OH + acid —> H2O + base

how does the Carbonic acid + bicarbonate buffer work

H+ + HCO3 ←→ H2CO3 + H2O ←→ 2H2O + CO2

• HCO3 = bicarbonate secreted in urine

• CO2 exhaled

• first reaction = acid base equilibrium

• second reaction = dissociation reaction

what other systems in the body get rid of OH and H+

H+ and HCO3 can be removed via filtration of the blood by the kidney and then removed in the urine

• slow process

The lungs use respiration to remove CO2 in a much quicker process

• why respiration increases when we exercise to battle pH change

under what conditions is buffering optimal

When we have relatively equal concentrations of acid and conjugate base

• works best when the pKa of the buffer is within one pH unit of the pH

• can still work outside of range, but not as effectively

how to find the pH of a buffer solution

can be done using the Henderson-Hasselbalch equation

• can also be used to determine how much of an acid and base buffer to add to a solution to get a certain pH

how to prepare a buffer solution

1. Determine the pH you want

2. choose a buffer that is within 1 of the desired pH ( can be multiple)

3. use the Henderson-Hasselbalch equation to find the ratio of base to acid (A-/HA) bufer needed to get pH

4. write out the number of moles of each needed

what are some examples of buffers

• Acetic acid = pka of 4.76

• pyridine = pka of 5.23

• HEPES = pka of 7.66

• Dihydrogen phosphate = pka of 7.21

• phenol = pka of 9.89

• lactic acid = pka of 3.85

what are acid base indicators

Large organic molecule that acts as dyes and change colour depending on the pH of a solution

• Switch between deprotonated and protonated forms to change colour

what are some examples of acid base indicators

Methyl red: starts as an acid (pka of 5.01) and turns red as it converts to a base

Bromothymol blue: starts as an acid (pka of 7.3) and turns blue as it converts to a base

what is an amino acid

The building blocks of proteins that bind together using peptide bonds or amide bonds

• contain a chiral centre bound to an amine, a carboxylic acid and a R group, which differs depending on the amino acid

amino acids and zwitterions

amino acids contain both acidic and basic groups meaning they are zwitterions aka dipolar ions

• ions that are neutral as they have both a negatively and positively functional group ( amine and carboxylic acid) that cancel each other out

• are salts making them very water soluble with a high mp

what are the types of amino acids

• nonpolar: side chains are hydrocarbons, hydrophobic (alanine)

• Polar uncharged: contains a polar side chain with no charge (serine)

• acidic: contains an extra carboxylic acid that has donated its H+ and is now charged ( aspartic acid, cysteine)

• basic: contains an extra amine that has been protonated and is now charged (lysine)

• aromatic: contains some form of ring structure (phenylalanine, histadine)

why is the COOH on an amino acid so acidic

The pKa of COOH in the main structure of an amino acid is very strong, and the amine group withdraws electrons, hence reducing electron density and weakening the OH bond

how does pH and pka effect the structure of an amino acid

Since amino acids have both acidic and basic groups, they never exists in an uncharged form ( the acids and bases can interact with one another)

• Whether or not functional groups are protonated or deprotonated depends on the pH of the solution

• pH > pka = deprotonated

• pH < pka = protonated

what is a heterocylic amine

an aromatic ring that conaisn nitrogen or amines in teh pace of some of the carbons in the ring

• creates new function groups like pyrrole and pyridine

• will generally have higher pKa as the Carbon in the ring will donate electrons and stabilise the conjugate acid of an amine

what is pyrrole

A 5-membered, non-basic molecule whose lone pairs become delocalised into the ring

• prevents the lone pair from being donated as if they did the ring would loose its aromacity

what is pyridine

A 6-membered basic molecule whose lone pairs exist outside the sp2 overlap allows it to bond to further molecules

• The lone pairs can be used in donation, making it a basic molecule

What is an imidazole ring

A functional group found in histidine that contains both pyridine and pyrrole

• The pyrrole has no pKa, and it is neither an acidic nor a basic molecule it can’t accept or donate electrons without compromising its structure

isoelectric points

measured in pl, is the pH at which an amino acid exists as a dipolar zitterion ( everything is charged

• is the midway between pka

how to determine the pl of an amino acid

neutral: the average of the pKa values of the acidic and basic groups

• includes non-polar, polar, uncharged or aromatic

acidic: the average of the two lowest pKa

basic: the average of the two highest pka

what is electrophoresis

a method used to separate amino acids, DNA/RNA or proteins based on charges

how does electrophoresis work

1. AAs are embedded in a gel medium

2. A +ve or -ve electrode is placed in each of the tanks containing a running buffer

3. The amino acids will move towards the oppositely charged electrode

what directions will amino acids move in electrophoresis

• -vely charged AAs will have a lower pl than the buffers pH and move towards the +ve electrode

• The positively charged AAs will have a high pl than the buffers pH and move towards the negative electrode

what is the primary structure of a protein

a linear sequence of AAs that are encoded directly from DNA nd held together using covalent bonds

• The type of bonds can be peptide or amide bonds between the carboxylic acid of one AA (C-terminus) and the amine of another AA (N-terminus)

what are proteinogenic amino acids

the amino acids used to make proteins

what are peptides

Shorter strings of amino acids that can be 1 to 2 amino acids long

• di-peptides are 2 long

• tri-peptides are 3 long

what is the secondary structure of a protein

a more complex structure of a protein whose arrangement is determined by the pattern of H-bonds found in its originating primary structure

• can form either beta-pleated sheets or alpha helices and occasioannly random coils

what is an alpha helis structure

a coil structure of proteins formed using H-bonds or ionic interactions between every 3rd and 4th amino acid’s R group

• any R-groups not used to bending then point outwards from the structure

what allows the alpha helix to bend

The overlapping sp2 orbitals between the amine group and the carbonyl group in the amide bond form a planar resonance structure

• This structure is rigid and prevents the molecule from bending at that point, allowing it to form a coil

• Instead, it twists at the chiral carbons attached to the R groups

what is a beta pleated sheet

A flat sheet of amino acids made of multiple linear structures bound parallel or anti-parallel to one another (anti-parallel like the 3’ and 5’ ends of DNA)

• Bonded using the O of the carbonyl groups and the H attached to the nitrogen in the amide bond

• R groups are in alternating wedge and dashed bonds to reduce steric strain by placing bulky groups far from one another

What can cause protein structures to form loops

Disulphide bonds formed between the thiol groups on cysteine can create a loop in a chain

• Stabilises the structure by acting as an anchor that locks the 3D structures in place

how can kinks and bends be formed in helixes

kinks: occur when a C-terminus bonds to the nitrogen in proline’s R-group found in a helix structures

bends: when adjacent charged basic groups repel from one another due to their charges causing the structure to bend

what is a tertiary structure

A 3D protein made by combining multiple secondary structures

• can be a mixture of helices and sheet or can be just 1 kind of 2ndary structue

• is stabilised by the bonding between functional groups eithe covalently or non-covalently

what type of bonds can be found in tertiary structures

• H-bonds

• Hydrophobic interactions between hydrocarbons

• Salt bridges( bond between oppositely charged molecules)

• disulphide bonds

what is a quaternary structure

a structure of proteins made up of multiple tertiary structures

protein structure and genetic illness

A change in the AA sequence can create a non-functional protein or cause it to lose its structure hence affecting its function

• in sickle cell, the worng amino acid is placed in the sequence, allowing it to form non-polar interactions with other proteins hence distorting hemoglobin strutcures

proteins structure and substrate specifity

change in the AA sequence can distort a binding site for a particular protein, preventing the binding of substrates

• distorts the shape of the binding site prvent substarte from binding

• asparate has a -vely charge R- group that it needs to bind to trypsin

what types of bonds are used in each structure

Primary: peptide/amide bonds

Secondary: peptide + hydrogen bonds (sometimes disulphide bonds)

Tertiary structures: peptide + hydrogen bonds + disulphide bonds + hydrophobic interaction ( between hydrocarbons) + salt bridges ( between oppositely charged molecule)

pKa and pH’s effect on amino acid structure

The interaction between pH and pKa can determine whether a certain group on a amino acid/protein are ionised

• ionisation can then effect the structure of the protein as +ve charges can repel one another causing bending and opposite charge can bind together causing the formation of salt bridges

pKa and pH’ effect on drug intercations

the bonding of the keratin group can cut off drugs from their binding site by creating a barrier or using their charges to repel the drug

• This is why it is important to consider the structure of the protein at the pH of certain areas of the body before creating drugs

what is the degree of ionisation

What percentage/ How much of the compound is ionised/ has a +ve/ - ve charge due to the loss or gain of electrons

why is knowing the degree of ionisation useful

The degree of ionisation of a molecule can effect its

• protein/enzyme structure

• protein binding

• stability and reactivity of a molecule ( the more charged the more reactive)

• the absorption into the body

• the formation of the drug (injection or tablet)

what is method 1 for calulating degree of ionisation

Method one is used when the concentrations of the acid and conjugate base in known and provides the percentage of the molecules that will be in conjuate base form

• to find the ph that this ratio occurs in you can used the hednerson hasselbalch

• %A^- = [A^-]/([HA] + [A^-]) x 100

what is method 2 for calculating degree of ionisation

can be used when concentrations aren’t known but the pka of the molecule and Ph of the environment is known

• two versions of the equation so you can determine the percentage of either and compare to see if they = 100%

equations for method 2

%A^- = 1/(10^pka-pH + 1) x 100

%HA = 1/(10^{pH -pka} + 1) x 100

trends in the ratio of formation

• pH = pKa the [HA] = [A^-] (50 - 50)

• if pH = pKa +1 then [HA] = 10% and [A^-] = 90%

• if pH = pKa + 2 then [HA] = 1% and [A^-] = 99%

• opposite percentage for if pKa = pH +1 or 2

Monoprotic acids in titration

Have 1 pKa and 1 equivalent point, as one group on the molecule is able to be in a conjugate base or acidic form

• at the equivalence point the pKa of the group will = pH of the environment

diprotic acids in titration

Have 2 pKa values (one for each group) and 2 equivalence points for each group

• at the first point the pKa of one group will equal the pH of the environment and at the second point the pH of the second group = the pH

methods used to determine the structure of a molecule

• X-ray crystallisation ( give a snapshot of what the molecule looks like)

• Infrared spectrometry (shows functional groups of the molecule)

• Nuclear magnetic resonance spectrometry ( show the carbon hydrogen framework of a molecule)

• Mass spectrometry( show molecular formula by looking at mass of he various components)

• Ultraviolet-visible spectroscopy ( show the presence of conjugated systems

How to certain wavlength of light effect samples

X-ray cab sometime be damaging to sample making the less retrievable compared to using infrared, ultraviolet and microwaves

how does spectroscopy work

A compound is irradiated with electromagnetic radiation, moving the molecule from a low to high-energy state or exciting it

• The molecule will then move back down to a low-energy state and by doing so emit energy at a certain wavelength that is picked up by a machine

• does not effect sigma bonds but can effect conjugated systems

what is a conjugate system

the overlaping of sp² orbitals that is displayed in alternating doubdle bonds

how can ultraviolet spectroscopy be used in biology

Can be used to determine

• concentration of DNA

• Base pair ( G or C) content of DNA/ complementarity of DNA

• progression of a enzymatic redox reaction

what is the beer lambert law

a law that states that the absorbance of light of a particular compound is dirrectly proportional to its concentration

• compared sample of known concentration put into a standard curve to determine the concentration of an unknow sample based on its absorbance

what is the beer lambert equation

A = εcl

• A = absorbance at a particular wavelength

• ε = molar absorptivity ( specific for the molecule)

• c = concentration ( flip the equation to c = A/εl)

• l = path length or the width of the cuvet in cm

How can ultraviolet be used to find conjugate systems

if molecule absorb light between 200-400nm then they have conjugated systems

• Shorter wavelengths = less conjugation

• longer wavelengths = more conjugation

what is infrared spectroscopy

a technique used to determine the functional group of a molecule by the way the absorb IR light

• the IR light causes the bond in a molecule to stretch or bend / vibrate

what bonds are sensitive to IR

Covalent bonds are naturally vibrating; however, we can use infrared to excite polar bonds like the ones seen in functional groups

• IR is absorbed more intensely by polar bonds

• The vibration due to IR can lead to a change in dipole direction as atoms move

what types of vibrations can occur

stretching vibration which can occur symmetrically or asymmetrically

bending vibrations which can be rocking, scissoring or wagging or twisting

how many different vibrations can occur in a molecule

Non-linear atoms will have 3n - 6 fundamental vibrations larger molecules have a more complex IR spectrum

• n = number of atoms

why can vibration be seen at c-c or c=c bonds despiet the fact that they are not polar

These bonds can produce small vibrations as IR light can cause the electrons moving around them to form dipoles

• the vibrations are small but they can add up as there are lot of them

what is the fingerprint region of an IR diagram

A region on an infrared spectrum that represents a unique pattern or fingerprint for a particular molecule

• found between 400-1500cm^-

• ignored when analysing the spectrum

at what wavenumber can you see certain functional groups

• c=c - 1600cm

• c=o - 1700cm

• o-h = 3100 - 3500 cm

how to read an infrared spectrum

1. Ignore any section of the graph that shows wavenumbers below 1500 cm ¹ (fingerprint region)

2. find the lowest peak in transmittance that does not match the transmittance of a particular functional group ( is often not characteristic of the sample)

3. look for any characteristic peaks

what is mass spectrometry

A technique used to determine the molecular formula mass, or certain structural features of a compound

• can be used to distinguish between molecules with the same functional group but different masses

what are the step of Mass spectrometry

1. Ionisation of the sample ( to a +ve charge)

2. The separation of the molecule into fragments ( slowly deteriorates the molecule)

3. The detection of the fragments

Ionisation of the sample

The sample is placed in a high vacuum chamber, vaporised and exposed to a high-energy electron source taht dislodges and electron from the sample causing it to form a moleclar ion

• is a radical cation, as it now has 1 unpaired electron but the same mass as the original molecule

fragmentation

The molecular ion is split into fragments or neutral particles

• neutral or -ve particles are removed

detection of the fragments

The fragments are then separated from one another using an electromagnetic field to differentiate mass

• molecules that reach the detector the quickest have the smallest molecular mass

what are the resulst given from a mass spectrometer

provide amd mass to chrage ration with charge often = +1 as 1 electron has been removed

• the x axis = mass and the y axis = its abundance

how to read the resulst of a mass spectrometer

The peak furthest to the right, which is often the highest, is the molar mass of the molecular ion (aka the original molecule), while smaller peaks represent that molecule after losing a particular fragment

• The taller the peak, the greater the presence

• to determine the fragment lost, look at the difference between a peak and the previous peak and then determine which group has a molar mass close to that number

Iosotope and mass spectrometry

can be used to represent the presence of diffrent isotope form in molecules

• when a molecule has iosomer you will seen two peak with one being the molecular ion and the other being the molecular ion + 2 atomic mass units

• the height of the peaks will differ based on natural abundenc

an example of hiehgt difference in isotopes

³⁵Cl and ³⁷Cl have a natural abundance of 76% and 24%, leading to a 3: 1 ratio of abundance

• This means that Cl is present in the molecule if 35Cl peak is at M is 3 times higher that 37Cl at M+2