B1 Introduction to Biochemistry

Metabolism:chemical reactions that go on in cells

Types metabolic
of
processes
-catabolism:the breakdown larger
of molecules into smaller ones with the release ofenergy e.g. respiration
- Anabolism:process synthesising
of molecules needed by cells which requires energy e.g. photosynthesis

Names metabolic
of
processes
1. Condensation:joining together of two molecules with the formation a
of covalent bond with elimination of water

sugar -> disaccharides and polysaccharides

- amino acid -> proteins

2. Hydrolysis:breaking a covalent bond by the addition of

water, usually with an acid/alkali/ enzyme

B2 Proteins

Amino acids -
monomers proteins:
of

General chemical formula:HINCH(R)COOH

Amino acids are amphoteric because they contain both acidic (100H) and basic (NH2) groups

What is a zwitterion?
• The carboxylic acid group in the amino acid can protonate an amino group in the same molecule
• When the proton is transferred from the COOH to the NH2, an ion with no overall charge can be formed, this form of an
amino acids is known as a zwitterion

Explaining why I amino acids have different isoelectric points:

side chain - lower isoelectric
-
vneutral/hydrocarbon point
-presence e.g.-COOH
of lower isoelectric point
=
What would happen to an amino acid if an acid and alkali is added respectively at its isoelectric point?

Compare the melting point of amino acids (in the zwitterionic form) and pure acids.
The melting point of amino acids is higher, because they exist in the zwitterion form so there are stronger electrostatic
attractions between oppositely charged groups on adjacent zwitterions (COO- on one amino acid with H3N+ on another)

Outline the solubility of amino acids in water and organic solvents.

• Soluble in water: amino acids exist as ions which can form ion-dipole interactions with water molecules
• Insoluble in organic solvents: weak London forces between the amino acid and organic solvent molecules cannot pay
back the energy needed to overcome the stronger eletrostatic forces between ions

How is a protein formed by two amino acids, and what is the linkage between amino acid molecules?

Describe the secondary structure of proteins.

Linear folds into alpha-helices and beta-pleated sheets
• Alpha-helix: twists in a clockwise direction from the carboxyl terminus, forming the shape of a corkscrew, helical structure
stabilized by hydrogen bonds (intramolecular hydrogen bonds)
• Beta-pleated sheets: zig-zag stretches of amino acids, intramolecular H bonds formed

Identify the bonds within the tertiary structure of proteins.

• Hydrogen bonds: between amino acids bearing side chains e.g. OH and N
• London forces: between amino acids bearing non-polar side chains
• Electrostatic attractions: between COO+ and NH3+ groups in side chains
• Disulfide bonds: covalent S-S bonds formed by the oxidation (of SH groups) within two cysteine residues
Describe how the tertiary structure differs from the quaternary structure in hemoglobin. [N20]
• Tertiary: folding/shape of a single «polypeptide/protein» chain
• Quaternary: arrangement/folding of four/several chains/proteins/polypeptides «held together by IMF

Explain how paper chromatography separates the components.

Components strongly adsorbed by stationary phase (water in the chromatography paper) move less, components very soluble
in mobile phase move more

Outline how the amino acids may be identified from a paper chromatogram. [M18]

A mixture of amino acids is separated by gel electrophoresis at pH 6.0. The amino acids are then stained with ninhydrin.
Suggest why glycine and isoleucine separate slightly at pH 6.5. [N16]
Different sizes/molar masses/chain lengths «So move with different speeds»

Outline the behavior of an amino acid in gel electrophoresis.

• pH = isoelectric point: does not move
• pH < isoelectric point: acts as a base and receive H+, becomes positively charged and move towards the negative electrode
• pH > isoelectric point: acts as an acid and loses H+, becomes negatively charged and move towards the positive electrode
 B3 Lipids

Types of lipids in the body:

① Triglyceride -

energy store

② Phospholipid -
in cell membranes

③ Steroid -
e.g. cholesterol, steroid hormones

Fats have a higher energy value per mole than carbohydrates

fats contain less and are in a less oxidized state (i.e. undergo more oxidation) so more
energy released
oxygen
-

more
*
energy per mass released when lipids are oxidised be ratio 0
of to C in lipids lower

① Triglycerides and fatty acids ester link

⑧
11
0
11
HO C -
R 0 R
HcC
-

H2C -
0H
- -
C -

⑧ 0

1- 0H t Ho-c-R"
11
-> Hc- 0 - -
R" +
3H 20

Hid-0H
0

-
⑧
3
11

HO-C -
R Hi 0 - c -
R

glycerol 3 fatty acids triglyceride

Fatty acids:

group at one end

contain a
long hydrocarbon chain with a COOH
-

major types:saturated, monounsaturated (1C=)bond) polyunsaturated (2 +C C bonds)

=
-
or

-
London forces saturated
in
fatty acids are
stronger
:no C=C/ straight chain/no kinks => chains
pack more closely together

Iodine number:mass iodine

of react
that with 100g of the fat/oil
& the
higher the iodine number, the more unsaturated the fatty acid
ix =

I
+
+
- - -

Isaturated fats 0) =
calculate using DBE
~
calculating iodine number
e.g. linoleic acid:2 =C, Mr 280.50
=

-
2 double bonds -> 2 mol IC
of will react with I mol of acid
<Mr Of Iz)
-
Mass iodine
of
reacting with I mol of 2x253.80
acid= 507.609
=

Mass iodine
of
reacting with 100g acid
of
507.60x,58% 180.969
= =
-

:. Iodine number of linoleic acid 181

=

Hydrolysis triglycerides
of

alkali:
Heating a triglyceride with an

-
ester bonds are broken, yielding glycerol and sodium salts of the fatty acids -

saponification (make soaps

-

advantage over acidic hydrolysis:higher yield

H ⑧

"
H2C -
0H

ri-oH
heat
3NGOH
+ c C,H3,COONA
+

H2C -
0H

H glycerol salt of
fatty acid
 Rancidity of fats/ fatty acids

② Phospholipids
0
phosphate group
phosphate-ester linkage
+ - -
0 - i - 0 -
H

I ↓-

g-
H - -
0 -

H -
- -
H !
H 0
H
11
Formation phosphodiester
of H-C-0-p -0 - c-
I
↓ -
it

of
Hydrolysis phospholipids
Heating a phospholipid with a concentrated acid:

ester bonds between fatty acids and the backbone broken down into all its
glycerol are components
-

n -

-ofifo_"-i-c i i drs H2C 0H

4
-

&
H-OH + CrHs,COOH H3POp+HOCHzCHiFNCCHa)s
+

H2C -
0H

Heating a phospholipid with a mild acid:

0-2 0 broken to yield 2 fatty acid and

linkages molecules phosphodiester
=
-
ester are a

H
I I CHS
n 0 x-
+

cHs
i
- - -
- -
-c -

I ↓- it is
H -) -
0 -
H

I
H - -
0 -
H
③ Steroids

mostly hydrophobic
-
steroid backbone made up of 3 six-membered rings and a five-membered ring
-used to build up depleted muscle due to lack of activity, of inflammation
treatment

compare and
* contract:

W W

v v ~

~ ~

Effects of lipids on health:

 carbohydrates
B4

① Monosaccharides
contain carbonyl group) 0
=
-

have at least two

-

hydroxyl groups 0-H

empirical formula is CH20

Straight chain form: H2O aldehyde (CHO)/ CH20H

I
the end
b- oH C 0 at
=

H - 2 0
=
ketone (RCOR' / 2 0 =

ofthe chain
Ho--H Ho - d -
H
in middle of chain

H - b -
0H H - b -
0H

H - -
0H H - -
0H

H - d- or 'HOH
i
Glucose Fructose

(Aldose sugar) (ketose sugar)

Straight chain form -> ring form

double-bonded oxygen (C) in glucose/C2 fructose) joins to 15, forming
-
carbon with in an ether linkages-0->

H2'c 0 ·CHOH
r 5
0

-
H - -

Ho! -
H
H
H
H
*
- 0H 7
H
H -

H - -
0H OH OH 0H

H - -or 3 2

i H OH

Glucose

'CH,0H
21
2 0
=

I ⑧
-H
Ho

I M CHOH
-

H -
*
- 0H 7
A

H -
0H
Ol
-

H
·CHOH H HO

Fructose
OH H

&- glucose:C-1OH downwards &

3 glucose:C-1 OH
upwards is
-
 B5
Vitamins

water-soluble vitamins Lipid-soluble vitamins

contain OH (and C 0) contains

mainly hydrocarbon parts (and only 10H)
=

many
- -

-
can form extensive H-bonds with water molecules -less polar long non-polar hydrocarbon chain

① Vitamin A -
important for night vision

deficiency causes acue

② Vitamin B1 -
essential for energy production within cells

deficiency causes beriberi

③ Vitamin B3 -
importantfor oxidation -
reduction processes in
cells

-
deficiency causes dementia

④
Vitamin) -

important for collagen formation

-

deficiency causes scurvy

⑦
Vitamin D -
facilitates uptake of
calcium and phosphorus
-deficiency causes rickets

Preventions of vitamin deficiencies:

-adding nutrients missing in commonly consumed foods

genetic modification foods

of

providing nutritional supplements

 B6 Biochemistry and the Environment

mass of atoms desired

in product
Atom economy -

measuring efficiency of a reaction - x 100%

mass of reactants/products
all atoms in

Greener methods:

higher atom economy

-

-non-toxic reactants

-use of catalysts more

+
products in a shorter period of time

-
single-stepsynthesis -> reduce formation derivatives
of

Use of enzymes reducing

in environmental problems:
-breakdown of oil spills
industrial waste
-treatment of

biological detergents ->

improve energy efficiency

Biodegradable:can be broken down by bacteria or other living organisms

Ladd starch to e.g. plastic to allow digestion by micro-organisms -> more

biodegradable

Biomagnification e.g. pesticide (DDT), mercury and other heavy metals

species be
cannot metabolised/broken down

(hot biodegradable)
-Aconcentration as one species feeds on another in
the food chain
(passing up food chains