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Introduction:

 In order to understand the topics in our course, you have to understand the
structure of different molecules because the structure is important to understand
the function.
 The function will be reflected from the structure, any abnormality in the structure
of proteins it will affect its function.

 Like sickle cell disease

- The reason of the sickle cell disease is a defect in a polypeptide in the cell
(The beta globin polypeptide chain).
- So, if we have a poly peptide chain consist of 46 Amino acids, and we
have defect in one of them we will have an abnormal protein.
- What is the function of beta globin?
It is a part of the hemoglobin (which is composed of 4 chains) 2 of them are
beta globin and 2 of them are alpha globin, that is important to carry O2 to
the tissue and to carry CO2 (toxic) from the tissue to the lungs.

 Enzymes
- They are very important catalysts (we need them to do everything).
- One of the protein functions is to speed up reactions. So, enzymes are
proteins.
- We use enzymes in metabolic reactions.
- For example, if we have an amino acid out its own (OH hydroxyl group) the
mutation will pear. HOW?
- The formation of polypeptide chain happens after the transcriptions of DNA to
make RNA. So, if we have any errors in the transcriptions like substitution or
deletion of nucleotides, we will have a mutation.
- So, biochemistry is concerned with three things (Enzymes, metabolism and
proteins).

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 - We have 20 Amino acids and every amino acid has its own genetic code or more
than one.

- Examples for amino acids that carry OH group:

1- Serine
2- Threonine
3- Tyrosine

 Oxidation and Reduction

 The lecture started by talking about this topic because it occurs a lot in our bodies.
 Metabolism is two types:
1- Anabolism
2- Catabolism

 Reduction  Gain of electrons

 Oxidation  Loss of electrons

 See the equation below:

H3CHC=O + NADH + H+ <==> H3CH2COH + NAD+

(Aldehyde) (Alcohol)

- What is NADH?
It is one of the molecules in the electron transport chain. It carries protons
and, in this case, it is in reduced
form of the NAD+ that carries 2
protons. The other is called
NADH + H+.
NAD+ is the oxidized form of
NADH

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 - The oxidized form of the aldehyde has been reduced to alcohol, which is
called ethanol. This is how methanol is metabolized by REDOX reaction.
- This process is catalyzed by an enzyme called alcohol dehydrogenase in
which ethanol is converted into acetaldehyde and the NAD+ into NADH.

 Gibbs Free Energy

 You don’t need to memorize the equation BUT remember the benefit of it.

∆G = ∆H - T∆S

- The benefit and importance of this equation is the direction of the reaction.
All metabolism that we are going to talk about are composed of a reversable
reaction.
Metabolism and
Catabolism are reversible
reaction.
- The ∆G for each reaction will determine where is
the direction of the reaction, either toward
anabolism or catabolism or toward oxidation or
reduction. All of that depends on the value of ∆G.

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 - If the value of ∆G is negative  The reaction is forward.

- If the value of ∆G is positive  The reaction is backward.

- The value of ∆G can be calculated for any chemical reaction by the equation:
c d a b
ΔG = ΔG°’ + RTln {[C] eq[D] eq]} / {[A] eq[B] eq}

- ∆G (value and direction) depends mainly on the concentration of the product

and the concentration of the reactant.

- ∆G is standard and constant and it only changes when the concentration of

the reactant or product changes.

- So, changing the product or the reactant will change ∆G value and that will
determine the direction of the reaction.

- If you are given a chemical reaction and you are asked about the
direction of it, you are now able to answer such questions.

 Water and Buffers

- Unequal sharing of electrons
- Uneven Charge Distribution
- Covalent bonds:
1- Dipolar
2- Hydrogen Bonds: always involve hydrogen. They are most important as they’re
weak enough to be breakable and strong enough to hold things together.

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 Hydrophilic vs Hydrophobic

 Amphiphilicity

 Amphipathic molecules: they are molecules with two parts – hydrophilic and
hydrophobic, such as, soap and detergent.
 Hydrophilic means that this compound is dissolved in water.
 The ability of the compound to dissolve in water depends on the compound
and its functional group, whether they’re able to form H-bonds or not. If it is
able to do so, the compound is hydrophilic and can dissolve in water. And
vice versa, if it is not able to form H-bonds, that means it is hydrophobic and
can’t dissolve in water.
 Some compounds have both, hydrophobic and hydrophilic parts in the same
molecule. These compounds are called amphipathic as they have the two
sides (hydrophobic and hydrophilic).
 This is an example of an amphipathic compound. (It is a fatty acid compound)

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  Other Amphiphilic Substances

 Cell membrane  Composed of amphiphilic molecules such as

phospholipids
 Glycerophospholipids Sphingolipids are examples of amphiphilic molecules
that constitute cell membrane.
 Phospholipids are composed of a Glycerol molecule (3 carbon atoms) +
2 Fatty acids + Phosphoric acid[
- In the previous sentence, the three elements together are called
Phosphatidic acid.
 Next to the phosphoric acid there is a base “x” (like choline)
 The acid and the base represent the hydrophilic face while the other face,
which is two fatty acids, represents the hydrophobic face.
 If phosphoric acid attaches to
choline we call it phosphatidic
choline so we can make a lot of
phosphatic acid by binding some
groups (different bases) to
phosphoric acid part.

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  If we take these phospholipids and we put them an aqueous medium, they
will form Micelles, which are lipid molecules that arrange themselves in a
spherical shape. (B)
 The hydrophobic region is inside between the two layers.
 One of the hydrophilic regions facing the outside aqueous environment and
the other facing the cytoplasm (which is also aqueous).
 Why this happened?
- Because of the hydrophobicity which is important for forming cell
membrane and folding the proteins.

A B

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  Polypeptide consists of a
specific sequence of amino
acids linked together by peptide B
bonds.
 For a protein to function, it must
A
be folded.
 Unfolded protein is not functional
(inactive). After it is synthesized,
it must be folded in the ER.
 Why do they fold?
- Due to the hydrophobicity  Important:
 They can fold automatically or by - The force responsible for the folding
the help of other proteins. of protein is the hydrophobic forces.
 As you can see, (A) is not folded,
thus, not functional.
 Black balls represent the hydrophobic amino acids while yellow balls represent
the hydrophilic amino acids. When the polypeptide chain is in
aqueous solution, all the hydrophobic
amino acids remain inside away from water (escape) while the hydrophilic amino
acids remain on the surface of the molecule interacting with water making
hydrogen bonds.
 Folding means making the proper tertiary structure in the two dimensions.
 There are millions but billions of the tertiary structures that the protein could
make but only one structure is the functional one, due to the hydrophobic forces.
 Hydrophobic amino acids will interact with each other noncovalently by
hydrophobic interactions like, Van der Waals forces and other hydrophobic
forces.
 What are the functional group of hydrophilic amino acids?
- (COOH /OH /SH/NH)
- All of these groups can form hydrogen bonds with water and in most cases,
they are polar amino acids.

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  Hydrogen bonds could form between water molecules themselves and also
between water molecules and other molecules “these are soluble in water”.

 In every H bond there is a donor and an acceptor, the donor is the atom to which
the H atom involved in the bond is covalently bonded.
 The acceptor is the electronegative atom which the H atom is electrostatically
attracted to and has a lone pair of electrons.

 This is how salts dissolve in water as their

ions will be separated by their dipole
interaction with water.

 This is a hydrogen bond between nucleic

acids in DNA “3 H bonds between Guanine
which is a purine and a Cytosine which is a
pyrimidine” as you see O with H and N with
H l Adenine (purine) makes 2 H bonds with
thymine (pyrimidine).

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  This table compares between the strength of bonds, where Bond Energy is the
energy required to break the bond. We can tell H bonds are very weak but they
can still stabilize proteins and DNA because they are numerous.

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