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Samenvatting Metabolisme en Biochemie Deeltentamen 1 & 2
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Alle behandelde stof voor deeltentamen 1 en 2 van Metabolisme en Biochemie, inclusief de stof uit de Xerte modules.
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Chapter 1: Unity of biochemistryAll organisms:
- Use ATP as energy currency
- Use the same flow from DNA to RNA to protein
- Are build up from the same components
o Sugars, nucleotides, proteins and fats
Bacteria are unicellular and therefore do not develop in tissues.
The fundamental groups pf organisms include Eukarya, Bacteria and Archaea.
- The distinguishing feature of Eukarya is the well-defined nucleus in each cell.
Factors that determine the reaction pathway and product structure:
1. Intermolecular bonds
2. Reaction solvent
3. Thermodynamics
4. pH of the solution
The DNA backbone is made from repeating sugar-phosphate units. The formation of a
double helix is driven by the following forces:
- A base on one DNA strand interacts via hydrogen bonds with the complementary
base in the other DNA strand
- In the double helix, the base pairs are parallel and stacked on top of one another.
This allows for van der Waals interactions
- The non-polar regions of DNA end up being inside the DNA and out of reach of
water. These are hydrophobic interactions
- The negatively charged phosphate groups lead to electric repulsion forces
The water molecules can form hydrogen bonds with the negative phosphate groups. This
stabilizes the DNA double helix.
Adenine and thymine form two hydrogen bonds.
Cytosine and guanine form three hydrogen bonds.
All bonds on molecular and atomic level are electric in nature. These forces arise due to the
existence of charge Felectronegativity (Coulomb energy) = (k*(q1*q2))/d*r
Intramolecular bonds:
1. Non-polar covalent
a. A bond formed between two atoms through the equal sharing of electrons.
The electronegativity value of the two atoms is equal.
2. Polar covalent
a. A bond in which there is an unequal sharing of electrons that arises due to
different electronegativity values.
3. Ionic bond (4-20 kJ/mol)
, a. One atom is much more electronegative than the other and pulls the electron
completely to its side. This creates a full separation of charge holding the
atoms together.
Intermolecular bonds:
1. Hydrogen bonds (dipole-dipole) (4-20 kJ/mol)
a. A hydrogen atom is shared by two electronegative atoms
b. The group that contains the H-atom is the H-bond donor, while the group
that accepts it is the H-bond acceptor (N- and O-atoms are often involved)
2. Van der Waals forces (2-4 kJ/mol)
a. The electron density around atoms fluctuates. The asymmetric distribution of
one molecule can cause the electron density of a nearby molecule to change
accordingly. The molecules can then bond through the instantaneous dipole
moments.
Angstrom (A) is the unit used to describe the distance between atoms in a bond.
First law of thermodynamics: the total energy of an isolated system is constant; energy can
be transformed from one form to another, but can be neither created nor destroyed.
- Esystem + Esurroundings = Euniverse
The most likely arrangement is always the one with the highest entropy.
Second law of thermodynamics: the entropy of the universe always increases. When the
entropy of the system decreases, the reaction releases enough energy into its surroundings
to increase the entropy of the surroundings by a greater amount.
- Ssystem + Ssurroundings = Suniverse > 0
If a reaction has a negative G, the reaction can occur spontaneously.
pH = -log[H+]
pH = pKa + log(A-/HA) (Henderson-Hasselbach equation)
[H+] = 10^-pH
[OH] = 10^-14 / [H+]
At a pH higher than the pKa less will be protonated than deprotonated.
At a pH lower than pKa there will be more protonated than deprotonated.
There are several molecular representations:
- Space-filling model
o Indicates the volume occupied by a biomolecule
- Ball-and-stick model
o Shows the bonding arrangement in small biomolecules
- Skeletal model
o Shows the bond framework in macro
,The difference between biological macromolecules and metabolites is that metabolites are
low-molecular weight molecules that are transformed in biological processes, whereas
biological macromolecules are large molecules such as proteins and nucleic acids.
Base pairing provides an accurate means for reproducing DNA sequences, because if a DNA
molecule separated into two strands, each strand can act as the template for the generation
of its partner strand.
Chapter 2: Protein composition and structure
Key properties of proteins:
1. Proteins are linear polymers build of monomer units called amino acids
a. These are linked to each other by peptide bonds
i. Peptide bonds form via dehydrolysis reactions
ii. Peptide bond formation is thermodynamically not favorable (requires
ATP)
iii. Peptide bonds are kinetically stable (because of the high activation
energy)
2. Proteins contain a wide range of functional groups
3. Proteins can interact with one another and with other biological macromolecules to
form complex assemblies
4. Some proteins are quite rigid, whereas others display considerable flexibility
Alpha amino acids contain a chiral (alpha) carbon that is bound to an amino group, a
carboxylic acid group, a hydrogen atom and a R-group that is unique to that particular
amino acid.
- Most amino acids in proteins are L isomers. The majority of amino acids, with the
exception of two, have the (s)-absolute configuration .
Amino acids differ from one another based on their side chain groups. The variations
determine the chemical reactivities of the amino acids. They vary in:
1. Size
2. Polarity
3. Structure and shape
4. Change
5. Hydrophobic properties
6. Ability to hydrogen bond
At a neutral pH, amino acids exist in their zwitterion (dipolar) form, which means they
contain a positive and a negative charge.
- At a low pH both groups are protonated, so the ion has a positive charge
- At a high pH both groups are deprotonated, so the ion has a negative charge
Proline is an aliphatic (not aromatic) amino acid, but it differs from others because its side
chain is bonded to both the nitrogen and the alpha carbon of the backbone.
An amino acid has an average mass of 110 dalton.
, There are seven amino acids with ionizable side chains:
1. Alpha-carboxyl - pKa = 3.1
2. Alpha-amino - pKa = 8.0
3. Aspartic acid - pKa = 4.1
4. Glutamic acid - pKa = 4.1
5. Histidine - pKa = 6.0
6. Cysteine - pKa = 8.3
7. Lysine - pKa = 10.8
8. Tyrosine - pKa = 10.9
9. Arginine - pKa = 12.5
Ionizable amino acids are important because:
1. They can readily exchange hydrogen atoms
2. They can interact via ionic bonds
Cysteine can stabilize protein structures by forming covalent cross-links between
polypeptide chains due to its sulfhydryl group. Disulfide bonds are formed.
The beginning of any polypeptide chain is the alpha amino group, which functions as the
hydrogen-bond donor, and the end is at the alpha carbon group, which functions as the
hydrogen-bond acceptor.
Peptide bonds can be resonance-stabilized due to a partial double-bond character,
preventing rotation and making the bond planar.
Trans peptide bonds are often more energetically favorable than cis because there is no
steric hindrance.
Phi and psi rotations ultimately allow the protein to fold into its three-dimensional
structures. Not all phi and psi combinations are possible because of steric hindrance.
These can be investigated in a Ramachandran plot.
- Phi: angle of rotation about the single bond between the nitrogen and alpha-
carbon atom
- Psi: angle of rotation about the single bond between the alpha-carbon and the
carbonyl carbon atom
Primary structure: unique sequence of amino acids linked together by peptide bonds
Secondary structure: repetitive arrangement of amino acids that are near each other in
the linear sequence
- Alpha helix
o Rod-like structure containing the backbone on the inside portion of the helix
and the residues on the outside portion
o Each turn contains 3.6 amino acids
Every residue has around 1.5 Angstroms height
o A right-hand helix rotates clockwise, whereas a left-hand helix rotated
counter clockwise
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