This document contains detailed lecture notes with extra explanation for all lectures given except for the guest lectures. The book used in the lectures is Principles of Biochemistry by Lehninger.
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Test Bank For Lehninger Principles of Biochemistry, 7th Edition by LEHNINGER Chapter 1-28
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Radboud Universiteit Nijmegen (RU)
Biology
Cellular Biochemistry (BPOO7C)
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Cellular Biochemistry
2020/2021 Quarter 2
1
,Biochemistry lectures
Lecture 1: Interactions in aqueous systems and amino acids .................................................................... 6
Introduction .............................................................................................................................................. 6
Hydrogen bond ......................................................................................................................................... 6
Van der Waals interactions ....................................................................................................................... 9
Acid and base ............................................................................................................................................ 9
Henderson-Hasselbalch equation ....................................................................................................... 11
Titration curve ..................................................................................................................................... 12
Buffer .................................................................................................................................................. 13
Lecture 2: Amino acids, peptides and protein structures ......................................................................... 14
Amino acids ............................................................................................................................................. 14
Classification ....................................................................................................................................... 15
Acids and bases ................................................................................................................................... 17
Structures of peptides and proteins ....................................................................................................... 19
Peptides .............................................................................................................................................. 19
Peptides and proteins ......................................................................................................................... 20
Three-dimensional structure of proteins ............................................................................................ 20
Secondary structure ............................................................................................................................ 21
Tertiary structure ................................................................................................................................ 23
Quaternary structure .......................................................................................................................... 26
Post-translational modifications ............................................................................................................. 26
Protein and function summary ............................................................................................................... 26
Lecture 3: Working with proteins; Detection and purification ................................................................. 28
Protein detection and purification.......................................................................................................... 28
Column chromatography .................................................................................................................... 29
Electrophoresis for protein analysis ................................................................................................... 35
Isoelectric focusing ............................................................................................................................. 37
2D electrophoresis .............................................................................................................................. 37
Quantification of protein concentration................................................................................................. 38
Quantification of purification efficiency ................................................................................................. 39
Analysis with antibodies ......................................................................................................................... 39
Summary (mentimeter) .......................................................................................................................... 39
2
,Lecture 4: Protein function: enzymes working mechanisms, kinetics & inhibitors ................................. 41
What are enzymes? ................................................................................................................................ 41
Bioenergetics and thermodynamics ....................................................................................................... 41
Working mechanism ............................................................................................................................... 42
How do enzymes reduce the activation energy ..................................................................................... 44
Catalytic mechanisms of enzymes .......................................................................................................... 45
Kinetics .................................................................................................................................................... 46
Reaction rate ....................................................................................................................................... 47
Two-substrate reactions ......................................................................................................................... 51
Enzyme inhibition ................................................................................................................................... 51
Lecture 5: Catabolism of fatty acids and amino acids............................................................................... 55
Metabolism ............................................................................................................................................. 55
Fatty acids ............................................................................................................................................... 56
Different types of lipids........................................................................................................................... 59
What are mitochondria? ......................................................................................................................... 62
Fatty acid oxidation................................................................................................................................. 63
Amino acid oxidation .............................................................................................................................. 65
Dietary proteins .................................................................................................................................. 66
Lecture 6: Principles of bioenergetics ........................................................................................................ 71
Introduction ............................................................................................................................................ 71
Important concepts from chapter 1 ....................................................................................................... 72
ATP .......................................................................................................................................................... 72
Reaction speed........................................................................................................................................ 73
Catalysts .................................................................................................................................................. 74
Bioenergetics and reactions.................................................................................................................... 76
Laws of Thermodynamics apply to living organisms .............................................................................. 76
Reaction and free energy ........................................................................................................................ 76
Chemical logic and common biochemical reactions ............................................................................... 78
Inside the cell .......................................................................................................................................... 78
Key concepts for the exam...................................................................................................................... 83
Lecture 7: Protein function and interaction .............................................................................................. 84
The cytoskeleton ..................................................................................................................................... 84
Actin .................................................................................................................................................... 84
3
, Myosin................................................................................................................................................. 87
Intermediate filaments ........................................................................................................................... 90
Keratin ................................................................................................................................................. 90
Collagen............................................................................................................................................... 92
Lamin................................................................................................................................................... 93
Adhesion ................................................................................................................................................. 94
Lecture 8: Carbohydrates and glycoconjugates ........................................................................................ 96
Carbohydrates......................................................................................................................................... 96
Mono- and disaccharides ........................................................................................................................ 96
Polysaccharides ..................................................................................................................................... 101
Cellulose ............................................................................................................................................ 102
Human dietary .................................................................................................................................. 102
Organisms ......................................................................................................................................... 102
Glycosaminoglycans (also called GAG’s) ........................................................................................... 103
Glycoconjugates .................................................................................................................................... 104
Relevance in health and disease ........................................................................................................... 106
Lecture 9: Receptors and signal transduction ......................................................................................... 109
Signal molecules.................................................................................................................................... 109
Ionotropic receptors ......................................................................................................................... 110
G-protein-coupled-receptors ............................................................................................................ 110
Kinase receptors................................................................................................................................ 111
Nuclear receptors.............................................................................................................................. 111
Receptors .............................................................................................................................................. 112
Tyrosine kinase receptor................................................................................................................... 113
IGF ..................................................................................................................................................... 118
TGFB receptors.................................................................................................................................. 120
Quick look-back to the receptors discussed ..................................................................................... 122
Signal transduction ............................................................................................................................... 122
Lecture 10: Signal transduction II ............................................................................................................ 126
Signal transduction ............................................................................................................................... 126
PLC gamma........................................................................................................................................ 126
PI3K ................................................................................................................................................... 128
SHC .................................................................................................................................................... 130
4
, Ok, but now in real life ...................................................................................................................... 132
Signal transduction to the nucleus ....................................................................................................... 133
Nuclear receptors.............................................................................................................................. 133
Signal transduction to the nucleus via ERK ....................................................................................... 133
Effect of growth factors .................................................................................................................... 135
G-protein-coupled-receptors ............................................................................................................ 136
LPA .................................................................................................................................................... 139
TGFB receptor downstream signaling ............................................................................................... 140
Cytokines ........................................................................................................................................... 140
Lecture 11: Tumor suppressors and oncogenes ...................................................................................... 142
Oncogenes ............................................................................................................................................ 142
RNA tumor virus ................................................................................................................................ 142
Oncogenes in human ........................................................................................................................ 144
DNA tumor viruses ............................................................................................................................ 145
Tumor suppressor genes....................................................................................................................... 148
RB ...................................................................................................................................................... 149
P53 .................................................................................................................................................... 150
Different effects of mutations can be observed ............................................................................... 150
Haplo-insufficiency............................................................................................................................ 150
PTEN .................................................................................................................................................. 152
Lecture 12: Cell cycle regulation .............................................................................................................. 153
Influence of oncogenic mutations on the cell cycle ............................................................................. 153
General characteristics of cancer development and cancer cells ........................................................ 159
Normal cells vs tumor cells ................................................................................................................... 161
Anchorage independent growth ....................................................................................................... 162
Loss of contact-inhibition.................................................................................................................. 162
Stem cells vs tumor cells ................................................................................................................... 162
5
,Lecture 1: Interactions in aqueous systems and amino acids
Introduction
Water has different important functions regarding life and the study of life. Water is over 70% of an
organisms’ total weight. Water is also one of the reasons why life is possible. Biochemical reactions are
studied in aqueous solution. We will look at water for most of the examples used in this lecture. Water
consists of two H atoms and one O atom. A few weak interactions will be discussed. These are the
hydrogen bond, the Van der Waals interactions, and ionic and hydrophobic interactions. We will also
discuss the weak acid and weak bases and how to calculate with them.
Hydrogen bond
Hydrogen bonds give water its unusual properties. These bonds can be formed when there is an
electrostatic attraction between an oxygen atom of one water molecule and the hydrogen atom of
another water molecule. Hydrogen bonds are weaker than ionic- and covalent bonds because it takes
less energy to break these types of bonds. Nevertheless, a lot of these bonds together can form a strong
bond. Hydrogen bonds are the result of an unequal distribution on a molecule, these molecules are said
to be polar. If we look at water molecules, we can see that the oxygen atom shares electrons with two
different hydrogen arms.
Figure 1: Electronstatic attraction
In total, this molecule has 10 protons, 8 from oxygen and 1 each from the hydrogen atoms, and a total
of 10 electrons, 2 shared between the oxygen atom and the hydrogen atom number one, 2 shared
between the oxygen atom and hydrogen atom number 2, and the other 6 non shared electrons from the
oxygen atom.
This water molecule is electrically neutral, but it has a partial positive side, the hydrogen side, and a
partial negative side, the oxygen side of the molecule. The electrons are not shared equally within the
molecule, as they have a higher probability of being found closer to the nucleus of the oxygen atom,
giving that end a slightly negative charge. So, the hydrogen atoms end of the molecule will have a
slightly positive charge.
In solid form there are many bonds (each water molecule can form 4 bonds in ice), and when water is
steam or gas, there are no bonds. This is because the molecules are too far apart to form bonds.
Hydrogen bonds only form between hydrogen atoms that are covalently bonded, or bonds where
electrons are being shared and not transferred, to an oxygen, nitrogen, or fluorine atom. These bonds
make water ideal for the chemistry of life. Hydrogen bonds are also important in the structure of
proteins and nucleic acids.
Now we know that water molecules are polar or have slightly positive and slightly negative ends. Many
lipids, or fats and oils are not polar. Their molecules share electrons equally in their bonds, they are also
called nonpolar molecules. This means that when water and oil come together, they do not form bonds
with one another. Even when we try to mix them, the water molecules will eventually separate because
6
, their polar molecules are attracted to one another and will form hydrogen bonds, separating the water
and the nonpolar oil molecules.
In the end, the oxygen molecule will attract electrons more strongly which makes them electronegative.
The H molecules are more electropositive.
Figure 2: Hydrogen bond between water molecules
Hydrogen bons are weak when you compare them with covalent bonds. The covalent are the bonds with
the atoms within the molecules. The energy of the covalent bond is much higher. The hydrogen bond is
for a great amount responsible for the cohesion (the action or fact of forming a united whole) of liquid
water.
Hydrogen bonds are the strongest when they are linear, when they are not linear they are (much)
weaker. How weak or how strong the hydrogen bond is, depends thus on the angle between the
hydrogen acceptor, the hydrogen donor, and the other molecules. To have a hydrogen bond, there has
to be a hydrogen acceptor and a hydrogen donor. The hydrogen acceptor is an electronegative atom of
a neighboring molecule or ion that contains a long pair that participates in the hydrogen bond. It always
is an important interaction between macromolecules.
Figure 3: Angle within molecules with hydrogen bonds
Molecules can be hydrophilic or hydrophobic. Hydrophilic means that the molecule(s) is easily dissolved
in water, they have polar compounds. Hydrophobic means that it is difficult to dissolve the molecule in
water, they have nonpolar compounds. An example of a hydrophilic compound is NaCl. Water can
7
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