Biochemistry Lecture Slides PDF

Biochemistry Yves Bollen Overview Lecture 1: thermodynamics Energy, entropy, enthalpy, work. Lecture I.2: Interactions This is an extension of chapter 5 of the book. The book chapter is rather shallow, I...

Biochemistry Yves Bollen Overview Lecture 1: thermodynamics Energy, entropy, enthalpy, work. Lecture I.2: Interactions This is an extension of chapter 5 of the book. The book chapter is rather shallow, I explain some covalent bond aspects in more detail. With this knowledge, you hydrogen bond should be able to study chapter 5 by yourself. Chapter 4 is considered prior knowledge. ionic bond Chapters 1-3 will be covered later. polarity Vanderwaals interactions hydrophobic effect Biochemistry 3 Atoms Refresh your memory: atoms consist of positively charged nucleus surrounded by orbiting electrons. Bohr model (outdated) Orbitals (first five) Biochemistry 4 Electronegativity Some atoms have a strong tendency to attract electrons. Other atoms only attract their outer electrons weakly, they have a tendency to loose electrons. This property of an atom is called electronegativity. Strong electronegativity means a strong attraction of its outer electrons, and therefore a tendency to gain electrons upon interaction with other atoms. Electronegativity correlates with the position in the periodic table. Biochemistry 5  Electronegativity of elements high low From Wikipedia Biochemistry 6  Electronegativity of elements high low The top rows are most interesting for biochemistry. Some rules of thumb: Noble elements are inert; perfectly happy. The others want to become as noble as possible. The ones on the left (low value, yellow) have one electron in their outer shell. They tend to loose one electron. (Li will “look like” He, Na will “look like” Ne) The ones on the right (high value, red) will try to gain one (F, Cl, Br), two (O, S) or even three (N) electrons to fill their outer shell. The large majority does neither. They will tend to share electrons equally. Biochemistry 7 Covalent bond Two atoms share an electron pair This requires two atoms with similar electronegativity Images: Wikimedia creative commons license. Biochemistry 8 Carbon Carbon is an important element in life. Most biochemical compounds are built around a carbon backbone. Carbon has 4 electrons in its outer shell, which can harbor 8. Therefore, carbon can make 4 covalent bonds. This is perfect for making branched or ring-shaped structures with side-chains. Biochemistry 9 See the C-C bond Atomic Force Microscopy (AFM) can visualize covalent bonds. Like here, carbon-carbon bonds. From L. Gross et al. (2009) Science 325(5944):1110-4. Biochemistry 10 Ionic bond If two atoms interact that have a large difference in electronegativity, one electron will hop from one to the other. This results in an ionic bond: a positive and a negative ion. In water they will dissociate completely. Example: NaCl (table salt). Na donates an electron to Cl: Na+ Cl- high low Biochemistry 11  Example: NaF Na donates electron to F. They end up by both having a nicely filled (identical) outer shell. Due to their differently charged nucleus, they both have a net charge: Na+ and F-. They will form a salt crystal. In water, they will dissolve completely into ions. Wikimedia by Wdcf. CC BY-SA 3.0 Biochemistry 12 Ionic interactions or salt bridges Ions of opposite charge strongly attract each other. That is what keeps the salt solid. This is also widespread in biomolecules. DNA, RNA, phospholipids, proteins: they all contain charged atoms. Interactions between two charges are called “electrostatic”, because the charges are permanent. can be attractive (+-) or repulsive (++ or --) Attractive electrostatic interaction inside a protein Biochemistry 13 Polarity What if two atoms interact that have an intermediate difference in electronegativity? δ+ δ- They will form a covalent bond, but the electrons in the bond will be more on one side of the molecule. The molecule will therefore be polar: it Hydrogen fluorine (HF). The more will have a partial charge separation. electronegative fluorine (yellow) has a partial negative charge; the hydrogen a partial positive charge. Biochemistry 14 Polarity in molecules A polar bond does not automatically lead to a polar molecule. Is carbon dioxide (CO2) polar? No. The C=O bonds are both polar. Due to the linear geometry, their effects cancel out: the molecule is not polar. Polarity in a molecule requires: 1) partial charge separation 2) some form of a-symmetry Biochemistry 15 Water Is water polar? Yes! Both H-O bonds are polar, and water is not linear. The O in water is partially negatively charged. The H’s are partially positively charged. Biochemistry 16 Hydrogen bond In water, the partially positive H’s are electrostatically attracted to the partially negative O’s. This is called a hydrogen bond. The hydrogen remains with its original molecule, H-bond but it is pulled a bit towards the other molecule. H-bonds occur for molecules containing N-H, O-H or F-H bonds because N, O and F have strong electronegativity. Also the acceptor of the bond must be substantially electronegative. Biochemistry 17 Hydrogen bond O-H and N-H groups are very common in biomolecules. They can all form H-bonds; with water molecules or other biomolecules: intermolecular H-bonds INTERmolecular H-bond within the molecule: INTRAmolecular H-bond intramolecular H-bonds in biomolecules: α-helix in a protein; double-stranded DNA Biochemistry 18 Strength of a hydrogen bond The strength of an H-bond depends on the distance and on the angle: short and straight bonds are strongest. Typical enthalpies (∆H) for binding in a favorable orientation: O−H···:N (29 kJ/mol or 6.9 kcal/mol), e.g. water-ammonia O−H···:O (21 kJ/mol or 5.0 kcal/mol), e.g. alcohol-alcohol N−H···:N (13 kJ/mol or 3.1 kcal/mol), e.g. ammonia-ammonia N−H···:O (8 kJ/mol or 1.9 kcal/mol), e.g. amide-water Biochemistry 19  Non-hydrogen dipole interactions Dipoles, being partially charged, can exert forces on each other. Those can be attractive or repulsive, depending on their relative orientation. For example C=O group C=O image: LibreText CC 3.0 Biochemistry 20 Induced dipoles An ion or a dipole can induce a dipole in a neighboring group that, by itself, is not polar. For example, C and H have very similar electronegativity values. Hence a methyl group (CH3) is not polar. An ion or a dipole in the vicinity can push the electrons of the methyl groups to a more favorable position. As a result, the methyl group becomes polar: an induced dipole. The interaction of an induced dipole with the ion or dipole is always attractive and is called Debye force (after Dutch Noble laureate). Biochemistry 21 Induced dipole A carbonyl group induces a dipole in a nearby methyl group. The induced dipole is always weaker than the permanent dipole. Similarly, also an ion can induce a dipole. H3C C=O H3C Biochemistry 22 Induced dipole Induction of a dipole is particularly easy in larger electronic systems, for example ring structures with delocalized electrons. Biochemistry 23 Two induced dipoles? The weakest attractive force is the one between two non-polar groups. This force is called London dispersion force. It arises from a fluctuation of the electrons in one group inducing a transient dipole in a neighboring group. This leads to a weak attraction. In large molecules like proteins they are H3C still relevant due to their large number. CH3 H3C Biochemistry 24 Van der Waals interactions Van der Waals (Dutch Noble laureate) demonstrated the distance dependence of non-ionic, non-covalent interactions. At very short distance, atoms repel each other (collision). At long distance, atoms do not sense each other. At intermediate distance (“contact distance”), they attract each other. Biochemistry 25 Van der Waals interactions are a collection of weak, distance-dependent attractive forces between atoms and molecules. Covalent bonds and ionic interactions are not VdW interactions. London dispersion forces are definitively VdW interactions. Sometimes also dipole-dipole interactions and Debeye forces (dipole - induced dipole) are considered VdW interactions. Always double-check what people mean by “VdW interactions”. We will use Van der Waals for London dispersion only. Biochemistry 26 Strength of interactions Those were all the interactions that you need to know. Here is an overview of their strength. Dissociation energy Dissociation energy Bond type Note (kcal/mol) (kJ/mol) Ionic lattice 250–4000 1100-20000 Covalent bond 30–260 130–1100 About 5 kcal/mol Hydrogen bond 1–12 4–50 (21 kJ/mol) in water Dipole–dipole 0.5–2 2–8 Estimated from the London dispersion forces