分子与细胞生物学 1 - L1ab: Elements and Bonds
新坑！这一类专栏需要一点化学基础，比如说基本的元素、结构、化学键、氧化还原等等，不是很需要物理化学的基础。但是到需要化学的地方都会有小复习，所以对化学不是很熟悉的朋友们也欢迎来看喔~ 不太明白的或者有错误的地方随时来找UP主喔~
文集本部分的参考文献Essential Cell Biology, 5th ed. Alberts, et al. 2019. 部分内容来自khanacademy与维基百科.
封面图 http://static02.mediaite.com/themarysue/uploads/2013/08/periodic-table-640x480.png
L1 Elements and Bonds
1a Bioelements
Biochemistry Themes:
Structure - How? Chemical Properties
Function - Why? Evolutionary Purpose
Elements required for life: 20 are known as necessary for life
Backbones of biological molecules: H 氢, C 碳, N 氮, O 氧 - make of 99% of living cells
B 硼, Si 硅, Ni 镍
Na 钠, Mg 镁, P 磷, S 硫, Cl 氯, K 钾, Ca 钙
F 氟, V 钒, Cr 铬, Mn 锰, Fe 铁, Co 钴, Cu 铜, Zn 锌, Se 硒, Mo 钼, I 碘
- The elements required for life (C) are not the most abundant elements on Earth (which is O/Si)
Biological System:
Combination of (1) a small number of building blocks;
(2) varied structures
- organism in parts gives evolutionary flexibility
A balance between a.stability & b.dynamics
So in the molecule level - chemical bond can rearrange, break & reform
How do elements fill these evolutionary needs?
H, C, N, O, (S, P) - form covalent bonds
From “backbones” of molecules / stable in H2O
C - most common, C-based life!
Many complex shapes, up to 4 bonds!
Covalent Carbon Backbones form molecules with many shapes: Kinked / Linear / Rings / Branched ......
Charge Properties
C uncharged; O often (-); N(attract H) often (+)
Why Carbon not Silicon? Why N / O? P and S form moderately stable covalent bonds.
Elements in 3rd row of periodic table form less stable covalent bonds than the 2nd row
Si - too unstable
P, S - moderately unstable, allows molecular re-arrangements
eg phosphorous forms covalent bonds that are readily rearranged (ATP hydrolysis)
Summary:
Most common elements in living organisms:
H, O, N, C: Covalent backbones of molecules
Variety in chemical shape, charge
P, S: Covalent bonds that can be rearranged easily
1b Chemical Bonds
Bonds
- Covalent - Share an e- pair
Covalent bonds form the backbone of a molecule - stable in the water
- Polar covalent - very stable in H2O
- Non-covalent - electrostatic interactions less stable in H2O
Non-covalent bonds affect its conformation and dynamic interactions
- Ionic (Salt Bridge)
- H-Bonds
Polar - partial charges, can interact with other polar molecules
3 partially charged atoms in a straight line; an H is in the middle of O’s/N’s
- Dispersion forces (Van der waals interactions)
Between any atoms when very close
Weak attractive force due to the electrons in two adjacent atoms being off center from the nucleus, making the atoms form temporary dipoles
Bond strength in water (compare energy to break vs environmental energy)
Covalent bond - 100x greater than thermal energy (cannot break the bond)
Non-covalent bond < thermal energy (may break)
Many non-covalent bond together > thermal energy (fairly strong)
Which one is stronger?
Covalent > Non-covalent: Ionic bonds > H-Bonds > Dispersion Forces
Many weak electrostatic bonds
- Together stabilize a molecular interaction
- Covalent backbone pinned into one conformation by many weak non-covalent bonds.
Nearby charged / polar molecules weaken electrostatic interactions (eg salt, H2O)
Weaken both electrostatic repulsions and attractions
Example
DNA - electrostatic repulsion between negatively charged phosphates in DNA
- K+ / Na+ salts weakens this repulsion in DNA
Negative carboxyl group - (Na+)/(Cl-) - Positive amino group
Water (polar) (+) - O / H - (-)
In water, 4 possible H-bonds per H2O
In liquid water (moving around, constantly form & break bonds), only 2 H-bonds per H2O at any one time: 2 H-bonds to Hydrogen, 2 H-bonds to unshared e- pairs.
The hydrophobic effect (water-hating)
Uncharged molecules - clump together, separate from water
Less contact with water, less partial charges - block the fewest H-bonds between waters
Salt molecules (charged) dissolve easily in water, as the water is more charged.
