新坑！這一類專欄需要一點化學(xué)基礎(chǔ)，比如說基本的元素、結(jié)構(gòu)、化學(xué)鍵、氧化還原等等，不是很需要物理化學(xué)的基礎(chǔ)。但是到需要化學(xué)的地方都會有小復(fù)習(xí)，所以對化學(xué)不是很熟悉的朋友們也歡迎來看喔~ 不太明白的或者有錯誤的地方隨時來找UP主喔~

文集本部分的參考文獻(xiàn)Essential Cell Biology, 5th ed. Alberts, et al. 2019. 部分內(nèi)容來自khanacademy與維基百科.

封面圖 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

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Elements required for life: 20 are known as necessary for life

Backbones of biological molecules: H?氫, C 碳, N 氮, O 氧?- make of 99% of living cells

B 硼, Si 硅, Ni?鎳

Na 鈉, Mg?鎂, P 磷, S 硫, Cl 氯, K 鉀, Ca?鈣

F?氟, V 釩, Cr 鉻, Mn?錳, Fe 鐵, Co 鈷, Cu 銅, Zn 鋅, Se 硒, Mo 鉬, I?碘

- The elements required for life (C) are not the most abundant elements on Earth (which is O/Si)

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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

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How do elements fill these evolutionary needs?

H, C, N, O, (S, P) - form covalent bonds

From “backbones”?of molecules / stable in H2O

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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 ......

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Charge Properties

C uncharged; O often (-); N(attract H) often (+)

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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

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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

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Many weak electrostatic bonds

- Together stabilize a molecular interaction

- Covalent backbone pinned into one conformation by many weak non-covalent bonds.

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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 - (-)

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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.

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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

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Salt molecules (charged) dissolve easily in water, as the water is more charged.