Chapter 3 Water: The Matrix of Life Overview

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1 Chapter 3 Water: The Matrix of Life Overview
Section 3.1: Molecular Structure of Water Section 3.2: Noncovalent Bonding Section 3.3: Thermal Properties of Water Section 3.4: Solvent Properties of Water Section 3.5: Ionization of Water

2 3.1 물의 분자구조 -산소원자가 sp3혼성으로 사면체 기하학구조(그림3.1) -산소의 전기음성도가 더 커 전자를 자기;쪽으로, 부분적인 음전하 (그림3.2) 극성(전자의 분포가 비대칭) -물분자는 구부러져 (그림3.3) -전하가 분리된 쌍극자여서 전기장에서 반대방향(그림3.4) -수소결합: 극성 분자사이의 정전기적 상호작용(그림3.5)

3 Section 3.1: Molecular Structure of Water
Water is essential for life Water’s important properties include: Chemical stability Remarkable solvent properties Role as a biochemical reactant Hydration

4 Section 3.1: Molecular Structure of Water
Water has a tetrahedral geometry Oxygen is more electronegative than hydrogen Figure 3.1 Tetrahedral Structure of Water

5 Section 3.1: Molecular Structure of Water
Larger oxygen atom has partial negative charge (d-) and hydrogen atoms have partial positive charges (d+) Figure 3.2 Charges on a Water Molecule Figure 3.3 Water Molecule

6 Section 3.1: Molecular Structure of Water
Bond between oxygen and hydrogen is polar Water is a dipole because the positive and negative charges are separate Figure 3.4 Molecular Dipoles in an Electric Field

7 Section 3.1: Molecular Structure of Water
An electron-deficient hydrogen of one water is attracted to the unshared electrons of water forming a hydrogen bond Can occur with oxygen, nitrogen, and fluorine Has electrostatic (i.e., opposite charges) and covalent (i.e., electron sharing) characteristics Figure 3.5 Hydrogen Bond

8 3.2 비공유결합 -약한 결합(표3.1) -생체분자의구조와 기능에 영향줌 (1)이온화 상호작용 상반된 전하를 띤 원자나 화합그룹사이 NaCl, 양전하, 음전하 아미노산곁사슬의 인력을 염다리 혹은 반발력: 단백질접힘, 효소작용, 분자인식 등 (2)수소결합 -수소와 산소, 질소 또는 유황사이의 공유결합은 매우 극성이어, 수소원자가 인접된 O, N, S에 약하게 끌림(그림3.6) -물은 3차원적으로 집합체를 이룸; 높은 끓는점, 녹는점, 기화열

9 Section 3.2: Noncovalent Bonding
Noncovalent interactions are electrostatic Weak individually, but play vital role in biomolecules because of cumulative effects

10 Section 3.2: Noncovalent Bonding
Three most important noncolvalent bonds: Ionic interactions Van der Waals forces Hydrogen bonds

11 Section 3.2: Noncovalent Bonding
Ionic Interactions Oppositely charged ions attract one another Ionized amino acid side chains can form salt bridges with one another Biochemistry primarily investigates the interaction of charged groups on molecules, which differs from ionic interactions like those of ionic compounds (e.g., NaCl)

12 Section 3.2: Noncovalent Bonding
Hydrogen Bonds Electron-deficient hydrogen is weakly attracted to unshared electrons of another oxygen or nitrogen Large numbers of hydrogen bonds lead to extended network Figure 3.6 Tetrahedral Aggregate of Water Molecules

13 (3)반데르발스힘 -일시적인 정전기적 상호작용, -영구적이거나 일시적으로 유도된 쌍극자사이에 일어남 -거리에 따라 인력 혹은 반발력, 반데르발스 반경에서 가장 큼 -3가지 형태 쌍극자-쌍극자 상호작용: 수소결합이 이의 한 형태(그림3.7a) 쌍극자-유도된 쌍극자 상호작용 -영구적인 쌍극자는 인접한 분자의 전자분포를 뒤틀리게하여 일시적인 쌍극자형성을 유도한다(그림3.7b) 3. 유도된 쌍극자-유도된 쌍극자(그림3.7c) -인접된 무극성분자 내 전자이동은 인접분자 내에 일시적인 분자불균형을 초래한다. -런던 분산력:DNA분자 내 위아래 염기고리의 상호작용

14 Section 3.2: Noncovalent Bonding
Van der Waals Forces Occur between neutral, permanent, and/or induced dipoles Three types: Dipole-dipole interactions Dipole-induced dipole interactions Induced dipole-induced dipole interactions Figure 3.7 Dipolar Interactions

15 3.3 물의 성질 -녹는점 끓는점이 높다(표3.2); 수소결합 -물 한 분자는 4개의 수소결합(그림3.8) -물 온도를 증가시키는데 에너지가 높다(표3.3) -물은 높은 기화열과 열용량 3.4 물의 용매성질 -이온, 당, 많은 아미노산 등을 녹인다 1)친수성 -용매화 구형(그림3.9) 구조화된 물 (그림3.10) 졸-겔(그림3.11): 아메바의 위족, G-actin F-actin의 가역적중합반응 2)소수성분자 -물의 용매화망상에서 배제되어 작은 방울로 뭉친다 -물이 무극성분자 주위에 새장모양(그림3.12) -무극성물질사이의 인력: 소수성 상호작용 3) 양극성 -극성그룹과 무극성그룹을 포함 -예: 이온화 지방산(카르복실기와 탄화수소, 미셀형성 그림3.11)

16 Section 3.3: Thermal Properties of Water
Water’s melting and boiling points are exceptionally high due to hydrogen bonding Each water molecule can form four hydrogen bonds with other water molecules Extended network of hydrogen bonds

17 Section 3.3: Thermal Properties of Water
Figure 3.8 Hydrogen Bonding Between Water Molecules in Ice Maximum number of hydrogen bonds form when water has frozen into ice Open, less-dense structure

18 Section 3.3: Thermal Properties of Water
Water has an exceptionally high heat of fusion and heat of vaporization Helps to maintain an organism’s internal temperature

19 Section 3.4: Solvent Properties of Water
Figure 3.9 Solvation Spheres Water is the ideal biological solvent Hydrophilic Molecules, Cell Water Structuring, and Sol-Gel Transitions Water can dissolve ionic and polar substances Shells of water molecules form around ions forming solvation spheres

20 Section 3.4: Solvent Properties of Water
Structured Water Water is rarely free flowing Water is associated with macromolecules and other cellular components Forms complex three- dimensional bridges between cellular components Figure 3.10 Diagrammatic View of Structured Water

21 Section 3.4: Solvent Properties of Water
Figure 3.11 Amoeboid Movement Sol-Gel Transitions Cytoplasm has properties of a gel (colloidal mixture) Transition from gel to sol important in cell movement Amoeboid motion provides an example of regulated, cellular, sol-gel transitions

22 Section 3.4: Solvent Properties of Water
Figure 3.12 The Hydrophobic Effect Hydrophobic Molecules and the Hydrophobic Effect Small amounts of nonpolar substances are excluded from the solvation network forming droplets This hydrophobic effect results from the solvent properties of the water and is stabilized by van der Waals interactions

23 Section 3.4: Solvent Properties of Water
Amphipathic Molecules Contain both polar and nonpolar groups Amphipathic molecules form micelles when mixed with water Important feature for the formation of cellular compartments Figure 3.13 Formation of Micelles

24 (4)삼투압 -반투막에의 물의 통과현상 (그림3.14) -삼투압은 용질농도에 의존(그림3.15) -삼투압=iMRT (i=용질의 이온화정도, M=몰랄농도) -예: 0.1M NaCl의 I 값? (82페이지) -저장,등장, 고장액(그림3.16) -막전위; 세포막표면상의 이온의 불균형으로 전기전도, 능동수송, 수동수송 -삼투압의 조절, 식물은 팽압 -리포트?(문제 )

25 Section 3.4: Solvent Properties of Water
Figure 3.14 Osmotic Pressure Osmotic Pressure Osmosis is the spontaneous passage of solvent molecules through a semipermeable membrane Osmotic pressure is the pressure required to stop the net flow of water across the membrane Osmotic pressure depends on solute concentration

26 Section 3.4: Solvent Properties of Water
Can be measured with an osmometer or calculated (=iMRT) Cells may gain or lose water because of the environmental solute concentration Solute concentration differences between the cell and the environment can have important consequences Isotonic solution Hypotonic solution Hypertonic solution Figure 3.16 Effect of Solute Concentration on Animal Cells

27 Section 3.4: Solvent Properties of Water
Proteins with ionizable amino acid side chains affect cellular osmolarity by attracting ions of opposite charge There is asymmetry of charge across the membrane due to ions forming an electrical gradient (membrane potential) Unlike animal cells, plant cells use osmotic pressure to drive growth via turgor pressure

28 3.5 물의 이온화 -물의 이온화 Keq, 평형상수 Keq x 55.5 은 이온적 Kw pH=-log[H+] (1)산, 염기 그리고 pH -강산 강염기 -약산 약염기 약산과 이의 짝염기 Ka, 산의 해리상수(클수록 강산) pKa= -logKa (pKa가 낮을수록 강산)(표 3.4) - pH척도(그림3.17), 수소이온 농도의 음성로그: pH= -log[H+]

29 Section 3.5: Ionization of Water
Water can occasionally ionize, forming a hydrogen ion (H+) and a hydroxide ion (OH-) In an aqueous solution, a proton combines with a water molecule to form H3O+ (hydronium ion) H2O  H+ + OH- (reversible)

30 Section 3.5: Ionization of Water
The ion product of water is referred to as Keq[H2O] or Kw = [H+][OH-] Kw at 25°C and 1 atm pressure is 1.0  10-14 Kw is temperature-dependent; therefore, pH is temperature-dependent as well

31 Section 3.5: Ionization of Water
Acids, Bases, and pH An acid is a proton donor A base is a proton acceptor Most organic molecules that donate or accept protons are weak acids or weak bases A deprotonated product of a dissociation reaction is a conjugate base

32 Section 3.5: Ionization of Water
The pH scale can be used to measure hydrogen ion concentration pH=-log[H+] Figure 3.17 The pH Scale and the pH Values of Common Fluids

33 Section 3.5: Ionization of Water
pKa is used to express the strength of a weak acid Lower pKa equals a stronger acid pKa=-logKa Ka is the acid dissociation constant Figure 3.17 The pH Scale and the pH Values of Common Fluids

34 Section 3.5: Ionization of Water

35 (2) 완충액 -산독증, 알칼리혈증 -완충액 -르샤트리에르의 원리: 평형상태에서 한 반응에 어떤 변화를 주면 그 변화를 제거하는 방향으로 평형이 일어난다. -예: 아세트산과 아세트산염나트륨으로 구성된 아세트산염완충액(그림3.18) 완충용량(buffer capacity) -완충액성분의 농도에 비례 Henderson-Hasselbalch방정식 -HA= H+ + A- -pH=pKa + log[A-]/[HA] [A-]=[HA]이면, pH=pKa (그림3.18) 가장 효과적인 완충액은 pKa값 위아래 1pH범위 리포트?, 문제

36 Section 3.5: Ionization of Water
Buffers Regulation of pH is universal and essential for all living things Certain diseases can cause changes in pH that can be disastrous Acidosis and Alkalosis Buffers help maintain a relatively constant hydrogen ion concentration Commonly composed of a weak acid and its conjugate base

37 Section 3.5: Ionization of Water
Buffers Continued Establishes an equilibrium between buffer’s components Follows Le Chatelier’s principle Equilibrium shifts in the direction that relieves the stress Au: What exactly establishes an equilibrium between buffer’s components? Figure 3.18 Titration of Acetic Acid with NaOH

38 Section 3.5: Ionization of Water
Henderson-Hasselbalch Equation Establishes the relationship between pH and pKa for selecting a buffer Buffers are most effective when they are composed of equal parts weak acid and conjugate base Best buffering occurs 1 pH unit above and below the pKa Henderson-Hasselbalch Equation pH = pKa + log [A-] [HA]

39 Section 3.5: Ionization of Water
Worked Problem 3.5 (Page 91) Calculate the pH of a mixture of 0.25 M acetic acid (CH3COOH) and 0.1 M sodium acetate (NaC2H3O2) The pKa of acetic acid is 4.76 Solution: pH = pKa + log [acetate] [acetic acid] pH = log [0.1] [0.25] = = 4.36

40 *한 개 이상의 이온화그룹을 갖는 약산 -인산(phosphoric acid, H3PO4), 약한 다양성자 산 -NaOH로 적정(그림3.19), 단계적 이온화 -가장 산성 그룹의 pKa를 pK1으로 표기 -낮은 pH에서 대부분 분자들이 양성자화된다 -pH와 pK1이 동일할 때 H3PO4와 H2PO4-의 양이 동일함 -아미노산의 이온화: 두 기능기, 적정시 –COOH가 먼저 양성자를 잃고 다음으로 –NH3가 다음으로

41 Section 3.5: Ionization of Water
Figure 3.19 Titration of Phosphoric Acid with NaOH Weak Acids with Multiple Ionizable Groups Each ionizable group can have its own pKa Protons are released in a stepwise fashion

42 (3)생리적인 완충액 중탄산염완충액 CO2 + H2O ↔ H2CO3, Carbonic acid H2CO3 ↔ H+ + HCO3-, Bicarbonate CO2 + H2O ↔ H++ HCO3-, 실제 혈액내 인산완충액 H2PO4-(인산이수소)= H+ + HPO42+ (인산수소) *단백질완충액 -곁사슬의 이온화기 -농도가 많음, 헤모글로빈 알부민 등 *세포의 부피조절과 물질대사 (그림3A) 삼투몰 농도의 작은 변화를 보정하는 기작: 막을 통한 무기이온의 교환 -단백질합성 시: 아미노산 감소로 물 유출, 무기이온의 이입 -단백질분해 시; 반대 -삼투질이라는 다량의 삼투활성물질의 합성: 스트레스를 받으면 다량의 알코올(소비톨 등), 아미노산, 타우린(아미노산유도체)를 만듦

43 Section 3.5: Ionization of Water
Physiological Buffers Buffers adapted to solve specific physiological problems within the body Bicarbonate Buffer One of the most important buffers in the blood CO2 + H2O  H+ + HCO3- (HCO3- is bicarbonate): This is a reversible reaction Carbonic anhydrase is the enzyme responsible

44 Section 3.5: Ionization of Water
Phosphate Buffer Consists of H2PO4-/HPO42- (weak acid/conjugate base) H2PO4-  H+ + HPO42- Important buffer for intracellular fluids Protein Buffer Proteins are a significant source of buffering capacity (e.g., hemoglobin) Figure 3.20 Titration of H2PO4- by Strong Base

45