Essential Chemistry for Biologycontents.kocw.net/KOCW/document/2014/hanyang/bertbinas/4.pdf ·...

CHAPTER 2

Essential Chemistry for Biology

Today:

• Refresher of basic chemistry

• Radioactive isotopes in biology and medicine

• The role of water in biology

Last time:

• Diversity of life

• Evolution

• Life and machines

Matter: Elements and Compounds • Matter (물질) is anything that occupies space and has mass. • Matter is found on the Earth in three physical states:

– Solid – Liquid – Gas

• Matter is composed of chemical elements (원소).

– Elements are substances that cannot be broken down into other substances.

– There are 92 naturally occurring elements on Earth. 참고: naturally occurring: 자연계에 존재하는

• All the elements are listed in the periodic table.

http://www.privatehand.com/flash/elements.html

http://www.youtube.com/watch?v=ox68UGTQ03k&feature=related

http://www.youtube.com/watch?v=GFIvXVMbII0&feature=related

Just for fun: The element song

Copyright © 2007 Pearson Education Inc., publishing as Pearson Benjamin Cummings

• Twenty-five elements are essential to life. – Four of these make up about 96% of the weight of the human body. (O, C, H, N) This is something you should know – Next seven: 4% Ca, P, K, S, Na, Cl, Mg – 14 trace elements occur in smaller amounts : account for less than 0.01% (B,

Cr, Co, Cu, F, I, Fe, Mn, Mo, Se, Si, Sn, V, Zn)

Human body, by weight

http://en.wikipedia.org/wiki/Liebig%27s_law_of_the_minimum

• Living organisms maintain a constant ratio of the essential elements. – Therefore biomass is limited by the

availability of the least abundant of the essential elements.

– Animals get the right ratio of elements from their food (eventually plants).

– Plants get H and O from water (H2O) and C from air (CO2), but usually N is limiting (most plants cannot obtain N from N2) Providing N in suitable form (“fertilizers”) can dramatically increase plant yield in agriculture

Water level symbolizes biomass

Maximum possible water level


• Trace elements are essential for life.

• An iodine deficiency in the diet prevents normal functioning of the thyroid gland and results in goiter [= an enlargement of the thyroid gland (갑상선종)]

Needs only a tiny amount (0.15 mg/day)

• Iron (Fe) is a component of hemoglobin, the transporter of oxygen in the blood. An iron deficiency leads to a deficiency of hemoglobin reduced number of red blood cells


• Elements can combine to form compounds (화합물). – These are substances that contain two or more elements in a fixed ratio. – Example: NaCl (salt), H2O, Organic compounds

Atoms • Each element consists of one kind of atom (원자).

– An atom is the smallest unit of matter that still retains the properties of an element.

The Structure of Atoms Helium Atoms are composed of

subatomic particles

• A proton (양성자) is positively charged

• An electron (전자) is negatively charged (1/2,000 the mass of a proton)

• A neutron (중성자) is electrically neutral


• Atoms have protons and neutrons packed tightly into the nucleus. – The nucleus is the atom’s central core. – The electrons orbit the nucleus.

• Elements differ in the number of subatomic particles in their atoms.

– The number of protons, the atomic number (원자번호), defines the element.

– Mass number (질량) = number of protons + number of neutrons.


Isotopes are alternate mass forms of an element

Isotopes (동위원소)

• They have the same number of protons and electrons but different number of neutrons

• They are forms of an element that differ in mass

99% 1% minute quantity

stable stable unstable (radioactive)

Half life 5,730 ± 40 years

• In radioactive isotopes (방사선 동위원소), – The nucleus decays, giving off particles and energy.

Radioactive isotopes have many uses in research and medicine

• Living cells cannot distinguish radioactive isotopes from non-radioactive isotopes.

Useful as tracers: The location and concentration of radioactive isotopes can be detected because of the radiation they emit

• To destroy cells (tumors) • Uncontrolled exposure to radioactive isotopes can harm organisms by damaging DNA.

– 1986 Chernobyl nuclear accident dramatic increase of malformed children and of thyroid cancer

Need careful monitoring of radioactive isotopes

Example 1: Tumor diagnosis: PET image of 18-FDG (Fluoro-Deoxy-Glucose) metabolism (half life 110 min)

OOH

OH

HO

HO

OHO

OH

F

HO

HO

OH

glucose 2-fluoro-2-deoxyglucose (FDG)

18

Normal

Lung tumor

Examples for using radioactive isotopes as tracers

Example 2: Figuring out metabolic pathways

Example: Photosynthesis - The metabolites of radioactive (14C) CO2 were identified using two-dimensional chromatography and autoradiography of plant extracts

http://www.sigmaaldrich.com/content/dam/sigma-aldrich/life-science/biochemicals/migrationbiochemicals1/27.gif http://5e.plantphys.net/article.php?ch=8&id=77

After 5 seconds

After 30 seconds

Example 3: Dating fossils – the radiocarbon method

• 14C is produced by cosmic rays at constant rate from 14N in the stratosphere and troposphere.

• It is incorporated into CO2 and then by photosynthesis into plants and eventually eaten by animals.

• 14C also decays constantly, and hence a steady state results: 1.5 parts of 14C for 1012 parts of 12C.

• A living plant or animal has the same 14C/12C ratio as the atmosphere.

• A dead plant or animal does not incorporate 14C, but its 14C continues to decay the 14C/12C ratio decreases with time .

• 14C has a half life of about 5,730 years, and the accuracy of radiocarbon dating allows to determine age until ~60,000 years ago.

http://news.bbc.co.uk/2/hi/uk_news/england/dorset/8260072.stm

Bones dated between 890 and 1030 AD

Electron Arrangement and Chemical Properties • Electrons determine how an atom behaves when it encounters other atoms. • Electrons orbit (전자궤도) the nucleus of an atom in specific electron shells. • The number of electrons in the outermost shell determines the chemical properties of an atom.

s p d Number of electrons

1st shell (K) 2 Up to 2 2nd shell (L) 2 6 Up to 8 3rd shell (M) 2 6 10 Up to 18

Main shells

Subshells (orbitals)


The outer shells of the atoms of the four elements most abundant in life are not full are highly reactive.

Chemical Bonding and Molecules

• When possible, atoms give up or acquire electrons in order to complete their outer shells. • These interactions usually result in atoms staying close together. • The result are chemical bonds

• The nature of the chemical bond depends on the difference in electronegativities

• Electronegativity is the ability of an atom to attract a foreign electron in a chemical bond • Large difference in electronegativities ionic bonds • Small difference in electronegativities covalent bonds


Ionic Bonds • Example NaCl

• Large difference in electronegativities electron transfer from one atom to the other • The electron transfer results in full outer electron shells of both ions • The electron transfer changes the atoms (neutral) into ions (charged) • The opposite charges attract each other ionic bond


• A covalent bond forms when two atoms share one or more pairs of outer-shell electrons • Atoms held together by covalent bonds form a molecule (A covalent bond connects each hydrogen

atom to the carbon in the molecule of CH4) • The number of covalent bonds an atom can form is equal to the number of additional electrons

needed to fill its outer shell

Covalent Bonds (공유결합)

• H2 and O2 are molecules, but not compounds

• Examples H2, O2, CH4


Chemical Reactions • = the rearrangement of chemical bonds (breaking existing bonds, forming new bonds)

http://www.youtube.com/watch?v=mRIMO35b-t8&feature=related

– Reactants (반응물) = starting materials – Products (생성물) = end materials

• Chemical reactions cannot create or destroy matter, they only rearrange it.


The electrons of the covalent bonds are not shared equally between oxygen and hydrogen

• This unequal sharing makes water a polar molecule (oxygen attracts the electrons of covalent bonds much more strongly than does hydrogen)

• A polar molecule has opposite charges on opposite ends (the oxygen end of the molecule has a slight negative charge, while the two hydrogen atoms are slightly positive)

The structure of water consists of two hydrogen atoms joined to one oxygen atom by single covalent bonds

Hydrogen Bonds (수소결합)

Oxygen atom has strong electronegativity


The polarity of water results in weak electrical attractions between neighboring water molecules

• These interactions are called hydrogen bonds (H-bonds)

• Weak forces (about 1/10 of covalent bond)

• Short-lived property (life span: 10-12 sec) • In a liquid state, each water molecule

form H-bonds with 3.4 other water molecules

(−)

(+)

(+) (−)

(−)

(+)

(+) (−)

Hydrogen bond 0.177 nm

0.0965 nm

Water and Life • Life on Earth began in water and evolved there for >3 billion years.

– Modern life still remains tied to water. – Our cells are composed of 70%–95% water.

•The abundance of water is a major reason that Earth is habitable – Water is the only common substance that exists in the natural environment in

three physical states – The attraction forces between water molecules and the slight tendency to

ionize are crucial for the structure and function of biomolecules

The Life-Supporting Properties of Water

• The polarity of water molecules and the resulting hydrogen bonds explain most of water’s life-supporting properties:

– Water’s cohesive nature – Water’s ability to moderate temperature – Floating ice – Versatility of water as a solvent


Water molecules stick together as a result of hydrogen bonding (=H-bond)

The Cohesion of Water

Microscopic tubes • The sum of all the H-bonds between water molecules

confers great internal cohesion on liquid water • Cohesion is vital for water transport in plants

• Although H-bonds are VERY short-lived, at any given moment many water molecules are H-bonded

• Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid (Hydrogen bonds give water an unusually high surface tension, making it behave as though it were coated with an invisible film)

How Water Moderates Temperature Water molecules stabilize temperature as a result of hydrogen bonding (=H-bond)

• Mechanism: When water is heated, the heat energy first disrupts H-bonds (= energy is absorbed) and then makes water molecule move faster (= temperature rises)

– Water temperature does not go up until water molecules start moving faster – Because heat is first used to break H-bonds rather than raise temperature, water

absorbs and stores large amounts of heat while warming up only a few degrees in temperature

– Conversely, when water cools, H-bonds form, a process that releases heat. Thus water can release a relatively large amount of heat to the surroundings while water temperature drops only slightly

– Water’s resistance to temperature change stabilizes ocean temperatures, creating a favorable environment for marine life

– Oceans also cause land temperatures to stay within limits by storing a huge amount of heat during warm period and giving off heat during cold conditions

• Global role of water’s ability to moderate temperatures

• Evaporative cooling – another way to keep temperature constant

– When a substance evaporates, the surface of the liquid remaining behind cools down. – This occurs because the molecules with the greatest energy (the “hottest ones”)

evaporate first – On a scale of individual organisms: “Sweating”


Biological Significance of Ice Floating

• The density of ice is lower than liquid water ice floats.

– Since ice floats, ponds, lakes, and even the oceans do not freeze solid – Mechanism: Ice insulates the liquid water below

Ice protects the biosphere


Water as the Solvent of Life • Solution (용액) = a liquid consisting of two or more substances evenly mixed.

– Dissolving agent = solvent (용매) = water in living cells – Dissolved substance = solute (용질).

• Water can dissolve an enormous variety of solutes necessary for life • As a solvent, water is a medium for chemical reactions • The competence of water as solvent is due to the ability to form “hydration shell”

around a solute molecule. Illustration how water polarity facilitates

dissolving salt http://www.learnerstv.com/animation/ani

mation.php?ani=122&cat=chemistry

Units of concentration • Mass concentration: 1 g/ 100 ml = 1% (w/v) • Volume concentration: 1 ml / 100 ml = 1% (v/v) • Molar concentration: 6 x 1023 molecules / liter = 1 mol / liter = 1M (Weight of 1 mol = molar mass = molecular weight in grams)


Water and pH

• Acid: A chemical compound that donates H+ ions to solutions.

• Base: A compound that accepts H+ ions and removes them from solution.

• To describe the acidity of a solution, we use the pH scale.

• pH = -lg[H+]

• Most water molecules are intact. However, some water molecules dissociate into ions H+ + OH-

• H+= hydrogen ions, OH¯= hydroxide ions http://dwb4.unl.edu/ChemAnime/AUTOWD/AUTOWD.html

Even a slight change in internal pH can be harmful because a balance of H+ and OH− ions is critical for the proper functioning of chemical processes within organisms Buffers (완충용액) are substances that resist pH change

• They accept H+ ions when they are in excess • They donate H+ ions when they are depleted • One of the major buffers in our body is H2CO3, the hydrated form of CO2

• Many small organic molecules in the cell also have buffer activity

Buffering is not foolproof (절대 안전한)

• Example: acid precipitation

Illustration how buffers work http://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/buffer12.swf

Summary – The chemical foundation of life

• Of 25 life-essential elements, the most abundant are O, C, H, N. Slightly less abundant key elements are Ca, P, K, S, Na, Cl, Mg. The others are called trace elements.

•Elements are groups of atoms sharing the same “atomic number” (= numbers of protons = number of electrons = minimum number of neutrons). Elements with the same atomic number but different “mass numbers” (= number of protons + number of neutrons) are called isotopes.

• Isotopes are chemically nearly identical but tend to be unstable (=radioactive) when the number of neutrons is larger than the number of protons.

•As tracers, radioisotopes are used to elucidate metabolic pathways, date fossils, etc. •In medicine, short lived radioisotopes are used to obtain images or to treat some cancers. But radioisotopes are also dangerous (especially when incorporated into the body).

•Atoms “want” to fill their outer electron shells, which is achieved by sharing (covalent bonds) or receiving /donating (ionic bonds) electrons, leading to formation of molecules.

•The most abundant “bio-elements” H, O, N, C are very reactive because their outer electron shells lack 1, 2, 3, 4 electrons, respectively. •The character of the chemical bonds is determined by the differences in electronegativity: large difference ionic; small or no difference covalent.

• Because of its abundance and unique physical-chemical properties, water (H2O) plays a dominant role in all aspects of life.

•Polarity leads to hydrogen bonding leading to high surface tension, temperature-density abnormality, ability to buffer temperatures, insulate, be a versatile solvent. •Weak ability to dissociate supports pH buffering by other molecules.

• 25개의 생명에 필수적인 원소 중, 가장 풍부한 것은 O, C, H, N 이다. 약간 적지만 필수 원소는 Ca, P, K, S, Na, Cl, Mg 이다. 다른 것들은 미량원소라고 부른다.

• 원소는 같은 “원자번호” (=양성자의 수=전자의 수=중성자의 최소 개수)를 공유하는 원자 집단이다. 원자번호는 같지만 다른 “질량수” (=양성자의 수 + 중성자의 수)를 가진 원소는 동위원소라고 부른다.

• 동위원소는 화학적으로 거의 동일하나, 중성자의 수가 양성자의 수보다 클 때, 불안정한 (방사성) 경향이 있다.

• 추적자처럼, 방사성동위원소는 대사 과정이나, 화석 나이 등을 밝히기 위해 사용된다.

• 의학에서, 반감기가 짧은 방사성 동위원소는 영상을 얻거나 특정 암을 치료하기 위해 사용된다. 그러나 방사성 동위원소는 특히 체내에 흡수되었을 때 위험하다.

• 원자들은 외곽의 전자껍질을 채우려는 “경향”이 강하고, 이것은 공유하거나 (공유결합), 받거나/주면서 (이온결합) 이루어지며, 분자를 형성하게 되면서 충족된다.

• 가장 풍부한 “생체 원소” 인 H, O, N, C 는 각각 1, 2, 3, 4 개 전자가 없어, 반응성이 매우 크다.

• 화학결합의 특징은 전기음성도의 차이에 의해 결정된다: 차이가 클 때→이온성; 차이가 작거나 없을 때→ 공유성.

• 물의 풍부함과 독특한 물리·화학적 특성은 생명의 모든 부분에서 중요한 역할을 한다.

• 극성은 수소결합을 만들며, 이는 물이 높은 표면장력과 비열, 온도에 대한 완충역할, 절연역할, 다양한 용매로서의 역할을 가지게 만든다.

• 약한 분리능은 다른 분자들에 의한 pH의 완충역할을 지원한다.

요약- 생명의 화학적 기초

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