lecture ia h2o

7/17/2019 Lecture Ia H2O

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LECTURE Ia

General introduction & water

BCH 101

STRUCTURE OF BIOMOLECULES

Course Outline

BCH 101: STRUCTURE OF BIOMOLECULES

Structure o !io"olecule#: Structure$ c%e"i#tr$ occurrence$

cla##iication and unction o !io"olecule#$ water$ 'H and

!uer#( carbohydrates, amino acids and proteins; Introduction to

enzymes: classification, properties, specificity, theories of binding

to substrates and the active site concept; Lipids and

Eicosanoids: functions, properties, classifications; the

nucleosides; nucleotides and the nucleic acids structure, functions

and properties; Chemical and 3! structures of !"# and $"#;

%ualitative and &uantitative identification of lipids, carbohydrates,nucleic acids and proteins; #nalysis of biochemical components of

naturally occurring materials by separation methods'

(chematic relationship bet)een biochemistry, genetics and molecular biology

Function

Gene#)rotein#

Bioc%e"i#tr

Molecular Biolo*

Genetic#

+ Biochemistry is the study of molecules (e.g. proteins).

Biochemists take an organism or cell and dissect it into itsmolecular components, such as enzymes, lipids and DNA,and reconstitute them in test tubes (in vitro).

+ Genetics is the study of the eect of genetic dierences onorganisms. ften this can be inferred by the absence of anormal component (e.g. one gene).

+ !olecular biology is the study of biology at a molecularle"el. #he $eld o"erlaps %ith other areas of biology,particularly genetics and biochemistry. !olecular biology

concerns itself %ith understanding the interactionsbet%een the "arious systems of a cell, including theinterrelationship of DNA, &NA and protein synthesis andlearning ho% these interactions are regulated.

Macromolecules

Car!o%drate#

+ucleic ,cid#)rotein#

2 : e o ecu e at upports

All of Life

+ 'ater is the biological medium on arth

+ All li"ing organisms reuire %ater more thanany other substance

+ !ost cells are surrounded by %ater, and cellsthemsel"es are about *+-/ %ater

+ #he abundance of %ater is the main reason thearth is habitable

0he 1ater olecule

+ 'ater is a simple tri0atomic molecule, 12

+ ach 01 bond is highly polar , because of the highelectronegati"ity of the o2ygen

+ bond angle of %ater 3 4+o

+ due to the bent shape, the 01 bond polarities do notcancel. #his means5 water is a polar molecule.

T%e -ater Molecule

6 is the lo%ercase 7reek symbol delta

68 68H H

5 means a

partial negative

charge

56 means a

partial positive

charge

0hus, )ater has a partialnegative end (0xygen) and

a partial positive end

(Hydrogen), and it is called

7polar8 because of these

areas of difference

Hdro*en!ond

'ater9s bentshape and abilityto hydrogen

bond gi"es itmany specialproperties:

T%e 'ro'etie# o -ater Molecule

• Four of ater!s properties thatfacilitate an en"ironment for life are5

9 ;ohesi"e beha"ior

9 Ability to moderate temperature

9 2pansion upon freezing

9 <ersatility as a sol"ent

Cohesion

+ ;ollecti"ely, hydrogen bonds hold %ater

molecules together, a phenomenon calledcohesion

+ ;ohesion helps the transport of %ater againstgra"ity in plants

+ Adhesion is an attraction bet%een dierentsubstances, for e2ample, bet%een %ater andplant cell %alls.

-ater/conductin*

,d%e#ion

Co%e#ion

2irection

o water

"o3e"ent

+ Surface tension is a measure of ho% hard it is

to break the surface of a liuid+ =urface tension is related to cohesion

+ ne %ater molecule can hydrogen bond to

another because of this electrostatic attraction.+ Also, hydrogen bonding occurs %ith many other

molecules surrounding them on all sides.

(urface 0ension

A %ater molecule in themiddle of a solution ispulled in all directions.

Surace Ten#ion

+ "ot true at the surface.

+ #hey are pulled down and to each side, notup%ard since the %aterand air are not

attracted to each other.+ #his holds themolecules at thesurface together tightly.

+ #his causes surfacetension#

Surace Ten#ion

+ 'ater drops are

rounded, becauseall molecules onthe edge are pulledto the middle, notout%ard to the air:

+ A drop has theleast amount of

surface area forany gi"en "olume.

Moderation of Temperature

+ 'ater absorbs heat from %armer air andreleases stored heat to cooler air

+ 'ater can absorb or release a large

amount of heat %ith only a slight changein its o%n temperature

' 9 1i h = i$ 1

'ater9s 1igh =peci$c 1eat

+ #he speci$c heat of a substance is theamount of heat that must be absorbed orlost for 4 g of that substance to changeits temperature by 4>;

+ #he speci$c heat of %ater is 4 cal?g?>;

+ 'ater resists changing its temperature

because of its high speci$c heat

i h i$

+ 'ater9s high speci$c heat can be tracedto hydrogen bonding

9 1eat is absorbed %hen hydrogen bonds break

9 1eat is released %hen hydrogen bonds form

+ #he high speci$c heat of %ater minimizestemperature @uctuations to %ithin limitsthat permit life

'ater9s 1igh =peci$c 1eat

"aporati"e ;ooling

+ Evaporation is transformation of a substance

from liuid to gas+ Heat of %apori&ation is the heat a liuid

must absorb for 4 g to be con"erted to gas

+ As a liuid e"aporates, its remaining surfacecools, a process called e%aporati%e cooling

+ "aporati"e cooling of %ater helps stabilize

temperatures in organisms and bodies of%ater

' i f i

'(pansion upon free&ing

+ ce @oats in liuid %ater because hydrogenbonds in ice are more ordered,C making iceless dense

+ 'ater reaches its greatest density at E;

+ f ice sank, all bodies of %ater %oulde"entually freeze solid, making lifeimpossible on arth

Hdro*en

!ondLi4uid water

Hdro*en !ond# !rea5 and re/or"Ice

Hdro*en !ond# are #ta!le

ig' 3a

Hdro*en

!ondLi4uid water Hdro*en !ond# !rea5 and re/or"

IceHdro*en !ond# are #ta!le

h S l f if

The Sol%ent of Life

+ A solution is a liuid that is a homogeneous

mi2ture of substances

+ A sol%ent is the dissol"ing agent of asolution

+ #he solute is the substance that is dissol"ed+ An a)ueous solution is one in %hich %ater

is the sol"ent

+ 'ater is a "ersatile sol"ent due to its polarity,

%hich allo%s it to form hydrogen bonds easily+ 'hen an ionic compound is dissol"ed in

%ater, each ion is surrounded by a sphere of%ater molecules called a hydration shell

+ 'ater can also dissol"e compounds made

of nonionic polar molecules+ "en large polar molecules such as

proteins can dissol"e in %ater if they

ha"e ionic and polar regions

8a9 L#o"e "olecule in a

nona4ueou# en3iron"ent

8!9 L#o"e "olecule 8'ur'le9 in an a4ueou#

en3iron"ent

8c9 Ionic and 'olar re*ion#

on t%e 'rotein;# #urace attract water "olecule#<

=ubstances

+ A hydrophilic substance is one that hasan aFnity for %ater

+ A hydrophobic substance is one that

does not ha"e an aFnity for %ater+ il molecules are hydrophobic because

they ha"e relati"ely nonpolar bonds

+ A colloid is a stable suspension of $neparticles in a liuid

=olutions

+ !ost biochemical reactions occur in %ater

+ ;hemical reactions depend on collisions ofmolecules and therefore on the concentrationof solutes in an aueous solution

+ Molecular mass is the sum of all massesof all atoms in a molecule

+ Numbers of molecules are usuallymeasured in moles, %here 4

mole *mol+3 G.+H 2 4+HI molecules

+ A"ogadro9s number and the unit dalton %ere de$ned such that G.+H 2 4+HI daltons3 4 g

+ Molarity *M+ is the number of moles ofsolute per liter of solution

S l ti C t ti

Solution Concentrations

2pressed as a ratio of the amount ofsolute to the total amount of solution5

Concentration < #mount of solute

0otal amount of solution

=>, w/v ?

2pressed as a ratio of the amount ofsolute to the total amount of solution5

Concentration < #mount of solute

0otal amount of solution

Liters

= molarity, M ?

/ ;oncentration has multiplier of 4++ toplace ratio on parts per 4++C basis5

@rams of solute

mL of solution>, w/v < A 44

Jractice situation5*'- grams of "aCl is dissolved in sufficient )ater to

maBe -4 mL of solution'

1hat is the > =w/v ? concentration of this solution

@rams of solute

> <*'- g

-4 mLA 44 < 4'33 >

0he gDmL units are understood but not included' 3.

0he concentration is0he concentration is

4'33 > =4'33 > =w/v w/v ?'?'

*'- grams of "aCl is dissolved in sufficient )ater to

1hat is the > =w/ v? concentration of this solution

Another52' grams of 2(F* is dissolved in sufficient )ater to maBe

4'44 liters of solution'

1hat is the > =w/ v? concentration of this solution

@rams of solute

> <2' g

44 mLA 44 < 2'4 >

0he gDmL units are understood but not included'

(olution volume units must be converted from liters to mL

before doing calculations: 4'44 L < 44 mL'

nce kno%n, the solution concentration%ork as a con"ersion factor.

EGamples =all are wt/vol percents?:

4'. > "aClmeansH

4'. g "aCl < 44 mL solution

and the conversion factors areH

4'. g "aCl

44 mL solution

Ksing the concentration as a con"ersionfactor5

1hat mass of "aCl is present in 2444 mL of 4'.>"aCl solution

o) much dissolved "aCl is ino) much dissolved "aCl is in

this 2444 mL of saline solutionthis 2444 mL of saline solution

EGamples =all areEGamples =all are wt/vol wt/vol percents?:percents?:

4'. g "aCl

44 mL solution

2444 mL soln2444 mL soln AA << -'4 g "aCl-'4 g "aCl

-'4 grams of dissolved "aCl is

present in 2444 mL of this

solution

1hat volume of 4'.> "aCl solution should contain 2'4

grams of dissolved "aCl

1hat volume )ill contain1hat volume )ill contain

2'4 grams of dissolved2'4 grams of dissolved

"aCl"aCl

1hat volume of 4'.> "aCl solution should contain2'4 grams of dissolved "aCl

2'4 g "aCl2'4 g "aCl AA << 2/* mL soln2/* mL soln4'. g4'. g "aCl"aCl

44 mL44 mL solutionsolution

EGamples =all areEGamples =all are wt/vol wt/vol percents?:percents?:

1hat volume of 4'.> "aCl solution should contain2'4 grams of dissolved "aCl

2/* mL of this solution contains2/* mL of this solution contains

2'4 grams of dissolved "aCl'2'4 grams of dissolved "aCl'

MolaritMolarit

< <oles of soluteoles of solute

Liters of solutionLiters of solution

*'- grams of "aCl is dissolved in sufficient )ater to maBe

-4 mL of solution'

1hat is the molarity of "aCl in this solution

1e previously determined this solution to be 4'33>;

)hat is its molarity*.

olarity

<oles of solute

Liters of solution

0he *'- grams of "aCl )ill need to be converted to moles

before the calulations are done'

(imilarly, to maBe units match, the -4 mL )ill be

converted to liters'

olarity

<oles of solute

Liters of solution

*'- grams of "aCl is dissolved in sufficient )ater to maBe-4 mL of solution' <

*'- g "aCl A < 4'4.2 mole "aCl

.' g "aCl

mole "aCl

-4 mL A < 4'-4 L444 mL

*'- grams of "aCl is dissolved in sufficient )ater to maBe

-4 mL of solution' <

4'4.2 mole "aCl

4'-4 L

<oles of solute

Liters of solution

< 4'4. M "aCl

< 4'4. moles "aClDL

<4'4.2 moles "aCl

4'-4 Liters of solution

4'4. M

0he concentration is

4'33 > =w/v ? and H

is 4'4. M

*'- grams of "aCl is dissolved in sufficient )ater to

1hat is the > =w/ v? concentration of this solution and

)hat is its molarity

-4 mL2

lecture ia h2o

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