26697606 biochemistry introduction

8/19/2019 26697606 Biochemistry Introduction

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MARISOL A. LAGUARDIA

Teacher-in-Charge

myra_laguardia @ yahoo.com


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BIOCHEMISTRY

the study of the chemical compositionof living matter

the study of the biochemical processesthat underlie life activities duringgrowth and maintenance.

Seeks to describe the structure,organization, and functions of livingmatter in molecular terms.


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3 Principal Areas:1. structural chemistry of the components

of living matter and the relationships ofbiological function.

2. study of metabolism (totality of chemical

reactions that occur in living matter).3. molecular genetics (chemistry of

processes and substances that store andtransmit biological information) tounderstand heredity and the expression of

genetic information in molecular terms.


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Development ofBiocemistr!

Living matter was generally believedas composed of substancesualitatively different from those foundin nonliving matter, substances thatdid not behave according to the knownlaws of physics and chemistry.

VITALISM held that living things areendowed with a mysterious and divine

life force.


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Mi" #$t cent%r!investigations of the chemical composition of plant

and animal tissues

Friedrich Wohler showed that urea (of biological

origin) could be synthesized in the laboratory fromthe inorganic compound ammonium cyanate.

!

II

"#$%"&!' #" & "#

Ammonium cyanate urea


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Cent%r!

studies of respiration, fermentation and uantitative analysis

of naturally occurring substances.

#$()' chromosomes were discovered by Walter Fleming and identified as genetic elements by *+.

#$'*' Friedrich Miescher isolated nucleic acids, but theirchemical structures were poorly understood and were

regarded as simple substances.

#$'( ' duard and !ans "uchner found that extractsfrom broken and thoroughly dead yeast cells could carry outthe entire process of fermentation of sugar to ethanol.

-his discovery opened the door to analysis of biochemicalreactions and processes in #itro (Latin, in glass/) in a testtube, rather than in intact living matter (in #i#o).


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&ate #$t an" earl! #'t Cent%r!

#'++' genes are found in chromosomes.

#'+3 $arl %euberg was the first to formally introducebiochemistry.

#',+s isolation, determination of other chemical structure

synthesis of vitamins and certain hormones

concepts of the essential amino acids in citric acid cycle

elucidation of metabolic pathways by means of isotope tracers

#',*- &.". Sumner showed that protein urease (enzyme from 0ack beans) could be crystallized, like any organic compound.


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Mi"-#'t

Cent%r!genes were discovered as the unit

of hereditary information as derivedfrom the works of 1regor 2endel.

#'.+s-#')+s' 3"4 is the bearer ofgenetic information.


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Earl! #')+s development of new and improved research techniues

and euipment

#'3,- #')+ ' development of electron microscopeproviding a whole new level of insight into cellularstructure (mitochondria and chloroplasts).

#')3' &ames Watson and Francis $ric' describedthe double'helical structure of the 3"4.

Scientists /o pioneere" te st%"! of0iocemistr! 5riestly Lavoisier

Liebig 6erzelius 6ernard

-heir studies were concerned with the whole animalsand gross tissue samples answering the what/ type ofuestions


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&ater A"vances in

Biocemistr! involves:2odern refinement of

biochemical techniues

3evelopment of more

sophisticated and sensitiveinstrumentation7ltracentrifuge by Svedberg

made possible the investigation atcellular levels

2ade possible the exploration of

chemical mechanisms involved inthe development anddifferentiation of cells

2ade possible the study of thephysiology and mechanismswithin the cell.


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&ater A"vances in

Biocemistr! involves:6iochemical elucidation of the

structures of deoxyribonucleic acid(3"4) and ribonucleic acid (8"4)5rovide fuller understanding of the

structure of genes and thetransmission of genetic information

Study of the precise mechanisminvolved in the metabolic reactionsin cells Studies on the chemical transformation

by which glucose, amino acids andlipids derived from foods aretransformed into essential bodycomponents (anabolism) by way ofmetabolic pathways or are used forenergy (catabolism) in cells.


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&ater A"vances in

Biocemistr! involves:9isualization of changes in molecular transformation

by x'ray diffraction techniues

3iscovery of the use of: isotropic tracers in metabolic pathways

chromatographic procedures in isolating intermediatesinvolved in the metabolic reactions

radioimmunoassay techniues in determining uantities of

certain biomolecules such as insulin and hormones


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DISTI12ISHI12 CHARACTERISTICS

O4 &I5I12 MATTER1. They are complicated

and highly organized.Their cells possess

intricate internalstructures containingmany kinds ofmolecules.They occur in an

enormous number ofdifferent species withstructural organization.

(a) 2icroscopic complexity andorganization are apparent in this

thin section of vertebrate muscletissue, viewed with the electronmicroscope.


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2. They undergo constant renewal ofa highly ordered structure often

acco!"anied #y an increase in theco!"le$ity of that structure #ycreating an elegant !olecular order

within the! and "ass a "attern ofthat order on to descendentorganis!s.


O4 &I5I12 MATTER


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%. &ach co!"onent "art a""ears to

ha'e a s"ecific "ur"ose or function.

DISTI12ISHI12 CHARACTERISTICSO4 &I5I12 MATTER


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O4 &I5I12 MATTER(. They ha'e the

ca"acity toe$tract andtransfor! energyfro! theiren'iron!ent #y

interacting withtheirsurroundings.

-he lion uses organic compoundsobtained by eating other animals tofuel intense bursts of mus;cularactivity. -he zebra derives energyfrom com;pounds in the plants itconsumes< the plants derive theirenergy from sunlight.


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O4 &I5I12 MATTER). They ha'e the ca"acity

for "recise self*

re"lication #y "assing

on infor!ation

descri#ing the

organis!+s structure

fro! one generation tothe ne$t.

6iological reproduction occurswith near'perfect fidelity.


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6HY DOES THE &I5I12 OR2A1ISM

APPEAR TO BE MORE THA1 THE SM O4ITS I1A1IMATE PARTS7

1. VITALISM( living things are endowed with amysterious and divine life force.

2. M$!A%I$S( the living body is a complexmachine capable of producing energy to dowork.


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6HY DOES THE &I5I12 OR2A1ISMAPPEAR TO BE MORE THA1 THE SM

O4 ITS I1A1IMATE PARTS7

3. "I)$!MIST*+( collections of

inanimate molecules interact witheach other to constitute, maintain,and perpetuate the living state.

governed by set of principlescalled the molecular logic o, theli#ing state.


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Complete Definition of &I4E inMolec%lar Terms

Molecular "iology '

study of nucleic

acids structure andfunction and thegenetic aspects ofbiochemistry.

"iochemistry '

structure,organization,and functions ofliving matter in

molecular terms.


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MO&EC&AR &O2IC O4&I4E

*. 4ll living organisms have thesame kinds of monomericsubunits.

. -here are underlying patterns

in the structure of

biological macromolecules.

=. -he identity of each organism

is preserved by its possession ofdistinctive sets of nucleic acids

and of proteins.


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tecni8%es %se" 0!0iocemists:

electron

microsco-y ' remarkable

details of cellularstructure.

(ray di,,raction

5recise ='dimensional

structures of huge biologicalmolecules.


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SES O4

BIOCHEMISTRY

*. )n human and animalnutrition/ it relates the dietaryreuirements of an animal to themetabolic utilization and fates ofa nutrient. (e.g. why vitamins areessential to health)


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2. )n clinical chemistry/ biochemicalmeasurements reveal clues to

diagnoses of illnesses or allowmonitoring responses to treatment.(e.g. detection of certain enzymes in

blood serum is a clue to internaldamage to a tissue, which releasedthat enzyme from its cells.)

SES O4

BIOCHEMISTRY


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3. )n -harmacology andtoicology/ it is concerned with

the effects of external chemicalsubstances on metabolism. (e.g.drugs and poisons act by

interfering specific metabolicpathways)

SES O4

BIOCHEMISTRY


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$. )n en#ironmental science/ it isinvolved in the understanding the

actions of herbicides and pesticides,in trying to increase theirselectivity, and in understanding

and dealing with mechanisms bywhich target organisms becomeresistant to agents.

SES O4

BIOCHEMISTRY


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>. )n manu,acturing/ the dissectionof the structures of enzymes reveals

general mechanism by whichproteins catalyze reactions, speedingthem up enormously under mildreaction conditions. (e.g.development of new synthetic orsemi'synthetic catalysts, eitherprotein or non'protein in nature)

SES O4

BIOCHEMISTRY


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BIOMO&EC&ES9

MACROMO&EC&ES

found in living matter with very

large molecular weights whichare composed of simple small

building block molecules strungtogether in long chains.


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0inds and their identical,unctions in all s-ecies o, cells

1. nucleic acid( store and transmit geneticinformation.

2. -roteins( direct products and effectors of geneaction, structural elements, and have specificcatalytic activity and functions as enzymes

3. -olysaccharides( storage forms of energy fuelfor cell activity and as extracellular structural

elements (cellulose) . li-ids( structural components of membranes and

storage form of energy' rich fuel.

Primor"ial


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Primor"ialBiomolec%les

simplest ancestors from which all other organicbiomolecules have been derived during thecourse of biochemical evolution.

1rouped according to their chemical structure:amino acids( building blocks of proteins -yrimidines/ -urines/ and (ribose(

precursors of nucleic acids.

(glucose( precursor of many polysaccharides.4lycerol/ choline/ and -almitic acid( building

blocks of lipids


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"I)M)L$5LS

2any different organic compounds occurred in relatively highconcentrations (warm soup) in the surface waters of theocean wherein the first living cells arose.

A.I. )-arin (Soviet biochemist) in the *+s suggested that: natural chemical and physical processes could have led to the

spontaneous formation of simple organic compounds (amino acidsand sugars) from $, "#$%, and #! vapor, which he postulated to

be components of the primitive atmosphere.

-hese gases were activated by the radiant energy of sunlight or bylightning discharges to react with each other to form simple organiccompounds condensed and dissolved in the primitive ocean, whichgradually became enriched in variety.

#e postulated that the *st living cell arose spontaneously from thiswarm, concentrated solution of organic compounds.


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&.".S. !aldane in ?ngland

independently put forwardthe same view of !parin.

)*I4I% )F

"I)M)L$5LS


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Stanley Miller

6 in *+>=) carried out experiments on the abiotic origin

of organic molecules.

sub0ected mixtures of gases (methane, ammonia,

water and hydrogen believed to be predominant in theprimitive atmosphere) in a closed flask at @& toelectric sparking across a pair of electrodes, tostimulate lightning, for periods of a week or more.

)*I4I% )F

"I)M)L$5LS

http://en.wikipedia.org/wiki/Image:UreyMillerExperiment.jpeg


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A0ioenesis: Evol%tion of&ife

http://en.wikipedia.org/wiki/Image:UreyMillerExperiment.jpeg


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http://en.wikipedia.org/wiki/Image:Miller-Urey_experiment-en.svg


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-hen he collected and analyzed the contents ofthe system which were as follows:

A. GAS PHASE B. DARK-COLORED CONDENSATE

!. C"#. C"#$. %#

!. &lycine#. alanine α -amino acids$. aspartic acid'. glutamic acid(. formic acid

). acetic acid*. propionic acid organic acids+. lactic acid,. succinic acid

)*I4I% )F

"I)M)L$5LS


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$hemical *eactions in

S-ar' ischarges*. $ % "#= #&" % = #

. &#$ % #&" =&" (a nitrile)

=. =&" % "#= =&!!#

(propionic acid) % "#=

$. =!#&" % "#= ="#&"

(aminonitrile) % #!

>. ="#&" % #! ="#&!!#

(alanine) % "#=


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A#B &42? CB8S-, 3"4 !8 58!-?B"D


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1. Precursors from the environment

(mol. wt. 18-44) - very simple low molecular weight

C"# #" %$ %

. !eta"olic #ntermediates (mol. wt. $%-$%)- converter seuences of precursors into building

block molecules/yruvate citrate malate glyceraldehyde

$-phosphates

&. 'uilding 'locs (mol. wt. 1%%-&$%)- organic compounds of somewhat larger molecular

weight.%ucleotides amino acids

monosaccharides fatty acids glycerol

4. !acromolecules ( mol. wt. 1% &-1% 4 )- covalently linked chains of building block

molecules with relatively high molecular weight%ucleic acids /roteins /olysaccharides

0ipids

$. upramolecular *ssem"lies (mol. wt. 1% + - 1% , )

- association of macromolecules of differentclasses.

0ipoproteins 1ibosomes 2nzymeComple3es Contractile systems

4icrotubules

+. ell rganelles- highest level of organization in the cell structure. %ucleus 4itochondria Chloroplasts

&olgi 5odies

IERARC Y OF T E MOLECULAR

ORGANIZATION OF CELLS


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C i f i f


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,ro"erties ,ro-aryotic ells &u-aryotic ellsSi/e 6.#7( µ m in diameter 4ost are !6-(- µ m in

diameter

ontain!ent ofD0A

8ree in cytoplasm as nucleoid In nucleus condensed withproteins into multiplechromosomes

,loidya

9sually haploid :lmost always diploid or /olyploid

Mechanis! of cellre"lication

;imple division following


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Subcellular ,ractionation o, Tissue.4 tissue such as liver is first mechanicallyhomogenized to break cells and dispersetheir contents in an aueous buffer. -hesucrose medium has an osmotic pressuresimilar to that in organelles, thus preventing

diffusion of water into the organelles, whichwould swell and burst.

-he large and small particles in the suspensi

can be separated by centrifugation at differspeeds.


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-he particles of different densitycan beseparated by isopycniccentrifugation.4 centrifuge tube is filled with asolution the density of whichincreases from top to bottom< asolute such as sucrose is

dissolved at differentconcentrations to produce thedensity gradient. Ahen a mixtureof organelles is layered on top ofthe density gradient and the tubeis centrifuged at high speed,

individual organelles sedimentuntil their buoyant densityexactly matches that in thegradient. ?ach layer can becollected separately.


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26697606 biochemistry introduction

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