8/10/2019 3303 3Amino Acids

1/37

Chapter 3-Amino Acids, Peptides and Protein

3-d structure of a protein

tertiary structure

3-d structure is related to ___

function

tertiary structure determines function, what is an example?

the enzyme catalytic site which forms a pocket for a specific substrate

4 examples of tertiary structures

H-bonds, ionic bonds, hydrophobic interactions and disulfide bonds

quaternary structure involves more than ___ su!unit "a#a monomer$

polypeptide

3 examples of quaternary structure

H-bonds, ionic bonds and hydrophobic interactions

in quaternary structure, the de%ree of su!unit ___ affects function

association

found in &'Cs( hemoprotein

hemoglobin

hemo%lo!in) ___ polypeptides of * classes( each su!unit has a ___

adult +!A) alpha*!eta*

fetal +!) alpha*___*

4; heme; gamma

___-handed alpha-helices in each alpha su!unit

right

___ ri%ht-handed alpha-helices in each !eta su!unit

7

8/10/2019 3303 3Amino Acids

2/37

functions of hemo%lo!in

O2 and O2 transport, buffer

what !inds .* as it relates to hemo%lo!in function?

!e2"; His #!$%; His #&7% --' specifically hinders O binding

hemo%lo!in contains 4 su!units held !y ___ !onds --/ ___ structure

non-co(alent; )uaternary

___ and ___ hemo%lo!in structures are flexi!le

secondary; tertiary

___-form of hemo%lo!in !inds .*, ___-form cannot

*; +

!indin% of first .* ta#es the lon%est time000the rest %et pro%ressively faster0 this is

!1c !indin% .* chan%es conformation of other su!units, facilitatin% further

.* !indin%

cooperati(e allosterism

2-conformation has a ___ .* affinity( &-conformation has a ___ .* affinity

low; high

sic#le-cell anemia ?

reduced O-carrying capacity of blood

myo%lo!in found in ___( hemo___( polypeptide of ___ amino acids( ___ ri%ht-

handed alpha-helices "A-+$ with heme !1t helices ___ and ___

muscle; protein; .; &; !

.* !ound to ___ is a reserve for when p.* of tissues is low000it is then released for

___ synthesis

myoglobin; /+0

most a!undant protein in the !ody

collagen

8/10/2019 3303 3Amino Acids

3/37

mature ___ composed of 3 alpha-chain su!units

tropocollagen

colla%en consists of ___ su!units held to%ether !y ___-!onds

.; H

re) colla%en, different tissues have different ___ ___ compositions, e0%0 type

colla%en is ___ alpha- and ___ alpha-* chain

amino acid; 2;

___ is the most a!undant amino acid in colla%en, with lots of proline and ___

glycine; lysine

amino acids definition

monomeric unit of peptides and proteins

most amino acids occur as?

1-alpha amino acids

ideal formula of amino acid has ___ char%es and practical formula has ___ and ___

char%es and the ___ from the car!oxyl %roup shifts

zero; "; -; hydrogen

acronym to descri!e the essential amino acids is?

0henylalanine

aline+hreonine

+ryptophan3soleucine #3le%

ethionine

Histidine/rginine

1eucine

1ysine

essential amino acids ___ !e synthesi5ed !y the !ody

cannot

8/10/2019 3303 3Amino Acids

4/37

adults can synthesi5e which * essential amino acids "children cannot$?

histidine and arginine

amino acid classification !y nutritional criteria includes the ___ amino acids

non-essential

what are the * non-essential AAs?

5lycine; alanine; serine; aspartic acid; tyrosine; asparagine; cysteine; proline; hydro6yproline;hydro6ylysine; glutamic acid; glutamine

which * AAs are not required for protein synthesis since they are formed after

protein is synthesi5ed?

hydro6yproline hydro6ylysine

amino acid classification !y chemical criteria incorporates the use of ___ ___

properties "&-%roup$

side chain

AA classification !y chemical criteria includes which 6 %roups of amino acids?

/liphatic, hydro6yl, sulfur, carbo6yl8amide, basic, aromatic and pyrrolidine

7 aliphatic AAs

5ly, /la, al, 1eu, 3le

7 hydroxyl AAs

9er, +hr, +yr, Hyl, Hyp

* sulfur AAs

ys, et

3 car!oxyl1amide AAs

/sp, 5lu8/sn, 5ln

4 !asic AAs

1ys, /rg, His, Hyl

4 aromatic AAs

His, 0he, +yr, +rp

8/10/2019 3303 3Amino Acids

5/37

* pyrrolidine AAs

0ro, Hyp

which 4 AAs 8.9:2 occur in proteins?

Homocysteine, ornithine, citruline and arginosuccinic acid

req:d for ;et synthesis

functions with

8/10/2019 3303 3Amino Acids

6/37

when the 4 %roups on a car!on are different

chiral carbon

there is more ___ char%e at low p+ and more ___ char%e at hi%h p+

"; -

a p+ with lots of protons would favor the ___ form at the !ottom of the ratio and

would !e ___ and for a hi%her p+ it would !e the opposite

uncharged; less than

if &-%roups are hydrocar!ons then they are ___ and can form ___ !onds

hydrophobic; hydrophobic

if &-%roups are polar "C..+, 9+3, .+$ then they are ___ and can form ___

!onds "salt !rid%e$ or ___ !onds

hydrophilic; ionic; hydrogen

if r-%roups are aromatic then they possess stron% ___ a!sorption( this is used for

quantitation of ___ in solution

+ "usually Cys$ then they are oxidi5ed to form ___ !onds

disulfide

if a compound has hydro%en it:s in ___ form and w1o hydro%en it:s ___

reduced; o6idized

!1t C..+ and 9+3

in vivo, cataly5ed !y en5ymes

a#a peptide !ond

amide bond

8/10/2019 3303 3Amino Acids

7/37

usually formed !1t * cysteines

involved in redox reactions

antioxidants

%eneral 38 protein structure

disulfide bond

if r-%roups are -.+ or -9+* they can form ___ !y covalently !ondin%

car!ohydrates via ___ !onds

glycoproteins; glycosidic

+!Ac stands for?

Hemoglobin adult carbohydrate attached

%lycohemo%lo!in is ___ or ___ hemo%lo!in

glycosylated; glycated

less than1equal to amino acids

peptide

more than AAs

polypeptide

many AAsmay !e comprised of multiple polypeptides

protein

9-terminal a#a? C-terminal a#a?

amino terminal and carbo6y terminal

intracellular antioxidant( will prevent oxidation of other compounds, thus it must

reduce other compounds while it is !ein% oxidi5ed

glutathione #59H%

tripeptide of %lutathione

5lu ys 5ly; ys contains 9 so can possibly form disulfide bond

tripeptide form hypothalamus, stimulates pituitary

thyrotropin-releasing hormone #+*H%

8/10/2019 3303 3Amino Acids

8/37

8/10/2019 3303 3Amino Acids

9/37

3 steps of colla%en synthesis

=translation of m*>/ into pro-alpha chain in fibroblasts

2=hydro6ylation of pro-alpha chains

proline by prolyl hydro6ylslysine by lysyl hydro6ylase

.=three hydro6ylated pro-alpha-chains H-bond to form pro-collagen #hydro6yproline, hydro6ylysine,

glycine%4= secretion of pro collagen out of cell by e6ocytosis

= clea(age of > and -terminal segments by procollagne peptidases --'tropocollagens

?= o6idation of some lysine@s to lysyl aldehydes by lysyl o6idase

!oth reactions in the colla%en synthesis *nd step require which 3 components?

(it , iron, O2

%enetic mutation where Bly is replaced !y Cys( easy !one !endin% and fracture,

hump!ac# "twisted spine$( delayed wound healin%osteogenesis imperfecta

step of colla%en synthesis requires which 3 components?

u, (it ?, O2

re) step of colla%en synthesis, the ___ functional %roup leads to cross lin#in% of

tropocolla%en--/colla%en fi!rils "the ___ structure$

aldehyde; )uaternary

due to deficiency of lysyl oxidase( deformed spine( !one deminerali5ation( =oint

dislocation( aortic aneurysms

lathyrism

protein classification !ased on which 4 factors?

!unction,conAugation,shape and solubility

which 4 contractile proteins are resp0 for contraction relaxation?

actin, myosin, tropomyosin, troponins

%lo!ular actin polymeri5es into actin ___

filaments

8/10/2019 3303 3Amino Acids

10/37

B-actin ? -actin?

globular actin; actin filaments

f-actin is wrapped with a dimer of rope-shaped ___ and is attached !y ___

troponins--/thin filament of the ___

tropomyosin; .; sarcomere

___ is the thic# filament

myosin

found in lun%, lar%e aa0, s#in and other C2

many random coils "* de%ree structure$ --/ elasticity and extensi!ility

pralines are hydroxylated "as in colla%en$

some lysine:s oxidi5ed to aldehydes "as in colla%en$

elastin

___ formed from condensation of ___ lysine aldehydes plus ___ unmodified lysine--

/mar#er of elastin meta!olism1turnover "i0e0 emphysema$( comes out of ___

desmosine; .; ; urine

due to lac# of A2P( actin cannot !e released( the actin-myosin complex remains

contractd

rigor mortis

whenever you see A2P there:s %oin% to !e ___ involved

g2"

al!umins are ___, e0%0 serum al!umin

%lo!ulins are ___ ___ solutions with low water solu!ility, e0%0 anti!odies

%lutelins are ___ or ___ solu!le, e0%0 %luten

!asic proteins are ___ or ___ solu!le, e0%0 histones

water-soluble; dilute salt; acid or base; acid or salt

most proteins, when classified accordin% to shape, !elon% to this class

globular

8/10/2019 3303 3Amino Acids

11/37

elon%ated proteins, %enerally structural e0%0 actin, myosin, colla%en, elastin, #eratin,

etc0

fibrous

no attachment of non-protein component

simple proteins

apoprotein D prosthetic %roup

conAugated #comple6% proteins

7 con=u%ated proteins

hemo Hb, cytochromes, glyco antibodies, glycophorin, lipo chylomicrons, 1:1, H:1, 1:1

phospho casein metallo some hemoproteins #!e%, 35!0- protease

E types of proteins !ased on function

enzymes; structural proteins; contraction; transport; hormones; protection; storage; receptor; cross-

membrane transporter

* protein su!-classifications !ased on con=u%ation

simple conAugated

* su!-classes of protein !ased on shapeglobular fibrous

Part *

0 All proteins in humans are polymers made up of ____ different __________0

= 2B different amino acids=

Fhat types of functions to structural proteins provide? Bive * examples0

+hey pro(ide structural components= &g= ollagen in tendons and cartilage and Ceratin in hair, skin,wool, and nails=

Fhat types of functions to contractile proteins provide? Bive * examples0

+hey pro(ide mo(ement of the muscles= &g= yosin and actin control muscle fibres=

Fhat types of functions to transport proteins provide? Bive * examples0

+hey carry essential substances throughout the body= &g= Hemoglobin transports o6ygen and

8/10/2019 3303 3Amino Acids

12/37

lipoproteins transport lipids=

Fhat types of functions to stora%e proteins provide? Bive * examples0

+hey store nutrients= &g= asein stores protein in milk and !erritin stores iron in the spleen and li(er=

0 Fhat types of functions to hormone proteins provide? Bive * examples0*0 +ormones can !e either protein !ased or _______ !ased0

= +he regulare body metabolism and ner(ous system= &g= 3nsulin regulates blood glucose le(els and

growth hormone regulates the body@s growth=

2= steroid=

Fhat types of functions to en5yme proteins provide? Bive * examples0

+hey catalyze biochemical reactions in cells= &g= 9ucrose catalyses the hydrolysis of sucrose= +rypsin

catalysez the hydrolysis of protein=

Fhat types of functions to protection proteins provide? Bive * examples0

+hey recognize and destroy foreign obAects= &g= 3mmunoglobulins stimulate immune responses=

0 Fhat are the functional %roups in amino acids "AAs$?

*0 Fhat three thin%s are !onded to a central car!on atom in the * AAs

found in proteins?

30 AAs with this structure are called _______0

40 2he unique characteristics of these * AAs are due to the side chain "&-

%roup$ which occupies _______________0

= an amino group #>H % and a carbo6ylic acid group #OOH%

2= an amino group #>H % and a carbo6ylic acid group #OOH% and a hydrogen.= D amino acids

4= the 4th bond to the central carbon atom

8/10/2019 3303 3Amino Acids

13/37

Fhat is a 5witterion and what is its char%e?

/ molecule with a positi(e and a negati(e charge on the same structure= 3t has a net charge of zero=

EEE /ll amino acids are e6amples of zwitterions=

0 +ow are atoms com!ined in proteins?

*0 Fhat is important to remem!er a!out them?

30 Fhat is the nature of the side chain in the AA? Fhy is this important?

= +he carbo6yl and amino groups are combined in peptide linkage=2= +hey are not a(ailable for chemical reaction, e6cept for H-bonding

.= 3t dictates the //s role in the protein and F is useful to classify // according to the properties of the

chain=

0 Fith the exception of ___________, all AAs are "G, *G, or 3G$ amines?

*0 Fhat are primary amines?

= 0roline= G=

2= 0rimary amines arise when one of three hydrogen atoms in ammonia is replaced by an alkyl=

9on-polar AAs)

0 2he 9P side chain "does1does not$ !ind, %ive off protons, or participate in

+ or ionic !onds0*0 Fhat ma#es these AAs hydropho!ic?

= +he >0 side chain does >O+ bind, gi(e off protons, or participate in H or ionic bonds=

2= +he Hs are >0 and, therefore, not soluble in water= EEE +hese //s can be thought of as lipid-like=

+herefore, they are soluble in lipids=

8/10/2019 3303 3Amino Acids

14/37

9on-polar AAs)

0 Fhat happens with the side chains in proteins that are in aqueous solution

and why?

*0 Fhat happens with the side chains in lipid cell mem!ranes and why?

= +he side chains cluster together in the interior of the protein= +his is due to the hydrophobicity of the

non-polar *-groups=

2= hen in a lipid cell membrane, the non-polar * groups are then found on the surface of the protein

Polar AAs)

0 Fhy are they hydrophilic?

30 Fhich 3 AAs contain a polar hydroxyl %roup that can participate in +-

!ondin%?

40 Fhich 3 AAs exhi!it some de%ree of polarity in the & %roups0

= 8c the &> atoms in the side chains form H-bonds with water=.= +he first .I 9erine, threonine, and tyrosine=

4= +he last .I /sparagine, cysteine, and glutamine=

Fhat does the side chain of cysteine contain? Fhy is this important?

3t contains a sulphydryl group #-9H%= 3t is an important component of the acti(e site of many enzymes=

!or e6ample, in proteins, the -9H groups of two cysteines can become o6idized to form a co(alent

cross-link called a disulphide bond #9-9%=

Acidic AAs)

0 Fhat do they contain?

*0 2hey can ioni5e as a "stron%1wea#$ acid$0

30 Fhich two amino acids are proton donors?

= a carbo6ylic acid group #OOH%2= weak

.= aspartic acid and glutamic acid= +hey become aspartate and glutamate=

'asic AAs)

0 Fhat do these AAs contain?

*0 ____________ is only wea#ly !asic in comparison to the other two0

= /n amino group that can ionize as a weak base, by accepting proton#s%=

8/10/2019 3303 3Amino Acids

15/37

2= Histidine=

0 2he H-car!on of each AA is attached to _____________, except for %lycine0 2his

ma#es it a ________0

*0 Fhy is %lycine an exception?

= 4 different chemical groups= hiral carbon=2= 8c its D-carbon has two hydrogen substituents=

0 AAs that have an asymmetric centre at the H-car!on can exist in two forms0

Fhat are they? 2his ma#es them ___________0

*0 +ow are they drawn and identified?

30 Fhich is most dominant in !iolo%ical systems?

= : 1= 9tereoisomers of each other=2= :rawn using !isher 0roAections= ut for the 1 isomer, the amino group #>H % is on the left and for

the : group, it@s on the right

.= 1-amino acids= : amino acids are in nature, but not in proteins=

0 Fhat is the isoelectric point "p$?

*0 Fhat happens when the p+ is different from the p?

30 n a solution that is more acidic than the p, what happens with the -C..

%roup?

40 Fhat a!out in a solution more !asic than the P?

= +he point at which an // e6ists as a zwitterion #" and - charge%=2= +he zwitterion accepts or donates H =

.= 3t acts as a base and acceps an H , gi(ing an o(erall positi(e charge to the amino acid=

4= +he H> group acts as an acid and loses an H , gi(ing the // an o(erall negati(e charge=

Fhen the con=u%ate !ase and acid are present in equal concentrations, their ratio is

_____, the lo% is _____, and so the p+ ______0

*0 A !uffer has maximum !ufferin% capacity at its _______, when the acidic

and !asic forms are present in ______ concentrations0

30 Iach AA has * pJa:s, referred to as ________ and ______0

40 An AA has minimal !ufferin% capacity when the p+ _____ and it has

maximal !ufferin% capacity at each of its ______0

= one, zero, pCa=2= pCa, e)ual

.= pCa and pCa

4= p3= pCa@s #i=e= when JbaseKLJacidK

8/10/2019 3303 3Amino Acids

16/37

.f the * AAs, which are considered essential, meanin% not producea!le !y the

!ody?

mnemonic device) PH group of the ne6t //= terminal

.= dipeptide

4= >-terminal // , the -terminal //=

0 As a consequence of resonance contri!utors, the peptide !ond has K4L

________ character0 Fhat does this mean for it:s structure and function?

= double bond F the peptide bond is shorter than a regular chemical bond, making it rigid and planar=

+his characteristic pre(ents free rotation about the bond=

0 2he peptide !ond is %enerally a _____ !ond due to the steric hinderance of the &-

%roups when in the __________0

*0 2he C. and the 9+ %roups of the peptide !ond are polar and are

involved in _______ !onds0

= trans, cis position

2= hydrogen

8/10/2019 3303 3Amino Acids

17/37

+ow do you name peptides?

*0 Fhat would !e the name for a tripeptide consistin% of alanine, %lycine, and

serine !e named?

= &ach // beginning from the >-terminal is named in order with its .-letter abbre(iated name=2= /la-5ly-9er

0 Fhen is a polypeptide "PP$ chain called a protein?

*0 Fhat are the levels of protein structures?

= hen there are more than B //s=

2= 0rimary #G%, secondary #2G%, tertiary #.G%, and )uaternary=

0 +ow is a G protein structure determined?

= 9imply by the order of the amino acids held together by peptide bonds=

0 +ow is a *G protein structure determined?*0 Fhat are the most common secondary protein structures?

= +he secondary structure of a protein describes the way the //s ne6t to or near each other along the

polypeptide are arranged in space=2= /lpha-heli6, beta-pleated sheet, and the triple heli6= &ach type looks atI #a% the H-bonding between

the H atom of an amino group and the polypeptide chain and #b% the o6ygen atom of the carbonyl group

in another part of the chain=

8/10/2019 3303 3Amino Acids

18/37

0 Ixplain the H-helix structure of protein0 "4 points$

*0 Fhat types of tissues have this structure?

= 9trong, spiral, tightly coiled like a telephone cord2= &6tensi(e H-bonding between each >H group and the O of a LO group in the ne6t turn of the

heli6, 4 //s down the chain=

.= 3ndi(idually bonds are weak, but together they are strong #like a zipper and its indi(idual links%4= /ll side chains #*-groups% are located on the outside of the heli6=

2= skin and hair

0 Ixplain the M-Pleated >heet structure of protein0 "4 points$

*0 Fhat types of proteins have this structure?

= 00 chains are held together side by side by H-bonds between the peptide chains

2= 9urfaces of the M-sheet appear pleated.= M-sheet ha(e 2 or more peptide strands that are almost fully e6tended and held together by H-bonds

4= H-bonds are perpendicular to the 00 backbone

2= 9ilk

0 Ixplain the 2riple +elix structure of protein0 " point$0

*0 Fhat is the most a!undant protein and where is it found?

30 Fhat does this protein have a hi%h content of and how does it contri!ute to

the stren%th of the helix?

= E +he result of three polypeptides wo(en together like a braid=

2= ollagen= !ound in connecti(e tissue, blood (essels, skin, tendons, ligaments, the eye and cartilage=.= 5lycine, proline, alanine, and hydro6ylproline and hydro6ylysisine= +he -OH groups present in their

8/10/2019 3303 3Amino Acids

19/37

hydro6yl forms in proline and lysine form H-bonds across the peptide chains gi(ing strength to the

heli6=

Fhat happens when a diet is deficient in 0 side chains are located in the centre of the 00 chain=

2= Hydrophilic portions of the 00 chain are located on the surface.= 0roteins located in >0 #lipid% en(ironments ha(e the re(erse arrangement #i=e= 0olar parts on surface

and Hydrophilic parts in interior%=

8escri!e hydropho!ic interactions0 "* points$

= /ttractions between the e6ternal, a)ueous en(t and //s that ha(e polar or ionized side chains=

2= 0olar side chains pull twd the outer surface of the protein and hydrogens bond with water=

8escri!e +-'ond interactions0 "* points$

= H-bonds form between polar amino acids=

8/10/2019 3303 3Amino Acids

20/37

2= &g= /n H-bond can occur between the -OH group of serine adn the ->H group of glutamine=

8escri!e onic "salt !rid%e$ interactions0 "* points$

= 3onic bonds between side groups of basic and acidic amino acids, which ha(e " and - charges=2= +he attraction of the oppositely charges side chains forms a strong bond called a salt bridge=

8escri!e 8isulphide 'ond interactions0 "* points$

= o(alent linkage between the -9H group of each two cysteine //s=2= +he cysteines may be separated by many //s or may be located in different 00 chains altogether=

>econdary and tertiary structures are li#e the !ric#s and mortar of protein

architecture0

0 Blo!ular proteins have ______ shapes !1c of their secondary structures of

the PP chain fold over on top of each other0

*0 Blo!ular proteins perform much of the wor# of the cells includin% these 3

functions?

30 +eme proteins are speciali5ed %lo!ular proteins0 Fhat * are the most

a!undant in humans?

= compact, sphirical

2= synthesis, transport and metabolism.= myoglobin and hemoglobin= +hey ser(e to bind o6ygen re(ersibly=

0 Fhat is a porphyrin?

*0 Ixplain the properties of +eme0 "7 points$

= yclic compounds that readily bind to metals, particularly !eN and !e = 2=a% 3t@s a porphyrin ring with !eN at centre=

b% *esponsible for the red colour of blood=

c% 3ron is held in centre of the heme molecule by bonds to the 4 nitrogens of the porphyrin ringd% !eN can form 2 additional bondsI One on either side of the ring

e% &ach heme group can bond one molecule of O

8/10/2019 3303 3Amino Acids

21/37

0 Fhat are fi!rous proteins?

*0 Fhat are the two types? 8escri!e them0

= 1ong, thin, fibre-like shapes of proteins that are in(ol(ed in the structure and cells of tissues=

2= D M-keratins

0 8escri!e H-#eratins0 "* points$*0 8escri!e M-#eratins0 "* points$

D-keratinsI

= ake up hair, wool, skin and nails=

2= ithin the fibril, the D-helices are held together by disulphide #9-9% linkages btwn the * groups of

the many cystein //s in hair= 9e(eral fibrils bind together to form a strand of hair=M-keratinsI

= !ound in feathers and scales=

2= +he proteins consist of large amounts of M-pleated sheets=

0 Fhat is the quaternary structure of protein?

*0 +ow do they wor#? "3 points$

= +he spacial arrangement of the 00 subunits #i=e= a single chain, or 2 or more chains that may8may notbe related%=

2=a% Held together by non-co(alent interactions #ie= hydrophobic, ionic, etc=%= b% F interactions that

stabilize the tertiary structure also stabilizes the )uaternary= c% 9ubunits may work together orindependently of one another=

8/10/2019 3303 3Amino Acids

22/37

0 +ow does protein denaturation occur? Fhat happens?

*0 Fhat are some denaturin% a%ents?

30 s denaturation reversi!le? Ixplain0

= +he disruption of any of the bonds that stabilize the 2G, .G, 4G of the protein= Howe(er, co(alentbonds of the primary structure are unaffected= hen denatured, proteins lose their shape and ability to

be functional=

2=Heat, strong acids, bases, and hea(y metals=.= >o= +he protein is unable to retain its original structure=

0 Fhat proteins sequester and deliver . to the cells?

*0 Fhere are they found and what are they responsi!le for?

= yoglobin #b% and Hemoglobin #Hb%

2= b found in skeletal and striated muscle=

Hb found in erythrocytes= *esponsble for mo(ement of O between lungs and other tissue=

Fhat is the maximum p. "partial pressure of oxy%en$ in arterial !lood? Fhata!out in air?

BBmm Hg #mercury% and B mm Hg

0 Fhat is myo%lo!in?

*0 +ow many AAs in a sin%le PP chain of myo%lo!in with a!out 314 of the

chain in the H-helix secondary structure?

= a% / storage protein= / globular heme protein present in heart and skeletal muscle=

b% functions as a reser(oir for o6ygen as an o6ygen carrier that increases the rate of transport of

o6ygen within the muscle cell=2= .=

0 +emo%lo!in is composed of ___ PP chains or su!units) ___ H chains and __ M

chains, denoted as _____0

*0 +ow are the chains held to%ether?

30 Iach su!unit of +! contains a heme %roup %ivin% the molecule ___ heme

%roups in total "compared to for ;!$0

40 2e complete quaternary structure of +! can !ind and transport ___

molecules of oy%en0 t can transport C. from tissues to lun%s and carry .

from lun%s to tissues0

= 4= 2= 2= denoted as D M =

2= y non-co(alent interactions=

.= four

4= four=

8/10/2019 3303 3Amino Acids

23/37

0 @i#e . , C. !inds to heme %roups0 2he affinity for C. is more than x that

of . 0 Fhat implications does this have if there was prolon%ed exposure of

+! to C.0

Fhat would !e the treatment of choice?

= 3t would be irre(ersible and lead to highly to6ic le(els of arbo6yhemoglobin=

2= Hyperbaric O

0 Fhat unique role does +! play in the !ody and why is

= 3t gather incomming O from lungs and releases it to tissues=

0 Fhat is an en5yme?

*0 +ow do en5ymes affect the !rea#down of proteins in our diet?

30 +ow are en5ymes named? Fhat is the exception?

= / protein that is a catalyst= 1arge protein molecules that speed up the rates of chemical reactions

without themsel(es undergoing any change= +hey lower the /& re)uired= F less energy is re)d tocon(ert reactant molecules to products=

2= &nzymes speed up the breakdown of proteins= ithout them they wouldn@t break down )uicklyenough to meet the body@s needs=

.= *eplace the end of the name of the reaction8reacting compound with -ase= &6ceptionI &arly enzymes

sometimes used the -in suffi6, such as pepsin and trypsin which are used to break down proteins=

0 or the en5yme class oxidoreductases0 Fhat reaction is cataly5ed?

*0 or example, what do oxidases,

reductases, and dehydro%enases do?

= O6idation-reduction *P>s2= &g= O6idases o6idize a substance= *eductases remo(e a substance= :ehydrogenases remo(e atoms,

to form a double bond=

0 or the en5yme class transferases0 Fhat reaction is cataly5ed?

*0 or example, what do transaminases and #inases do?

= +ransfer a group between two compounds= 2= &g= +ransaminases transfer amino groups #>H %=

Cinases transfer phosphate groups #0O N %

0 or the en5yme class +ydolases0 Fhat reaction is cataly5ed?

*0 or example, what do proteases, lipases, car!ohydrases, phosphatases, and

nucleases do?

= Hydrolysis *P>s2= &g= 0roteases hydrolyze peptide bonds= 1ipases hydrolyze ester bonds in lipids=

arbohydrases hydrolyse glycosidic bonds in carbohydrates= 0hosphatases hydrolyze phosphate-ester

bonds=

>ucleases hydrolyze nucleic acids=

8/10/2019 3303 3Amino Acids

24/37

0 or the en5yme class @ysases0 Fhat reaction is cataly5ed?

*0 or example, what do car!oxylases and deaminases do?

= /dd or remo(e groups in(ol(ing a double bond without hydrolysis=

2= &g= arbo6ylases add O and :eaminases add >H

0 or the en5yme class somerases0 Fhat reaction is cataly5ed?*0 or example, what do somerases and Ipimerases do?

= *earrange atoms in a molecule to form an isomer=

2= &g= 3somerases con(erts cis to trans or (ice (ersa and epimerases con(ert : to 1 isomers or (ice

(ersa

0 or the en5yme class @i%ases0 Fhat reaction is cataly5ed?

*0 or example, what do synthetases do?

= !orm bonds between molecules using /+0=2= &g= 9ynthetases combine two molecules=

0 Fhat are su!strates?

*0 Fhat structure of an en5yme plays an important role in how the en5yme

cataly5es &N9s?

30 +ow do en5ymes wor#? Fhat models do they use?

= *eacting molecules=2= +he tertiary structure=

.= +hey bind to a substrat (ia its acti(e site= +hey use a lock and key 3nduced fit models=

0 Fhat is the *-step reaction of an en5yme cataly5ed reaction?*0 Fhat happens?

30 Fhat factors affect en5yme activity?

= & " 9 --' &9 --' & " 0

2= 1ea(es the e6zyme and produces a product #i=e= sucrase " sucrose --'sucrase-sucrose comple6 --'

sucrase " glucose " fructose

.= +emp=, pH, substrate concentration, competiti(e non-competiti(e inhibitionQ

0 +ow does temperature affect en5yme activity?

*0 +ow does p+ affect en5yme activity?30 >pecifically, how does pepsin wor# in the stomach?

= 1ow temp L little acti(ity= 3ncrease temp L increased acti(ity until O0+3

8/10/2019 3303 3Amino Acids

25/37

we eat, it triggers the release of Hl to stomach, lowering the pH=

+ow does su!strate concentration affect en5yme activity?

hen enzyme J K is kept constant, increasing the substrate J K increases the rate of the catalyzed r6n aslong as their are more enzyme molecules than substrate molucules= /t some point, the substrate J K

saturates the enzyme= /ll a(ailble enzyme molecules are then bonded to the substrate, the rate of

catalyzed reaction reaches its ma6 7 adding more substrate cannot increase the rate any further=

+ow does competitive inhi!ition affect en5yme activity?

ompetiti(e inhibitionI /n inhibitor has a structutre so similar to the substrate that it competes for the

same acti(e site as the substrate= 3f the J K of the inhibitor is substantial, there is a loss of enzymeacti(ity= 3ncreasing the substrate J K displaces more of the inhibitor molecules= /s more enzyme

molecules bind to substrate #&9%, enzyme acti(ity is regained=

+ow does en5yme inhi!ition affect en5yme activity?

+hey pre(ent the acti(e site from binding with a substrate=

+ow does non-competitive inhi!ition affect en5yme activity?

>on-competiti(e inhibitionI +he inhibitor acts on a site that is not the acti(e site= 3t doesn@t resemble the

substrate and doesn@t compete for the acti(e site=

+he binding causes the shape of the enzyme to be distorted, including the shape of the acti(e site=

3nhibition occurs b8c substrate cannot fit8does not properly fit the acti(e site F no catalysis can occur=8c a non-competiti(e inhibitor isn@t competing for the acti(e site, te addition of more substrate does

not re(erse this type of inhibition=

&6amples include hea(y metal ions that bond with // *-groups=

atalytic acti(ity is restored when chemical reagents remo(e the inhibitors=

0 Fhat are simple en5ymes?

*0 Fhat are en5yme cofactors?

30 Fhat is an apoen5yme?

40 Fhat are coen5ymes?

= hen their functional forms consist only of proteins with tertiary structures #eg= +rypsin and pepsin%

2= >on protein portions of enzymes re)uired for carrying out a catalyzed reaction= +hey may be

metallic ions or organic compounds=

.= +he protein #polypeptide% portion of the the enzyme=4= Organic cofactors= 3=e (itamins= 3f tan enzyme re)uires a cofactor, neither the protein structure or

the cofactor aloe has catalytic acti(ity=

0 Fhat are proen5ymes or 5ymo%ens? Bive an example0

= &nzymes that are manufactured by the body in inacti(e form= 3n order to make them acti(e, a small

part of their 00 chain must be remo(ed=

+he body does this as a protecti(e mechanism so that it will acti(ate the enzyme where it wants it towork=

8/10/2019 3303 3Amino Acids

26/37

&g= +rypsin is a protease #clea(es proteins%= e want it to work in our stomachs on the proteins we eat=

3f it worked outside the stomach in its acti(e form, it would destroy our body@s own proteins=

0 Fhat is allosterism?

*0 Fhat can happen if a su!stance !inds non-covalently reversi!le to a site

other than the active site?

30 2he su!stance that !inds the allosteric en5yme is called ____________0

= hen enzyme regulation takes places by means of an e(ent that occurs at a site other than the acti(e

site, but will effect the acti(e site= +he enzyme regulated by it is called an allosteric enzyme=

2= 3t may inhibit enzyme action #/C/ negati(e modulation% or stimulate enzyme action #/C/ positi(emodulation%

.= / regulator=

0 Fhat are isoen5ymes?

*0 8ifferent forms of the same en5yme are called ____ or ____0

= &nzymes that perform the same function but ha(e (ery different combinations of subunits indifferent tissues= #i=e= different )uaternary structures%2= isozyme or isoenzyme=

0 +eme has only up to a ___________ protein structure0

tertiary

Part 3

5witterion

dipolar ion; can act as either an acid or base; o(erall net zero charge, but molecule contains positi(ely

and negati(ely charged regions

isoelectric point

characteristic pH at which the net electric charge is zero #p3%

side chain

* group of an amino acid; (ary in structure, size and electric charge which influence the solubility of th

amino acid in water

sequence "of a protein$

order of amino acids in a polypeptide chain

peptide

two or more amino acids Aoined by a peptide bond

8/10/2019 3303 3Amino Acids

27/37

protein

polypeptide with a molecular weight abo(e B,BBB

dialysis

a procedure that separates proteins from small solutes by taking ad(antage of the proteins@ larger size;

small molecules transfuse across a semipermeable membrane while protein cannot

con=u%ated protein

protein that contains permanently associated chemical components in addition to amino acids

prosthetic %roup

non-amino acid part of a conAugated protein

primary structure

description of all co(alent bonds #mainly peptide bonds and disulfide bonds% linking amino acid

residues in a polypeptide chain

secondary structure

the particularly stable arrangements of amino acid residues gi(ing rise to recurring structural patterns

tertiary structure

all aspects of the three-dimensional folding of a polypeptide

quaternary structure

arrangement of polypeptide subunits in space when a protein has two or more subunits

electrophoresis

important techni)ue for the separation of proteins based on the migration of charged proteins in an

electric field

concensus sequences

se)uence that reflects the most common base or amino acid at each position when a series of relatednucleic acid or protein se)uences are compared; contains much of the functional information in protein

se)uences; parts of the se)uence that ha(e particularly good agreement often represent e(olutionarilyconser(ed functional domains

cation-exchan%e chromato%raphy

column matri6 that contains negati(ely charged polymer beads that cause positi(ely charged proteins tomigrate more slowly through the column

8/10/2019 3303 3Amino Acids

28/37

anion-exchan%e chromato%raphy

column matri6 that contains positi(ely charged polymer beads that cause negati(ely charged proteins to

migrate more slowly through the column

isoelectric focusin%

procedure used to determine the p3 of a protein; proteins placed in pH gradient in presence of electricfield so that each protein migrates until it reach the pH that matches its p3

>8>-PABI electrophoresis

electrophoresis that uses 9:9 #sodium dodecyl sulfate% to gi(e each protein a similar charge-to-mass

ratio and unfolds protein so that proteins are separated almost e6clusi(ely on the basis of size in gelelectrophoresis

si5e exclusion chromato%raphy

aka gel filtration; separates proteins according to size with larger column emerging from the columnsooner than small ones due to polymer beads with engineered pores

affinity chromato%raphy

based on binding affinity; beads in column ha(e a co(alently attached chemical group #ligand% thatbinds to the desired protein; protein eluted by adding solution with high concentration of salt or ligand

Part 4

38 "primary$ structure of a protein is determined !y its

amino acid se)uence

2he function of a protein depends on its

structure

+ow many sta!le structural forms does a protein usually have

one or a small number

the most important forces sta!ili5in% the specific structures maintained !y a %ivenprotein

non-co(alent interactions

the spatial arran%ement of atoms in a protein, achieved !y rotation around sin%le

!onds

conformation

8/10/2019 3303 3Amino Acids

29/37

proteins in functional conformations

nati(e proteins

the tendency of a protein to maintain its native conformation

stability

forces counteractin% hi%h entropy in unfolded state

disulfide #co(alent, 9---9% and weak #non-co(alent, hydrogen bonds, hydrophobic and ionicinteractions%

Fhy aren:t disulfide !onds common in most cells and where are they commonly

found in eu#aryotes?

reducing en(ironment, secreted e6tracellular proteins #hormones%

>olvation layer occurs due to

less water order due to less hydrophobic material in contact #surface area% Lincreased entropy

release of free ener%y from this counteracts loss of entropy due to folded

conformation

increased entropy in surrounding a)ueous en(ironment

Fhy is the C-9 !ond in a peptide !ond shorter and more ri%id than in a classic C-

9 amine structure?

resonance between amide nitrogen and carbonyl o6ygen, no rotation between and >

what does each dihedral !ond an%le represent

phi-alpha carbon8nitrogen rotation

psi-alpha carbon8carbon rotation

omega-nitrogen8carbon rotation #usually $B%

why can:t phi and psi !oth !e

steric interferences

2he secondary structure of a protein refers to

+he path or shape of the main chain polypeptide atoms in a segment, without regard to side chains or

other segments

8/10/2019 3303 3Amino Acids

30/37

n an alpha helix, the typical phi and psi an%les are ____ and _____ and there are

_____ amino acids and a len%th of ______ per turn of the helix?

-7, -47, .=?, =4 angstroms

Fhy is the alpha helix such a sta!le conformation?

optimal use of hydrogen bonding #>-H and -O%

which amino acid has the %reatest tendency to form alpha helices

alanine

Fhat effect does ad=acent char%ed amino acids at char%ed ph:s have on the

sta!illity of the helix?

unstable8will not form

what amino acids are not compati!le !ein% close to%ether in a chain due to

!ul#1shape?

/sn, +hr, 9er, ys

critical interactions occur !etween amino acid side chains ____ and sometimes

_____ residues away from each other0 2hese interactions include

., 4= Oppositely charged residues, aromatic hhydrophobic

Amino acids least li#e to form alpha helices areproline and glycine

why is proline not favora!le for an alpha helix?

n in #n--- alpha% bond is part of rigid ring, no rotation possible for bond

why is %lycine not favora!le for an alpha helix?

more conformational fle6ibility than other amino acids

Fhich terminus has which char%e of the helix dipole?

carbo6yl -amino "

what five constraints affect the sta!ility of an alpha helix?

% indi(idual residue@s propensity to form heli62% interactions between r groups, particularly those . or 4 residues apart

8/10/2019 3303 3Amino Acids

31/37

.% bulkiness of adAacent r groups

4% occurrence of pro and gly residues

% interactions between charged residues with dipole of the heli6 at ends

Part 7

* common amino acids) @ehnin%er !oo#0 i%ures from other set, names fixed0

Ar%inine-A&B, &

+istidine-+>, +

8/10/2019 3303 3Amino Acids

32/37

@ysine-@O>, J

Aspartate-A>P, 8

Blutamate-B@, I

8/10/2019 3303 3Amino Acids

33/37

>erine->I&, >

2hreonine-2+&, 2

Aspara%ine-A>9, 9

8/10/2019 3303 3Amino Acids

34/37

Blutamine-B@9, Q

Cysteine-CO>, C

Blycine-B@O, B

8/10/2019 3303 3Amino Acids

35/37

Proline-P&., P

Alanine-A@A, A

8/10/2019 3303 3Amino Acids

36/37

soleucine-@I,

@eucine-@I, @

;ethionine-;I2, ;

8/10/2019 3303 3Amino Acids

37/37

Phenylalanine-P+I,

2yrosine-2O&, O

2ryptophan-2&P, F