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Chapter 4

BIOL 243 Chapter Notes - Chapter 4: Carbohydrate, Release Factor, Start Codon

Course Code
BIOL 243
Gordon Chua

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Chap te r 4 Note s
- Section 4.1: Mole cula r Structure of Prote ins
- The exa ct order of a mino acids in a prote in dete rmine s the protein’s s ha pe a nd function
- Structure of Amino acids
- Centra l ca rbon atom, ca lle d the a lpha carbon, conne cte d by cova le nt bonds to four
diffe re nt chemica l groups : an a mino group (NH2), a ca rboxyl group (COOH), a nd a
varia ble s ide chain or R group
- In the e nvironment where the pH range is 7.35-7.45, the amino group ga ins a proton
to be come NH3+, a nd the ca rboxyl group loses a prote in, to be come COO-
- Covale nt bonds from the a lpha carbon a re bonded a t e qual a ngle s , there fore , a mino
acids form a te tra he dron, a pyra mid with with four tria ngula r fa ce s
- The R groups are the only fe ature of a mino a cids tha t makes e a ch a mino a cid unique
- Amino a cids diffe r in their chemica l a nd physica l prope rties
- The R groups are chemica lly dive rs e a nd are groupe d a ccording to the ir prope rtie s,
with a particula r e mphas is on whe ther the y a re hydrophobic or hydrophilic, or have
spe cial chara cte ris tics that might affe ct a protein’s s tructure . These prope rties
influe nce how a polype ptide folds , a nd he nce the three-dime nsiona l s ha pe of the
prote in
- Most hydrophobic a mino a cids ha ve non pola r R groups compos e d of hydrocarbon
cha ins or uncha rge d carbon rings. Be ca use wate r mole cule s in the ce ll form hydroge n
bonds with e ach othe r ins te a d of with the hydrophobic R groups, the hydrophobic R
groups te nd to aggregate with e a ch othe r. Their a ggrega tion is a ls o s ta bilize d by we a k
van de r waa ls force s, in which a s ymme tries in ele ctron dis tribution cre ate tempora ry
cha rge s in the inte racting mole cule s , which a re the n attra cte d to e a ch othe r
- Most hydrophobic a mino a cids te nd to be burie d in the inte rior of folde d prote ins,
whe re the y a re ke pt a way from wate r
- Amino a cids with pola r R groups ha ve a perma ne nt charge s epa ra tion, in which one
end of the R group is s lightly more nega tively cha rge d than the othe r
- R groups of basic and a cidic a mino acids are ve ry pola r
- The a bility to bind a nother mole cule of opposite cha rge is one importa nt way in which
prote ins ca n a s s ocia te with e ach othe r or with othe r ma cromole cule s such as DNA
- The propertie s of s e ve ra l a mino a cids (ie. glycine , proline , a nd cyste ine ) a re note worthy
be ca us e of their e ffe ct on prote in s tructure
- Glycine is diffe re nt from othe r a mino acids beca use its R group is hydroge n, e xa ctly
like the hydrogen on the other s ide of the a lpha ca rbon, a nd the refore it is not
as ymme tric. All othe r a mino a cids have four diffe re nt groups a tta ched to the alpha
ca rbon a nd a re as ymmetric. Also, glycine is non polar a nd sma ll e nough to tuck into
spa ce s whe re other R groups would not fit. The small s ize of glycine’s R group als o
allows for freer rotation around the C-N bond s ince its R group doe s not ge t in the way
of the R groups of ne ighbouring a mino a cids . Thus , glycine incre ase s the fle xibility of
the polypeptide ba ckbone, which ca n be an importa nt thing in the folding of the prote in
- Proline is a lso dis tinctive for a diffe re nt re ason. It’s R group is linked ba ck to the amino
group. This linka ge crea te s a kink or be nd in the polypeptide chain a nd re s tricts
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rotation of the C-N bond, there by impos ing cons tra ints on protein folding in its vicinity,
an e ffe ct the very opposite of glycine’s
- Cysteine make s a spe cial contribution to prote in folding through its -S H group. Whe n
two cyste ine side cha ins in the s ame or differe nt polype ptide s come into proximity,
the y ca n re act to form a n S -S dis ulphide bond, which cova le ntly joins the s ide cha ins .
Such dis ulfide bonds a re s tronger tha n the ionic inte ractions of other pa irs of a mino
acid, a nd form cross -bridge s that ca n conne ct differe nt pa rts of the s a me prote in or
even diffe re nt proteins . This property contributes to the overa ll s tructure of s ingle
prote ins or combina tions of prote ins
- The bond forme d betwee n two amino a cids is a pe ptide bond
- In forming the pe ptide bond, the ca rboxyl group of one a mino a cid re a cts with the a mino
group of the ne xt amino acid in line, a nd a mole cule of wate r is re le a s e d. Note that, in
the re s ulting mole cule , the R groups of e a ch amino acid point in diffe rent dire ctions
- The C=O group in the pe ptide bond is known a s a ca rbonyl group, and the N-H group is
an a mide group. The e le ctrons of the pe ptide bond are more a ttra cte d to the C=O group
tha n to the NH group beca us e of the gre ater e lectronega tivity of the oxyge n atom. The
re s ult is that the pe ptide bond ha s s ome of the cha racteris tics of a double bond. The
pe ptide bond is s horte r tha n a s ingle bond, for e xample, a nd it is not fre e to rota te like a
single bond. The other bonds a re fre e to rota te a round the ir ce ntra l a xes
- Polyme rs of amino acids s ha re a chemical fea ture common to individua l a mino a cids :
tha t the e nds a re chemica lly distinct from e ach othe r. One e nd, ha s a fre e a mino group;
this is the amino e nd of the mole cule . The other end ha s a fre e ca rboxyl group, which is
the carboxyl e nd of the mole cule
- A polyme r of amino a cids connecte d by pe ptide bonds is known a s a polypeptide.
Typica l polypeptide s produce d cells cons ist of a fe w hundred a mino a cids. In huma ns ,
the s horte st polypeptide s a re about 100 a mino acids in le ngth
- The te rm prote in is often us ed a s a s ynonym for polype ptide , e s pe cia lly whe n the
polype ptide chain ha s folde d into a sta ble , thre e-dime ns iona l conforma tion. Amino a cids
tha t a re incorporated into a protein are often referred to a s amino a cid res idue s . In a
polype ptide chain a t physiologica l pH, the amino a nd ca rboxyl ends are in their cha rged
sta te s of NH3+ and COO-. For s implicity, the e nds a re de note d a s NH2 and COOH
- The s e quence of a mino a cids in a protein is its primary structure . The s eque nce of
amino a cids ultima te ly de termine s how a prote in folds . Intera ctions betwe e n s tre tches of
amino a ids in a prote in form loca l s e condary s tructure s. Longer-range inte ra ctions
be tween these s e condary s tructure s in turn support the overa ll 3D sha pe of the
polype ptide , which is its te rtia ry structure . Fina lly, s ome prote ins a re made up of se veral
individua l polype ptide s that intera ct with each othe r, and the re sulting e ns e mble is the
qua te rnary s tructure
- No matte r wha t the function of a protein is, the a bility to ca rry out this function depe nds
on the 3D s ha pe of the protein. Whe n fully folde d, s ome prote ins conta in pockets with
pos itively or nega tively charge d side chains a t just the right pos itions to tra p sma ll
mole cule s ; othe rs have surfa ces that ca n bind a nothe r prote in or a s e quence of
nucle otide s in DNA or RNA; some from rigid rods for s tructura l s upport; a nd still others
ke e p their hydrophobic s ide cha ins a wa y from wate r mole cule s by ins e rting into the ce ll
me mbra ne
- By convention, the amino a cids in a prote in a re lis ted in orde r from left to right, s tarting a t
the a mino e nd a nd proce e ding to the ca rboxyl e nd
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