RNA
RNA mol ecul es a re s i ngl e s tra nds containing the nucl eoti des : a deni ne (A), gua ni ne (G), cytos i ne (C), a nd ura ci l (U). RNA mol ecul es often form s econda ry (2°) s tructures much l i ke protei ns a nd ma y i ntera ct wi th DNA, other RNA mol ecul es , a nd protei ns . Thes e i ntera cti ons hel p to defi ne the pa rti cul a r functi on of ea ch type of RNA.
In genera l , there a re four di s ti nct types of RNA mol ecul es , ea ch wi th a pa rti cul a r functi on (Ta bl e 4-2). Messenger RNA (mRNA) mol ecul es ,
whi ch ca n be 100s –1000s of nucl eoti des l ong, functi on a s the tra ns mi tter of geneti c i nforma ti on from the DNA geneti c code to the res ul ti ng protei n. In thi s ta s k, mRNA i s often bound by protei ns tha t hel p to protect a nd regul a te thes e i mporta nt geneti c mes s a ges . Transfer RNA (tRNA) mol ecul es , norma l l y 65–110 nucl eoti des l ong, ca rry i ndi vi dua l a mi no a ci ds a nd ma tch them wi th a s peci fi c mRNA s equence duri ng protei n s ynthes i s . tRNA mol ecul es ha ve a very cha ra cteri s ti c “T” s ha pe tha t i s opti mi zed for thi s functi on. Ribosomal RNA (rRNA) i s a s s oci a ted wi th protei ns a nd ma kes up the a ctua l worki ng “ma chi nery” res pons i bl e for the s ynthes i s of protei n mol ecul es . The exa ct mecha ni s m of protei n s ynthes i s a nd the rol es of ea ch i ndi vi dua l type of RNA wi l l be di s cus s ed i n more deta i l i n Secti on II. A fourth type of RNA, often referred to a s regulatory RNA, i s i nvol ved i n regul a ti on of DNA expres s i on, pos ttra ns cri pti ona l mRNA proces s i ng, a nd the a cti vi ty of the tra ns cri bed mRNA mes s a ge (s ee Cha pter 9).
TABLE 4-2. Cha ra cteri s ti cs of mRNA, tRNA, a nd rRNA
DNA
DNA mol ecul es a re compos ed of two s i ngl e s tra nds of deoxynucl eoti des , adenine (A), guanine (G), thymidine (T), a nd cytosine (C), i n whi ch the two s tra nds a re pa i red to form a l a dder-type mol ecul e referred to a s a double helix (Fi gure 4-6A). Thi s doubl e hel i x forms when a toms i n the ni trogenous ba s es of the nucl eoti des form hydrogen bonds (G bondi ng wi th C a nd A bondi ng wi th T) (Fi gure 4-6B) whi l e the hydrophi l i c phos pha te a nd hydroxyl groups of the s uga r “ba ckbone” a re expos ed to the wa ter envi ronment.
Figure 4-6. Basic Structure of DNA. A. Doubl e hel i x model (l eft fi gure), i l l us tra ti ng the wi ndi ng “l a dder” s tructure wi th the i ns i de “rungs ” crea ted by nucl eoti de pa i ri ng a nd the outs i de “runners ” crea ted by cha rged phos pha te groups . B. Deta i l (top) of how the doubl e hel i x s tructure protects the i nner hydrophobi c a rea a nd a l l ows hydrogen bondi ng between pa i red G–C a nd A–T nucl eoti des whi l e expos i ng the outer hydrophi l i c deoxyri bos e a nd phos pha te groups to the wa ter envi ronment. Bondi ng (bottom) i n DNA onl y between T a nd A a nd G a nd C, whi ch hel ps to di cta te the geneti c code a nd fi del i ty i n i ts repl i ca ti on a nd expres s i on. [Reproduced wi th permi s s i on from Na i k P: Bi ochemi s try, 3rd edi ti on, Ja ypee Brothers Medi ca l Publ i s hers (P) Ltd., 2009.] Deta i l (bottom) of hydrogen bondi ng (a rrows ) between puri ne a nd pyri mdi ne pa i rs . C. Mecha ni s m of DNA Repl i ca ti on. Unwi ndi ng of DNA to a l l ow a cces s to new nucl eoti des duri ng DNA repl i ca ti on. [Reproduced wi th permi s s i on from Murra y RA, et a l .: Ha rper’s Il l us tra ted Bi ochemi s try, 28th edi ti on, McGra w-Hi l l , 2009.]
The double-helix s tructure of DNA i s es s enti a l for i ts functi on beca us e thes e two bonded s tra nds ca n tempora ri l y s epa ra te a t s peci fi c pa rts of the DNA mol ecul e to a l l ow for DNA repl i ca ti on (s hown i n Fi gure 4-6C). mRNAs a nd a s s oci a ted protei ns ca n a l s o a cces s the DNA s tra nds to copy the conta i ned geneti c s equence a s the fi rs t s tep, l ea di ng to protei n s ynthes i s (s ee Cha pter 9). Thi s proces s i s di s cus s ed i n more deta i l i n Secti on II. The uni que doubl e hel i x ca n then rebond to a ga i n protect the vi ta l DNA mes s a ge. A s epa ra te type of DNA i s found i n mi tochondri a . Thi s mitochondrial DNA (mtDNA) codes for onl y a few protei ns (13 tota l protei ns i n huma n mi tochondri a ) i nvol ved i n the producti on of energy wi thi n the mi tochondri a . Unl i ke DNA found i n the nucl eus , mtDNA forms a s ma l l ci rcul a r s tructure wi th the s a me bondi ng a nd s tra nd s epa ra ti on s een i n l i nea r doubl e-hel i x DNA mol ecul es .
The s peci fi c s equence of A, G, C, a nd T nucl eoti des or “genome” defi nes a l l the functi ona l mol ecul es of a l i vi ng crea ture a nd, a s s uch, DNA i s the bl uepri nt of l i fe. The genome of huma ns i s es ti ma ted to conta i n a pproxi ma tel y 20,000–25,000 di fferent genes . Conta i ned wi thi n the chromos omes (Fi gure 4-7) a re the nucl eoti de s tra nds , whi ch conta i n the mes s a ge or “code” for every s i ngl e protei n. The s equences of A’s , G’s , C’s , a nd T’s or “genes” tha t code for mRNA mol ecul es a nd, s ubs equentl y, thes e protei ns a re referred to a s “expres s ed s equences ” or “exons.”
Sequences tha t do not code for a protei n a re ca l l ed “interveni ng s equences ” or “introns.” In fa ct, i ntrons compri s e over 90% of the tota l DNA s equence found i n huma ns a nd a re bel i eved to be l eftover, nonfuncti ona l remna nts of evol uti ona ry cha nges or, perha ps , i mporta nt regul a tory s equences whos e functi ons a re yet to be determi ned. Introns a re removed or “s pl i ced” from the s equence duri ng the ea rl y s ta ges of protei n s ynthes i s (s ee Secti on II).
Figure 4-7. Relationship between Chromosomes (right) and a Gene. Ea ch huma n chromos ome (fa r l eft, whos e DNA content i s gra phi ca l l y i l l us tra ted a s fa r l eft ba r) conta i ns a pproxi ma tel y 1000–2000 genes a rra nged i n cl us ters of a pproxi ma tel y 20 genes . Wi thi n the gene a re “expres s ed s equences ” (exons , da rk ora nge) a nd “i nterveni ng s equences ” (i ntrons , l i ght ora nge). The i nterveni ng s equences a re removed duri ng expres s i on of the pri ma ry mRNA tra ns cri pt a nd proces s i ng to the fi na l mRNA product. Introns do not a ppea r to code for a ny protei n a nd thei r rol e, i f a ny, i s s ti l l unknown. Length of mol ecul es i s i ndi ca ted a s bp (ba s e pa i rs ) or nt (nucl eoti des ). [(Left pa rt) Reproduced wi th permi s s i on from Mes cher AL: Junquei ra ’s Ba s i c Hi s tol ogy Text a nd Atl a s , 12th edi ti on, McGra w-Hi l l , 2010. (Ri ght pa rt) Ada pted wi th permi s s i on from Murra y RA, et a l .: Ha rper’s Il l us tra ted Bi ochemi s try, 28th edi ti on, McGra w-Hi l l , 2009.]
Ribozymes: Ribozymes (ribonucleic acid enzymes) repres ent a uni que depa rture from the ori gi na l thought tha t enzymes ca n onl y be protei ns . Li ke thei r protei n counterpa rts , pa rti cul a r RNA s equences pos s es s s econda ry or terti a ry s tructure tha t ena bl es them to ca ta l yze a rea cti on.
Mos t ri bozymes a ct on ei ther thems el ves or a nother RNA mol ecul e. However, s ome ri bozymes , i ncl udi ng thos e i n ri bos omes (s ee Cha pter 9), ca ta l yze the tra ns fer of a mi no groups to a growi ng protei n s equence a nd a s s i s t new protei ns to fol d i nto thei r a ppropri a te conforma ti on.
The devel opment of potenti a l s ci enti fi c a nd medi ca l a ppl i ca ti ons of ri bozymes i s ongoi ng, i ncl udi ng pos s i bl e trea tments a ga i ns t i ni ti a l HIV i nfecti on. Theori es s ugges ti ng tha t RNA, not DNA, mol ecul es were the ori gi na l geneti c code mol ecul es a l s o i nfer tha t ri bozymes ma y ha ve been s ome of the i ni ti a l enzyma ti c mol ecul es tha t a l l owed propa ga ti on of ea rl y l i fe.
Knowi ng the exa ct s equence of a n orga ni s m’s DNA genome woul d a l l ow one to dupl i ca te or “cl one” tha t orga ni s m exa ctl y. “Cloning” i s s i mpl y the a bi l i ty to copy the DNA s equence a nd repl i ca te i t to form the pa rti cul a r orga ni s m. Is ol a ti ng s peci fi c s equences tha t a re the code for a pa rti cul a r protei n a l l ows res ea rchers to s tudy a nd ma ni pul a te thes e protei ns (s ee Appendi x II), a nd i s vi ta l for s ci enti fi c a nd medi ca l purpos es .
Adenosine Deaminase Deficiency and Gene Therapy: Defi ci enci es i n the brea kdown of nucl eoti des a nd nucl eos i des l ea d to often fa ta l di s ea s es ea rl y i n l i fe i n whi ch the i mmune res pons e i s ma rkedl y decrea s ed. Severe combined immunodeficiency syndromes encompa s s s evera l
exa mpl es of thes e di s ea s es but a l mos t ha l f of pa ti ents ha ve a defi ci ency i n the brea kdown of a denos i ne by adenosine deaminase. Pa ti ents ha ve been trea ted by bone ma rrow tra ns pl a nt but a l s o by the emergi ng technol ogy of gene thera py wi th s ome s ucces s . Gene thera py offers the potenti a l for produci ng a “good” copy of a gene a nd us es i t to repl a ce the defecti ve copy. The i mpl i ca ti ons of thi s trea tment a re va s t.