Biology PDF - Nucleic Acids

*hapter 1: ilNA $tructure, $ynthe*is, and Repair L*$SSn 't."1 Nwm&m6m &m&dw lntnodue{ion Deoxyribonucleic acid (DNA) is the heritable material passed from parent fe i-rji:-:1::'!*1,: that allows for the transmission of genetic information from one generation to another. DNA stores the informa...

*hapter 1: ilNA $tructure, $ynthe*is, and Repair L*$SSn 't."1 Nwm&m6m &m&dw lntnodue{ion Deoxyribonucleic acid (DNA) is the heritable material passed from parent fe i-rji:-:1::'!*1,: that allows for the transmission of genetic information from one generation to another. DNA stores the information needed for an organism's development and vital processes, and it plays a role in regulating the expression of that information. The expression of the information encoded in DNA is mediated by ribonucleic acid (RNA), a related molecule. Both DNA and RNA are composed of building blocks called nucleotides. The order in which nucleotides are joined together is the mechanism by which genetic information is stored and transmitted. This lesson explores DNA and RNA structure and function. 1"1"fr1 Overview sf DNA and R,NA Function DNA can be transferred from one generation to the next via t:;i);''i:?'t:61 i1:1':r^:-iiii i*i:::'i''ij';i';il:*i:' Asexual reproduction involves a single parent organism that produces offspring genetically identicalto the parent. ln contrast, sexual reproduction involves two parent organisms that both contribute genetic material to produce genetically unique offspring. In prokaryotic cells, DNAis typically stored as a single circular chromosome, whereas in eukaryotic cells, DNA is organized into several distinct linear chromosomes (Figure 1.1). Each chromosome contains coding DNA and noncoding DNA. Goding DNA consists of genes, which are specific sequences of DNA that contain information needed fot" the production of ,,:i"i,ri.r':i:":',: and other molecules (eg, tt:,ritliilr' li'i'.il': ttRNAl) that carry out many of the essential functions of the cell. Prokaryotic cell Eukaryotic cell I i i _j Figure 1.1 DNA in prokaryotic cells versus eukaryotic cells'  ehapter 1: ilNA $truc{rJr*, $ynthesis, and Repair The information contained in a gene can be converted to a related molecule known as ribonucleic acid (RNA) through a process called tr*n**ripti*n. For genes that encode a protein, the RNA is transcribed and processed to become messenger RNA (mRNA), which leaves the nucleus and enters the cytosol aftertranscription. The mRNA is then trans!*te*l by a ribosome to produce a protein. Lessons 2.2 and 2.3 explore transcription and translation in more detail. In addition to genes, each chromosome contains noncoding DNA (Figure 1.2), which accounts for the majority of human genetic material (ie, the g*r:nme). Noncoding DNA does not code for proteins or other known functional biomolecules. While the function of some noncoding regions remains unknown, many regions are known to be involved in maintenance of chromosomal integrity (eg, te tomeres) or regulation of gene expi sssict-r. Noncoding ONA Figure r.z cooing,;ersus noncoding DNA. 1.1.02 l\ucNeotides and Nucleic Acids DNA and RNA are composed of nucleotides, which are naturally occurring molecules that can be classified as either deoxyribonucleotides (found in DNA) or ribonucleotides (found in RNA). Each nucleotide consists of a sugar linked to a nitrogenous base and one, two, or three phosphate (PO+-) groups (Figure 1.3). PhffiFhat$ greup " A, T, C, 6 in 0NA and A, U, C, S in RNA. H in $NA {aooxyribose sugar} and OH in RNA (ribaBe $ugsr}. * ' Figure 1.3 General structure of a nucleotide.  f;hapt*n t: *lltA $truc*urs, Synih**is, a*d ffi*pair Deoxyribonucleotides differ from ribonucleotides primarily in the type of incorporated into the =,-:;,,,:i structure. Ribonucleotides contain ribose, whereas deoxyribonucleotides contain deoxyribose. In both types, each carbon is numbered 1'(1-prime)through 5'(S-prime). In nucleotides, a negativelycharged phosphate group is attached to the sugar at the 5'carbon, and a hydroxyl (OH) group is attached to the 3' carbon, as shown in Figure 1.3. The i,iiir-r,;;,rl ii:t:.1 t').:::::,::i is attached to the '1 ' carbon of the sugar. Nitrogenous bases may be either purines (containing two rings) or pyrimidines (containing one ring). Both DNA and RNA contain the purines adenine (A) and guanine (G), and the pyrimidine cytosine (C). However, DNA contains thymine (T) and RNA contains uracil (U), which are both pyrimidines. Nucleotides are the building blocks of nucleic acids, which are polymers composed of multiple nucleotide monomers linked together by covalent bonds (Figure 1.4). Linkages between nucleotides form when the 3'end of one nucleotide reacts with the 5'end of another. formino a dinucleotide. "9u. 9-':- u 5,--:. 3, 6-.cts - u' ,"'f" $l*.r. u,_g G 5'- -* 3, i.- ; 5,-*_. 3' -------+ S, A J Nucleotides Nucleic acid (RNA) Figure 1.4 Nucleotides join to form nucleic acids. The 3'end of the resulting dinucleotide can then react with the 5'end of another nucleotide to form a trinucleotide, and so on. This process can eventually lead to the formation of nucleic acids that contain thousands of individual nucleotides linked together by a repeating ;.ii,::::::," ,;ir,,:::,1.;:-r.'l:;::: :.::::i.ili.:i,*i';;:+. The linkage of nucleotides is the basis,for both DNA synthesis (replication) and RNA synthesis (transcription). 1.1.*3 Nr*lc$eim Aald $tnueture DNA is made up of two distinct nucleic acid strands that wrap around one another to form a double helix. The strands are aligned in an antiparallel direction, meaning that the 5'end of one strand aligns with the 3' end of the other strand. As shown in Figure 1.5, the double helix is arranged such that the sugar- phosphate backbone of each strand faces outward and the nitrogenous bases face the inside of the double helix, towards one another. Strands are Backbone antiparallel faces outward ' i'r*{I"'- 3.::... ; 1.. l.: :a: : i..,: r:r.r::;. _.iiji: ' :+:.lri.. ;d" i'';:iil t: ''.:,f t lt'r,,r,. Nitmgenous basesl. inward face -o'--, Figure 1.5 General structure of a DNA double helix.  Ch*pter 1: ilhiA $tt'ucture, $ynthesls, arid Ropair in the Each nitrogenous base in one strand of the double helix forms h'oriit*51*n [:'lr:-:*; with a base pair (ie, a purine pairs with a pyrimidine). The pairing of nitrogenous opposite sirand to produce a base bases is highly specific. tn DNA, adenine (A) always pairs with thymine (T), and guanine (G) always pairs G and C with cytosine iC) (f igure 1.6). Therefore, A and T bases should always be equal in number, and basesshould always be equal in number. This complementarity guides DNA replication. i{, (, Fyrimidines have a ' Purinen have a single-ringed structure double-ringed structure 0 \l\{:r'. * o=J-o. e t,; 'n--i,- [- | , '' ' ;"u J ffiy.-_'-* { ,l cr '*)^')? '** i s*p:il I '1i-l * ',' Y s! ^-,**i, --, *-*t,; ;1- *=i-o" ; ]W-.'_g{-- q,* -0_. I x 4o 'F,t*ti---'---s t 0--p:* i rfI s ,, 0 {"{ i-ll i:!-t I *,.l.. Y"o 'i' WW - o=p*O\ il 0 ,'=, /N*rj"r''." --t*"j:)'. -* l* n -* t T*v ll{Hr} I i f1 **$-u- 0- A_ ,* m/*-n'."* *T* s*N." \r., i\* T M i -*-i@o-J=o ' ryY- n**u:*'; 3' I -" / ,.i, "l-t*,{ ,l S, o *, I ^ Purines pair with pyrimidines, making width of DNA consiant A * Adenine; C* Cytosine; G* Guanine; T * Thymine' Figure 1.6 The pairing of nitrogenous bases is highly specific' acid Unlike DNA, which is made up of two nucleic acid strands, RNA is composed of a single nucleic strand. Both double- and single-stranded nucleic acids may exhibit complementary base pairing. For example, during ii;alr*i:iipti**, ribonucleotides in the growing mRNA strand pair with deoxyribonucleotides in the portion of the DNA strand being transcribed (see Lesson 2.2). The complementarity of this pairing is the same as in DNA, with the exception that A in the DNA strand pairs with uracil (U), instead of t in tne mRNA strand. During transcription, A in the RNA strand continues forms io pair with r in the DNA strand. RNA base pairing with itself occurs primarily when an RNA strand ii,,riiiljn by bringing complementary bases within the strand into proximity of one another. a loop called a  Chapt*r 1: DNA Structure, $ynthesis, ancl Repeir A fragment of DNA contains 157 adenine (A) bases and 225 guanine (G) bases. What is the total number of nucleotides present in this DNA fragment? fi Note: The appendix contains the answer. 1.1.S4 h!uclclc Aa:id [-'lyb ridiraticn mnd ffienmturati*n When two nucleic acid strands are joined in a double helix, they are said to be hybridized, or annealed. Within a cell, DNA not being used for replication or transcription is fully hybridized. However, for '.r:,::- to provide the replication or transcription to occur, portions of the DNA double helix must :;:.,,,:-, necessary enzymes and incoming nucleotides access to nitrogenous bases in the DNA. The process of separating hybridized DNA strands is known as ;'i,ir ':, Of melting. DNA can be denatured by enzymes or due to environmental factors such as high temperatures, pH levels well outside of physiological levels, and changes in salt concentrations. These environmental factors cause denaturation by disrupting hydrogen bonds and other interactions between bases. The temperature required to separate half of the double helices in a sample into single strands is referred to as the melting temperature In,' of the DNA being assessed (Figure 1.7). An increased number of hydrogen bonds between bases increases the stability of a double helix and therefore increases the I' for that double helix. Low temperature: ,{ll DNA hybridiead i#$',?$#,f*ffiS.b#q,id uX;#ti*{ 100% Half of the DNAstrands F ($ are denatured N r't,",f \.." tlr.,,rfllrr" ttoo,l"t',, High temperature; €, so"r" \o$!, All DNAdenat{.,rcd s t"lrfe! ti\*rfhn* o tt.r*ftt,rr "'.*l"ro,.s ',.../'.. '. t..uf '' ' )i"' "..f;" Temperature Figure 1.7 Effect of temperature on DNA hybridization' G-Cbasepairinginvolvesmore,r.i'r,,,,:,:;:.'.':.:thanA-TorA-Ubasepairing,soadoublehelixwitha higher percentage of G-C pairs tends to have a higher I, than a double helix with a lower percentage of G-C pairs. Similarly, longer double helices have more total intermolecular interactions than shorter helices with similar G-C levels, so longer double helices tend to have a higher I' than shorter helices. When denatured DNA strands in a solution are returned to temperatures well below their Im, the strands quickly reanneal. The speed with which reannealing occurs can be influenced by certain factors, includlng length of the DNA (ie, annealing takes longer when strands are longer), pH g.f the solution (ie, annealing takes less time when pH is near 7.4lie, physiological pH in most cell nucleil), and salt  eFrapt*r t: DNA $tructr-rre, Slnthesis, a*el NQ*{:air concentration of the solution (ie, annealing is more stable when cations in a salt interact with the negatively charged phosphate groups in DNA). These factors must be considered when optimizing conditions for molecular techniques that rely on DNA annealing and denaturation, such as PCR (see Concept4.1.02).