Bio 2.1-2.2.PDF

Chapter 2: Gene Expression Lesson 2.1 The Central Dogma of Molecular Biology lntroduction As presented in Chapter 1, the information needed for an organism's development and vital processes is stored in its genetic code (DNA), and the transmission of genetic information from one generation to the...

Chapter 2: Gene Expression Lesson 2.1 The Central Dogma of Molecular Biology lntroduction As presented in Chapter 1, the information needed for an organism's development and vital processes is stored in its genetic code (DNA), and the transmission of genetic information from one generation to the next cannot proceed without DNA replication. However, the expression of an organism's genetic code is dependent on the flow of information from DNA to RNA to proteins, mediated by the processes of transcription and translation. This lesson provides an overview of the mechanism by which genes are expressed, otherwise known as the central dogma of molecular biology. The expression of genes is the highly regulated manifestbtion of a set of genetic instructions (DNA) into a physical form. lt is the link between the genetic code of an organism (its genotype) and the organism's physical and biochemical attributes (its phenotype), as illustrated in Figure 2.1. Genotype Phenotype *l** "/ --u%u & '.w" Gene ,@" - exprossron 1ir-:'rci., "'o' 3' Genetic code (DNA) Figure 2.1 An organism's physical and biochemical attributes are a consequence of gene expression. The central dogma of molecular biology explains how genetic information, stored as DNA, is used to regulate the synthesis of proteins (polypeptides). ln turn, the proteins made using this genetic information control the activities of the cell and organism. 2.1.02 Gene Expression According to the central dogma of molecular biology, gene expression can be divided into two stages: transcription and translation (Figure 2.2). During transcription, information stored in DNA is copied, or transcribed, into a more mobile form known as RNA. lr4Lrltiple types of RNA are involved in gene expression, but only messenger RNA (mRNA) contains the information needed to synthesize a protein via translation. During translation, a ribosome and two other forms of RNA (transfer RNA IIRNA] and ribosomal RNA [rRNA]) are used to decode the information in mRNA, resulting in a protein product.  Chapter 2: Gene ExPression Transcription : The central dogma t,i!$ of molecular biologY , ,,'1 ,,1 Translation.li' Figure 2.2 The central dogma of molecular biology. of one protein In general, the information encoded in an individual mRNA results in the synthesis (piypeptide), consisting of a single chain of amino acids. However, some proteins consist of multiple associaieO polypeptide-chains (subunits), which may be derived from more than one gene. Each unique protein subuniiis translated from its own mRNA, associating with additional subunits once translation is complete. The basic mechanisms of transcription and translation are the same in all organisms. In eukaryotic occurs first, organisms, transcription and translation are separated in both space and time. Transcription in the nucleus, and translation occurs later, outside of the nucleus. One important difference between prokaryotic and eukaryotic gene expression is that prokaryotrc organisms generally do not have membiane-bound organelles, so DNA is not separated from the rest of the cell in a nucleus' focuses on While prokaryotic and eukaryotic gene expression have many similarities, this chapter about prokaryotic gene regulation is eukaryotic gene expression and regulation. Additional information presented in ConcePt 6.3.05.  Chapter 2: Gene Expression I aqclnn 9 ? Transcription Introduction Genomic DNA can be classified based on characteristics such as nucleotide composition, sequence structure, and coding potential (ie, whether a region of DNA contains information for generating a product). Only a small fraction of eukaryotic DNA contains coding information, giving rise to different types of RNA (eg, mRNA, rRNA, IRNA). While alltypes of RNA may be created via transcription, this lesson focuses on the transcription of mRNA, which is the only type of RNA that contains the information needed to synthesize proteins. 2.2.01 Mechanism of Transcription The process of gene expression (ie, DNA ) mRNA ) protein) begins when the cell receives signals indicating that transcription should take place. Because the majority of DNA is noncoding, certain boundaries exist that define a transcription unit (ie, where a coding region begins and ends). These boundaries are marked by specific sequences of nucleotides called promoters and terminators, which identify where transcription should begin and end, respectively (Figure 2.3). The promoter and the DNA sequences before the transcription unit are considered upstream, and the region to be transcribed is considered downstream. These terms also describe the position of nucleotides within a tran'scription unit. For example, the terminator is downstream of the coding region. Transcription unit Promoter Gene Terminator 5' 3' 5' Transcription start site Figure 2.3 A transcription unit. Transcription is similar to DNA replication (see Lesson 1.2) in that the enzyme that synthesizes mRNA molecules (RNA polymerase ll) can assemble nucleotides in the 5't 3'direction only. However, unlike DNA polymerase lll, RNA polymerase ll does not need a primerto begin assembling nucleotides. Transcription occurs in three broad stages: initiation, elongation, and termination. Initiation begins with the recognition of the promoter sequence, which is generally located approximately 25-50 nucleotides upstream of the transcription start site (Figure 2.4). A transcription initiation complex is formed when RNA polymerase ll and other regulatory proteins known as general (basal) transcription factors bind to a specific nucleotide sequence called the promoter. There are a variety of promoter sequences, but the most well-known is the TATA box, which consists of a sequence of thymine (T) and adenine (A) nucleotides. Once the transcription machinery is assembled at the promoter, RNA polymerase ll unwinds the DNA helix and transcription begins at the transcription start site. One strand is known as the"coding (sense) strand (5'> 3'), and the other is the noncoding (antisense) strand (3') 5').  Chapter 2: Gene Expression General transcription factors RNA polymerase ll { a Promoter Terminator Transcription start site Transcription initiation complex Figure 2.4 Transcription initiation. During elongation, the noncoding DNA strand (ie, the 3't 5'DNA strand) is used as a template to build the mRNA molecule, as shown in Figure 2.5. The mRNA transcript is synthesized in the 5' ) 3'direction by RNA polymerase ll through complementary base pairing with the noncoding DNA strand. Accordingly, the DNA coding strand has a similar sequence and directionality (5' ) 3') as the newly synthesized mRNA transcript, except that the mRNA transcript has uracil (U) nucleotides where the DNA has thymine (T) nucleotides. As RNA polymerase ll progresses along the temi:late strand, the DNA double helix reforms behind the enzyme, and multiple RNA polymerase ll molecules can transcribe a single gene at the same time. 30  Chapter 2. Gene Hxpression polymerase ll Coding DNA strand Noncoding DNA strand c' mRNA strand -t) Direction of transcription Figure 2.5 Transcription elongation. Termination of transcription occurs when the transcription complex reaches the terminator sequence in the DNA (Figure 2.6). In prokaryotes, the mRNA transcript then detaches from the DNA and is available for translation with no further modification. In eukaryotes, RNA polymerase ll transcribes a sequence in the DNA known as the polyadenylation signal sequence (3'-TTATTT-5'), which is then bound by proteins that separate the mRNA transcript from RNA polymerase ll. At this time, the mRNA transcript is considered pre-mRNA (ie, primary transcript) and must undergo further processing before it can be exported from the nucleus as a mature mRNA transcript. Promoter Gene Terminator *,,mfi itrfry **^" Cod g A stra nd...,."--,Aii j\ a\js.E i n DN r ** 2' 3' *.,ryff fFAf,Agn-*NoncodingDNAstrand-.-*,.r;;r1ni'Tu..,..."- Pre-mRNA transcript Transcription is released machinery t dissociates *-.e*' ***f11**' 3. 5, *--** PolYadenYlation signal sequence General lt',f : transcription factors RNA polymerase ll Figure 2.6 Transcription termination. JI  Chapter 2: Gene HxPression 2.2.A2 Modifications to mRNA Ends eukaryotic while prokaryotic mRNA is immediately available for translation once transcription is complete, pre-mRNA must undergo certain modifications before it can be exported from the nucleus and translated' in Figure 2'7' Modifications to both eiOs of pre-mRNA are the first steps in RNA processing, shown of a 5'cap, The 5,end of pre-mRNA is modified almost immediately after it is transcribed with the addition which is a modified guanosine triphosphate (GTP) nucleotide (7-methylguanoslne [rntG]). This 5'cap is recognized by the ribosome during translation and prevents degradation of mRNA in the cytoplasm' When transcription is complete, a chain of adenine nucleotides known as the poly'A tail is added to the 3,end of mRNA, direcfly downstream of the transcribed polyadenylation signal sequence' Like the 5'cap, ln addition, the poly-A tail facilitates export of the poly-A tail also funclions to prevent mRNA degradation. mature mRNA from the nucleus to the cytoplasm' Pre-mRNA r-T-l a Polyadenylation 5'cap mRNAend. processlng.,, ,j! signalsequence ,{W Poly-Atail ,J$f'G. ffi ry l \.u, 3' t/ c Figure 2.7 5' and 3'mRNA end processing' 2.2.03 RNA SPlicihg Mechanisms In eukaryotes, gene structure is considerably more complex than in prokaryotes. The vast majority of DNA in eut