Human Genome PDF 2024

Human Genome Dr. Madona Akhobadze 2024 Gene Structure and Function. Information Content of the Human Genome. The Central Dogma: DNA → RNA → Protein. Gene Organization and Structure, Fundamentals of Gene Expression. Gene Regulation and Changes in A...

Human Genome Dr. Madona Akhobadze 2024 Gene Structure and Function. Information Content of the Human Genome. The Central Dogma: DNA → RNA → Protein. Gene Organization and Structure, Fundamentals of Gene Expression. Gene Regulation and Changes in Activity of the Genome. Variation in Gene Expression and its Relevance to Medicine Reading: Ch. 11 - Principles of Genetics, by Snustad & Simmons Ch. 3 - Thompson & Thompson Genetics in Medicine, Robert L. Nussbaum,Roderick R. McInnes  GENOME CONTAINS ABOUT 20 000 - 25 000 PROTEIN-CODING GENES PRODUCT OF MOST GENES IS A PROTEIN  3-BILLION-LETTER DIGITAL CODE HUMAN ANATOMY, PHYSIOLOGY, AND BIOCHEMISTRY INFORMATION MOVES FROM GENES IN THE GENOME TO PROTEINS OF THE PROTEOME THAT ORCHESTRATE THE MANY FUNCTIONS OF CELLS, ORGANS, AND THE ENTIRE ORGANISM  1. MANY GENES ARE CAPABLE OF GENERATING MULTIPLE DIFFERENT PROTEINS, NOT JUST ONE 2. INDIVIDUAL PROTEINS DO NOT FUNCTION BY THEMSELVES COMBINATORIAL NATURE OF GENE NETWORKS RESULTS IN AN EVEN GREATER DIVERSITY OF POSSIBLE CELLULAR FUNCTIONS  GENES ARE LOCATED THROUGHOUT THE GENOME CLUSTER IN SOME REGIONS AND ON SOME CHROMOSOMES CHROMOSOME 11 GENE-RICH CHROMOSOME WITH ABOUT 1300 PROTEIN-CODING GENES  THE HUMAN GENOME AND ITS CHROMOSOMES The genome contained in the nucleus of human somatic cells consists of 46 chromosomes, arranged in 23 pairs Of those 23 pairs, 22 are alike in males and females and are called autosomes, numbered from the largest to the smallest. The remaining pair comprises the sex chromosomes: two X chromosomes in females and an X and a Y chromosome in males.  GENES LOCATED ON THE AUTOSOMES TWO COPIES OF EACH GENE BOTH COPIES ARE EXPRESSED AND GENERATE A PRODUCT  FUNCTIONS OF THE GENETIC MATERIAL THE GENETIC MATERIAL MUST REPLICATE, CONTROL THE GROWTH AND DEVELOPMENT OF THE ORGANISM, AND ALLOW THE ORGANISM TO ADAPT TO CHANGES IN THE ENVIRONMENT THE CENTRAL DOGMA: DNA → RNA → PROTEIN  THREE ESSENTIAL FUNCTIONS: 1. THE GENOTYPIC FUNCTION, REPLICATION. THE GENETIC MATERIAL MUST STORE GENETIC INFORMATION AND ACCURATELY TRANSMIT THAT INFORMATION FROM PARENTS TO OFFSPRING, GENERATION AFTER GENERATION. 2. THE PHENOTYPIC FUNCTION, GENE EXPRESSION. THE GENETIC MATERIAL MUST CONTROL THE DEVELOPMENT OF THE PHENOTYPE OF THE ORGANISM. THAT IS, THE GENETIC MATERIAL MUST DICTATE THE GROWTH OF THE ORGANISM FROM THE SINGLE-CELLED ZYGOTE TO THE MATURE ADULT. 3. THE EVOLUTIONARY FUNCTION, MUTATION. THE GENETIC MATERIAL MUST UNDERGO CHANGES TO PRODUCE VARIATIONS THAT ALLOW ORGANISMS TO ADAPT TO MODIFICATIONS IN THE ENVIRONMENT SO THAT EVOLUTION CAN OCCUR. TRANSFER OF GENETIC INFORMATION: THE CENTRAL DOGMA The central dogma of biology is that information stored in DNA is transferred to RNA molecules during transcription and to proteins during translation. According to the central dogma of molecular biology, genetic information usually flows (1) from DNA to DNA during its transmission from generation to generation and (2) from DNA to protein during its phenotypic expression in an organism During the replication of RNA viruses, information is also transmitted from RNA to RNA.  THE TRANSFER OF GENETIC INFORMATION FROM DNA TO PROTEIN INVOLVES TWO STEPS: (1) transcription, the transfer of the genetic information from DNA to RNA (2) translation, the transfer of information from RNA to protein. the transfer of genetic information from DNA to RNA is sometimes reversible, whereas the transfer of information from RNA to protein is always irreversible ribonucleic acid (RNA) Messenger RNA (mRNA) Ribosomal RNA (rRNA) Transfer RNA (tRNA) Genetic Code FIVE TYPES OF RNA MOLECULES Messenger RNAs, the intermediaries that carry genetic information from DNA to the ribosomes where proteins are synthesized. Transfer RNAs (tRNAs) are small RNA molecules that function as adaptors between amino acids and the codons in mRNA during translation. Ribosomal RNAs (rRNAs) are structural and catalytic components of the ribosomes, the intricate machines that translate nucleotide sequences of mRNAs into amino acid sequences of polypeptides. Small nuclear RNAs (snRNAs) are structural components of spliceosomes, the nuclear organelles that excise introns from gene transcripts. Micro RNAs (miRNAs) are short 20- to 22-nucleotide single-stranded RNAs that are cleaved from small hairpin-shaped precursors and block the expression of complementary or partially complementary mRNAs by either causing their degradation or repressing their translation. All five types of RNA—mRNA, tRNA, rRNA, snRNA, and miRNA—are produced by transcription. Unlike mRNAs, which specify polypeptides, the final products of tRNA, rRNA, snRNA, and miRNA genes are RNA molecules. Transfer RNA, ribosomal RNA, snRNA, and miRNA molecules are not translated. GENE ORGANIZATION AND STRUCTURE During transcription, one strand of DNA of a gene is used as a template to synthesize a complementary strand of RNA, called the gene transcript - 3′ to 5′ transcribed template strand of DNA noncoding, antisense strand 5′ to 3′ strand of nontranscribed DNA is sometimes called the coding, or sense DNA strand TRANSFER OF GENETIC INFORMATION: THE CENTRAL DOGMA During the replication of RNA viruses, information is also transmitted from RNA to RNA. The transfer of genetic information from DNA to protein involves two steps: (1) transcription, the transfer of the genetic information from DNA to RNA, and (2) translation, the transfer of information from RNA to protein. TRANSFER OF GENETIC INFORMATION: THE CENTRAL DOGMA In addition, genetic information flows from RNA to DNA during the conversion of the genomes of RNA tumor viruses to their DNA proviral forms Thus, the transfer of genetic information from DNA to RNA is sometimes reversible, whereas the transfer of information from RNA to protein is always irreversible. During translation, the sequence of nucleotides in the RNA transcript is converted into the sequence of amino acids in the polypeptide gene product. This conversion is governed by the genetic code, the specification of amino acids by nucleotide triplets called codons in the gene transcript  PROPERTIES OF THE GENETIC CODE 1. The genetic code is composed of nucleotide triplets. Three nucleotides in mRNA specify one amino acid in the polypeptide product; each codon contains three nucleotides. PROPERTIES OF THE GENETIC CODE 2. The genetic code is nonoverlapping. Each nucleotide in mRNA belongs to just one codon except in rare cases where genes overlap and a nucleotide sequence is read in two different reading frames. PROPERTIES OF THE GENETIC CODE 3. The genetic code is comma-free There are no commas or other forms of punctuation within the coding regions of mRNA molecules. During translation, the codons are read consecutively.  PROPERTIES OF THE GENETIC CODE 4. The genetic code is degenerate All but two of the amino acids are specified by more than one codon. PROPERTIES OF THE GENETIC CODE 5. The genetic code is ordered. Multiple codons for a given amino acid and codons for amino acids with similar chemical properties are closely related, usually differing by a single nucleotide. PROPERTIES OF THE GENETIC CODE 6. The genetic code contains start and stop codons. Specific codons are used to initiate and to terminate polypeptide chains.  PROPERTIES OF THE GENETIC CODE 7. The genetic code is nearly universal. With minor exceptions, the codons have the same meaning in all living organisms, from viruses to humans. The RNA molecules that are translated on ribosomes are called messenger RNAs (mRNAs). In prokaryotes, the product of transcription, the primary transcript, usually is equivalent to the mRNA molecule In eukaryotes, primary transcripts often must be processed by the excision of specific sequences and the modification of both termini before they can be translated. So, primary transcripts usually are precursors to mRNAs and, as such, are called pre-mRNAs. Most of the nuclear genes in higher eukaryotes and some in lower eukaryotes contain noncoding sequences called introns that separate the expressed sequences or exons of these genes. The entire sequences of these split genes are transcribed into pre-mRNAs, and the noncoding intron sequences are subsequently removed by splicing reactions carried out on macromolecular structures called spliceosomes In eukaryotes, primary transcripts often must be processed by the excision of specific noncoding sequences - introns and the modification of both termini before they can be translated. So, primary transcripts usually are precursors to mRNAs and, as such, are called pre-mRNAs. EUKARYOTIC GENE EXPRESSION the primary transcripts or pre-mRNAs often must be processed by the excision of introns and the addition of 5 7-methyl guanosine caps (CAP) and 3 poly(A) tails (A)n. In addition, eukaryotic mRNAs must be transported from the nucleus to the cytoplasm where they are translated. KEY POINTS The central dogma of molecular biology is that genetic information flows from DNA to DNA during chromosome replication, from DNA to RNA during transcription, and from RNA to protein during translation. Transcription involves the synthesis of an RNA transcript complementary to one strand of DNA of a gene. Translation is the conversion of information stored in the sequence of nucleotides in the RNA transcript into the sequence of amino acids in the polypeptide gene product, according to the specifications of the genetic code. THE PROCESS OF GENE EXPRESSION Information stored in the nucleotide sequences of genes is translated into the amino acid sequences of proteins through unstable intermediaries called messenger RNAs. GENE ORGANIZATION AND STRUCTURE Translation takes place on intricate macromolecular machines called ribosomes, which are composed of three to five RNA molecules and 50 to 90 different proteins AN MRNA INTERMEDIARY The genetic information stored in the sequences of nucleotide pairs in genes must somehow be transferred to the sites of protein synthesis in the cytoplasm. Messengers are needed to transfer genetic information from the nucleus to the cytoplasm. Although the need for such messengers is most obvious in eukaryotes, the first evidence for their existence came from studies of prokaryotes. GENERAL FEATURES OF RNA SYNTHESIS RNA synthesis occurs by a mechanism that is similar to that of DNA synthesis Except: (1) the precursors are ribonucleoside triphosphates rather than deoxyribonucleoside triphosphates, (2) only one strand of DNA is used as a template for the synthesis of a complementary RNA chain in any given region, and (3) RNA chains can be initiated de novo, without any requirement for a preexisting primer strand. RNA SYNTHESIS The RNA molecule produced will be complementary and antiparallel to the DNA template strand and identical, except that uridine(U) residues replace thymidines(T), to the DNA nontemplate strand If the RNA molecule is an mRNA, it will specify amino acids in the protein gene product. They are also called sense strands of RNA because their nucleotide sequences “make sense” in that they specify sequences of amino acids in the protein gene products. An RNA molecule that is complementary to an mRNA is referred to as antisense RNA. Most of the nuclear genes in higher eukaryotes and some in lower eukaryotes contain noncoding sequences called introns that separate the expressed sequences or exons of these genes. The entire sequences of these split genes are transcribed into pre-mRNAs, and the noncoding intron sequences are subsequently removed by splicing reactions carried out on macromolecular structures called spliceosomes RNA SYNTHESIS The synthesis of RNA chains, like DNA chains, occurs in the 5 → 3 direction, with the addition of ribonucleotides to the 3-hydroxyl group at the end of the chain The reaction involves a nucleophilic attack by the 3-OH on the nucleotidyl (interior) phosphorus atom of the ribonucleoside triphosphate precursor with the elimination of pyrophosphate, just as in DNA synthesis. This reaction is catalyzed by enzymes called RNA polymerases. The process of transcription can be divided into three stages: (1) initiation of a new RNA chain, (2) elongation of the chain, and (3) termination of transcription and release of the nascent RNA molecule INITIATION OF RNA CHAINS involves three steps: (1) binding of the RNA polymerase holoenzyme to a promoter region in DNA; (2) the localized unwinding of the two strands of DNA by RNA polymerase, providing a template strand free to base-pair with incoming ribonucleotides; and (3) the formation of phosphodiester bonds between the first few ribonucleotides in the nascent RNA chain. The midpoints of the two conserved sequences occur at about 10 and 35 nucleotide pairs, respectively, before the transcription-initiation site Thus they are called the --10 sequence and the --35 sequence The nucleotide sequences that are present in such conserved genetic elements most often are called consensus sequences The sigma subunit initially recognizes and binds to the --35 sequence; thus, this sequence is sometimes called the recognition sequence. Nucleotide sequences preceding the initiation site are referred to as upstream sequences; those following the initiation site are called downstream sequences. Other promoters that are recognized by RNA polymerase II contain some, but not all, of these components. The conserved element closest to the transcription start site (position 1) is called the TATA box. it has the consensus sequence TATAAAA (reading 5 to 3 on the nontemplate strand) and is centered at about position 30. The TATA box plays an important role in positioning the transcription startpoint. The second conserved element is called the CAAT box; it usually occurs near position 80 and has the consensus sequence GGCCAATCT. RNA PROCESSING IN EUKARYOTES The nucleotide sequences of some RNA transcripts are modified posttranscriptionally by RNA editing RNA transcripts undergo three important modifications, including: 1. the excision of noncoding sequences called introns. 2. RNA CHAIN ELONGATION AND THE ADDITION OF 5 METHYL GUANOSINE CAPS Once eukaryotic RNA polymerases have been released from their initiation complexes, they catalyze RNA chain elongation by the same mechanism as the RNA polymerases of prokaryotes 3. CHAIN CLEAVAGE AND THE ADDITION OF 3 POLY(A) TAILS The 3’ ends of RNA transcripts synthesized by RNA polymerase II are produced by endonucleolytic cleavage of the primary transcripts rather than by the termination of transcription After cleavage, the enzyme poly(A) polymerase adds poly(A) tails, tracts of adenosine monophosphate residues about 200 nucleotides long, to the 3’ ends of the transcripts The addition of poly(A) tails to eukaryotic mRNAs is called polyadenylation ELONGATION OF RNA CHAINS Elongation of RNA chains is catalyzed by the RNA polymerase core enzyme, after the release of the subunit. The covalent extension of RNA chains takes place within the transcription bubble, a locally unwound segment of DNA. The RNA polymerase molecule contains both DNA unwinding and DNA rewinding activities. RNA polymerase continuously unwinds the DNA double helix ahead of the polymerization site and rewinds the complementary DNA strands behind the polymerization site as it moves along the double helix TERMINATION OF RNA CHAINS Termination of RNA chains occurs when RNA polymerase encounters a termination signal. When it does, the transcription complex dissociates, releasing the nascent RNA molecule. There are two types of transcription terminators in E. coli. One type results in termination only in the presence of a protein called rho; such termination sequences are called rhodependent terminators. The other type results in the termination of transcription without the involvement of rho; such sequences are called rho-independent terminators KEY POINTS RNA synthesis occurs in three stages: (1) initiation, (2) elongation, and (3) termination. RNA polymerases—the enzymes that catalyze transcription—are complex multimeric proteins. The covalent extension of RNA chains occurs within locally unwound segments of DNA. Chain elongation stops when RNA polymerase encounters a transcription–termination signal. Transcription, translation, and degradation of mRNA molecules often occur simultaneously in prokaryotes. INITIATION OF RNA CHAINS The initiation of transcription by RNA polymerase II requires the assistance of several basal transcription factors. Still other transcription factors and regulatory sequences called enhancers and silencers modulate the efficiency of initiation Each basal transcription factor is denoted TFIIX (Transcription Factor X for RNA polymerase II, where X is a letter identifying the individual factor). RNA CHAIN ELONGATION AND THE ADDITION OF 5 METHYL GUANOSINE CAPS Once eukaryotic RNA polymerases have been released from their initiation complexes, they catalyze RNA chain elongation by the same mechanism as the RNA polymerases of prokaryotes TERMINATION BY CHAIN CLEAVAGE AND THE ADDITION OF 3 POLY(A) TAILS The 3’ ends of RNA transcripts synthesized by RNA polymerase II are produced by endonucleolytic cleavage of the primary transcripts rather than by the termination of transcription After cleavage, the enzyme poly(A) polymerase adds poly(A) tails, tracts of adenosine monophosphate residues about 200 nucleotides long, to the 3’ ends of the transcripts The addition of poly(A) tails to eukaryotic mRNAs is called polyadenylation KEY POINTS Three to five different RNA polymerases are present in eukaryotes, and each polymerase transcribes a distinct set of genes. Eukaryotic gene transcripts usually undergo three major modifications: (1) the addition of 7-methyl guanosine caps to 5 termini, (2) the addition of poly(A) tails to 3 ends, and (3) the excision of noncoding intron sequences. The information content of some eukaryotic transcripts is altered by RNA editing, which changes the nucleotide sequences of transcripts prior to their translation. INTERRUPTED GENES IN EUKARYOTES: EXONS AND INTRONS Most eukaryotic genes contain noncoding sequences called introns that interrupt the coding sequences, or exons. The introns are excised from RNA transcripts prior to their transport to the cytoplasm. Noncoding sequences intervening between coding sequences. They were subsequently found in the nontranslated regions of some genes. They are called introns (for intervening sequences.) The sequences that remain present in mature mRNA molecules (both coding and noncoding sequences) are called exons (for expressed sequences). INTRONS: BIOLOGICAL SIGNIFICANCE? variable in size, ranging from about 50 nucleotide pairs to thousands of nucleotide pairs in length. This fact has led to speculation that introns may play a role in regulating gene expression. Although it is unclear how introns regulate gene expression, new research has shown that some introns contain sequences that can regulate gene expression in either a positive or negative fashion. introns may provide a selective advantage by increasing the rate at which coding sequences in different exons of a gene can reassort by recombination, thus speeding up the process of evolution KEY POINTS Most, but not all, eukaryotic genes are split into coding sequences called exons and noncoding sequences called introns. Some genes contain very large introns; others harbor large numbers of small introns. The biological significance of introns is still open to debate. REMOVAL OF INTRON SEQUENCES BY RNA SPLICING The noncoding introns are excised from gene transcripts by several different mechanisms For genes that encode proteins, the splicing mechanism must be precise; it must join exon sequences with accuracy to the single nucleotide to assure that codons in exons distal to introns are read correctly require precise splicing signals, presumably nucleotide sequences within introns and at the exon–intron junctions. splicing and intron sequences can influence gene expression mutations at these sites are sometimes responsible for inherited diseases in humans, such as hemoglobin disorders. three distinct types of intron excision from RNA transcripts: 1. The introns of tRNA precursors are excised by precise endonucleolytic cleavage and ligation reactions catalyzed by special splicing endonuclease and ligase activities. 2. The introns of some rRNA precursors are removed autocatalytically in a unique reaction mediated by the RNA molecule itself. (No protein enzymatic activity is involved.) 3. The introns of nuclear pre-mRNA (hnRNA) transcripts are spliced out in two-step reactions carried out by complex ribonucleoprotein particles called spliceosomes. protein folding involves interactions with proteins called chaperones that help nascent polypeptides form the proper three-dimensional structure. The two most common types of secondary structure in proteins are alpha-helices and beta-sheets გმადლობთ , ყურადღებისთვის !!!