DNA and Protein Synthesis - Summary for Biology Students PDF PDF

Here is the conversion of the document/image into a structured markdown format: ### DNA replication: * DNA replicates semiconservatively. * The two strands of the DNA Parental molecule separate. * Each strand acts as a template for the synthesis of a new complementary strand. * The replicat...

Here is the conversion of the document/image into a structured markdown format: ### DNA replication: * DNA replicates semiconservatively. * The two strands of the DNA Parental molecule separate. * Each strand acts as a template for the synthesis of a new complementary strand. * The replicated double helix DNA consists of one old strand and one newly made strand. ### 10.1.1 DNA strand separation: * DNA replication begins at the origins of replication. * DNA Helicase binds to the origin of replication and breaks the hydrogen bonds. * DNA separates, unwinds, forming replication ‘bubble’ (has two replication forks). * Replication fork is formed at the junction of single and double-stranded regions. * Single-stranded binding proteins bind to single-stranded DNA which prevents reformation of the double helix. ### 7.1.2 Synthesis of RNA primer: * Both parental strands serve as templates for synthesizing new DNA strands. * Primase synthesizes RNA primer at a point where replication begins. * The synthesis occurs in the 5' to 3' direction. * Adds RNA nucleotides complementary to the DNA. * Forms RNA primer with 5 to 10 RNA nucleotides on both strands. ### 10.1.3 DNA synthesis in the 5' to 3' direction: * DNA polymerase III catalyzes the synthesis of new DNA by adding DNA nucleotides to the 3' end of an existing polynucleotide chain. * Catalyzes formation of phosphodiester linkage between DNA nucleotides. * New DNA strand is synthesized in the 5' to 3' direction. * DNA nucleotides added are complementary to the template strand (A-T, G-C). ### 10.1.4 Leading and lagging strands: * There are two types of new strands because DNA strands are antiparallel to each other, leading and lagging strands. * **Leading strand**: DNA nucleotides are added continuously, and the strand grows toward the fork (same direction as the helicase). * **Lagging strand**: DNA nucleotides are added discontinuously in the small segments called Okazaki fragments and grows away from the fork (opposite direction of the helicase). * Each segment is initiated by a separate RNA primer. ### 10.1.5 Replacement of RNA primer: * DNA polymerase I removes RNA nucleotides of the primer and replaces them with DNA nucleotides. ### 10.1.6 Ligation of DNA fragments: * DNA ligase joins Okazaki fragments of the lagging strand. * Forms phosphodiester linkages. * Two daughter DNA are formed and each consists of one old strand and one newly synthesized strand. ### 10.2 PROTEIN SYNTHESIS * Gene expression is the process by which DNA directs the synthesis of proteins (or, in some cases, just RNA). The expression of genes that code for proteins includes two stages: | DNA | Pre-mRNA | Mature RNA | | :----------- | :--------------- | :----------- | | Transcription | | Translation | | | Genetic information | Protein | ### 10.2.1 Transcription * "Goal form RNA". * Transcription is the synthesis of RNA using information in the DNA. * DNA double helix separated into: * Template/antisense/- strand → (Transcribed). * Coding/sense/ + strand → (Not transcribed). * RNA is synthesized in the 5' to 3' direction. * No RNA primer is needed. * Bacteria - single type of RNA polymerase. * Eukaryotes - three types: * RNA polymerase I synthesizes rRNA * M RNA polymerase II synthesizes mRNA * \+ RNA polymerase III synthesis tRNA * 3 stages in transcription: Initiation, Elongation, Termination * \*\* Initiation * The start point of initiation of transcription is the promoter. * The binding site of RNA polymerase on the template strand. * Transcription factors bind to the promoter, enabling the binding of RNA polymerase. * RNA polymerase does not need a primer. * RNA polymerase unwinds and separates the DNA helix. * \*\* Elongation * RNA polymerase moves along the template strand, unwinding the DNA. * Exposing 10-20 DNA nucleotides for pairing with RNA nucleotides. * Add ribonucleotides to the 3' end of RNA strands (complementary) to the template strand. * A in DNA pairs with U in RNA, C in DNA pairs with G in RNA, T in DNA pairs with A in RNA. * As RNA elongates, the earlier formed RNA strand separates from the DNA template strand. * DNA template strand rewinds and reforms the double helix. * \*\* Termination * RNA polymerase reaches 'stop' signal. * RNA-DNA hybrid within the transcription bubble separates. * DNA rewinds, and transcription stops. ### 10.2.2 Posttranscriptional Modification * For prokaryotes, the process of translation begins while transcription is in progress. * Can you explain why this occurs? * Prokaryotes do not membrane. * Both the bacterial DNA and ribosomes are located in the cytoplasm. * Eukaryotes have a nuclear membrane which separates the DNA and ribosomes. * The pre-mRNA produced must be modified before leaving the nucleus. * To prevent degradation of hydrolytic enzymes in the cytoplasm. * Posttranscriptional modification only occurs in the eukaryotes. * Before moving from the nucleus to the cytoplasm, each end of pre-mRNA is modified. *Alteration of MRNA ends * 5' caps: A modified form of a guanine (G) nucleotide is added onto the 5' end. * 3' poly-A tails: At the 3' end about 50-250 adenine nucleotides are added | | | | :----------------------------------------- | :------------------------------------------------ | | A modified guanine nucleotide added to | 50-250 adenine nucleotides added to the 3' end | | Region that includes protein-coding segment | Polyadenylation signal | | 5' Cap 5' UTR Start codon Stop codon 3'UTR | AAAAAA | **(b) RNA splicing** * Eukaryotic gene is made up of: * Exons -coding segments * Introns - non-coding segments * Initial transcription produces pre-mRNA transcript (contains both exons and introns). * Spliceosome cuts introns and joins the exons, forming shorter mature mRNA transcript. | Pre-mRNA | | | :----------- | :------- | | 5' Cap Intron | Intron 3 | | 1-30 | | | | Poly-A | | Introns cut out. Exons spliced together | | ### 10.2.3 THE GENETIC CODE * Code = 64 codons → language for protein synthesis. * Codon = sequence of 3 constitutive mRNA bases which specifies an amino acid or signal to start/terminate the poly-peptide chain. * Code is read continuously without ‘gaps’ separating the codons ### The genetic code: | | Second mRNA base | | | | | :---- | :--------------- | :---- | :---- | :---- | | | **U** | **C** | **A** | **G** | | **U** | UUU Phe | UCU | UAU Tyr | UGU Cys | | | UUC | UCC Ser | UAC | UGC | | **C** | CUU Leu | CCU | CAU His | CGU | | | CUC | CCC PRO | CAC | CGC Arg | | **A** | AUUAUC Ile | ACU | AAU Asn | AGU Ser | | | AUC | ACC Thr | AAC | AGC | | **G** | GUUGUC val | GCU | GAU Asp | GGU | | | GUC | GCC Ala | GAC | GGC Cly | * Genetic code is degenerate. * More than one codon may specify a particular amino acid. * No codon specifies more than one amino acid. * Example: Leucine- CUU, CUC, CUA, CUG, UUA & UUG. * Certain Condons are: * 'start: signal for initiation of polypeptide chain-AUG. *(codes for methionine) =start codon. *'Stop' signal for termination of polypeptide chain UAA, UAG, & UGA. *= stop/non-sense codons. * The genetic code is nearly universal, sheared by the simplest bacteria and the most complex animals. * Genes can be transcribed and translated after being transplanted from one species to another. ## 10.2.4 Translation * Translation is the synthesis of polypeptide using the genetic information encoded in an mRNA molecule. * There is a change of "Language" from nucleotides to amino acids. * The translator of the "language" is carried out by tRNA at the ribosome. ### 10.2.4.1 Structure and Function of Ribosome * Ribosome provides site for assembly of polypeptides * Rimosome: * Consists of large and small subunits * Made of rRNA and protein * 3 sites for protein synthesis- P, A, & E sites * A ribosome has: * An mRNA binding site * Three tRNA binding sites, known as be E, P, and A sites (this sequence) #### 10.2.4.2 STUCTURE AND FUNCTION OF tRNA *Transfer RNA (tRNA) * Transfer an amino acid from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome. * One end has an anticodon- sequence of 3 nucleotides complementary to codon of mRNA. * At the opposite end, a specific anino acid is added by actruating enzymes called amineacyl -tRNA synthetase. * Specific amino acid binds to 3' end of tRNA by covalent bond ( Aminoacy) tRNA complex mino and FRNA *No tRNA with anticodon complementary to nonsense codon. ### 10.2.4.3 Process of Translation * There are 3 stages in translation: * Initiation * Elongation * Termination * Initiation * MRNA. Mall + large rubunits, TRNA spuitar amino acid. * The small ribosomal subunits bind to the mRNA at the AUG start codon. \* The initiator tRNA or methionine - tRNA (I RNAmet) with Anticodon UNC binds to the start codon (AUG) an mRMA. \* The large ribosomal subunits binds to the small Subunit (b) Elongation: * 2nd TRna * with Complementary Anticodon and attched amino acid binds and ASITE * Peptidy transterase * Breaks bond between * the amino acid and IRNA and Asite by beotide bond * 1 is empty 2nd has amino aids * Translocation * Ribsome mones one codon 3-6 * ISTIRNA * istina is shified too esit 2nd INA shified to P'SITE * A'site is empty * 2rd is bound to a site * beotid transterase * breaks bond of all holding 2nd * Amino of Acid2 and INA * attches it to amino acide * then 3rd amino acid * trans is empty then RNA has three amino acides. * Ribbone means one codon. * shirfts 1st IRNA - Everything dissacrates (c) Termunation: * Release factor binds to stop cordon at (a site)s releases facts * Prondytes and other compostions. * The process is repeated and over and over. ## 10. 2.5 DIFFERENCES OF GENE EXPRESSION BETWEEN PROKARYOTES AND EUKARYOTES | | | | :------------------------------------------ | :----------------------------------------- | | PROKARYOTE gene expression | EUKARYOTE gene expression | | Rna is translated as soon as it is transcribed | must be transported out of Nucleus for | | translation | gene contain introns | | Doesn’t contain introns | before Translation | Modified before Translation | | ### 10.3.1 GENE EXPRESSION * Genes or Regulatory are only genes that are directly needed or are transcribed. * Genes can cause Protein constitutive (meaning causes)Genes E-Genes for Elicitic Genes) enzyme. * are directed to proudce or stop Proudcing, that is * Orgenes expressible for genes or is called A**OPERON(E** **Operon (Lactase inducible** * that are only neadeed IRNA trasumbers * are is aunit of genetic functions. found in (bacteria and pages) in promolter. A specifis nucliode sequence * are Dna where Rna polymasrase binds. * and iniliatescription openates. Suitch that controls tramscription - of Structural gene ### 10.3.2 Inducible Operon: * Usually on switched off (for repression) **Ex-lack operon** * It means * genes only neaded IRNA trasumbers #### When fed with glucose and lactas, E Coil uses all up the glucoses first then its finish, it will take a lactas.