Indwiani Astuti Dept of Pharmacology & Therapy Fac of Medicine Universitas Gadjah Mada
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DNA
Deoxyribonucleic Acid Double helix Carries genetic information Located in the nucleus The monomer is a nucleotide
A phosphate A ribose sugar A nitrogenous base
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Genes are located on the chromosomes which are found in the nucleus of a cell. When a cell is undergoing cell reproduction, the chromosomes are visible. Chromosomes appear when the chromatin condenses and become visible. Most of the time (90%) the genetic material in the form of chromatin. A genome is the complete genetic information contained in an individual.
(gene + chromosome)
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post-translational modifications of histone tails: control compaction of DNA and serve as docking sites for trans-acting factors
Range: Can act at the level of a single gene, often acts over groups of genes and over larger domains (20-200kb), and can affect gene expression over an entire chromosome
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Protein degradation
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cis-acting factors: promoters/regulatory sequences of genes trans-acting factors: proteins and RNAs that bind cis-elements and promote or repress gene expression DNA methylation: methylation of CpG islands promotes silencing
Range: Usually functions at level of single gene, or at most a local group of genes
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Gene expression takes place differently in prokaryotes and eukaryotes. What is a prokaryotes? Eukaryotes?
Prokaryotes
No membrane bound organelles (nucleus) More primitive organisms Only one circular chromosome Bacteria are the only organisms that are prokaryotes.
Eukaryotes
Membrane bound organelles ( specialize in function nucleus, mitochondria, chloroplast) Chromosomes are in pairs and not circular All organisms that are not bacteria: protist, fungi, plants and animals
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Translation converts the information in mRNA into the amino acid sequence of a protein using ribosomes, large complexes of rRNAs and proteins.
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In Eukaryotes, following mitosis or meiosis, DNA recoils but certain regions remain relaxed for transcription. The areas of relaxed DNA are called euchromatin.
Transcription is the Reading of the DNA and Changing the code to mRNA. Translation is changing The mRNA into a trait by Using tRNA to interpret the mRNA (The synthesis of a polypeptide chain using the genetic code on the mRNA molecule as its guide).
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DNA in eukaryotes has regions of coding and noncoding DNA. The regions of DNA that code for proteins or traits are called EXONS, while the regions that do not code for proteins are called INTRONS.
cytoplasm cytoplasm
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Eukaryotic Transcription
General transcription factors bind to the promoter region of the gene. RNA polymerase II then binds to the promoter to begin transcription at the start site (+1). Enhancers are DNA sequences to which specific transcription factors (activators) bind to increase the rate of transcription.
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GU at 5 end of intron
AG at 3 end of intron
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Eukaryotic Transcription
Coactivators and mediators are also required for the function of transcription factors.
coactivators and mediators bind to transcription factors and bind to other parts of the transcription apparatus
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Enhancer Control
Eukaryote genes on a DNA strand also have noncoding control sequences that facilitate transcription. These are called enhancers. Transcription factors are additional proteins that bind to RNA polymerase and enhancers to help with transcription.
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In prokayotes, transcription and translation occur in the cytoplasm. In eukaryotes, transcription occurs inside the nucleus in a two step sequence of events.
Pre-mRNA includes both introns and exons for the gene. mRNA is only the coding portion (exons).
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Types
Messenger RNA (mRNA) <5% Ribosomal RNA (rRNA) Up to 80% Transfer RNA (tRNA) About 15% In eukaryotes small nuclear ribonucleoproteins (snRNP)
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mRNA
A long molecule 1 million Daltons Ephemeral Difficult to isolate mRNA provides the plan for the polypeptide chain
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rRNA
Coiled Two subunits: a long molecule 1 million Daltons a short molecule 42 000 Daltons Fairly stable Found in ribosomes Made as subunits in the nucleolus rRNA provides the platform from protein synthesis
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tRNA
Short molecule about 25 000 Daltons Soluble At least 61 different forms each has a specific anticodon as part of its structure. tRNA translates the message on the mRNA into a polypeptide chain
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Posttranscriptional Regulation
Control of gene expression usually involves the control of transcription initiation. But gene expression can be controlled after transcription, with mechanisms such as:
RNA interference alternative splicing RNA editing mRNA degradation
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Posttranscriptional Regulation
RNA interference involves the use of small RNA molecules The enzyme Dicer chops double stranded RNA into small pieces of RNA
micro-RNAs bind to complementary RNA to prevent translation small interfering RNAs degrade particular mRNAs before translation
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Posttranscriptional Regulation
Introns are spliced out of pre-mRNAs to produce the mature mRNA that is translated. Alternative splicing recognizes different splice sites in different tissue types. The mature mRNAs in each tissue possess different exons, resulting in different polypeptide products from the same gene.
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Posttranscriptional Regulation
RNA editing creates mature mRNA that are not truly encoded by the genome. For example
apolipoprotein B exists in 2 isoforms one isoform is produced by editing the mRNA to create a stop codon this RNA editing is tissue-specific
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Posttranscriptional Regulation
Mature mRNA molecules have various halflives depending on the gene and the location (tissue) of expression. The amount of polypeptide produced from a particular gene can be influenced by the halflife of the mRNA molecules.
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Translation
RNA
Single stranded Does not contain thymine but has uracil instead.
tRNA carries 3 base pair code for specific amino acid. Amino acids compose polypeptid chains. One or more polypeptide chains compose a protein proteins provide the blueprints for our characteristics and functions.
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Transcription plan
Nucleus Gene
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Translation plan
Complete protein Polypeptide chain TRANSLATION
Ribosomes
Stop codon
2007 Paul Billiet ODWS
Start codon
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SKEMA TRANSLASI
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Translation
Location: The ribosomes in the cytoplasm that provide the environment for translation The genetic code is brought by the mRNA molecule
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This is enough combinations to code for the 20 amino acids but is the code actually made of triplets?
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Nature is logical!
Over 10 years biochemists synthesised bits of mRNA with different combinations Then they used them to synthesise polypeptides The results proved the logical answer was correct The genetic code is made of triplets of bases called codons
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Ribosomes initiate translation at ribosome-binding sites in polycistronic procaryotic mRNAs, which can encode more than one protein
07_33_mRNA.encode.jpg
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Important points: No direct binding between mRNA and rRNA Small ribosome subunit binds directly to cap requires specific initiation factor eIF4e Other initiation factors can unwind double stranded regions in the mRNA eIF4 group Small subunit scans mRNA till it finds correct AUG Correct AUG is embedded in preferred sequence GccAccAUGG G indwiani@gmail.com
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Proteins
Essential for all biological events
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