Biochem Review - Bacani PDF

ORGANIC COMPOUNDS Study of compounds that contain the element carbon. CLASS OF COMPOUNDS: Carbon can share Four (4) valence electrons and form four strong covalent bonds. VALENCE ELECTRON - used to share. Carbon can form bonds to one another, forming long...

ORGANIC COMPOUNDS Study of compounds that contain the element carbon. CLASS OF COMPOUNDS: Carbon can share Four (4) valence electrons and form four strong covalent bonds. VALENCE ELECTRON - used to share. Carbon can form bonds to one another, forming long Chains and rings. Carbon is able to form an immense diversity of compounds. METHANE is the simplest compound. Natrium is the old term for sodium. PROPERTY ORGANIC INORGANIC (Salt) Bonding usually covalent Usually lonic Forces weak Strong Normal state Gas. Liquids Colids Flammability Flammable Non-flammable Solubility Insoluble in water Soluble NON METALS - transfer METALS - share INORGANIC have stronger bonding forces than organic because INORGANIC transfers elections while organic only shares. WHERE DO ORGANIC COMPOUNDS CAME FROM? Friedrich wohler First to synthesize an organic compound from inorganic substances. In 1828, He synthesized UREA slowly evaporating a water solution of ammonium cyanate. which he had prepared by adding silver cyanite. FUNCTIONAL GROUP an atom or group of Naming of Functional atoms which determined compounds group the chemical and physical properties of an *Meth 1 carbon organic compound. *Eth 2 carbons METHANE: Simplest *Prop 3 carbons *But 4 carbons Pent 5 carbons Hex 6 carbons CH4 INTRO TO BIOCHEM : BIO - light CHEMISTRY -scientific study of basic characteristics of substance. SIGNIFICANCE IN NURSING - It helps to identify Alterations. - Rationale. on how medication works.  BIOMOLECULE most essential organic molecules, includes mainte- nance and metabolic process of Living organisms. carbohydrate lipids Proteins Nucleic Acids ❖ CARBOHYDRATES most abundant organic Compound in the world. storehouse of chemical energy. ELEMENT: C, H, O MONOMER: monosaccharides ❖ LIPIDS compound found in living organisms that are insoluble in water. Storage of energy. MONOMER: Fatty Acids ELEMENT: CHO CELL membrane bound structure building blocks of life. ❖ PROTEINS basic unit of life. greek word Proteios" means "af first Important" Functions can be structure catalysis movement, transport, “CELLA" means small room. hormones protection, storage and regulation. cell - tissue-organ-organ system-organ system MONOMER: Amino Acids ELEMENTS: C,H,O,N PROKARYOTES unicellular, 0.2/2 size, cell wall usually present, no ❖ NUCLEIC ACIDS nucleus, no mem- brane, no bound organelles. bio molecules that are important for the continuity of life. EUKARYOTIC major functions of NA are to store and express genomic info. for uni / multicellular, 10-100 size, cell wall is present in protein synthesis. fungi/plants, with nucleus and with membrane bound MONOMER: Nucleotide organelles. ELEMENTO: C, H, O, N, P - Large biomolecule that play essential role in all cells and Human cells contains 46 CHROMOSOMES viruses A major functions; - storage and expression of genomic information. CELL MEMBRANE - Composed of group of nucleotides - outermost layer that decide the structure (Nitrogenous base, sugar and phosphoric Acids) - Composed of phospholipid bi-layer. - Maintain the internal environment of the cell. 1. NITROGENOUS BASE NUCLEUS - center of the cell, more than 90% cellular DNA in the nucleus. CYTOPLASM - part of the cell contains cell membrane organelles. MITOCHONDRIA - The powerhouse of the cell contains energy. LYSOSOMES - small vesicles found in cytoplasm. - Also known as "Suicidal bags" of the cell. - Program cell. PEROXISOMES - responsible for metabolism of hydroperoxide in the cells. ROUGH ENDOPLASMIC RETICULUM - consist of a network of tubules and platte- hed sacs. site of protein production via Ribosome (where protein produced) (Outside) SMOOTH ENDOPLASMIC RETICULUM - production of lipids. GOLGI APPARATUS - help package protein and lipids molecules which will be exported to various locations. such as lysosome, cell 2. SUGAR membrane, secretion. RIBOSOME - Site of protein synthesis.  3. PHOSPHORIC ACIDS DEOXYRIBONUCLEIC ACIDS Double helix models proposed by JAMES WATSON and FRANCIS CRICK. CHARACTERISTICS 1. NITROGENOUS base pairing 2. CHARGAFF’S rule 8. Anti- parallel 4. Backbone of the model = NUCLEOTIDE: 1. NITROGENOUS BASE PAIRING - A based pair is a connection between nitrogenous bases that help 2 nucleotides together in DNA. - "Rung of the ONA ladder." - The standard arrangement of bases in nucleotides is THYMINE being paired with ADENINE and CYTOSINE paired with GUANINE.. Example of PAIRING: DNA STRAND 5'-A-T-T-C-C-A-A-G-3’ 3’-T-A-A-G-G-T-T-C-5’ 2. ANTI- PARALLEL DNA is more stable than RNA because the attachment has - One strand runs from 5’ prime 3’ prime and the other (hydrogen) Easy to attach. strands run from 3' to 5'. - This configuration allows the DNA Strands to form Types of Nucleic Acids: complementary pairs. 3. CHARGAFF’S RULE Deoxyribonucleic Acids Ribonucleic Acids - DNA from any cells of all organisms should have a 1:1 ratio of pyrimidine and purine bases. - Carries genetic info - Single stranded. - the composition of DNA varied from one species to for development and - Present in all living another. functioning. cells. (A, C, G, U ) - adenine, cytosine, - TYPES: 4.BACKBONE OF THE MODEL guanine, phosphate, 1. Messenger RNA - The backbone of DNA is based on a repeated pattern of Thymine. 2. Ribosomal RNA sugar group and phosphate group. 3. Transfer RNA - Sugar - phosphate backbone provides structural support to the molecule. Ribonucleic Acids - Carries the DNA in the nucleus to cytoplasm. CENTRAL DOGMA OF MOLECULAR BIOLOGY - Makes up 60% structure of RNA (responsible for protein The dogma states that the information contained in DNA synthesis) molecules is transferred to RNA molecules, and then from the - Pick up amino acids from RNA molecules the information is expressed in the structure of cytoplasm. mRNA proteins. - To carry the code of DNA from nucleus to Ribo. rRNA - Catalyzes the formation of a peptide bond between two amino acids. tRNA - Brings in amino acids from the cytoplasm to the ribos DNA REPLICATION  Topoisomerase prevents the DNA double helix ahead of the replication fork from getting too tightly wound. Enzymes involved in DNA Replication: Helicase - Breaks down the hydrogen bonds between base pairs Topoisomerase - Prevents the supercoiling of the DNA strands. Single-strand Binding Protein - Proteins that coat the DNA strands to prevent rewinding Primase synthesizes RNA primer. Primase - Make a short section or RNA that acts as a primer. DNA Polymerase III - Responsible for the synthesis of new strands DNA Polymerase I - Removes primers and replace the gaps by relevant nucleotide DNA Ligase - Catalyzes the joining of two DNA ends The two strands of DNA unwind at the origin of replication Helicase opens the DNA and replication forks are formed DNA Polymerase III starts adding the complementary nucleotides at the end of the primer. Okazaki Fragments are short strands synthesized in the lagging strand during DNA Replication. The single strands are coated with SSB proteins to prevent rewinding of DNA Helicase opens the DNA and replication forks are formed  DNA Polymerase I removes the primers and proofreads Every double helix in the new generation of an the synthesized strand. organism consists of one complete “old” strand and one complete “new” strand wrapped around each other. Proven by the experiment of Meselson and Stahl. A fundamental, physical, and functional unit of heredity. DNA Ligase joins Okazaki Fragments in the lagging TRANSCRIPTION strand with the use of ATP. A fundamental, physical, and functional unit of heredity. A segment from the DNA that is responsible for the synthesis of a specific protein. Identified by Gregor Mendel as “factor”. Wilhelm Johannsen coined the word “gene”. Steps In Transcription - Initiation - Elongation - Termination INITIATION DNA is transcribed by an enzyme called RNA polymerase. Specific nucleotide sequences tell RNA polymerase where to begin and where to end. RNA polymerase attaches to the DNA at a specific area called the promoter region. The DNA in the promoter region contains specific sequences that allow RNA polymerase to bind to the DNA. ELONGATION Certain enzymes called transcription factors unwind the DNA strand and allow RNA polymerase to transcribe only a single strand of DNA into a single stranded RNA polymer called messenger RNA (mRNA). When RNA polymerase transcribes the DNA, guanine pairs with cytosine (G-C) and adenine pairs with uracil(A-U). TERMINATION RNA polymerase moves along the DNA until it reaches a terminator sequence. At that point, RNA polymerase releases the mRNA polymer and detaches from the DNA. SEMI-CONSERVATIVE DNA REPLICATION EXONS Gene segment that codes or genetic information. INTRONS Gene segment that DOES NOT code for genetic information. RNA SPLICING RNA splicing is a biological process where a newly synthesized pre-mRNA is processed into mRNA. It involves the removing of introns and the joining of exons. Done by the protein complex Spliceosome. INITIATION 5’ Cap and 3’ Poly-A Tail The ribosome assembles The 5’ cap is added to the first around the mRNA to be nucleotide in read and the first tRNA pre-mRNA. The which matches the start cap is a modified codon AUG. This setup, Guanine called the initiation nucleotide, and it complex, is needed in protects the order for translation to mRNA from being getstarted. broken down. The 3’ Poly-A Tail ELONGATION are group of stage where the amino Adenine acid chain gets longer. nucleotide that In elongation, the helps the mRNA mRNA isread one become more codon at a time, and stable and helps the amino acid it can be exported to the cytoplasm. matching each codon is added to a growing protein chain. TERMINATION starts when a stop codon enters the ribosome and is translated. It separates the tRNA and the polypeptide chain allowing it to drift out of the ribosome. Peptidyl Site -Translate the codon and release the amino acid. TRANSLATION Aminoacyl Site - Accepts the next tRNA with the amino acid. Steps In Transcription Exit Site - Site for uncharged tRNA before it is released - Initiation - Elongation - Termination back to the cytoplasm. CODON A codon is a DNA or RNA sequence of three nucleotides that forms a unit of genetic information encoding a particular amino acid. ANTICODON An anticodon is a trinucleotide sequence located at one end of a tRNA, which is complementary to a corresponding codon in the mRNA sequence.  MUTATION Changes occur in our DNA sequences, either due to mistakes when the DNA is copied or the result of environmental factors. Mutation can be harmful, beneficial, or have no effect. If they occur in cells that make eggs or sperm that can be inherited: if mutations occur in other types of cells, they are not inherited. MUTAGEN Any agent causing mutation. Mutagens can be physical mutagens, chemical mutagens or biological mutagens. A substance that induces alterations in the base pairs of the DNA MUTAGENESIS PRocess by which an organism’s DNA changes, resulting in a gene mutation. A mutation is a permanent and heritable SICKLE CEL:L ANEMIA change in genetic material, which can result in altered - In mutation, a single nucleotide is protein function and phenotypic changes. replaced in the portion of DNA which codes for a unit of POINT MUTATION hemoglobin. The substitution Is an alteration of a single nucleotide in a gene. mutation causes a Glutamic Acid FRAMESHIFT MUTATION in the protein to be changed to a Involves one or more nucleotide changes, altering Valine Amino Acid. the open reading frame of a particular gene. With lower ability to carry oxygen, these cells are also more prone to TYPES OF MUTATION: clot within the small capillaries of -Base substitution -Insertion -Deletion organs. This can lead to an increased risk of heart attack, BASE SUBSTITUTION: stroke and other cardiovascular - Type of replication error during DNA replication disease. which places the wrong nucleotide or sequence of nucleotides in the wrong position. - POINT MUTATION - Transition, Transversion, silent mutation, missense mutation, Nonsense mutation INSERTION TRANSITION If the nucleotide is purine that A type of frameshift mutation that occurs when an extra changes to purine or a pyrimidine to pyrimidine, it nucleotide is added to the DNA strand during replication. is called transition. This can happen when the replicating strand “slips”, or TRANSVERSION Nucleotide is Purine to wrinkles, which allows the extra nucleotides to be pyrimidine or Pyrimidine to purine. incorporated. DELETION A type of frameshift mutation that occurs when a wrinkle SILENT MUTATION NONSENSE MISSENSE forms on the DNA template strand and subsequently MUTATION MUTATION causes a nucleotide to be omitted from the replicated strand. Substitution of a base A base substitution A base that occurs on the that results in the substitution Types of MUTAGEN: third position of the generation of a gene that leads to Chemical Mutagen - group of naturally and synthetic codon. Thus there is sequence that the generation chemicals, which cause chemical mutation in the DNA by a positive possibility truncates the of a gene modifying the chemical composition and structure of DNA. that an identical translation or sequence that They generally induce errors in DNA replication machinery, codon will be alteration that leads codes for gene transcription, and transl;ation mechanisms. They generated that will to the generation of different amino induce mutations in several ways. code for the amino stop codon that acids and 1. Substitute the nucleotide sequence acid sequence. Thus, eventually forms a eventually a 2. Changes the normal bases no change in the nonfunctional different 3. Disruption of Hydrogen bond gene sequence protein. polypeptide Biological Mutagens - mutation agent in the form of an resulted in a silent sequence. organism which can include mutation in every living mutation. organism. Intercalating Agent - also mimic the nucleobases and intercalate Wavelength between the DNA nucleotide bases. The distance between any two corresponding points on - adjacent waves. Alkylating Agents Frequency - These chemicals add the alkyl group to the The number of waves that pass a certain point in a oxygen of guanine and adenine. Chemical like specified amount of time. dimethyl sulfate and ethyl methane sulfonate are alkylating agents *Guanine to Ethylguanine (acts like Adenine) = GC to AT Deaminating Agents - Common deaminating agent is NItrous Acid (HN02), which replaces an -NH2 or amino group with an -OH group, thereby altering the DNA base pairing. *Adenine to Hypoxanthine (acts like Guanine) = AT to GC *Cytosine to Uracil = CG to UA BASE ANALOGS Are the chemical derivatives that show analogy with the DNA Nucleotides and mimic DNA Nucleobases to varying extent. They pair with the corresponding bases in the DNA double helix and eventually induce point mutation by causing the insertion of wrong nucleotide bases during DNA replication. HEAT Heat can cause lethal effects on the DNA integrity and is termed as heat-stress induced DNA damage. Double stranded to single denatures. Heat can also cause inhibition of the DNA repair system. CYCLOBUTANE PYRIMIDINE DIMER The absorption of UV light makes the molecule potentially very reactive, and in certain situations can result in new bonds being made between different molecules. In particular. When thymine absorbs UV light, it becomes reactive with an adjacent thymine molecule in the DNA double helix and can lead to formation of a cyclobutane dimer in which the two thymine residues are covalently linked. Non-ionizing Radiation UV-radiation is a common example of non-ionizing radiation, which can induce DNA damage because of the skin cells' high absorption capacity. DNA readily absorbs UV-light of wavelength 280 nm. Thus, DNA acts as a target molecule of the UV-rays.