Molecules, Diet, Transport and Health PDF

# MOLECULES, DIET ## TRANSPORT AND HEALTH ### Notice: ATP (adenosine triphosphate molecule) It is a phosphorylated mono nucleotide, made from ribose (pentose sugar), adenine (nitrogen base), forming adenosine and can be combined with one, two or three phosphate groups to give, in turn, adenosine m...

# MOLECULES, DIET ## TRANSPORT AND HEALTH ### Notice: ATP (adenosine triphosphate molecule) It is a phosphorylated mono nucleotide, made from ribose (pentose sugar), adenine (nitrogen base), forming adenosine and can be combined with one, two or three phosphate groups to give, in turn, adenosine monophosphate (AMP), adenosine diphosphate (ADP) or adenosine triphosphate (ATP). ### What is ATP? A universal energy currency of cells as it is: 1. Small and water soluble so can easily diffuse between cell organelles. 2. Immediate energy donor as it is easily hydrolysed to ADP to release energy in presence of water. ### Uses of ATP: 1. Cell division. 2. Muscle contraction 3. Maintenance of body temperature. 4. Anabolic reactions such as protein synthesis. 5. Nerve impulse transmission. ## The formation of polynucleotide (in both DNA/RNA) Formed during interphase, where many nucleotides are linked together by a condensation reaction forming phosphodiester bond between phosphates of one nucleotide and carbon 3' in the sugar (ribose/deoxyribose) of the other nucleotide. Thus, the phosphodiester bond links the 5' carbon of one sugar with the 3-carbon of the next. Forming a sugar phosphate backbone with its bases at one side (pointing inwards from the 2 sugar phosphate backbones in case of DNA. ### FIRST: THE STRUCTURE OF DNA MOLECULE 1. 2 polynucleotide strands (each nucleotide =deoxyribose, phosphate & nitrogenous base. 2. Running in opposite direction (anti parallel). ex. strands are 3'to 5' and 5' to 3'. 3. Held together by Hydrogen bonds between the nitrogenous bases. between the amino and carbonyl groups of purine and pyrimidine bases on opposite strands. 4. Where the bases pair together according to a complementary base pairing rule where in each base pair there is a purine and pyrimidine Adenine pairs with thymine (A= I) and guanine pairs with cytosine (G:::C) 5. Each strand has a sugar phosphate backbone with phosphodiester bonds. _2n 6. The two strands twist forming a double helix(3D shape) I till--1 rrl 7. Each full turn in a DNA molecule has 10 base pairs, 3.4 nm length. ### Explain the importance of the hydrogen bonding between the 2 strands of DNA? 1. Hold the two polynucleotide strands together. 2. Important in contributing to 3D structure of DNA molecule (where the hydrogen bonds between bases stabilize the a-helix structure). 3. Many hydrogen bonds give stability. 4. H-bonds more easily broken than covalent bonds. So strands can be separated for replication(transcription) 5. H-bonds only formed between specific bases so few mistakes (faithful replication). 6. H- bonds can easily reform without chemical reaction. ### Structural feature of DNA making it stable molecule? 1. Complementary base pairing holds the strands together. 2. Because of many hydrogen bonds holding the strands together. 3. Sugar phosphate backbone with phosphodiester bonds. 4. Double helix structure protects bases. 5. Coiling protects from enzymes or any chemical attack. ### Why DNA should stay stable (not broken by enzymes or a chemical reaction)-i.e. genetic stability? 1. Sequence won't be spontaneously changed so decreasing chance of mutation--Ji- So Protein produced will always be functional. 2. Maintains all genetic information through Out life of cell, So same genetic information passed on to daughter cells (offspring). 3. Maintain size so still enclosed within the nucleus. ### Second: Semi-conservative replication of DNA: **semi conservative replication?** Its an increase in number of DNA molecules. where both strands of original DNA are replicated/copies. Each old parental strand acts as a template to form a new complementary strand Producing two genetically identical molecules (where the new DNA molecule has one old-and new strand) Occurs during S phase of cell cycle (late interphase). ### Steps of DNA replication (semiconservative) Watson and Crick hypothesis: 1. The DNA double helix unwinds. 2. The hydrogen bonds between complementary bases broken by enzyme DNA Helicase (strands separate). 3. The free activated nucleotides line up along both strands. 4. Where Both DNA strands act as templates. where each of the bases of activated DNA nucleotides pair up with its complementary base on each of the old DNA strand( A= T. c=(G) and hydrogen bonds formed between bases. 5. DNA polymerase enzyme lines Up the new nucleotides along the DNA template strand step by step Sequentially). 6. DNA ligase is an enzyme that catalyse the formation of phosphodiester bonds between adjacent mononucleotides. 7. Process continues along whole DNA molecule. 8. Producing two genetically identical DNA molecules. 9. Replication Is semi conservative where each newly formed DNA molecule contains one original and one newly synthesised DNA strand. 10. Where each of the two strands, the old and new complementary one will wind together Forming two DNA helices genetically identical to each other and to their mother ### Experimental evidence for the semi conservative replication of DNA by Meselson, and Stahl). In the 1950s, no-one knew exactly how DNA replicated. Three possibilities were suggested: **HYPOTHESIS: DNA replicates semiconservatively.** **METHOD** 1. Grow bacteria in N (heavy) medium. 2. Transfer some bacteria to N (ight) medium; bacterial growth continues. 3. Before the bacteria reproduce for the first time in the light medium (at 0 minutes), all DNA (parental) is heavy. 4. Take samples after 0 minutes, 20 minutes (after one round of replication), and 40 minutes (two rounds of replication). **RESULTS** After 2 generations, half the DNA was intermediate and half was light only, there was no heavy-only DNA. **CONCLUSION:** This pattern could only have been observed if each DNA molecule contains a template strand from the parental DNA; thus DNA replication is semiconservative. **conservative replication, in which one completely new double helix would be made from the old one semi-conservative replication, in which each new molecule would contain one old strand and one new one.** 1. Bacteria C. E. coli) were grown for many generations in a medium containing ammonium chloride with the heavy isotope's nitrogen-15 (. 15N). 2. This produces bacteria with heavy nitrogen-15 carried In both strands of the DNA molecule, this DNA would be heavier than DNA with nitrogen-14. 3. The bacteria with heavy nitrogen-15 strands in its DNA molecule were grown in a medium containing the normal nitrogen isotope N¹⁴ and were left to divide one generation. 4. The off springs showed DNA molecule with both strands N14 N15 5.. N14.4 15. 5. N14 The second generation had N N and NN ### Third: Genetic code Gene is a length of DNA containing a specific sequence of bases that codes for a specific sequence of amino acids to form specific protein, giving a particular characteristic/phenotype/feature. 1. **Triplets:** Each sequence of three bases (e.g CGA) DNA or RNA is referred to as Codon. With four different bases, there are 64 possible codons, which is more than enough to specify the 20 different amino acids that occur in proteins. 2. **Universal,** The same triplet genetic code codes for the same amino acid in all living organisms, which is strong evidence for the idea that all living organisms originate from one group. 3. **Degenerate:** it is that some amino acids have more than one genetic code. Which means there are more codons than number of amino acids. Where arranging the 64 bases in triplets gives 64 possible combinations. so, 61 possible codons for 20 amin? acids and (3 stop codons). so more than one codon specifies an amino acid ..... this minimizes the effect of mutation. 4. **Not overlap:** no base of a given triplet enter to be a part of the adjacent triplet. Proved using point mutation (a change in a single base of the DNA code) ### Properties of genetic code * CCA which codes for the amino acid valine * TTT which codes for the amino acid lysine * GAA which codes for the amino acid leucine * CCC which codes for the amino acid glycine ### DNA * **Acid Name:** Deoxyribo Nucleic * **Stability:** Very stable (long "life") * **Found in:** Nucleus, Mitochondria (most eukaryotes), Plastids (plant cells) * **Function:** Static, digital genetic data storage * **Copier Enzyme:** DNA polymerase * **Structure:** Two complementary strands A-, B- or C-form helix ### RNA * **Acid Name:** RiboNucleic * **Stability:** Less stable (short "life") * **Found in:** Nucleus and cytosols * **Function:** Dynamic, many varied functions * **Copier Enzyme:** RNA polymerase * **Structure:** One strand only A-form helix | Backbone | Inorganic phosphate | | ---------- | ------------------- | | Nucleobases | Deoxyribose (D in DNA), Ribose (R in RNA) | | Base Pairing | Thymine, Cytosine, Adenine, Guanine A=T (Adenine to Thymine) G-C (Guanine to Cytosine) | | Uracil replaces Thymine AU (Adenine to Uracil)| | EM Radiation | Somewhat UV sensitive | | EM Radiation | Relatively UV resistant | ### There two types of RNA that take part in protein synthesis: 1. mRNA (messenger RNA): forms a copy of the DNA code. 2. tRNA (transfer RNA) carries amino acids to the ribosomes to make the protein. ### Protein synthesis takes place in two stages: 1. Transcription (formation of mRNA from the gene in the nucleus) 2. Translation (Formation of polypeptide chain using mRNA ar mRNA and tRNA in the cytoplasm) ### Transcription 1. Part of the DNA (the gene) unwinds and unzip due to break of hydrogen bonds between the bases. 2. The antisense strand act as a template, where free activated RNA nucleotides line up against the template strand according to the complementary base pairing rules (A=U, C=G). 3. The free nucleotides join together by RNA polymerase.. 4. Forming mRNA molecule. 5. The process ends when the chain reaches stop codon, and mRNA separates from DNA template strand allowing the DNA chains of double helix to re-join. 6. Then mRNA leaves the nucleus through nuclear pores in nuclear membrane to the ribosome in the cytoplasm. ### Translation * This means converting the code in m.RNA into a protein in the ribosome in the cytoplasm. 1. The triplet code in mRNA is called codon, where each codon codes for a particular amino acid. 2. The mRNA attach to a ribosome. 3. Ribosome is made from -A and a small and a large subunit. ### t.RNA * tRNA has anticodon which is complementary to a particular codon on mRNA. * And at the other end of tRNA is a site where a specific amino acid can attach under the control of specific enzyme and with energy" from ATP giving tRNA-amino acid complex, * The tRNA molecule carries its amino acid to the ribosome, where its specific anticodon links up with corresponding mRNA codon. + A peptide bond is formed between amino acids by condensation reaction. + There are 20 different amino acids, so there must be at least 20 different codons and 20 different anticodons. In fact there mRNA are more than this, because some amino acids use more than one triplet code. ### Steps of translation: 1. The mRNA attaches to the small subunit of ribosome. six bases at a time are exposed to the large subunit. 2. tRNA with complementary anticodon UAC (carrying methionine amino acid ) bind with H-bond to the mRNA at the start codon(AUG). 3. Start codon: AUG is the first one coded in a polypeptide chain ( codes for methionine) 4. Another tRNA brings along a second amino acid. The anticodon of the second tRNA binds to the next codon on mRNA. Two tRNA molecules fit onto the ribosome at any one time. This brings two amino acids side by side 5. The two amino acids are held closely together, and a peptide bond is formed between methionine and the second amino acid. 6. This is a condensation reaction catalysed by peptidyl transferase which is found in the ribosome. 7. The first tRNA molecule is and goes off to collect another Acid, And the ribosome moves along the mRNA to bring the next codon in position of translation. And a third tRNA molecule binds. 8. More tRNA molecules arrive at the mRNA and add their amino acids to the growing chain forming polypeptide. Until a stop codon (UAA/UAG/UGA) is exposed on the ribosome preventing further translation. 9. Stop codons terminate translation and don't code for amino acids 10. Then the polypeptide is released (termination) and enters the ER and the 'stop' codon UAA prevents further translation and ribosomal subunits float independently in the cytoplasm Usually, several ribosomes work on the same mRNA strand at the same time. They are visible, using an electron microscope, as polyribosomes (mass production) 1. So a single mRNA can be translated by several by ril ribosomes at the same time. 2. thus several identical DRAMuude chains are synthesised from one mRNA.. ### Summary Role of m. Rna 1. Produced by transcription. 2. Important in translation by using base sequence to make polypeptide chain. 3. Where it leaves nucleus moving towards ribosome. 4. It attaches to the small subunit of ribosome. 5. Carry codons where each codon codes for a particular amino acid. 6. tRNA binds and bring specific amino acids to the ribosome. 7. where its specific anticodon links up with corresponding mRNA codon. 8. According to complementary base pairing (A= U, c:=G) 9. Example of codon mRNA AUC and its complementary anticodon will be UAG. 10. single mRNA can be translated by several by ribosomes at the same time (polyribosomes). 11. mRNA is short lived where it can produce proteins for short period of time. ### ROLE OF t.RNA 1. At the one end of tRNA there is a site where a specific amino acid can attach under the control of specific enzyme. 2. tRNA carries amino to ribosome. 3. where its specific anticodon links up with corresponding mRNA codon. 4. According to base pairing (A=U, C8G). 5. Two tRNA binds to the ribosome at the same time. 6. two amino acids are held closely together. 7. For peptide bond formation. 8. tRNA can be reused by binding to another amino acid. ### ROLE OF Ribosome 1. It's important for, translation. 2. Where The mRNA attaches to the small subunit of ribosom, six bases at a time are exposed to the large subunit. 3. mRNA has codes for specific sequence of amino acids in a polypeptide chain. 4. Ribosome moves along the mRNA one codon at a time. 5. Ribosome provides sites for attachment of the two tRNA at a time. 6. Where each tRNA carries specific amino acid, so 2-.amino acids are held close together. 7. With its specific anticodon links up with corresponding mRNA codon. 8. Peptide bond formed between 2 amino acids, through a condensation reaction catalysed by peptidyl transferase which is found in, ribosome. 9. Assembly of amino acids into rim- structure. ### m. Rna * **Straight** * **No hydrogen bonds** * **Codons** * **No amino acids binding site** * **Found in nucleus and cytoplasm** ### t. Rna * **Folded** * **Hydrogen bonds holding the structure together** * **Anticodons** * **Has amino acid binding site** * **Found in cytoplasm** ### COMPARISON BETWEEN DNA REPLICATION AND TRANSLATION | | Transcription | Translation | | --------- | ------------------------ | --------------------------------------------------------------------------- | | **Product** | Production of transcription occurs in mRNA | Product of translation is a polypeptide chain (that becomes a protein) | | | Occurs in the nucleus of a cell | Occurs in the ribosomes of a cell | | | Requires RNA polymerase | Uses various reagents to create a polypeptide chain | | **Process** | DNA to RNA | RNA to protein | ### Protein synthesis and release from cells 1. Gene in DNA transcribed forming mRNA using DNA as template in nucleus. 2. mRNA contains code for polypeptide. 3. mRNA leaves nucleus to cytoplasm where it binds/associates with ribosome. 4. tRNA molecules attached to specific amino acids. 5. tRNA with specific amino acid carried to ribosome. 6. pairing of codons on mRNA with anticodon on tRNA. 7. Formation of peptide bond between adjacent amino acid. 8. Protein formed enters the rough endoplasmic reticulum. 9. The proteins are then modified ( ex; glycosylation) 10. Then protein can be released from plasma cell where vesicles move to cell surface membrane via cytoskeleton, vesicle then fuse with cell surface membrane (exocytosis) using energy from ATP.