Biochemistry Lecture 6 & 7 PDF

Introduction to Molecular Biology 1- Nucleotides 2- DNA 3- RNA  1- NUCLEOTIDES 1- Structure of nucleotides 2- Importance (Functions) of nucleotides 3- Metabolism of nucleotides i. synthesis ii. degradation  Nucleotides Stru...

Introduction to Molecular Biology 1- Nucleotides 2- DNA 3- RNA  1- NUCLEOTIDES 1- Structure of nucleotides 2- Importance (Functions) of nucleotides 3- Metabolism of nucleotides i. synthesis ii. degradation  Nucleotides Structure Nucleotides = nitrogenous base + sugar + phosphate (1,2 or 3) 1-Nitrogenous base = Purine OR Pyrimidine Purine = Adenine OR Guanine Pyrimidine = Thymine (DNA only), Cytosine, Uracil (RNA only) 2-Sugar = Ribose (RNA) OR Deoxyribose (DNA)  Functions of nucleotides 1-Building blocks of RNA and DNA 2-Source of energy : ATP ,GTP act as source of Energy. 3-Mediate action of hormone : c.AMP and c.GMP are second messenger 4- Co-enzymes : as NAD,FAD, Co-enzyme A.  Metabolism of nucleotides 1- Synthesis (anabolism) i. sources of purine ring atoms ii. sources of pyrimidine ring atoms 2- Degradation (catabolism) i. end products of purine ring ii. end product of pyrimidine ring Synthesis of purines: Sources of atoms of purine ring Synthesis of pyrimidines: Sources of atoms of pyrimidine ring Degradation (catabolism) of purine ring : In human cells purine nucleotides is finally degraded to URIC ACID Uric acid is transported in blood to kidneys Finally, Uric acid is excreted in urine If uric acid is increased in blood, the case is called HYPERURICEMIA Hyperuricemia may lead to GOUT GOUT is a disease affects joints (arthritis) & kidneys (kidney stones) caused by deposition of uric acid in these tissues Degradation (catabolism) of pyrimidine : Pyrimidine nucleotides are degraded to highly soluble products : , β-alanine & β-aminoisobutyrate, CO2 and NH3  DNA 1- Importance of DNA 1- Storage of genetic material & information (material of GENES) 2- Transformation of genetic information to new cells (template for REPLICATION) i.e. synthesis of new DNA from parental DNA for new cells 3- Transformation of information for protein synthesis in cytosol (template for TRANSCRIPTION) i.e. synthesis of mRNA from DNA Gene in nucleus 2- Location of DNA in human cells (nucleus- mitochondria) 3- Structure of DNA molecule - Structure of a single strand of DNA (1ry) - Structure of double stranded DNA (2ry) - Packing of DNA (3ry tertiery)  1- Structure of Single strand of DNA Building Units: Polynucleotide sugar: deoxyribose Base: Purine: A or G OR Pyrimidine: T or C Phosphoric acid Mononucleotides are bound together by phosphodiester bonds In linear DNA Strand : two ends (5` = phosphate & 3` = OH of deoxyribose) In circular strand: no ends  2- Structure of double stranded DNA Hydrogen bonds link the two single strands together -Two strands are anti-parallel (in opposite directions). -Hydrogen bonds between bases of opposite strands (2 hydrogen bonds between A & T but 3 hydrogen bonds between C & G) A- Denaturation: breakdown (loss) of hydrogen bonds between two strands leading to formation of two separate single strands) Causes of denaturation : heating or alkaline pH. B. Renaturation: If strands of DNA are separated by heat and then the temperature is slowly decreased, base pairs reform gaian. C. Hybridization: A single strand of DNA or RNA pairs with complementary base sequences on another strand of DNA or RNA.  Linear & Circular DNA 1- Linear DNA in nucleus of eukaryotes (including human cells) i.e. DNA of chromosomes 2- Circular DNA i. in eukaryotes: mitochondria ii. in prokaryotic chromosomes (nucleoid of bacteria) iii. in plasmids of bacteria (extrachromosomal element) iv. in plant chloroplasts  Mitochondrial DNA A. The mitochondrial genome is a double-stranded circular DNA molecule found within the mitochondrial matrix. B. Mitochondrial DNA is maternally inherited: Mitochondria from the egg contribute exclusively to the zygote. C. Mitochondrial DNA has a high mutation rate (about 5 to 10 times greater than the nuclear genome).  General RNA structure Building units: Polyribnucleotides (bound together by PDE) Single strand Linear (but may fold into complex structure) with two ends: 5`(phosphate) & 3`(-OH end) Sugar: Ribose Purine bases: Adenine & Guanine Pyrimidine bases: Cytosine & Uracil  RNA versus DNA RNA differs from DNA a. The polynucleotide structure of RNA is similar to DNA except that RNA contains the sugar ribose rather than deoxyribose and uracil (U) rather than thymine. (A small amount of thymine is present in tRNA.) b. RNA is generally single stranded (in contrast to DNA, which is double stranded).  1- Ribosomal RNA (rRNA) 80% of total RNA in the cell (most abundant RNA) Location: cytosol Function: machine for protein biosynthesis Types: a. rRNA molecules differ in their sedimentation coefficients (S). They associate with proteins to form ribosomes b. Eukaryotes have four types of cytosolic rRNA: 18S, 28S, 5S, and 5.8S rRNA.  Functionally competent ribosome Ribosomes are large complexes of protein and rRNA. They consist of two subunits, one large and one small. The prokaryotic 50S and 30S ribosomal subunits together form a ribosome with an S value of 70. The eukaryotic 60S and 40S subunits form an 80S ribosome. prokaryotic ribosome Eukaryotic ribosome 70S 80S 50S 60S 30S 40S 5.8S 5S RNA 5S RNA RNA 23S 16S 28S 18S RNA RNA RNA RNA 32 Proteins 21 Proteins ~50 Proteins ~30 Proteins  2- Transfer RNA (tRNA) -tRNA has a cloverleaf structure ,relatively small (80 nucleotides). -At least 20 tRNA are present for 20 amino acids A. In eukaryotic cells, many nucleotides in tRNA are modified as pseudouridine (Ψ), dihydrouridine (D), and ribothymidine (T). B.tRNA has 3 loops and 2 ends (1) The middle loop contains the anticodon, which base pairs with the codon in mRNA. (2) The CCA sequence at the 3’ end carries the amino acid.  Messenger RNA (mRNA) synthesized in the nucleus (by transcription):mRNA is synthesized complementary to DNA but in RNA language i.e. U instead of T Carries the genetic information from the nuclear DNA (gene) to the cytosol In the cytosol, mRNA is used for protein biosynthesis by ribosomes …..This is called Translation or Protein Biosynthesis  3- Messenger RNA (mRNA) Messenger RNA (mRNA) contains a cap structure and a poly(A) tail. A. The cap consists of methylated guanine triphosphate (m-GTP) attached to the 5’ end of the mRNA. B. The poly(A) tail contains up to 40-200 adenine (A) nucleotides attached to the 3’ end of the mRNA.  The Genetic Code Base sequence on m.RNA which is translated to amino acid sequence of protein. Each 3 bases called codon in 5`-3` direction e.g. 5`-AUG-3`, which is translated to one amino acid. There are 64 different codons:  61 codons: code for the 20 common amino acids  3 codons (UAG, UGA & UAA): do not code for amino acids but are termination (stop) codons  First Second Nucleotide Third Nucleotide U C A G Nucleotide UUU UCU UAU UGU U Phe Tyr Cys U UUC UCC UAC UGC C Ser UUA UCA UAA Stop UGA Stop A Lue UUG UCG UAG UGG Trp G CUU CCU CAU CGU U His C CUC CCC CAC CGC Arg C Leu Pro CUA CCA CAA Gln GGA A CUG CCG CAG CGG G AUU ACU AAU AGU U Asn Ser A AUC Ile ACC AAC AGC C Thr Arg AUA ACA AAA Lys AGA Met A AUG ACG AAG AGG G GUU GCU GAU GGU U GUC GCC GAC Asp GGC G Gly C Val Ala GUA GCA GAA GGA Glu A GUG GCG GAG GGG G  Phe P E A fMET AAA UAC mRNA EF-Tu GDP + Pi EF-Ts fMET Phe Lys AAA U U C GDP + Pi EF-G