Molecular Biology I - Lecture 2 - BIO316 PDF

Molecular Biology I BIO316 Lecture 2 An introduction to Gene Function Prepared by Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  The Double helix structure of DNA  It is u...

Molecular Biology I BIO316 Lecture 2 An introduction to Gene Function Prepared by Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  The Double helix structure of DNA  It is useful to consider the structure of DNA at three levels of increasing complexity, known as:  Primary DNA structure.  Secondary DNA structure.  Tertiary DNA structure.  The primary structure of DNA refers to its nucleotide structure and how the nucleotides are joined together.  The secondary structure refers to DNA’s stable three- dimensional configuration, the helical structure worked out by Watson and Crick.  The tertiary structures refers to the packing and arrangements of double-stranded DNA in chromosomes. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli  The primary structure of DNA Associate Professor of Biochemistry and Molecular Genetics  The primary structure of DNA consists of a string of  This difference gives rise to  The pentose sugars of DNA and nucleotides joined together by phosphodiester their names: RNA are slightly different in linkages.  Ribonucleic acid (RNA). structure.  Nucleotides: DNA is a very long molecule and is  Deoxyribonucleic acid (DNA).  RNA’s sugar, or ribose, has a termed a macromolecule.  The additional oxygen atom hydroxyl group (–OH) attached to  DNA is a polymer chain made up of many repeating in the RNA nucleotide makes the 2ʹ-carbon atom. units linked together. it more reactive and less  DNA’s sugar, or deoxyribose, has  These repeating units of DNA are nucleotides, each chemically stable than DNA. a hydrogen atom (–H) at this comprising three parts: (1) a sugar, (2) a phosphate,  For this reason, DNA is better position. and (3) a nitrogen-containing base. suited to serve as the long- term repository of genetic information.  Dr. Rami Elshazli  The primary structure of DNA Associate Professor of Biochemistry and Molecular Genetics  The second component of a nucleotide is its  The third component of a nucleotide is nitrogenous base, which may be a purine or a the phosphate group, which consists of a pyrimidine. phosphorus atom bonded to four oxygen  Each purine consists of a six-sided ring attached to a atoms. five-sided ring.  Phosphate groups carry a negative  Each pyrimidine consists of a six-sided ring only. charge, which makes DNA acidic.  The phosphate group is always bonded to  Both DNA and RNA contain two purines, adenine (A) the 5’-carbon atom of the sugar in a and guanine (G). nucleotide.  Three pyrimidines are common in nucleic acids: cytosine (C), thymine (T), and uracil (U).  Cytosine is present in both DNA and RNA.  Thymine is restricted to DNA, and uracil is found only in RNA.   Secondary structure of DNA Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  DNA is made up of many nucleotides connected by covalent bonds, which join the 5’-phosphate group of one nucleotide to the 3’-carbon atom of the next nucleotide.  These bonds, called phosphodiester linkages, are strong covalent bonds.  The backbone of the polynucleotide strand is composed of alternating sugars and phosphates.  At one end of the strand, a free phosphate group is attached to the 5’-carbon atom of the sugar in the nucleotide.  This end of the strand is therefore referred to as the 5’ end.  The other end of the strand, referred to as the 3’ end.  Each polynucleotide strand has polarity, with a 5’ direction and a 3’ direction.  Dr. Rami Elshazli  Three-dimensional structure of DNA Associate Professor of Biochemistry and Molecular Genetics  The secondary structure of DNA refers to its three- dimensional configuration of helical structure.  The double helix:  DNA consists of two polynucleotide strands wound around each other to form its double helix.  The sugar–phosphate linkages are on the outside of the helix, and the bases are stacked in the interior of the molecule.  Antiparallel nature of DNA:  The two polynucleotide strands run in opposite directions, which means that the 5’ end of one strand is opposite the 3’ end of the other strand.  The strands are held together by two types of. Interactions:  Hydrogen bonds link the bases on opposite strands.  Phosphodiester bonds that connect the sugar and  Hydrogen bonds are relatively weak compared with the phosphate groups on the same strand. covalent phosphodiester bonds.  Dr. Rami Elshazli  Three-dimensional structure of DNA Associate Professor of Biochemistry and Molecular Genetics  Base pairing of DNA strand:  Adenine (A) normally pairs only with thymine (T) through two hydrogen bonds.  Cytosine (C) normally pairs only with guanine (G) through three hydrogen bonds.  C–G pairing is always stronger than A–T pairing.  The two polynucleotide strands of a DNA molecule are complementary and antiparallel.  Dr. Rami Elshazli  Other secondary structure of DNA Associate Professor of Biochemistry and Molecular Genetics  B-DNA structure:  The three-dimensional structure of DNA described by Watson and Crick is termed the B-DNA structure.  The B-DNA structure is the most stable configuration and the predominate structure for nucleotides.  B-DNA is an alpha helix, meaning that it has a righthanded (clockwise) spiral.  A-DNA structure:  The A-DNA is an alpha (right-handed) helix, but it is shorter and wider than B-DNA.  Their bases are tilted away from the main axis of the molecule.  Z-DNA structure:  The Z-DNA, forms a left-handed helix.  In this form, the sugar–phosphate backbone zigzags back and forth, giving rise to its name.   Secondary structure of DNA  There are approximately 10 base pairs (bp) per 360- degree rotation of the helix.  The base pairs are 0.34 nanometer (nm) apart; so, each complete rotation of the molecule encompasses 3.4 nm.  The diameter of the helix is 2 nm, and the bases are perpendicular to the long axis of the DNA molecule.  The lowest energy state for B-DNA is occurred when it has approximately 10 bp per turn.  The spiraling of the nucleotide strands creates major and minor grooves in the helix.  Function of DNA grooves:  These grooves are important for the binding of some proteins that regulate the expression of genetic information. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli  Tertiary structure of DNA Associate Professor of Biochemistry and Molecular Genetics  Chromosomal DNA must be tightly packed to fit into the small confines of a cell.  DNA is negatively supercoiled and packed with the aid of topoisomerase enzymes.  Prokaryotic chromosome:  Most bacterial genomes consist of a single circular DNA molecule.  Bacterial DNA is not attached to histone proteins as is eukaryotic DNA, but it is complexed to various proteins.  Bacterial DNA appears as a distinct clump, called the nucleoid, within the bacterial cell.  The prokaryotic chromosome is circular, and its length is very large compared to the cell dimensions, so it needs to be compacted to fit inside the cell.  Dr. Rami Elshazli  Packing of DNA Associate Professor of Biochemistry and Molecular Genetics  Eukaryotic chromosome:  Individual eukaryotic chromosomes contain enormous amounts of DNA.  Eukaryotic chromosome consists of a single, extremely long molecule of DNA.  Chromatin structure  Eukaryotic DNA is closely associated with proteins, creating chromatin.  Two basic types of chromatin:  Euchromatin.  Heterochromatin.  Euchromatin constitutes the chromosomal material.  Heterochromatin presents at the centromeres and telomeres.  The most abundant proteins in chromatin are the histones.  Dr. Rami Elshazli  Chromatin structure Associate Professor of Biochemistry and Molecular Genetics  The histones are small, positively charged proteins of five major types: H1, H2A, H2B, H3, and H4.  All histones have a high percentage of arginine and lysine, positively charged amino acids that give the histones a net positive charge.  The positive charges attract the negative charges on the phosphates of DNA.  This attraction holds the DNA in contact with the histones.  Nonhistone chromosomal protein such as chromosomal scaffold proteins may help in folding and packing the chromosome.  DNA is complexed to proteins called chromatin, that is the material makes up eukaryotic chromosomes.  The most abundant of these proteins are the five types of positively charged histone proteins: H1, H2A, H2B, H3, and H4.  Chromatin structure: Nucleosome Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  The nucleosome Chromatin has a highly complex structure with several levels of organization.  The simplest level is the double-helical structure of DNA.  Nucleosome:  The repeating core of protein and DNA is the simplest level of chromatin structure, the nucleosome.  The nucleosome is a core particle consisting of DNA wrapped about two times around an octamer of eight histone proteins (two copies each of H2A, H2B, H3, and H4).  This wrapping resembles a thread wound around a spool.  The DNA in direct contact with the histone octamer is between 145 and 147 bp in length.  Chromatin structure: Nucleosome  The histone proteins has a flexible “tail,” containing from 11 to 37 amino acids, that extends out from the nucleosome.  The fifth type of histone (H1) is not a part of the core particle but plays an important role in the nucleosome structure.  H1 binds to 20 to 22 bp of DNA where the DNA joins and leaves the octamer histone.  It helps to lock the DNA into place, acting as a clamp around the nucleosome octamer. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Chromatin structure: Nucleosome  Chromatosome:  The nucleosome octamer and its associated H1 histone are called the chromatosome.  Each chromatosome encompasses about 167 bp of DNA.  Chromatosomes are located at regular intervals along the DNA molecule and are separated from one another by linker DNA.  Linker DNA comprises from about 30 to 40 bp.  Nonhistone chromosomal proteins may be associated with:  The linker DNA.  Bind directly to the core particle of nucleosome octamer. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  High order of chromatin structure  Nucleosomes fold on themselves to form a dense, tightly packed structure that makes up a fiber with a diameter of about 30 nm.  The next-higher level of chromatin structure is a series of loops of 30-nm fibers.  Each loop encompasses 20,000 to 100,000 bp of DNA and is about 300 nm in length.  The 300-nm loops are compressed and folded to produce a 250-nm-wide fiber.  Tight helical coiling of the 250-nm fiber produces the chromatid of a chromosome, approximately 700 nm in width.  The nucleosome consists of a core particle of eight histone proteins.  Chromatosomes, which are nucleosomes bound to an H1 histone, are separated by linker DNA. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics   Centromere Structure  The centromere is a constricted region of the chromosome to which spindle fibers attach.  Centromeres display considerable variation in structure.  Function of centromere:  It is essential for proper chromosome movement in mitosis and meiosis.  Centromeric sequences are the binding sites for the kinetochore, to which spindle fibers attach. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics   Telomere Structure  Telomeres are the natural ends of a chromosome.  Telomeres are region of repetitive nucleotide sequences that stabilized the ends of linear chromosomes.  Function of telomeres:  Telomeres serve as a cap that stabilizes the chromosome, much like the plastic tips on the ends of a shoelace that prevent the lace from unraveling.  Telomeres also provide a means of replicating the ends of the chromosome.  These telomeric sequences consist of a series of guanine nucleotides followed by several adenine or thymine nucleotides or both.  The repeating unit in human telomeres is 5’-TTAGGG-3’, which may be repeated from 250 to 1500 times.  Telomere shortening refers to the process of the gradual reduction in the length of telomeres associated with aging. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli  Chromatin vs. Chromatid Associate Professor of Biochemistry and Molecular Genetics  Chromatin is a complex of DNA and protein found in eukaryotic cells.  Its primary function is to package long DNA molecules into more compact, denser structures.  Chromatid is one half of a duplicated chromosome.  Chromosomes are thread-like structures located inside the nucleus and made of protein and a single molecule of deoxyribonucleic acid (DNA). Chromosome Chromatin Chromosomes are condensed chromatin Chromatin is composed of nucleosomes, fibers. which are a complex of DNA and proteins. Chromosomes are thick and compact Chromatin is a thin and long fiber. structure. Distinctly visible during cell division. Found throughout the cell cycle.  Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics