Molecules of Heredity PDF

Content: Part A: DNA Molecules of Part B: Chromosome Heredity Content: There are 2 types of molecules of hereditary: Part A:...

Content: Part A: DNA Molecules of Part B: Chromosome Heredity Content: There are 2 types of molecules of hereditary: Part A: DNA DNA (Deoxyribonucleic acid) - in most organism 1. DNA structure, formation and its components 2. Properties of DNA & Variation in DNA structure RNA (Ribonucleic acid) - some viruses 3. Location of Nucleic Acid within the cell Both DNA and RNA are nucleic acids 4. Major differences between DNA & RNA 5. Describe the structural composition of Gene 1. DNA Structure 10 base pairs per turn Watson-Crick Model (1953) Major groove Diameter of the helix is 2 nm The double helix to accommodate a purine- Minor pyrimidine base pairing Two sides (strands) groove Twisted like a spiral ladder Major and minor groove are Sugar-phosphate (covalent) important in interaction of - Hydrogen bond between PO4 other molecules with DNA Helix diameter Anti-parallel DNA strands/chains helix 2nm Nitrogenous base point inward Complementary/specific base pairing 1  Anatomy of DNA Formation of the DNA Strand/Chain 5’ phosphate DNA Phosphate group 5’ o 5’ o o Components Deoxyribose (5-carbon sugar) Cyclic nitrogen base O O o Phosphodiester o bond / linkage 3’ OH O o o o o + pp OH OH OH o i 3’ OH nucleoside nucleotide OH Sugar- Sugar- Phosphate Base pairs Phosphate Bases in nucleic acids backbone backbone G C Adenine Purine Hydrogen bonds Guanine (double ring) 5’ 3’ 2 anti-parallel DNA strands held together Thymine Pyrimidine A T by hydrogen Cytosine 5’ bonding (single ring) Hydrogen bonds 3’ Uracil between the complementary bases Purine Pyrimidine U Guanine  Cytosine Uracil presents in Adenine  Thymine RNA in the place of Thymine in DNA nucleotide 1. DNA Structure DNA exists as a right-handed double helix, consists of Watson-Crick Model (1953) two anti-parallel yet complementary DNA strand/chains The double helix coil around one another in a spiral. The polynucleotide chain composes of repeating units of Two sides (strands) nucleotides. Twisted like a spiral ladder Each nucleotide consists a phosphate group, a pentose Sugar-phosphate (covalent) (deoxyribose) and a cyclic nitrogen base. - Hydrogen bond between PO4 The two chains are held together by hydrogen bonding Anti-parallel DNA strands/chains between the complementary purine-pyrimidine bases Nitrogenous base point inward (A = T and G  C). 3’OH end is important for adding nucleotide to the DNA Complementary/specific base pairing strand 2  DNA is a dynamic molecule 3 Forms of DNA 2. The Properties of DNA Watson-Crick We will discuss SIX properties model  most DNA with stable form in methyl-base living cells B-DNA A-DNA Z-DNA Helix direction R-handed R-handed L-handed Bp per turn 10.4 11 12 Helix diameter 1.9 nm 2.3 nm 1.8 nm DNA is flexible DNA denaturation and renaturation The structure of DNA can be distorted by proteins, drugs or chemical compounds that incorporated into the DNA strand. DNA Denaturation (melting) - separation of the two complimentary strands of DNA (eg. by ↑ temperature) Eg. Damage recognition proteins and anticancer drugs DNA Renaturation (re-annealing) - two DNA strands + coming back together to form double-stranded DNA protein, drug, (eg. when ↓ temperature) chemical cpd denaturation DNA-RNA hybrid (melting) Eg. DNA-RNA hybrid maybe an important intermediate in Hepatitis B viral DNA replication renaturation DNA (re-annealing) RNA + anneal DNA-RNA hybrid DNA codes for protein The sequence of DNA can determine the proteins Ribosome GAT Amino acid 3 nucleotides DNA variation 3  3. Location of Nucleic Acid Metaphase chromosome nucleus  Nucleus Mitochondria Chromosome condensation   RER  Cytoplasm Chromatin 30 nm chromatin loop fiber 10 nm fibre (active transcription)  Nucleolus Interphase chromatin  Nucleus  Mitochondria 5. Relationship Between DNA and Gene Gene A Gene B DNA RNA  Double strand  Single strand  Deoxyribose  Ribose Regulation of  Thymine  Uracil translation Signals for  A, B and Z  mRNA, rRNA, tRNA Regulation of Exon Intron Exon Intron Exon Transcription transcription 1 1 2 2 3 termination  nucleus  Cytoplasm/nucleus Regulation of RNA (Ribonucleic Acid) translation Signals for Regulation of Exon Intron Exon Intron Exon Transcription transcription 1 1 2 2 3 termination RNA = a single chain of ribonucleotides Genetic material for some viruses transcription Ribonucleotide consists of a ribose, a cyclic Primary transcript nitrogen base & phosphate AUG UAA 4 bases : A = U, G ≡ C RNA splicing o mRNA OH OH Translation This is a H in a polypeptide N C nucleotide of DNA 4  RNA is single-stranded but can form secondary structure containing double-stranded regions. Example of RNA with stem-loops structure : 5’----AGCUUCUUGGAAGGAGUCCAAGGCCAG---3’ Single-stranded G region G A (loop) A G A U double-stranded G C region G C (stem) U A U A C G tRNA Ribosomal RNA 5’---AGCUU GCCAG---3’ RNA-Protein Interaction Content: Specific protein interactions occur in the RNA major groove formed by Part B: Chromosome bulges and loops. 1. DNA and Chromosome G RNA-protein interactions are G A essential for many cellular G 2. Chromatin packaging A processes – transcription, RNA A U splicing and translation. G C 3. Heterochromatin and euchromatin G C Eg. Mechanism of gene U A 4. Centromere and telomere U A transcription of HIV-1 C G 5’---AGCUU GCCAG---3’ 5. Human karyotype 1.DNA and Chromosome Why should DNA be organized and packed in the cell? = a structure consisting of DNA and proteins well-organized and packed in a specific way A human cell contains 6 billion base of DNA  a total of about 2 meters long!!! telomere How to fit DNA into a nucleus? How to maintain DNA in a state so that it is centromere p arm accessible to enzymes and regulatory proteins? How to organize the long DNA so that it does q arm not tangle? Therefore DNA need to be organized and chromatids telomere packaged into 46 chromosomes 5  2. Levels of Chromatin Packing DNA double helix 3 nucleosomes “beads-on-string” 30 nm chromatin fiber Chromatin looped domains Section of metaphase chrom. Entire metaphase chrom. 1st: Nucleosomes 2nd: Chromatin Fibers Linker DNA Linker DNA Nucleosome core particle Nucleosome DNA + nucleosome core particle core particle Nucleosome core particle = histone octamer = dimers of Histone H1 interacts with linker DNAs (50-60 nucleotides each histone H2A, H2B, H3 & H4 long) and the tails of core histones interact with histone in DNA - (146 bp) wraps 2 turns around a nucleosome core the neighboring nucleosome particle +(with diameter of 10 nm) to form a nucleosome  coil nucleosome filament with 6-8 nucleosomes per turn forming solenoid Multiple nucleosomes are formed on a DNA with a region of linker DNA in between nucleosome cores  organize the 10 nm nucleosome filament into a tightly  forms the “beads-on-string” 10 nm nucleosome filament wound coil of 30 nm chromatin fiber 3rd: Chromatin Looped Domains 4th: Metaphase Chromosome chromatin loops Normally loops of chromatins are spread out within the nucleus, cannot be visualized. However, some segments of chromatin are nuclear highly compacted and some are more diffuse Scaffold/ matrix During metaphase, chromatin loops are further condensed/ packed The 30 nm chromatin fiber folds into a series of large (50- 100 kbp), supercoiled loops/domains A-T rich regions of the chromatin loops are attached to non- histone proteins in the nuclear scaffold/matrix Duplicated These proteins regulate the degree of coiling and untangle chromosome has 2 loops, prevent transcription of gene in a loop from affecting chromatids genes in other loops 6  2. Chromosome Packaging  Just before cell division (and after DNA synthesis) Metaphase the chromatin condenses further into individual chromosome nucleus metaphase chromosomes Chromosome condensation  The dividing chromosomes appear as two chromatids  An electron microscopic view of a chromosome is shown in this photo – the chromatids appear to be made of coiled loops of 20-30 nm nucleoprotein Chromatin 30 nm chromatin fibers loop fiber 10 nm fibre (active transcription) Interphase chromatin  Chromatin is the name that describes nuclear material that contains the genetic code  In fact, the code is stored in individual units called “chromosomes” Heterochromatin  This is the condensed form of chromatin organization 3. Heterochromatin & Euchromatin  It is seen as dense patches of chromatin  Sometimes it lines the nuclear membrane, however, it is broken by clear areas at the pores so that transport is allowed heterochromatin Euchromatin  Euchromatin is threadlike, delicate  It is most abundant in active, transcribing cells, thus the presence of euchromatin is significant because the regions of DNA to be transcribed or duplicated must uncoil before the genetic code can be read Euchromatin Heterochromatin Permanently inactive compacted chromatin = Constitutive heterochromatin - centromere and telomere Chromatins are compacted during mitosis Transiently inactive compacted chromatin Become diffuse when cells enter = Facultative heterochromatin – varies with cell’s activities interphase, except heterochromatins remain compacted even after mitosis Euchromatin = Regions of chromatin that remain condensed/compacted during interphase (10%) = Regions of chromatin that unpack into the diffuse form contain genes that are silent (inactive genes, genes that are during interphase, usually contains actively transcribed not being transcribed/expressed into proteins) genes Thus, heterochromatins are inactive chromatins Thus, euchromatins are active chromatin 7  Centromere The site of constriction of the chromosome Consists of constitutive heterochromatin Dividing chrom. into p (short) and q arm 4. Centromere and Telomere (long) Contains:  Short AT- rich sequence tandemly repeated thousands of times  Kinetochore = protein-containing structure that serve as the attachment site for microtubules during cell division Telomere 5. Human Karyotype = a display/image of a full set of paired homologous chrom. & Each chromosome contains a single, linear sex chrom. in a mitotic cell arranged according to decreasing continuous double-stranded DNA molecule size Telomere = a stretch of tandemly repeated Colchicine is used to DNA sequences at the tip of each chromatid accumulate metaphase chrom Function:  Required for the complete replication of the chromosome Staining for band  Protects the ends of chromosomes from nucleases (banding)  Prevent the ends of chromosomes from fusing with one another (maintain chrom. integrity) Microscope  Facilitates interaction between the ends of chromosome and the nuclear envelope 22 pairs of autosomes + 1 pair of sex chromosome = 23 pairs/46 of chrom. Human chromosomes can be classified into 3 types Chromosome Banding & based on the centromere position: Identification Metacentric Submetacentric Acrocentric For chrom identification & structural analysis Characteristic for each chrom, reproducible stalk satellite Staining methods: Ideogram G banding Q banding R banding Centromere near one end stained by Quinacrine Heat treatment Giemsa Centromere in or Centromere off near the center/ the center/median substantially small Giemsa mustard Light and dark R bands median Dark and light Examined by The reverse of G banding P and q arms with satellites attached to p by stalk G bands fluorescence P and q arms ≈ clearly different μscope equal length length Eg.chrom. 13, 14, 15, 21 Low GC content Bright and dim Widely used * Telocentric – centromere at one end, only 1 arm; not in human Q bands 8  1. How many types of RNA are there? 2. Identify their functions? 3. The implication of the hydrogen molecule at the 2nd carbon in the deoxyribose molecule in DNA compared to RNA. o OHOH This is a H in a nucleotide of DNA 4. Why not all proteins in human start with methionine? 5. Why is the diameter of DNA restricted to 2 nm? 1. What is Centriol? Reading References: 2. What is Centrosome? Cell and Molecular Biology – Gerald Karp; 3. What is Centromere? John-Wiley & Son 4. What is Tiamine? 5. What is Thymine? The World of the Cell – Becker, Reece and 6. What is Chromatid? Poenie; Benjammin/Cummings 7. What is Chromosome? Genetics in Medicine - Thompson, McInnes and 8. What is Homologous Chromosome? Willard; WB Saunders 9. What is a Metaphase Chromosome? 9