SACE44 Biology Semester 1 (SABG11) PDF

SACE44 BIOLOGY SEMESTER 1 (SABG11) MS FARAH ANIZA SHAHRI TOPIC 1: DNA AND PROTEINS 1.1 DNA Structure and Function  Cell Theory 1. All organisms are composed of one or more cells. 2. The cell is the structural unit...

SACE44 BIOLOGY SEMESTER 1 (SABG11) MS FARAH ANIZA SHAHRI TOPIC 1: DNA AND PROTEINS 1.1 DNA Structure and Function  Cell Theory 1. All organisms are composed of one or more cells. 2. The cell is the structural unit of life for all organisms. 3. Cells can arise only by division from a preexisting cell.  Basics of Cells most basic property of cells; (building blocks of life) they are the smallest units to exhibit this property; bounded or separated from outside world - cell membrane able to reproduce, respond to stimuli in their environment & transform energy able to stores DNA for biological information DNA stored in nucleus depending of type of cell  Characteristics of Prokaryotic and Eukaryotic cells Comparison between prokaryotic and eukaryotic reveals many basic differences and similarities The shared properties reflect the fact that eukaryotes evolved from prokaryotic ancestor. Share identical genetic language Common set of metabolic pathways Common structural features  Characteristics of Prokaryotic and Eukaryotic cells Two fundamentally different classes of cells 1. Size 2. The types of internal structures (Organelles) All cells share certain characteristics They are all enclosed by a membrane They all use DNA as genetic information  Prokaryotic Cells Pro (before) - karyote (nucleus) prokaryotes do not have a nucleus and (generally) no internal membranes (do not contain membrane-bound organelles) made up of the bacteria and cyanobacteria family most prokaryotes are microscopic prokaryotes are unicellular – aggregate singly or permanently in colonies diameter: 1 – 5 μm; small size (very high ratio of surface are to volume)  Bacteria prokaryotic cells are enclosed by a plasma membrane surrounded by rigid & chemically complex cell wall – maintain the shape of cells has an outer sticky coat (capsule) – enable bacteria to stick to certain surfaces DNA consists of single loop; double stranded & has plasmid (small, circular DNA) have projections; help bacteria to move 1. Short projections - pili (singular: pilus) 2. Longer projections – flagella (singular: flagellum) General Prokaryotic Cells General Prokaryotic Cells  Eukaryotic Cells Larger in size, 10-100 μm complex multicellular organisms more highly organised and specialised Eukaryotic Cells – Animal cells Eukaryotic Cells – Plant Cells  Eukaryotic Cells The function of organelles and other structure in cells may be divided into four major groups: 1. The manufacture of chemicals such as nucleic acids, polypeptides and lipids. Eg: nucleus, ribosomes, endoplasmic reticulum and Golgi apparatus 2. The breakdown of materials, which may include foreign materials which are ingested. Eg lysosomes & vacuoles 3. Energy processing, either using energy from the Sun in the process of photosynthesis or obtaining the energy from foods that the organism has ingested. Eg mitochondria (respiration) & chloroplasts (photosynthesis) 4. Support, movement & communication between & within cells, Eg cytoskeleton, cell walls & membrane surfaces Prokaryotic vs Eukaryotic  Organelles with their own DNA (Double-membrane organelles) All organelle have membranes such as golgi, vesicles, ER, and others. But only some organelle contain DNA. Mitochondrial DNA (mtDNA) and chloroplast DNA is double-stranded but circular. There is a theory said that mitochondria & chloroplast was once prokaryote. But they undergo evolution and become organelle. Organelles with their own DNA (Double-membrane organelles)  Structure and Function of DNA DNA carries genetic code Replicates to pass on genetic information Instructions for synthesis of proteins Proteins are required to build an organism and catalyze of its biochemical reactions – controlling all of functions of cell and organisms  History of DNA How was DNA discovered? in 1869, the Swiss chemist Friedrich Miescher isolated DNA he removed the nuclei of pus cells and found nuclein (self-named) nuclein: rich in phoshorus, no sulfur like protein further research by other chemists → nuclein found to have an acidic substance they called nucleic acid at that time, they were still unsure if DNA is the genetic material or proteins in the chromosomes: 4 nucleotides VS 20 amino acids  History of DNA Rosalind Franklin and her experiment in 1952  History of DNA Watson and Crick described the DNA molecule from Franklin’s X-ray (1953) Watson and Crick in 1953  History of DNA The Watson and Crick Model of DNA In 1952, Rosalind Franklin, a student at King’s College London was able to crystallize DNA and used X-rays to obtain an X-ray diffraction photograph of DNA this photograph is then used by James Watson (American) and Francis Crick (British) to formulated the model of the double helical structure of DNA In 1962, Francis and Crick won the Nobel Prize for their discovery  Structure and function of DNA Main features of DNA: 1. DNA is double-stranded ; two polynucleotide stands alongside each other and the strands are antiparallel, i.e. they run in opposite directions (5'→ 3’ and 3’→5’) 2. The two strands are wound round each other to form a double helix. 3. The two strands are joined together by hydrogen bonds between the complementary base pairs.  The Structure of DNA short for deoxyribonucleic acid composed of basic building block called nucleotides a nucleotide consists of : 1. phosphate(phosphoric acid) 2. a pentose sugar 3. a nitrogen-containing base Nucleotides – The building blocks of nucleic acids (DNA and RNA)  nucleotides are monomers of nucleic acid (polymer) the phosphate of one nucleotide is attached to the sugar of the next nucleotide in a line which results in a backbone of alternating phosphates and sugars so DNA (a nucleic acid) is 2 strands of long sugar phosphate chain/backbone with organic bases attached to the sugar Building the Polynucleotides  Nitrogenous bases There are 4 different bases that can attach to the pentose sugar of DNA: 1. Adenine (A) 2. Cytosine (C) 3. Guanine (G) 4. Thymine (T)  Complementary base-pairing each base on one strand of DNA can form weak hydrogen bonds with a specific base on the other strand Adenine only bonds with Thymine (A—T) Guanine only bonds with Cytosine (G—C) A=T are linked by 2 hydrogen bonds G≡C are linked by 3 hydrogen bonds this is called complementary base pairing  Complementary base-pairing the number purine bases (A + G) always equals the number of pyrimidine bases (T + C) also, the amount of A = T and C = G in all species  DNA Base pairing PO4 PO4 adenine thymine PO4 PO4 cytosine guanine PO4 PO4 PO4 PO4  DNA double-helix DNA is twisted around each other – double helix bases DNA has 2 strands in a double helix shape the strands are complementary due to the nitrogenous bases sugar-phosphate chain  Variation of DNA between species the sequence of bases varies for each molecule of DNA across species, the length of DNA also varies human DNA has ~3billion base pairs (bp), >40,000 genes and can be about 2m long if stretched out bacteria have much shorter length of DNA due to the simplicity of its form but the bigger the animal may not correspond to longer DNA or more genes  The Genome Totality of genetic information of an organism Encoded in the DNA (for some viruses, RNA) Comparison of chromosomes in prokaryotes and eukaryotes Comparison of chromosomes in prokaryotes and eukaryotes Genetics Materials of Life Double helix structure  What are chromosomes? Genes → DNA → CHROMOSOMES→ Nucleus→ Cells→ Organism found in the nucleus of cells not visible unless the cell is dividing when the cell is not dividing, the mass of chromosomes are called chromatin the whole DNA of an organism will be arranged into several chromosomes a whole set of chromosome in the cell of an organism is called a karyotype  Human Karyotypes Male Karyotype Female Karyotype 46 chromosomes (usually numbered 46 chromosomes (usually numbered from largest to smallest) from largest to smallest) Has one X and Y sex chromosomes each Has two X sex chromosomes and no Y chromosome  Genes genes are made up of DNA they are regions of the DNA that form hereditary units that will be passed on from parents to their offspring the variation and sequence of the four bases A,T,C,G will determine the actual type and nature of genes most genes carry information to allow the cell to synthesize proteins the specific proteins will manifest the organism’s inherited traits  Genes and chromosomes each gene (specific DNA sequence) has a specific location(locus) on a specific chromosome chromosomes have a p-arm and a q-arm which is important to map the location of a gene’s locus  on a chromosome, there can be hundreds or thousands of genes a specific location of a gene on a chromosome is called a gene’s locus  DNA Replication What is it? A mechanism for copying genetic material Why is it important? To produce an identical copy of genetic material Occurs before cell division (mitosis and meiosis) Replication doubles the DNA Essential in passing on the genetic information from one generation to the next  DNA Replication Three postulated method of DNA replication: Semi conservative Conservative Dispersive  Semiconservative replication ✓produce two copies that each contained one of the original strands and one new strand Conservative replication ✓leave the two original template DNA strands together in a double helix and would produce a copy composed of two new strands containing all of the new DNA base pairs Dispersive replication ✓produce two copies of the DNA, both containing distinct regions of DNA composed of either both original strands or both new strands Alternative models of DNA replication: Evidence for the semi-conservative method of DNA replication Semi-conservative replication : each new DNA molecule contains one new strand and one old strand Meselson and Stahl (1958) ❖performed an experiment using the bacterium E. coli together with the technique of density gradient centrifugation of 15N (heavy nitrogen) and 14N (light nitrogen) 1958: Matthew Meselson & Frank Stahl’s Experiment Semiconservative model of DNA replication (Fig. 3.2)  DNA Replication a single chromosome is duplicated to form a double unit composed of two chromatids, attached together at the centromere  Step 1: DNA double strands are separated DNA replication occurs in the nucleus of cells DNA replication starts when an enzyme called helicase unwinds/separates the two parent strands or old DNA strand (separation of double helix) Both of two strands will both serve as a template for the making of a new complementary strand  Step 2: The leading strand On one parent strand, which runs from 3’ to 5’, DNA replication will start when RNA primase lays down /synthesizes an RNA primer complementary to the strand After RNA primer has been synthesized, DNA polymerase will start adding free nucleotides to the 3’ end of the primer to form a new DNA strand (5’ → 3’) called the leading strand, complementary to the parent strand (3’→ 5’) formation of hydrogen bonds between the bases of complementary strands the replication on the leading strand is continuous towards the replication fork as helicase unzips the double stranded DNA being replicated  Step 3: The lagging strand The DNA replication on the other parent strand (5’ → 3’) is discontinuous, DNA replication must start at the replication fork – known as lagging strand RNA Primase will lay down & synthesize an RNA primer at the replication fork DNA polymerase will synthesize the new strand from the 3’ end of each primer and the polymerase will actually move away from the replication fork in the 5’ to 3’ direction as helicase unzips another portion of the double stranded DNA, RNA primase will lay down another RNA primer at the replication fork and DNA polymerase will synthesize the new strand again  Step 4: Okazaki Fragments and DNA Ligase lagging strand will be synthesized in fragments called Okazaki fragments an Okazaki fragment will have an RNA primer and also a short length of new DNA lastly, DNA ligase will join the Okazaki fragments together to form a new DNA strand (the lagging strand) complementary to the parent strand The end result of DNA replication is two double stranded helical DNA  DNA Replication: Key Enzymes 1. Helicase : unwinds DNA 2. RNA Primase : synthesizes RNA primers to start the replication process 3. DNA Polymerase : synthesizes new DNA strand/ add free nucleotide bind complementary to template strand 4. DNA Ligase : joins the Okazaki fragments Exercise 1. Enzyme ________ unzips and unwinds the DNA molecule. A. DNA polymerase B. Helicase C. Primase D. DNA ligase 2. Which of the following statements about DNA replication is TRUE? A. the leading strand is replicated continuously, while the lagging strand is replicated discontinuously B. the leading strand is replicated discontinuously, while the lagging strand is replicated continuously C. both the leading and lagging strands are replicated continuously D. both the leading and lagging strands are replicated discontinuously 3. DNA replication results in two identical daughter molecules each consisting of one old (original) strand and one newly-synthesized strand A. True B. False 4. The point where separation of the DNA occurs is called the replication fork. A. True B. False Central Dogma Theory  Gene Hypothesis 1: Genes specify enzymes 1930, George Beadle and Edward Tatum did experiments using bread mould which led to the one gene-one enzyme hypothesis the one gene-one enzyme hypothesis stated that each gene specifies the synthesis of one enzyme later on it was soon discovered that other proteins besides enzymes were also coded by their own respective genes Which led to……  Gene Hypothesis 2: Genes specify a polypeptide many proteins are made up of two or more different polypeptide (amino acids) chains and each chain of polypeptide has its own specific gene so, a gene can be said as a segment of DNA that specifies the sequence of amino acids in a polypeptide of a protein But even this second hypothesis is not fully correct…  Genes also specify RNAs there are some genes that do not code for protein but actually code for structural RNA (ribonucleic acid) molecules such as ribosomal RNA There are three types of RNA: 1. Ribosomal RNA (rRNA) - counts for 80% of cellular RNA - associates with proteins to form ribosomes 2. Transfer RNA (tRNA) - specific carriers of amino acids for protein synthesis 3. Messenger RNA (mRNA) - mRNA is transcribed from DNA to carry the gene message out to the ribosomes for translation into an amino acid sequence  RNAs The DNA Language is the language of bases (A,C,T,G)…. The Protein Language is the language of amino acids….  Amino acids monomers or building blocks of protein molecules a long chain of amino acids(monomer) will form a chain of polypeptide(polymer) cells make proteins from various combinations of 20 different kinds of amino acids proteins can be made out of one, two or more identical or different chains of polypeptides Consider this….  Triplet codes, codons and amino acids The genetic flow of information from DNA to protein uses the triplet code on DNA and codons on mRNA, which then translates to amino acids Most amino acids have more than one triplet code The triplets of nucleotide sequences on mRNA are specifically called codons So, as codons are triplets of bases, the number of nucleotides that make up the genetic message must be three times the number of amino acids specified in the protein “In coding for a gene, n=amino acids, 3n=nucleotides” Amino acids abbreviation The 20 amino acids can be abbreviated by a single letter or three letters a shown in the table The flow of information from DNA to protein is unidirectional in most organisms. i.e. from DNA → RNA → Protein  5 Key Molecules in Protein Synthesis 1. DNA 2. Messenger RNA (mRNA) 3. Transfer RNA (tRNA) 4. Ribosomal RNA (rRNA) 5. Protein  1. DNA double helix with 2 complementary strands 4 bases: A, C, G, T one strand acts as a coding strand one strand of the DNA acts as template for the production of a molecule of mRNA a gene represents a length of DNA that contains specific information for a particular polypeptide chain DNA  2. Messenger RNA (mRNA) Function: ❑takes a message from DNA in the nucleus to the ribosomes in the cytoplasm for protein synthesis it is made in the nucleus but will end up in the cytoplasm it is a single stranded sequence that is transcribed from a DNA coding strand similar to DNA except 2 differences: 1. The deoxyribose sugar is replaced by a ribose sugar 2. Thymine (T) is replaced by Uracil (U). So the bases are A, C, G, U mRNA and Codons When mRNA is transcribed from a molecule of DNA: Adenine(DNA) bonds to Uracil (mRNA) : A-U Thymine(DNA) bonds to Adenine (mRNA) : T-A Guanine(DNA) bonds to Cytosine (mRNA) : G-C Cytosine(DNA) bonds to Guanine (mRNA) : C-G DNA VS RNA RNA DNA Ribose sugar Deoxyribose sugar Bases: A, U, C, G Bases: A, T, C, G Single stranded Double stranded Not helical Helical  3. Transfer RNA (tRNA) also transcribed from DNA is a single RNA strand (~80 nucleotides long) and has a clover leaf shape Function ❑code amino acids that will be linked into the polypeptide molecule specified by a particular sequence of bases on the mRNA each type of tRNA will carry only one of the 20 amino acids some amino acids can be carried by more than one tRNA molecule a specific amino acid will be attached to one end of the tRNA molecule  the other end of the tRNA molecule has three nucleotides (the anticodon) which can attach to the matching set of three nucleotides (codon) on the mRNA molecule So, tRNA molecules have the same bases as the mRNA molecule (A, U, G and C) /tRNA – anticodon  4. Ribosomal RNA (rRNA) Function: ❑along with proteins, makes up the ribosomes, where polypeptides are synthesized produced from a DNA template in the nucleus combined with proteins to make up ribosomes in the endoplasmic reticulum or the cytoplasm ribosomes are made up of 2 subunits: a large subunit and a small subunit  5. Protein macromolecules (large complex molecule) made from 20 different types of amino acids amino acids are monomers or building blocks of protein two or more amino acids or peptides are called a polypeptide or protein one or more polypeptide chains can be combined and folded into a specific and unique shape the shape of a protein molecule is vital for the function of the protein molecule protein synthesis or translation takes place in the cytoplasm and require specific enzymes Pathway of Protein Synthesis DNA Transcription RNA Translation Amino acids Polypeptides PROTEIN  Two steps of Protein Synthesis Step 1: Transcription Step 2: Translation - initiation - elongation - termination  Key Points for Transcription it occurs in the nucleus the process where an mRNA molecule is formed that has a sequence of bases complementary to a portion of one DNA strand because DNA is double stranded, only one strand is used for the coding of protein this strand is called the template strand the other strand is called the complementary strand  The Process of Transcription 1. a segment of the double stranded DNA helix unwinds and unzips to separate the two strands. This is done by an enzyme called RNA Polymerase 2. using the template strand of DNA, RNA polymerase will bring RNA nucleotides and synthesize an mRNA strand complementary to the template DNA 3. RNA polymerase joins the RNA nucleotides together in the 5’→3’ direction 4. that means, RNA polymerase can only add RNA nucleotides at the 3’end of an RNA 5. the newly synthesized mRNA strand(RNA transcript) will undergo some processing steps before it leaves the nucleus and goes into the cytoplasm for the next step of protein synthesis Transcription  The Discovery of Introns In eukaryotic cells, most mRNAs (some tRNAs and rRNAs) contain introns introns = are the sequences within the primary transcript that do not appear in the mature, functional RNA a piece of the DNA in a gene which does not give rise to an amino acids sequence before mRNA become functional mRNA, it is edited by cut out the introns’s base sequences  Exon and Intron Introns and exons are parts of genes. Exons code for proteins, whereas introns do not exons are parts of DNA that are converted into mature messenger RNA (mRNA) - the process by which DNA is used as a template to create mRNA is called transcription this mRNA then undergoes a further process called translation where the mRNA is used to synthesize proteins, via another type of molecule called transfer RNA (tRNA) Introns are parts of genes that do not directly code for proteins  RNA Processing - Splicing The original transcript from the DNA is called pre-mRNA. Pre mRNA – the first (primary) transcript from a protein coding gene and contains both introns and exons Introns (intervening sequences) – the non- coding segments of nucleic acid that lie between coding regions Exons – the coding regions of a pre mRNA that are translated to produce proteins (expressed) The introns are removed by a process called splicing to produce messenger RNA (mRNA) by spliceosomes  Key Points for Translation occurs in ribosomes at the cytoplasm or the endoplasmic reticulum (where ribosomes are found) the process where the sequence of codons on the mRNA at a ribosome directs the formation of a sequence of amino acids or a polypeptide molecules that are involved: mRNA, ribosomes, tRNAs can be divided into 3 steps: 1. Initiation 2. Elongation 3. Termination  1. Initiation starts when the mRNA strand associates with a ribosome translation is initiated by a signal code and the “start” codon, AUG the initiator tRNA with the anti codon UAC will bring the amino acid methionine(met) which corresponds to the “start” codon (AUG) 1. Initiation  2. Elongation once the first amino acid, methionine, is brought to the ribosome, the ribosome will start to “read” the mRNA strand ribosomes “read” the mRNA strand one codon at a time (3 bases at a time) while “reading” the mRNA strand, the ribosome will direct the correct tRNA to the mRNA so that the correct amino acid will be synthesized so elongation can be said as a process which a long amino acid chain is produced from mRNA 2. Elongation  3. Termination Occurs when the ribosome reaches one of the stop codons (UAG, UAA or UGA) when this happens, the ribosome will stop reading the mRNA and stop bringing in tRNAs with amino acids the mRNA will then detach from the ribosome the newly synthesized amino acid chain or polypeptide chain is also released for further modifications or processing 3. Termination