BIO206 - Introductory Cell and Molecular Biology

Typical Prokaryotic Cell - Escherichia coli Single Cell Organism – organism on the face of the earth that we know the most about; best studied and understood organism (model that allows us to understand the workings of a prokaryote) Binary Fission – division of the cell which occurs in a nutrient rich environment every 20 minutes; in the entire earth, there are 1030 of these organisms Organisms undergo self-replication – increases in size and divides, then the same process repeats In a day, ther

Mostly unicellular, micro-organisms Even multi-cellular organisms are generated from single cells Characteristics of life Growth Metabolism Movement Response to stimuli-communications (even cells communicate) Reproduction The Cell Smallest unit of life All living things are made up of cells New cells arise only from pre-existing cells Cell and molecular biology + principles of evolution universal features All cells store their hereditary information in the same linear chemical code (DNA) (A) B

Central Dogma of Molecular Biology - Flow of Information DNA is a molecule that contains information – contains discreet portion of information, not a big, long piece of information but they are segments They are transcribed – creating a copy of information that serves as a template for protein synthesis Information encoded in DNA is information to make a protein – specifically encoding the series of amino acids At the molecular level, these functions are complex and more complicated All organis

Chemical Systems Living Creatures Components, environments, structure function 70% water in a cell, , polar molecule = 96.5% of organism's weight How do these interact together? Covalent bonds - stronger because of the way they share their electrons Non-covalent bonds - weaker bond interactions between molecules TYPES of non-covalent bonds: Electrostatic ionic bonds between components with charges (partial positive/negative) enhances interactions between components Hydrogen bonds enha

Nucleotide Structure & DNA This nucleotide is involved in a number of processes – it delivers energy to drive biochemical reactions It is also involved in forming part of the structure of DNA – not quite ATP but it is deoxy-ATP that is incorporated into the DNA We can see that a simple structure can be put together in a spiral shape molecule with repetitive structure to it Polymerization: 3’ to 5’ Phosphodiester bonds DNA/RNA: Linear polymer of nucleotides The substrate for the reaction is a nuc

Levels of Protein Structure Primary (1) Structure The amino acid sequence of polypeptide chain The linear sequence of protein sequence – N-terminal to C-terminal Typically finding proteins ranging in size from 50 amino acids to over 2000 amino acids Single letter abbreviations for the amino acids as well – for instance, cysteine is C or cys (three letter abbreviation) Chemical properties of amino acids that give the biological and chemical properties of proteins The primary sequence of amino aci

Nucleic Acids - DNA and RNA (also energy molecules...) Nucleotides structure Sugar -- glycosydic bonds-- Nitrogenous base -- Phospho and hydro bonds (good source of energy) -- # of Phosphates Nucleoside Phosphate - # Phosphates Name ( 3 phosphates = triphosphate) Purine - Nitrogen on 1, 3, 7, 9 (2 Rings) Pyrimidine - - Nitrogen on 1, 3 (1 Ring) Sugar - Hydroxylic group - Present - Rybonucleotide on - Absent = Deoxyribose When both hydroxyls are missing ( C-2', 3') = Dideoxyribose Pho

Initiation The origin of replication (Ori C)' is N245 base pairs long. DNA-A binding region and A-T rich region. For replication to begin, DNA needs to separate at the A-T rich region. This happens easilty because A-T are double bond (H-bond) DNA-A is a homotetramer - 4 identical monomers/subunits DNA-A proteins bind to the DNA-A binding site strand separation SSB- Single stranded binding proteins, bind to ssDNA to prevent the separated strands from re-annealing (Homotetramer). DNA-B: Helicase

Composition of Cells Hydrogen Carbon Common to all biological molecules Nitrogen Oxygen Phosphorus Sulfur Carbon and sulphur have 4 valence electrons, but carbon can form 4 stronger and stable bonds than sulfur. This is because the 4 valence electrons carbon have are closer to the nucleus.When carbon combines with other carbons, it forms strong skeleton structures composed of linear, branched, or ringed groups of carbons. Side groups of biological molecules are central to the function of a molec

RNA Polymerase has 5 subunits - Alpha (x2) Beta Beta' Omega For RNA Pol to bind to DNA, it must be in complex with the sigma factor. Different sigma factors are used for transcription of different genes. Holo-enzymes - All RNA Pol subunits together + sigma factor Promoter region has 3 binding sites. 10 - Here sigma factor binds. 35 - Here also sigma factor binds. Up-element - 10, 35, and 50 base pairs upstream of transcription start site. 2 Alpha subunits bind here. Once sigma factor is bound,

DNA/Protein Interactions EcoR1 – a protein that is capable of binding DNA, not randomly but at a specific nucleotide sequence and it is a protein catalyst – reaction that the protein catalyzes is phosphodiester bonds It is a homodimer – made up of two identical subunits; catalytic activity requires cofactor which is magnesium Presence of magnesium will cleave the phosphodiester bond in two places, breaking DNA apart Nucleases - (Proteins) EcoR1 is a part of this group Enzymes that cleave phospho

UTR’s flank the coding sequences and have specific functions Two terminators in prokaryotic genes – one that terminates translation and one that terminates transcription Prokaryotic genes lack introns Transcription with the end product of an RNA molecule (single stranded polynucleotides made up on nucleotides C, A, U and G) Transcription involves a complicated enzyme known as RNA polymerase which is an enzyme catalyst that we can describe the biochemical reaction that it participates in One of t

Replication Transcription Translation Central Dogma - DNA DNA RNA Protein RNA Synthesis Protein Synthesis Gene Sequences have many functions, the definition is less accurate. A segment of DNA that encodes information for a protein or functional RNA as a linear sequence of nucleotides. Each gene has a different product (a double strand has different parts - genes within it.) Different genes are transcribed/translated in different w

6.1.1 - 6.1.3: Introduction to Protein Trafficking The Protein Trafficking Machinery Proteins are machines that carry out virtually every function in the cell and are therefore required at every cellular location. The route from initial translation to final destination is highly regulated. Protein production, sorting, trafficking, and targeting are so fundamental to cellular function that the cellular machinery that performs these functions are usually the largest and most obvious components of

Nucleic Acid Polymers and Transcription The only strand RNA that can continue to interact with is the 3' 5' strand, this is the one being read in RNA synthesis: 5' 3' is the directionality of the RNA strand. DNA - Coding strand 5' 3', because it is almost identical to the synthesized RNA strand. Non-coding strand - 3' 5' dRNA transcription - 5' 3' synthesized direction template strand Coding - Non-template - (+) Strand Non - Coding - Template - (-) Strand mRNA transcript - Sense Upstream

Sigma factor allows them to identify where the protein is located on the DNA Core enzyme contains catalytic activity of the enzyme – beta subunit catalyzes It is the sigma factor that is the regulatory component and recognizes the promoter General functions include Alpha recognizes the upstream element in DNA Beta has the polymerase activity which includes chain initiation and elongation Beta prime is involved in binding DNA and stabilizes the structure on the template of DNA Omega is a molecula

Transcription Process Divided into 3 main stages - Initiation, Elongation, Termination RNA polymerase is needed to recognize the promoter region - Which involves amino acids (in RNA Pol) recognizing nucleotides in the DNA. Recognition process is essential by which the amino acid sequence and nucleotides have been conserved for evolutionary times. They have similar sequences in different species. With the help of factor, helps (RNA Pol) to bind and align To transcribe in the correct place To tra

Transcription of a Eukaryotic Gene II Transcription Initiation Complex Eubacteria - core RNA polymerase (5 subunits) requires sigma factor to recognize -10 & -35 regions of the promoter Eukaryotes - ‘NA polymerase II (5+7 subunits) also requires ‘help’ to recognize the promoter: requires general transcription factors Not as straightforward as eubacteria, there are 7 additional subunits which they add extra complexity RNA II polymerase cannot recognize the promoter and requires HELPERS – call

Process that involves the synthesis of a linear sequence of amino acids – proteins themselves are made up of a limited number of 20 L-amino acids Protein synthesis process has a directionality to it –very discreet, one step at a time process, one peptide at a time is formed Protein begins synthesis at N-terminus, guided by the mRNA which is translated from the 5’ end to the 3’ end of RNA Leads synthesis of protein from N-terminus to C-terminus Once the process is finished, there is post-translat

Regulation is in groups in the same pathway. Eukaryotes - Transcription 1) Only Monocistronic - The way messages come in. 2) 3 types of RNA Polymerase to produce different types of RNA. 3) More complicated than prokaryotes. Compartmentilazation Exons / Introns (Why Introns in the first place?) DNA organization: tightly condensed chromatin with many proteins. Bacterial DNA has far fewer proteins. More players - different molecules and subunits The more complex - the more need of regulation. Havin