Study

Since most of my education has taken place above the organism level, and since my current job concerns sub-organism processes, I want to get more familiar with those sub-organism things. So I’m reading and taking notes on my blog about the stuff I’m reading. First off is the PDF compiled by Franco Preparata from Brown University called “A Biology Primer for Computer Scientists” at https://web.stanford.edu/class/cs173/papers/bioprimer.pdf section 1 life is defined as being able to replicate, and that’s possible with DNA section 2 chemical composition chemical makeup of life is largely composed of carbon, hydrogen, nitrogen and oxygen. molecules have different binding strengths and therefore different energy levels to break them molecules are held together by many types of bonds, one of which is the covalent bond an agent that aids a chemical reaction is a catalyst; a biological catalyst is an enzyme an enzyme itself is a molecule; and enzyme has a specific shape that matches a specific reagent it will catalyze building blocks of living organisms are biomolecules; basic ones are sugars, fatty acids, amino acids, and nucleotides. two important types of sugars are ribose and deoxyribose amino acids are particularly important, of which there are 20 types amino acids make up proteins; polysaccharides made of large carbohydrates; section 3 nucleic acids building blocks of nucleic acids are nucleotides a nucleotide is made up of three components: a base B, a sugar S and a phosphoric acid P. there’s 8 different nucleotide types (G, A, C, and T in DNA, and G, A, C, U in RNA) the S sugar of each nucleotide is called ribose; nucleotides polymerize as nucleic acids, either DNA or RNA DNA Is double stranded; RNA Is single stranded in DNA the two strands orient opposite directions with 5’ to 3’ and the other strand going 3’ to 5' in DNA, each strand has nucleic acids that bind to the complementary nucleic acid in the other strand section 4 fundamental cell processes three major processes occur in the cell: DNA replication, DNA-RNA transcription and RNA-protein translation. section 5 DNA replication DNA replication is the process by which a double-stranded DNA sequences produces two double-stranded sequences identical to the original one replication always proceeds from the 5’ end to the 3’ end - therefore goes in opposite directions in each strand (leading strand is 5’-3’, lagging strand is 3’-5') DNA polymerases facilitate the replication For the leading strand a string of about 200 bases indicates where to start For the lagging strand each Okazaki fragment is initiated by an RNA string synthesized by a specific enzyme section 6 DNA-RNA transcription transcription only uses the so called “genomic” strand, the one that goes from 5’ to 3' machinery that does transcription is called RNA-polymerase. it separates two DNA strands along a short area and transcription occurs along the short exposed strand, and DNA strands rejoin as the process proceeds In DNA replication, DNA is replicated in its entirety, whereas transcription is selective both in space (only certain substrings of DNA are transcribed) and time (depending on environment). Different types of RNA: mRNA (messenger; involved in RNA-protein translation), rRNA (ribosomal; participate in the structure of the ribosome), tRNA (transfer; assume a rigid 3d configuration acting as linkages between mRNA and protein chains), snRNA (small nuclear; excision of introns and splicing of exons) section 7 RNA-protein translation aka Protein synthesis DNA is segmented into triplets of nucleotides; each triplet == codon; each codon is individually translated into an amino acid there are 64 codons there are 20 amino acids (so each amino acid is encoded by more than 1 codon) translation occurs in the ribosome. ribosome can be compared to a tape reader (an mRNA sequence) that also produces an output tape (a protein). tRNA is also required (and are specific to a codon/amino acid pair?) section 8 protein structure proteins are polymers (polypeptides) amino acids fully specify a protein, BUT it is its spatial arrangement that determines its function how polypeptides fold is not fully understood protein structure levels primary: the linear sequence of amino acids secondary: local folding patterns such as alpha helices and beta sheets tertiary: complete 3D shape of a single polypeptide chain quaternary: arrangement of multiple polypeptide subunits within a protein complex