The Molecular Machinery of Life

The Molecular Machinery of Life • “…I went to Cambridge and saw the model and met Francis and Jim. It was the most exciting day of my life. The double helix was a revelatory experience; for me, everything fell into place and my future scientific life was decided there and then. • When the paper appeared a few weeks later, it was not well received by the establishment, composed largely of professional biochemists. They could not see, at the time, how profoundly it would change their subject by offering us a framework for studying the chemistry of biological information.” James Watson & Francis Crick

What does the number 3298 mean? The Decimal Code It means three thousand two hundred and ninety-eight. Humans use the decimal code so frequently (possibly because we have ten fingers) and so unconsciously that most of us have forgotten that it is a place-based number based on powers of ten—or the decimal base. We owe this numbering system to Hindu scholars who invented it certainly by the 6th century CE and possibly earlier. 3298

The Binary Code Numbers stored in computers use the base two, or binary system, which requires only 2 digits … 0 and 1. Why? Modern day computers are electronic gadgets. It’s loaded with tiny electronic switches, which either allow the passage of electrical current or block its passage. Can 3298 be represented as a binary number, which in turn is represented by the physical state of twelve switches? Switch closed = “1” Switch open = “0”

Binary Representation of 329810 The binary number this pattern of switch states represents is—1100111000102 By the way…a binary digit is called a bit

Is Information Nothing But Bits? • Yes! How does Google work? • The information Google retrieves is stored somewhere in ‘memory’ which is essentially arrays of electronic switches…set in patterns that are sequences of binary bits…1’s and 0’s in the form of binary code. • Computers can retrieve this information…run a ‘program’, also represented by specific patterns of binary bits, designed to process some algorithm - a sequence of steps required to perform some kind of calculation or answer some question. • The necessary programmed instructions had to be translated into binary code…and ‘loaded into the computer’ so that it could execute the algorithm to perform a calculation…or in the case of Google…to find and retrieve the data that answers a question—presumably faster than could be accomplished by its human programmer.

Question All information could (in principle) be stored in a large enough digital computer in the form of a _______ binary code genetic code bar code secret code nasal code

Life • The process just described is analogous to the process of life—information is retrieved from storage and acted upon to produce a result. • The information that life uses is not stored in an electronic memory in the form of a binary code, nor is its ‘computer’ a bunch of electronic circuits. • The storage facility and ‘computer’ in living organisms are all molecular—produced by chemical reactions that take place in biological systems—these molecules are mostly DNA, RNA and proteins. • The energy necessary to process the information doesn’t come from the electric power company—it’s extracted from other molecules, which ultimately got its store of energy from the Sun.

DNA - The Basic Code of Life DNA has two jobs: • Make copies of itself • Carry the instructions on how to make proteins These instructions are called genes

A DNA Nucleotide • The sugar in DNA is deoxyribose. The phosphate is one phosphorous atom surrounded by 4 oxygen atoms. • Each DNA nucleotide • Contains one of four nitrogenous basesabbreviated by a letter— • A for adenine • T for thymine • C for cytosine • G for guanine. The nucleotide Adenine —A • The sugar and phosphate form the spine • The nitrogenous base forms ½ rung.

Four Nucleotides of DNA base-pairing rule: A—T and C—G adenine links to thymine and cytosine links to guanine. 4 possible links: (i) A—T (ii) T—A (iii) C—G (iv) G—C. The base-pairing rule makes it possible to store information via the genetic code.

How Information is Stored DNA is shaped like a double helix ‘ladder’ consisting of 2 spines held together by rungs. The spine and half of a rung of the DNA ‘ladder’ is made of a linked chain of nucleotides—the sugar-phosphate group of one nucleotide linked to the sugar phosphate group of another.The nitrogenous base “dangles” out on the side of each nucleotide forming half of a rung. Resembles the structure of a ladder—twisted into the shape of a double helix.

Question The molecule formed from 2 long nucleotide chains linked together by nitrogenous bases according to a base pairing rule and twisted into the shape of a double helix is called _____ RNA MTA ATP NBA DNA

RNA vs DNA The sugar ribose (OH instead of an H) replaces deoxyribose The base Uracil replaces the Thymine in RNA (H replaces H2C)

Question The molecule formed from a single nucleotide chain in which each nucleotide consists of (1) phosphate (2) the sugar ribose and (3) 1 of the 4 nitrogenous bases; (i) adenine (ii) uracil (iii) guanine and (iv) cytosine is called _____ RNA NBA MTA AAA DNA

Central Dogma of Molecular Biology Flow of information is a one-way street! • Information contained in DNA can be transferred to another DNA (replication) • Information contained in DNA can be copied into mRNA (transcription) • Proteins can be synthesized using the information in mRNA as a template (translation)

Transcription of DNA Transcription of DNA is catalyzed by the RNA polymerase enzyme (RNAP). The information that controls the construction of a specific protein lies along a segment of the DNA molecule called a gene. This information consists of essentially three parts: The result: a short strand called messenger RNA (mRNA) that contains the code of one gene used to string together amino acids to make a protein! • A sequence of nucleotides that make up a promoter region and a leader sequence that guides the beginning of the transcription—followed by— • A region that contains the nucleotides that code for the specific amino acid sequence that make up the protein to be constructed—followed by— • A series of nucleotides that make up a terminal sequence that stop the transcription.

The Genetic Code 3 Nucleotides in a row make up 1 codon. Each codon is the ‘information’ that specifies 1 of 20 possible amino acids that make up all possible proteins. How many unique combinations are there that can be formed out of 3 nucleotides in a row if there are 4 possible choices for each nucleotide? Answer: 4 x 4 x 4 = 43 = 64

DNA  mRNA  Protein

Translation of mRNA → Protein DNAATGACGGAGCTTCGGAGCTAGTACTGCCTCGAAGCCTCGATC mRNAAUGACGGAGCUUCGGAGCUAGProteinStart -Thr-Glu-Leu-Arg-Ser- Stop Codons 1 and 7 ‘decode’ as ‘Start’ and ‘Stop’ Codons 2 — 6 ‘decode’ as specific amino acids, which will be linked together to form a protein.

Building a Protein

Description of Process Amino acids ‘float’ around in the cytoplasm of a cell. They are attracted and attached to transfer RNA (tRNA). There is one unique tRNA molecule for each of the possible words 64 ‘words’ in the genetic code—thus there are different tRNAs that carry the same amino acid. Ribosomes are enzymes made from complexes of RNA’s and proteins. They are divided into two subunits, one larger than the other. The smaller subunit binds to the mRNA —the larger subunit binds to the tRNA (and the amino acid it carries). As a ribosome ‘reads’ a codon, it attracts the appropriate tRNA molecule to it. The tRNA molecule enters one part of the ribosome and binds to the mRNA codon being read (the binding of the tRNA molecule takes place because it contains the anti-codon corresponding to the mRNA codon). The attached amino acids are joined together by another part of the ribosome. The ribosome moves along the mRNA, ‘reading’ the gene sequence — producing an amino acid chain. The process terminates when a ‘stop’ codon is read. The two subunits of the ribosome then release a completed polypeptide chain—the protein.

Protein Synthesis Flow of information is a one-way street … from DNA→ protein. Transcription: Information contained in DNA ‘transcribed’ intomRNA Translation: mRNAinformation ‘translated’ by ribosomeaccording to genetic codeandamino acidslinked together to form proteins

Question The process in which information stored in DNA is transcribed to form mRNA, which is then translated by ribosomes to make proteins is called _____ natural selection Intelligent design the central dogma of molecular biology spontaneous generation evolution

HIV Virus-a ‘Retrovirus’ The virus is encapsulated by a phospholipid layer from which protrudes a complex of 70 proteins whose geometry is designed to mate with certain protein receptors in the host cell (uh-oh)! At this point, the host cell is infected—the cell’s replication machinery will now replicate the virus! Upon entry to the target cell, an enzyme contained within the virus called reverse transcriptase converts the virus’ RNA genome into a small, double stranded DNA genome. Another of the virus’ enzyme, called integrase, integrates, or inserts the virus DNA genome into the host cell DNA.

Question A virus is able to replicate _____ by itself without any ‘outside’ help by ‘co-opting’ a cell’s replication machinery sexually — with a willing partner by stealing energy stored in a cell’s supply of ATP cloning

Mutation: A change in DNA sequence We transmit 75-100 new DNA variants to each of our offspring.

Mutations: Mostly Harmful What happens if DNA is damaged or miscopied? As a heuristic example, consider miscopying a single letter in a string of text …THEFATCATSAT… There is no punctuation but each 3 consecutive letters are analogous to a codon in DNA and the properly transcribed and translated sentence would read— …THE FAT CAT SAT … Now, suppose that the C is miscopied as an R then the codon sequence becomes …THEFATRATSAT… and the decoded text, based on reading each triplet codon in sequence, would translate to—…THE FAT RAT SAT … This is analogous to an x-ray knocking out a nucleotide, say an A, in a gene and your cellular repair machinery ‘fixing it’ by replacing it with a T. Let’s see what can happen …

Mutations: Mostly Harmful This is what you can get …sickle-cell anemia, which kills 100,000 people per year Caused by the change of an A to a T in 6th codon of the gene for the hemoglobin molecule—from GAG to GTG, which codes for the hydrophobic amino acid valine instead of the hydrophilic glutamic acid This single mutation results in a disastrous change in the shape of the hemoglobin molecule

Control Genes Control genes determine when and where other genes are ‘turned on’ Mutations in these genes can affect the way different parts of an organism are assembled!

Hox Gene Mutation Hox genesdetermine where your head and appendages grow Mostly, a mutation is bad news! A hox gene mutationcould lead to an entirely new body typethat would be better adaptedto its environment than its predecessors. A mutation could cause eyes to be positioned more towards the front of an organism and away from the sides. Ultimately such mutant members of an ocean-going species might slowly migrate to the land. Such genes would tend to proliferate, while those that endow their ‘carriers’ with a lesser survivability out of water would tend to die away.

How much do we differ?(number of DNA base differences) • Identical twins 0 • Unrelated humans 1/1,000 • Human vs. chimp 1/100 • Human vs. mouse 1/30 • Human vs. broccoli 2/3 • 3 billion DNA bases  3 million differences between each pair of individuals

Information Storage + ‘Copying Error’ → Evolution • All living organisms are essentially ‘bags of information’—they are vessels that carry molecular genes that have endowed them with high survival probability. • The genesof the ‘vessels’ that survive … proliferate in the gene pool. The gene is the basic unit of information in DNA that drives the natural selection. • Understanding how genes control the characteristics of all living organisms completes and extends the explanation of natural selection given by Charles Darwin long before the basic mechanisms of genetics were understood. • Natural selection, or ‘survival of the fittest,’ is a genetically driven process—the fittest simply carry the ‘right genetic stuff.’!

The Molecular Machinery of Life