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Biochemistry I - Overview of Biological Information Flow

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    Study Guide Biochemistry I – Overview of Biological Information Flow 1. RNA Carries Genetic Information DNA stores genetic information in two complementary strands. Each strand carries information that can be used to build the other. However, during transcription , usually only one DNA strand is used as a template to make RNA. RNA is different from DNA in an important way — it is single - stranded , not double - stranded. How DNA Is Copied into RNA RNA is made by matching bases with the DNA template strand: • DNA base A pairs with RNA base U • DNA base T pairs with RNA base A • DNA base C pairs with RNA base G • DNA base G pairs with RNA base C For example: A DNA sequence 3′ ATCCG 5′ is transcribed into an RNA sequence 5′ UAGGC 3′ RNA Is Temporary and Flexible Unlike DNA, RNA is not permanent . A single DNA gene can produce many RNA copies , which are used to make proteins and then broken down into nucleotides again. This disposable nature of RNA allows cells to respond quickly to changes by making only the RNA they need at a given time.

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    Study Guide Promoters and Transcription Start Sites RNA synthesis does not begin randomly. Special DNA sequences called promoters tell RNA polymerase (the enzyme that makes RNA) where to start transcription . • In prokaryotes , common promoter regions are the – 35 region and – 10 region • In eukaryotes , promoter regions often include the – 70 region and – 25 (TATA box) Figure 1 Messenger RNA specifies the order of amino acids in proteins 1.1 Messenger RNA and the Genetic Code Proteins are long chains (polymers) of amino acids . The order of amino acids determines a protein’s structure and function. Codons: Reading the Message The message in mRNA is read in groups of three nucleotides , called codons . • There are 4 RNA bases (A, U, G, C) • Possible codons = 4³ = 64 • Only 20 amino acids exist

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    Study Guide This means: • More than one codon can code for the same amino acid • The genetic code is redundant Start and Stop Signals The genetic code includes special signals, similar to punctuation in language: • AUG → codes for methionine (Met) o Acts as the start codon o Signals where protein synthesis begins • UAA, UAG, UGA → stop codons o Signal the end of protein synthesis Methionine can appear both at the start and within proteins , just like a capital letter can appear at the start or inside a sentence.

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    Study Guide 1.2 Universality of the Genetic Code Almost all organisms use the same genetic code , from bacteria to humans. However, small variations exist. Example: Mycoplasma • Mycoplasma DNA is rich in A and T • The codon UGA , which is normally a stop codon, codes for tryptophan in Mycoplasma • This happens because the usual tryptophan codon ( UGG ) is rare in its genome Amino Acid Abbreviations Here are standard abbreviations used for amino acids: • phe – phenylalanine • leu – leucine

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    Study Guide • ile – isoleucine • met – methionine • val – valine • ser – serine • pro – proline • thr – threonine • ala – alanine • tyr – tyrosine • his – histidine • gln – glutamine • asn – asparagine • lys – lysine • asp – aspartic acid • glu – glutamic acid • cys – cysteine • trp – tryptophan • arg – arginine • gly – glycine Transfer RNA (tRNA) Transfer RNA ( tRNA ) acts as a bridge between mRNA and proteins . It ensures that the correct amino acid is added for each codon. Two Key Functional Parts of tRNA 1. Anticodon o A set of three nucleotides o Base - pairs with the complementary mRNA codon

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    Study Guide 2. Acceptor End o Located at the 3′ end o Holds the specific amino acid Charging the tRNA Each amino acid is attached to its correct tRNA by a specific enzyme called aminoacyl - tRNA synthetase . This step ensures accuracy in protein synthesis . Figure 2 Ribosomes and translation 1.3 Ribosomes and Translation Ribosomes are the cellular machines that build proteins. Structure of Ribosomes • Composed of about 2/3 RNA and 1/3 protein • Made of two subunits :

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    Study Guide o Small subunit o Large subunit Functions of Ribosomes Ribosomes perform several key tasks: • Start protein synthesis ( initiation ) • Match mRNA codons with tRNA anticodons • Form peptide bonds between amino acids • Move mRNA through the ribosome • Release the completed protein Role of Ribosomal Subunits • Small subunit o Binds mRNA o Helps in codon – anticodon pairing o Involved in initiation and termination • Large subunit o Catalyzes peptide bond formation o Extends the growing polypeptide chain

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