Chapter 10: Nucleic Acids and Protein Synthesis 10-1 DNA 10-2 RNA 10-3 Protein Synthesis

10-1 DNA I. Structure of DNA (stores INFORMATION for PROTEIN making) DOUBLE-stranded nucleic acid  backbone and nucleotide SEQUENCE.

(1) Deoxyribose (“The Backbone”) 5-C sugar of DNA that LINKS a PHOSPHATE with a NITROGENOUS BASE.

(2) Nitrogenous Bases (“The Instructions”) 4 TYPES of “RUNGS” of a DNA  1 part of a NUCLEOTIDE (Adenine, Thymine, Cytosine, Guanine ARE the bases)

(3) Purines (i.e., Adenine and Guanine) N-bases with TWO rings of C and N atoms (bond to a PYRIMIDINE).

(4) Pyrimidines (i.e., Cytosine and Thymine) N-bases with ONE ring of C and N atoms (bonds to a PURINE).

(A) The Double Helix (1953, James Watson and Francis Crick) Two backbones bonded by “rungs” (HYDROGEN Bonds)  a double SPIRAL (i.e., COVALENT bonds holding sugar-phosphate backbone together).

(B) Complementary Base Pairing (who bonds to who?) Base-pairing RULES of DNA  TWO base pairs form due to WEAK HYDROGEN bonding between bases: Adenine-Thymine (A-T) [2 H-bonds] Cytosine-Guanine (C-G) [3 H-bonds]

II. Replication of DNA (during S phase of cell cycle) TWO nucleotide strands UNZIP and UNWIND  EACH strand serves as a TEMPLATE for a new COPY.

(1) Replication Fork (marks a LOCATION for replication to begin) POINT where TWO chains are SEPARATED by enzymes (HELICASES).

Critical Thinking (1) A DNA molecule (labeled as A) replicates to produce two new DNA molecules (labeled as B). Both of the B DNA molecules then replicate to form four new DNA molecules (labeled as C). Are any nucleotide chains from A present in the C DNA molecules? Explain your answer. If you believe the answer is yes, how many of the A DNA nucleotide chains are present in the C DNA molecules?

(2) Helicases (nuclear enzymes used for replication AND transcription) Enzymes move along DNA, breaking H-bonds between base pairs, causing two DNA sides to SEPARATE.

(3) DNA Polymerase (nuclear enzyme used for BUILDING DNA) Enzyme BUILDS TWO new IDENTICAL strands from UNZIPPED DNA, using complementary BASE PAIRING.

(A) Accuracy and Repair (of DNA during Replication) During replication, about ONE error occurs in every 10,000 paired nucleotides (due to “proof-reading” enzymes).

(1) Mutation (caused by mutagens OR proofreading errors) A change in the ORIGINAL nucleotide (BASE) sequence due to a MISTAKE in replication. NOTE: The combination of DNA proofreading and repair processes help keep the ERROR RATE one per 1 BILLION nucleotides.

10-2 RNA I. Structure of RNA (Ribonucleic Acid) RNA is SINGLE-stranded, w/ Ribose, Uracil, and exists in 3 TYPES.

(1) Ribose (replaces deoxyribose, found in DNA) SUGAR of the sugar-phosphate BACKBONE in RNA.

(2) Uracil (NO Thymine in RNA) A new BASE bonds to ADENINE (in place of Thymine in RNA) [U-A in RNA].

(A) Types of RNA (mRNA, rRNA, and tRNA) 3 types are needed to complete PROTEIN SYNTHESIS, using original DNA.

(1) Messenger RNA (mRNA) Carries a COPY of DNA’s SEQUENCE out of NUCLEUS to CYTOSOL; (NOTE: mRNA is single stranded).

(2) Transfer RNA (tRNA) A single chain of RNA folded into a “ t ” shape  transfers an AMINO ACID (45 types of tRNA found floating in the CYTOSOL).

(3) Ribosomal RNA (rRNA  make up RIBOSOMES) RNA bound to GLOBULAR proteins where PROTEINS are ASSEMBLED (on the protein workbenches).

II. Transcription (DNA  mRNA in the NUCLEUS) Only the REQUIRED sequence of DNA BASES are copied onto mRNA and will LEAVE the nucleus for a RIBOSOME.

(A) Steps of Transcription (what to COPY, when?) GOAL = BEGIN copying and END copying the desired DNA sequence at the CORRECT LOCATION.

(1) RNA Polymerase (like DNA Polymerase) Enzyme (light blue) transcribes (copies) a specific sequence (dark blue) of DNA onto a new molecule (yellow) (mRNA).

(2) Promoters (promoter (BEGIN)  termination signal (END)) RNA polymerase INITIALLY binds to PROMOTER, in order to mark BEGINNING of the TRANSCRIPTION.

(3) Termination Signal (Polymerase releases DNA and mRNA) A specific SEQUENCE of bases that marks END of transcription.

Critical Thinking (2) Does it matter which of the separated DNA chains is used for transcription? Why or why not?

(B) Products of Transcription A SEQUENCE of mRNA must find a ribosome to be TRANSLATED.

10-3 Protein Synthesis I. Protein Structure and Composition (proteins are also called polypeptides) POLYPEPTIDE chain of AMINO ACIDS is linked by PEPTIDE BONDS.

NOTE: Although only 20 types of amino acids EXIST, a polypeptide can BE MADE OF 100s to 1,000s of AA in sequence, depending on size of protein. SEQUENCE of the AA determines 3-D SHAPE of protein Determines FUNCTION of protein. (shape influences ability to bind to other molecules)

II. The Genetic Code (RNA  Amino Acids) Translates mRNA sequences into AMINO ACID sequences, and ultimately PROTEINS. (1960’s) Note: DNA and RNA are read (interpreted) in TRIPLETS (3 nucleotides at a time) Ex: DNA may read “AAT CCG ATC”

(1) Codon (Triplet of mRNA  one mRNA may have MANY codons) Exists in 64 combinations AND each codes for amino acid (Ex: AUG codon). NOTE: Most code for an AMINO ACID, however there are TWO types of codons that do NOT code for an amino acid AND play a different role during protein synthesis.

(2) Start Codon (AUG) Coding for “Methionine”, and SIGNALS to RIBOSOME to START TRANSLATING.

(3) Stop Codon (Ex: UGA  NO Amino Acid at this location) SIGNALS to ribosome to STOP translating mRNA and RELEASE the polypeptide (protein).

III. Translation (Step FOLLOWING Transcription) “Translating” mRNA with tRNA into an AMINO ACID SEQUENCE for a specific protein. NOTE: Transcription and Replication (NUCLEUS) of a cell, Translation MUST occur in the CYTOSOL where the ribosomes are located.

Critical Thinking (3) How is a system composed of THREE bases per codon better suited to code for 20 amino acids than a system composed of TWO bases per codon?

(A) Anticodons and tRNA (codon-mRNA triplet, anticodon-tRNA triplet) Anticodon (tRNA) in cytosol will bond to its proper codon (mRNA)  Links AMINO ACIDS together  PROTEIN is made.

(1) Anticodon (“coat hanger” triplet of tRNA) CARRIES an amino acid and BONDS to mRNA codon found on the RIBOSOME. Ex: In a sequence of mRNA: AGG UUA CGA, there are 3 CODONS: Resulting 3 tRNA ANTICODONS that bond to THIS SEQUENCE, carrying with them, 3 AMINO ACIDS would be… tRNA: UCC AAU GCU

(B) Ribosomes (protein and rRNA  Nucleolus) Protein WORKBENCHES where proteins are ASSEMBLED. Hold THREE binding sites that are key: (1) ONE Site for mRNA codon. (2 and 3) TWO sites for tRNA anticodon.

Critical Thinking (4) What would translation of the mRNA transcript UAACAAGGAGCAUCC produce?

(C) Protein Synthesis (Rough ER  Exported, Free Ribosome  Used in cell) Once BUILT from amino acids, a protein can be MODIFIED. (typically Met gets removed, the 1st AA) NOTE: Several ribosomes (i.e., a polysome) can simultaneously translate same mRNA transcript (Ex: Imagine a rope overhanging 4 or 5 workbenches)

Extra Slides AND Answers for Critical Thinking Questions (1) Yes. Each replicated DNA molecule is a hybrid consisting of one new nucleotide chain and one original nucleotide chain. Two of the eight nucleotide chains would have originated from the A DNA molecule. (2) Yes. Because templates are complementary, they do not contain identical sequences of nucleotides. A sequence complementary to the template will code for different information. (3) No protein would be produced because the mRNA begins with a stop codon, not a start codon. (4) Three bases per codon provide more than enough units for the 20 amino acids that make up proteins. Two bases would provide only 42 or 16 units.