Chapter IV Genetics

DNA and Protein Synthesis

Yalun Arifin
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Basic definitions
DNA: The molecule that encodes genetic information. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. The four nucleotides in DNA contain the bases: adenine (A), guanine (G), cytosine (C), and thymine (T). In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner. RNA: A chemical found in the nucleus and cytoplasm of cells; it plays an important role in protein synthesis and other chemical activities of the cell. The structure of RNA is similar to that of DNA. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different purpose.

DNA and RNA

Biochemistry of DNA
Double Helix Two DNA strands are antiparallel. Held together by base pairs: •Hydrogen bonds between the nitrogen-containing bases •A = T, and G = C

DNA Structure Reveals Key to Replication
Each of the two original strands serves as a template for construction of a new matching strand.

carrying code for protein synthesis . thymine is replaced by uracil Nucleotides joined by covalent bonds between sugar and phosphate to make a chain Bases are laid out in specific and highly varied order.DNA and RNA In RNA.

DNA Nucleotide O S P O S G S A T PS PS S C G SP P GC S S P P AT PS T A S SP P S T P A G C T A A T S P PS S A C G P S G C P C O P S O P P O S A T S O P T A P A T PS S AT P S P S P T A G C S P SP .

DNA: Central dogma .

Central dogma in cells .

. DNA Transcription and RNA Translation are not physically separated.In the absence of a nuclear membrane.

heterogeneous RNA (hnRNA). undergoes extensive posttranscriptional processing to make mRNA. . The primary transcript. proteins are made in the cytoplasm.DNA undergoes replication and transcription in the nucleus. RNA must therefore travel across the nuclear membrane before it is translated: transcription and translation are physically separated.

AAA. TAA) that encodes a certain amino acid. G. C).T. Thus. •DNA ligase permanently attaches short sections to make one chromosome. Process catalyzed by enzymes: •DNA polymerase catalyzes addition of matching bases. DNA Replication New helices are composed of half old (original) and half new nucleotides. and proofreads. .How do DNA keep the information? The genetic information in DNA in kept in the sequences of bases in the nucleotides (A . This code consists of 3 nucletiodes (e. ATG. 64 codes are possible to give the infinite number of genetic sequences.g.

. Translation.Protein Synthesis How Proteins Are Made: Genetic Transcription. – Every protein has a unique amino acid sequence. and Regulation • Proteins: Polypeptides – Strands of amino acids (20 different) joined by peptide bonds.

H H H3N C H C O– O O C H3N C CH O– CH2 CH3 isoleucine glycine (gly) ile H3N gly glu cys ala cys val ser tyr leu asn cys C asn O O– val gln ser cys leu gln glu tyr .

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• Protein Synthesis: Two Stages – Stage 1—DNA contains information for protein but resides in the nucleus. proteins are made in the cytoplasm. – Stage 2—Amino acids added in correct order by using the information on the RNA (translation). Solution: Copy DNA into small strands of RNA (transcription). .

OVERVIEW OF TRANSCRIPTION AND TRANSLATION DNA TRANSCRIPTION (in nucleus) mRNA ribosomes tRNA mRNA TRANSLATION (in cytoplasm) protein .

RNA nucleotide O O– H C N H N H uracil (base) O ribose (sugar) DNA nucleotide O O– H3C C N H N H O HO P O CH2 H O O Phosphate H group OH OH HO P O CH2 H O O Phosphate H group OH H thymine (base) deoxyribose (sugar) RNA strand C U S P S P S P sugar-phosphate handrail Bases: cytosine (C) guanine (G) adenine (A) uracil (U) DNA strand G A P S P C T S P S sugarphosphate handrail Bases: cytosine (C) guanine (G) adenine (A) thymine (T) C S P S G A U U C S P S G T S C G C S S P A T A P S P P S A T G C .

each variety capable of combining with a specific amino acid) that attach the correct amino acid to the protein chain that is being synthesized at the ribosome of the cell (according to directions coded in the mRNA) Ribosomal RNA: RNA found in ribosome . these sequences are transcribed into RNA but are cut out of the message before it is translated into protein.coding sequences of a gene. Exons: the sequences in the DNA molecule that code for the amino acid sequences of corresponding proteins.Basic definitions Intron: The DNA base sequences interrupting the protein. the form of RNA that carries information from DNA in the nucleus to the ribosome sites of protein synthesis in the cell Transfer RNA: short-chain RNA molecules present in the cell (in at least 20 varieties. Messenger RNA: the template for protein synthesis.

– tRNA (transfer RNA) involved in matching correct amino acid to specific instructions in mRNA.• Three Types of RNA Transcribed – mRNA (messenger RNA) carries instructions for sequence of amino acids in a protein. – rRNA (ribosomal RNA) important component of ribosomes. .

transfers amino acids to ribosomes Transfer RNA (tRNA) Ribosomal RNA (rRNA) Cytoplasm Structural component of ribosomes .2 Types of RNA Type of RNA Messenger RNA (mRNA) Functions in Function Nucleus.Table 14. migrates to ribosomes in cytoplasm Cytoplasm Carries DNA sequence information to ribosomes Provides linkage between mRNA and amino acids.

. – RNA polymerase catalyzes addition of new nucleotides into a single strand of RNA (called a transcript) from one strand of the double helix.• Transcription Uses Base Pairing – DNA used as a template to match complementary bases. – C to G and A to U (not T).

mRNA CGUUCA GC A AGTAC C T GA RNA nucleotides DNA mRNA mRNA .

.• RNA Processing – mRNA is edited. – The remaining pieces (called exons) are joined together to make the finished product. – Parts to be cut out are called introns.

exon 1 INTRON exon 2 INTRON exon 3 enzyme enzymes cut into the introns edited mRNA transcript .

• Making Sense of “Junk” DNA – Only 1.5% of our DNA codes for proteins (1 inch out of 6 feet). 10% of DNA. . congregate in gene-rich areas. tips of chromosomes. – Rest is noncoding DNA—housekeeping (regulatory) sequences. and ―junk‖: • Introns • Repetitive Sequences   ―Selfish DNA‖ Primates have 1 million Alu (280 base pairs long) repeats.

etc. not oneto-one code. 20 amino acids in protein. . AC.• Genetic Code: How DNA Codes for Amino Acid Sequence – Four bases in DNA. AT.). – Not two to one either—There are only 16 possible combinations of two bases of DNA (AA. AG. CA. – Triplet code—three nucleotides (called a codon) signifying one amino acid.

THE TRIPLET CODE DNA G C A A G T A C C T G A TRANSCRIPTION mRNA C G U U C A U G G codon codon codon A C U codon TRANSCRIPTION protein arg ser trp thr .

– Redundant = several different codons signify the same amino acid. – Universal .• Codon Table – 64 different possible combinations of the four nucleotides—more than enough for the 20 different amino acids. UAA. – Carries instruction codons for stopping (UGA. UAG) and starting (AUG) translation.

Second Base U C phe leu UCU UCC UCA UCG ser UAU UAC UAA UAG A tyr stop stop his gln asn lys asp glu UGU UGC UGA UGG G cys stop trp arg U C A G U UUU UUC UUA UUG First Base C CUU CUC CUA CUG leu CCU CCC CCA CCG ACU ACC ACA ACG GCU GCC GCA GCG pro CAU CAC CAA CAG AAU AAC AAA AAG GAU GAC GAA GAG CGU CGC CGA CGG AGU AGC AGA AGG GGU GGC GGA GGG U C A G U C A G U C A G Third Base A AUU AUC ile AUA AUG met (start) GUU GUC GUA GUG val thr ser arg G ala gly .

– tRNA molecules (transfer RNA) are ―translator‖ molecule. – tRNA can match the appropriate amino acid with the codon in the mRNA.• Translation Requires Translator – mRNA carries the instructions in the codons for each of the amino acids. .

thr gly mRNA ribosome .

.• Structure of Transfer RNA – Part of the molecule binds an amino acid. – The other end has three nucleotides (anticodon) that form a base pair with the codon in the mRNA.

amino acid amino acid attached site tRNA molecule G CU anticodon CG A codon mRNA attachment site mRNA .

• Ribosomes: The Location of Protein Synthesis – Large conglomerate of enzymes and ribosomal RNA (rRNA) in two subunits. – P site—binds tRNA attached to growing chain of polypeptides. – A site—binds tRNA-carrying amino acids. .

mRNA large subunit protein small subunit protein large subunit mRNA P A site site small subunit .

• Steps of Translation .

met met AUG mRNA start codon leu leu met met CUG A P site site A P site site .

met leu met leu A P site site A P site site thr met Polypeptide chain leu A P site site .

– Bacteria (E.• Genetic Regulation: Lac Operon – Operon = multipart genetic system. – Example—lactose. called an inducer – Genes involved: • y (permease enzyme to help lactose enter the cell) • z (-galactosidase enzyme to cut lactose into galactose and glucose) • a gene • i (codes for repressor protein) . coli) synthesize certain enzymes only if substrate is present.

polymerase which clips lactose molecules codes for permease enzyme that transports lactose into cells .lac operon regulator gene promotor operator i gene codes for repressor protein p o z gene y gene a gene DNA binding site codes for of RNA -galactoseidase.

so no enzymes made. .• Lac Operon: Regulatory DNA Sequences – Upstream promoter (acts as a binding site for RNA polymerase) – Between promoter and first gene is operator. – No transcription. – Repressor binds operator: prevents RNA polymerase from binding to the promoter.

RNA polymerase i gene p o z gene repressor protein blocks binding of RNA polymerase y gene a gene DNA no transcription repressor protein .

• Lac Operon: Lactose Inducer Present – Cell needs to make enyzmes only when lactose is present. so transcription ensues. . it will not bind the operator. – Repressor binds lactose.

2 RNA polymerase binds to promoter i gene repressor p o z gene y gene a gene DNA 3 transcription proceeds mRNA transcript lactose -galactosidase 1 lactose the (inducer) inactivates the repressor so that it cannot bind to the operator permease galactose glucose lactose .

000 and 100.000 specifically required proteins. – Some are made continuously.• Magnitude of Metabolic Operations – Human cells have between 50.000 genes. – But one cell usually makes only 5. .000 to 20. and others are inducible.