Genetics Chapter 8

Front 1

Wobble Theory (1 of 2)

Back 1

Analysis of the translation of each resulting mRNA into protein enabled them to identify the amino acid encoded by a particular combination of bases. From such experiments it was shown that several codons could encode the same amino acid, revealing the redundancy of the genetic code. Furthermore, the redundancy appeared to reside in the third amino acid in the codon (reading from the same end of the codon each time). This pattern of redundancy of the genetic code suggests that the pairing between the bases of the codon on the mRNA and the bases of the anticodon (the region that recognizes the corresponding codon) on the tRNA is unusual.

Front 2

What is Translation (1 of 2)

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Translation involves taking the message that's in the messenger RNA and in a sense decoding the message from the language of nucleic acids to the language of proteins or polypeptides. For translation to happen, the messenger RNA goes to the cytoplasm where it is attached to a cellular structure called a ribosome. Ribosomes are two part molecular assemblies consisting of various proteins plus a special kind of RNA called ribosomal RNA. Ribosomal RNA is involved in catalyzing some of the chemical reactions of translation.

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The genetic code is degenerate

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Because there are only 20 amino acids and 61 codons this suggests that the genetic code is degenerate i.e. each amino acid has more than one codon, and in fact all amino acids except trp and met are degenerate. However, the reverse is not true, there are no codons that specify more than one amino acid. Degeneracy is not uniform e.g. leu is 6-fold degenerate i.e. has 6 codons whereas tyr is only 2-fold.

Front 4

The genetic code is non overlapping

Back 4

This means that successive triplets are read in order. Each nucleotide is part of only one triplet codon

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Initiation in
Prokaryotic ribosome

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at the ribosome binding site there is the shine dalgarno box (AGGAGG) and initiation codon AUG the special tRNA whose anticodon is CAU this initiator RNA carries (fMET) functions only at initiation site. The 3' end of the 16s rRNA in the 30s subunit binds to Shine Dalgarno box and fMet binds to the mRNA's initiation codon at the end the fmet trna sits in the p site of the completed ribosome certain initiation factors (proteins) play a transient role in this process

Front 6

Enlongation in Prokarotic
Ribosome (1 of 2)

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Proteins known as enlongation factors usher the appropriate tRNA into the A site. the next tRNA must recognize the next codon of the mRNA the ribosome holds the initiating tRNA at p site and second at A site where an enzyme peptidyl transferase can catalyze the formation of a peptide bond between amino acids carried by the tRNA at the a site it also disconnects fmeth the n terminus of this dipeptide is fmeth the c termius is the second amino acid

Front 7

Enlongation in Prokarotic
Ribosome (2 of 2)

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Once formation of the first peptide bond causes the initiating tRNA in the P site to release its amino acid the ribosome moves exposing next mrna codon this requires enlongation factors and the input of energy as the initiation tRNA loses its amino acid is pushed in the E site and leaves the ribosome peptidyl transferase then catalyzes formation of the second peptide bond the tripeptide is connected at the c terminus of the trna that is currently in the A site each tRNA move fro A site P site to E site except initiator tRNA in the proceeds from N terminus to C terminus the ribosome must move in the 5' to 3' direction for the peptide chain to grow in the N to C direction

Front 8

Polyribosome

Back 8

structures formed by the simultaneous translation of a single mRNA molecule by multiple ribosomes

Front 9

Termination
in Prokarotic ribosome

Back 9

The ribosome releases the completed polypeptide no normal tRNA's carry anit codons for the nonsense codons UAA, UGA, UAG thus when the come into to A site no trna can bind to it instead proteins called release factors recognize the termination codon and brings polypeptide synthesis to a halt during this three things must occur the tRNA specifying the c terminal aminoacod releases the completed polypeptide the same tRNA as well as the mRNA seperate from the ribosome and the ribosome dissociates into its large and small subunits

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Prokaryotic Ribosome (70s)

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consists of the subunit 50s which consist of the 23s RNA with 3000 nucleotides and 5s 120nucleotides and 31 proteins
the 30s subunit has 16s RNA 1700 nucleotides and 21 proteins

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Eukaryotic Ribosome (80s)

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consist of a 60 s subunit with 28s rna (5000 nucleotides 5.8 s rna ( 160 nucleotides) 5s rna (120 nucleotide) 45 proteins
and a 40 s subunits with an 18s RNA (2000 nucleotides) 33 proteins

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Mutagens and Carcinogens

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A mutagen is a substance physical or chemincal agent that raises the frequency of mutations in cells or organisms above the spontaneous rate. A carcinogen is a substance that induces unregulated growth processes in cells or tissues of multicellular animals, leading to cancer. Although mutagen and carcinogen are not synonymous terms, the ability of a substance to induce mutations and its ability to induce cancer are strongly correlated. Mutagenesis refers to processes that result in genetic change, and carcinogenesis (the processes of tumor development) may result from mutagenic events

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Gene Expression

Back 13

the process by which a genes information is converted into RNA and then for protein coding genes into a polypeptide

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Central dogma of molecular
biology

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DNA codes for the production of RNA.
RNA codes for the production of protein.
Protein does not code for the production of protein, RNA or DNA.
However, the "Central Dogma" has had to be revised a bit. It turns out that you CAN go back from RNA to DNA, and that RNA can also make copies of itself. It is still not possible to go from Proteins back to RNA or DNA, and no known mechanism has yet been demonstrated for proteins making copies of themselves.

Front 15

Transcription/transcript

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the conversion of DNA encoded information to its RNA encoded equivalent a transcript is the product of transcription

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Transcriptional factor

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protein or RNA whose binding to ir indirect association with a cis control element helps regulate timing location and level of a particular genes transcription

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Messenger RNA

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RNA that serves as a template for protein synthesis

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Translation

Back 18

the process in which the codon carried by mRNA direct the synthesis of polypeptides from Amino acids according to the genetic code

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Reverse Transcription

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the process by which reverse transcriptase synthesizes DNA strands complementary to an RNA template the product of reverse transcription is a cDNA molecule

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Reverse transcriptase

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an RNA dependent DNA polymerase that synthesizes DNA strands complementary to an RNA template the product of reverse transcriptase is a cDNA molecule

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cDNA

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complementary DNA has a base sequence that is complementary to that os the mRNA template and contains no introns

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B-form DNA

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the most common form of DNA in which molecular configuration spirals to the right

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Z form DNA

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DNA in which nucleotides sequence cause the structure to assume a zigzag shape due to the helices spiraling to the left

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Charles Yanofsky

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American geneticist who demonstrated the colinearity of gene and protein structures

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intragenic suppression

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the restoration of gene function by one mutation canceling the efects of another mutation in the same gene

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Reading Frame

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the partitioning of groups of three nucleotides from a fixed starting point such that the sequential interprentation of suceeding triplet generates the correct order of amino acids in the resulting polypeptide chain

Front 27

Frameshift Mutation

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insertions or deletions of base pairs that alter the grouping of nucleotides into codons

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In vitro transcription/translation

Back 28

The transcription of a DNA molecule into mRNA molecules, and the subsequent translation of the mRNA molecules into polypeptides, within a laboratory mixture which contains ribosomes, enzymes, and all of the necessary components

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Promoter

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DNA sequences in the beginning of genes that signal RNA polymerase where to begin transcription

Front 30

RNA like Strand

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strand of double helical DNA molecule that has the same nucleotide sequence as am mRNA except for the substitution of T for U and the complementary to the template strand

Front 31

Template Strand

Back 31

the strand of the double helix that is complementary to both the RNA like DNA strand and the mRNA

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Stop Codon (nonsense codons)

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the three codons that terminate translation UAA, UGA, UAG

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Initiation Codon

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nucleotide triplet that marks the precise spot in the nucleotide sequence of an mRNA where the code for a particular polypeptide begins

Front 34

Hairpin loops

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structures formed when a single stranf of DNA or RNA can fold back on itself because of complementary base pairing between different regions of the same molecule

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Poly A tail

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the 3' end of eukaryotic mRNA consisting of 100-200 A's believed to stabalize the mRNA and increase the efficiency of the initial steps of translation this process occurs in two steps first ribonuclease cleaves the primary transcript to form a new 3' end this depends on the sequence AAUAAA which is found 11-30 nucleotides upstream then PAP adds the A's to the end of exposed 3' end

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Methylated cap

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formed by the action of capping enzyme and methyl transferases at the 5' end of eukaryotic mRNA critical for efficient translation of the mRNA to protein

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PCR (Polymerase chain reaction)

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a fast inexpensive method of replicaing a DNA sequence once the sequence has been indentified based on a reiterative loop that ampplifies the products of each previous round of replication

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Exons

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sequences that are found both in a gens DNA and in the corresponding mature mRNA

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Introns

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the DNA base sequences of a gene that are spliced out of the primary transcript and are therefore not foundin the mature RNA

Front 40

Spliceosome

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a complicated intranuclear clear machine that ensures that all of the splicing reactions take place in concert

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Splice donors

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nucleotide sequences in a primary transcript at the border between an intron and the upstream exon that proceeds it required for proper RNA splicing

Front 42

Splice acceptors

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nucleotide sequences in a primary transcript at the border between an intron and the downstream exon that follows it required for proper RNA splicing

Front 43

Branch sites

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special sequence of RNA nucleotides within an intron that helps form the lariat intermediate required for RNA splicing

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Ribozymes

Back 44

RNA molecules that can act as enzymes to catalyze specific chemical reactions

Front 45

Alternative Splicing

Back 45

production of different mature mRNA's from the same primary transcript by joining different combinations of exons

Front 46

Anti codons

Back 46

group of three nucleotides on transfer RNA (TRNA) molecules that recognize codons on the mRNA by complementary base pairing and the wobble

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Charged tRNA

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a tRNA molecule to which a corresponding amino acid has been attached by an aminoacyltRNA synthestase

Front 48

AminoacyltRNA synthestase

Back 48

enzymes that catalyze the attachment of tRNAs to their corresponding amino acids forming charged tRNA's

Front 49

Peptidyl transferase

Back 49

the enzymatic activity of the ribosome responsible for forming peptide bonds between successive amino acids

Front 50

Polyprotein

Back 50

polypeptides produced by translation that can subsequently be cleaved by protease enzymes into two or more seperate proteins

Front 51

Post translational modifications

Back 51

changes such as phosphorylation that occur to a polypeptide after translation has been completed

Front 52

silent mutations

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mutations without effects on phenotype usually denotes point mutations that change one of the three bases in a codon but that do not change the identity of the specifed amino acid because the degeneracy of the genetic code

Front 53

Missense mutation

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changes in the the nucleotide sequence of a gene that changes the identity of the amino acid in the polypeptide encoded by a gene

Front 54

Non sense mutations

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mutational changes in which a condon for an amino acid is altered to a stop codon resulting in the formation of a truncated protein

Front 55

loss of function mutation

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DNA mutation that reduces or abolishes the activity of a gene most but not all loss of function alleles are recessive

Front 56

null or Amorphic mutation

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mutations that abolish the function of a protein encoded by the wild type allele such mutations either prevent synthesis of the protein or promote sythesis of a protein incapable of carrying out any function

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nonsense suppressor tRNA's

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tRNAs encoded by mutant tRNA genes these contain anticodons that can recognize stop codons thus suppressing the effects of nonsense mutations by inserting an amino acid into a polypeptide in spite of the stop codon

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Hypomorphic mutation

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produces either less of a protein or a protein with a weak but detectable function

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haploinsufficiency

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a rare form of dominance in which an individual heterozygous for a wild type allele amd a null allele shows an abnormal phenotype because the level of gene activity is not enough to produce a normal phenotype

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dominant-negative or antimorphic alleles or mutations

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alleles that block the activity of wild type alleles of the same gene causing a loss of function even in heterozygotes

Front 61

Gain of function alleles or mutation

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rare mutations that enhance a genes function or confer a new activity on the genes product

Front 62

Neomorphic mutations

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rare mutations that produce novel phenotype due to production of a protein with a new function or due to ectopic expression of the protein

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Ectopic expression

Back 63

gene expression that occurs outside the cell or tissure where the gene is normally expressed

Front 64

Wobble theory (2 of 2)

Back 64

The pairing between the first two bases of the tRNA with the bases on the mRNA occurs as normal--one base recognizes and pairs only with a certain other base. But, the third base of the tRNA, at the 5' end of the anticodon, seems to be less restricted in its ability to pair with other bases. The wobble theory, published in 1966, proposed that this third base can pair with more than one type of base at the 3' end of the mRNA codon. This was proposed to be possible due to the increased spatial flexibility that could be attained by the 5' base

Front 65

What is translation (2 of 2)

Back 65

In addition to the ribosome, another kind of RNA called tRNA carries amino acids to the mRNA when it is attached to a particular part of the ribosome's small subunit, called a binding site. A critical feature of mRNA and how it is translated is the fact that each three nucleotides in the mRNA is called a codon and it is the codon that is translated. Thus the sequence of codons corresponds to the sequence of amino acids in the polypeptide. You will see that the tRNA molecules have a set of three nucleotide bases at one end that are complementary to a corresponding codon. The bases on the tRNA are called the anti codon. This is critical because the anti codons make the connection between the codons and the correct amino acids that go with each codon.