Important words and concepts from Chapter 17, Campbell & Reece, 2002 (1/29/2005):

by Stephen T. Abedon (abedon.1@osu.edu) for Biology 113 at the Ohio State University

 

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(1) Chapter title: From Gene to Protein

(a)                    "The DNA inherited by an organism leads to specific traits by dictating the synthesis of certain proteins. Proteins are the links between genotype and phenotype."

(b)                    [from gene to protein (Google Search)] [index]

 

REPLICATION VS. TRANSCRIPTION VS. TRANSLATION

 

(2) Central dogma of molecular genetics (reverse transcription) (see also central dogma)

(a)                    The central dogma of molecular genetics is typically depicted as a shorthand review of how genetic information moves around a cell, or from parent to offspring.

(b)                    The central dogma looks like this:

(i)                     DNA <-- DNA --> RNA --> protein

(c)                    Note that we can give names to these various steps:

(i)                     DNA --> DNA = replication (direction of arrow is arbitrary)

(ii)                   DNA --> RNA = transcription (direction of arrow is not arbitrary)

(iii)                 RNA --> protein = translation (ditto)

(d)                   This chapter deals particularly with the last two, transcription and translation

(e)                    Description: central-dogma

(f)                     (reverse transcription serves as an exception to the central dogma as originally conceived; it consists of DNA <-- RNA, i.e., RNA --> DNA, and is employed by such things as retroviruses including the virus that causes AIDS; note in the above figure that, of course, proteins also serve as enzymes)

(g)                    [central dogma, central dogma molecular genetics (Google Search)] [index]

(3) RNA (uracil) (see also RNA and uracil)

(a)                    See Figure, Overview: the roles of transcription and translation in the flow of genetic information

(b)                    RNA is a nucleic acid polymer that resembles DNA except

(i)                     RNA uses the sugar ribose instead of deoxyribose; Ribose has an --OH group at the 2' carbon instead of the --H seen with deoxyribose found in DNA

(ii)                   RNA employs the nitrogenous base uracil (U) instead of the pyrimidine thymine; that is, T is approximate by U

(c)                    The analogous base-pairing is U-A

(d)                   Note that U is energetically cheaper to make than T but that U is also less stable than T

(e)                    [RNA, uracil (Google Search)] [index]

(4) One gene-one polypeptide hypothesis (see also one gene, one enzyme)

(a)                    Beadle and Tatum developed the one gene-one enzyme hypothesis in the 1940s

(b)                    The idea is that Mendel's hereditary units are found in DNA but work by specifying enzymes

(c)                    This hypothesis was modified to one gene-one protein since not all proteins are enzymes but genes work by specifying proteins

(d)                   Finally, this hypothesis was modified to one gene-one polypeptide since many proteins consist of more than one polypeptide

(e)                    Genes specify the construction of specific polypeptides

(f)                     (in fact, to deconstruct things further, genes specify the transcription of specific RNAs)

(g)                    See Figure, Beadle and Tatum's evidence for the one gene--one enzyme hypothesis

(h)                    ["one gene one protein", "one gene one polypeptide", "one gene one peptide" (Google Search)] [index]

 

SOME PRODUCTS OF TRANSCRIPTION

 

(5) Transcription--introduction (template strand) (see also transcription and template strand)

(a)                    The DNA --> RNA flow of genetic information is termed transcription

(b)                    The term transcription reflects that the information in DNA (i.e., nucleotide sequence) is copied into a similar code in RNA

(c)                    Only one strand of the two possible strands of DNA is typically copied (always one strand per transcriptional unit)

(d)                   In different places on a chromosome the other strand may be copied

(e)                    The DNA strand that provides the complementary template to RNA polymerization is called the template strand

(f)                     The RNA can be of a number of types including:

(i)                     Messenger RNA (mRNA)

(ii)                   Transfer RNA (tRNA)

(iii)                 Ribosomal RNA (rRNA)

(iv)                 Etc. (e.g., spliceosomes)

(g)                    See Figure, Overview: the roles of transcription and translation in the flow of genetic information

(h)                    (see transcription in detail, below)

(i)                      [RNA transcription, template strand (Google Search)] [index]

(6) Messenger RNA (mRNA) (see also messenger RNA and mRNA)

(a)                    If the RNA produced by transcription is to be used to code for the synthesis of proteins, it is called messenger RNA (a.k.a., mRNA)

(b)                    [messenger RNA, mRNA (Google Search)] [index]

(7) Transfer RNA (1) (tRNA) (see also transfer RNA and tRNA)

(a)                    Another category of RNA, used during protein synthesis to ferry amino acids to growing peptide chains, is called transfer RNA (a.k.a., tRNA)

(b)                    (for more information, see transfer RNA, below)

(c)                    [transfer RNA, tRNA (Google Search)] [index]

(8) Ribosomal RNA (rRNA) (see also ribosomal RNA and rRNA)

(a)                    Another category of RNA that together constitute about 60% of the mass of ribosomes is called ribosomal RNA or rRNA

(b)                    (in Escherichia coli cells, ribosomes make up 25% of the dry weight of cells)

(c)                    [ribosomal RNA, rRNA (Google Search)] [index]

 

THE GENETIC CODE

 

(9) Codons (see also codon)

(a)                    The DNA and RNA nucleotide sequence code consists of one of four types of nucleotides (4 each, that is)

(b)                    The amino acid sequence code consists of 20 amino acids

(c)                    In translating from nucleotide sequence to amino acid sequence there cannot be a one-to-one correspondence (4 < 20)

(d)                   There also cannot be a two-to-one correspondence (42 < 20)

(e)                    Instead there exists a three to one correspondence (43 > 20)

(f)                     The three nucleotides that specify an amino acid during translation are called codons

(g)                    See Figure, The triplet code

(h)                   See Figure, The dictionary of the genetic code

(i)                      [codons or codon (Google Search)] [the genetic code (the table of codons and what that means) (Shaun D. Black)] [index]

(10) Codons are a property of mRNA (see also codon, mRNA and sense codon)

(a)                    Note that codons exist in mRNA, but only their complement exists on the template strand of DNA

(b)                    (though note, additionally, that on the non-template strand of DNA the analogous DNA codons--though without uracil--exists)

(c)                    See Figure, The dictionary of the genetic code

(d)                   [codons mRNA (Google Search)] [index]

(11) Redundancy of triplet code (see also redundancy of the genetic code)

(a)                    43 = 64 >> 20

(b)                    Consequently, there are many more codons than there are amino acids

(c)                    However, 61 of the 64 possible codons do code for an amino acid

(d)                   This is because many amino acids are specified by more than one codon

(e)                    See Figure, The dictionary of the genetic code

(f)                     (no, you don't have to memorize the figure)

(g)                    [triplet code redundancy OR redundant (Google Search)] [index]

(12) Lack of ambiguity in the triplet code (see also lack of ambiguity in the genetic code)

(a)                    Note that while the code is redundant, it is not ambiguous

(b)                   That is, each codon specifies for one and only one amino acid, not more than one

(c)                    [triplet code ambiguity (Google Search)] [index]

(13) Codons don't overlap (see also codon)

(a)                    Another property of codons is that they are arrayed one after another in the mRNA

(b)                    That is, they do not overlap

(c)                    (note that there is an only slightly related exception in which codons can overlap and this is when reading frames of different genes overlap)

(d)                   See Figure, The triplet code

(e)                    [codons overlap (Google Search)] [index]

(14) There is no punctuation between codons (see also lack of punctuation between codons)

(a)                    Furthermore, codons do not have gaps between them (i.e., there is no punctuation)

(b)                   See Figure, The triplet code

(c)                    [punctuation codons (Google Search)] [index]

(15) Start codon (AUG, methionine) (see also start codon, AUG, and methionine)

(a)                    The codon AUG codes for the amino acid methionine

(b)                    See Figure, The dictionary of the genetic code

(c)                    AUG also specifies the initiation of translation

(d)                   Thus, all polypeptides initially begin with methionine (Met)

(e)                    Note that as a part of post-translational protein processing the Met amino acid is often clipped off

(f)                     (though I don't expect you to learn all of the codons and their assignments, you should memorize AUG, methionine, and the fact that it serves as the start codon of reading frames)

(g)                    [start codon, methionine (Google Search)] [index]

(16) Stop codons (nonsense codons) (see also stop codon, nonsense codon, and nonsense mutation)

(a)                    Only 61 of the 64 possible codons specify amino acids

(b)                    The other three specify what are known as stop codons

(c)                    (or nonsense codons to distinguish them from the other 61 sense codons)

(d)                   See Figure, The dictionary of the genetic code

(e)                    Stop codons instruct the ribosome to stop adding amino acids to the growing peptide chain

(f)                     [stop codon (Google Search)] [index]

(17) Reading frame (see also reading frame)

(a)                    The sequence of codons beginning with AUG and ending with a stop codon is called the reading frame

(b)                    Note that the reading frame consists of (x + 1) * 3 nucleotides where x is the number of amino acids found in the resulting polypeptide (prior to post-translational modification) and the additional 1 is a stop codon

(c)                    [reading frame, open reading frame (Google Search)] [index]

(18) (nearly) Universal triplet code (see also triplet code)

(a)                    The language of codons is nearly universal among extant organisms

(b)                    (e.g., AUG specifies Met and is the start codon in all or nearly all living organisms)

(c)                    This near-universality is taken as evidence that all extant organisms share a common ancestor

(d)                   Furthermore, the divergence from this common ancestor must have occurred at a time after the implementation of the triplet code

(e)                    Since the triplet code is somewhat arbitrary, the converse hypothesis, that all organisms somehow independently adopted the same codons for each amino acid, is much less likely

(f)                     As a consequence of the near-universality of the triplet code, genes from one organism may be transferred into unrelated organisms and still express (i.e., be transcribed then translated)

(g)                    [universal triplet code (Google Search)] [index]

 

THE PROCESS OF TRANSCRIPTION

 

(19) Transcription in detail (see also transcription)

(a)                    Transcription takes place in three steps

(i)                     DNA binding and initiation

(ii)                   Elongation of the RNA strand

(iii)                 Termination of transcription

(b)                    The primary enzyme involved is called RNA polymerase

(c)                    See Figure, The stages of transcription: initiation, elongation, and termination

(d)                   See Figure, A summary of transcription and translation in a eukaryotic cell

(e)                    [RNA transcription (Google Search)] [index]

(20) RNA polymerase (see also RNA polymerase)

(a)                    RNA polymerase works similarly to DNA polymerase

(b)                    Like DNA polymerase, RNA polymerase employs a DNA template (i.e., the template strand) but, of course, polymerizes RNA

(c)                    Just as with DNA polymerase, RNA polymerase synthesizes in the 5' --> 3' direction

(d)                   [RNA polymerase (Google Search)] [index]

(21) Promoter binding (transcription factor) (see also transcription initiation, promoter, and transcription factor)

(a)                    The first step in transcription is DNA binding

(b)                    In prokaryotes this involves the recognition of specific DNA sequences (promoters) by the RNA polymerase

(c)                    See Figure, The initiation of transcription in a eukaryotic promoter

(d)                   In either case, the promoter is found upstream from the start codon

(e)                    Once bound the RNA polymerase begins transcribing (i.e., polymerizing RNA from a DNA template)

(f)                     In eukaryotes this involves the binding of RNA polymerase to proteins, called transcription factors, that are involved in sequence recognition

(g)                    [promoter binding (Google Search)] [index]

(22) Elongation (1) (see also elongation (molecular genetics) and transcription)

(a)                    To initiate transcription, the RNA polymerase must separate the DNA strands of the double helix

(b)                    Throughout the elongation of the RNA transcript, the DNA strand is kept open approximately 10 bases

(c)                    Note that a given gene may be transcribed by more than one RNA polymerase simultaneously, with one RNA polymerase following another along on the transcribed DNA

(d)                   See Figure, The stages of transcription: initiation, elongation, and termination

(e)                    [transcription elongation (Google Search)] [index]

(23) Termination of transcription (see also termination (molecular genetics))

(a)                    Just as transcription is initiated at certain base sequences, it is similarly terminated at specific base sequences

(b)                    With termination the RNA transcript is released from the RNA polymerase and DNA template strand, and the RNA polymerase from the DNA

(c)                    See Figure, The stages of transcription: initiation, elongation, and termination

(d)                   [transcription termination (Google Search)] [index]

 

WEIRD MOSTLY EUCARYOTE STUFF

 

(24) mRNA processing (see also messenger RNA processing)

(a)                    The compartmentalization of the eukaryotic cell results in a separation of transcription and translation, both spatially and temporally

(b)                    Eukaryotic cells take advantage of this compartmentalization to modify RNAs prior to translation

(c)                    Modifications include

(i)                     Addition of a 5' cap

(ii)                   Addition of a poly-A tail

(iii)                 Removal of introns

(d)                   See Figure, RNA processing: addition of 5' cap and poly(A) tail

(e)                    mRNAs are allowed to leave the nucleus only once they have been processed

(f)                     (recall that translation occurs only in the cytosol)

(g)                    [mRNA processing (Google Search)] [index]

(25) Eukaryotic segregation of transcription and translation (see also segregation of transcription and translation)

(a)                    Note that due to the existence of the nuclear membrane in eukaryotes, there exists a temporal and spatial separation of transcription and translation

(b)                   See Figure, Overview: the roles of transcription and translation in the flow of genetic information

(c)                    Transcription occurs within the nucleus, where the DNA resides

(d)                   Translation occurs within the cytosol, where the functional ribosomes reside

(e)                    There is no such segregation of transcription and translation in prokaryotes

(f)                     [segregation of translation and transcription (Google Search)] [index]

(26) Introns and exons (see also intron and exon)

(a)                    Most eukaryotic genes do not exist as continuous reading frames

(b)                    Eukaryotic mRNAs, however, do exist as continuous reading frames

(c)                    The conversion of RNAs that do not possess continuous reading frames to ones that do is a form of mRNA processing

(d)                   The intervening sequences that disrupt reading frames in genes and in RNAs prior to their processing are called introns (i.e., intervening sequences)

(e)                    The sequences which are spliced together, upon the removal of introns, to form a continuous reading frame are called exons (i.e., expressed sequences)

(f)                     See Figure, RNA processing: RNA splicing

(g)                    [introns exons (Google Search)] [index]

(27) Spliceosome (see also spliceosome)

(a)                    There exists a nuclear structure involved in intron excision called a spliceosome

(b)                    Note that yet another form of RNA plays a functional role in spliceosomes

(c)                    See Figure, The roles of snRNPs and spliceosomes in mRNA splicing

(d)                   [spliceosome (Google Search)] [index]

 

TRANSLATION

 

(28) Translation--introduction (see also translation and genetic code)

(a)                    The RNA --> protein flow of genetic information is termed translation

(b)                    The term translation reflects that the information in mRNAs (i.e., nucleotide sequence) is translated into a new "language", i.e., amino acid sequence

(c)                    See Figure, Overview: the roles of transcription and translation in the flow of genetic information

(d)                   (see translation in detail, below)

(e)                    [protein translation (Google Search)] [index]

(29) Translation in detail (see also translation )

(a)                    Translation is far more complex than transcription, involving many dozens of distinct macromolecular players

(b)                    See Figure, Translation, the basic concept

(c)                    These players include

(i)                     Transfer RNAs

(ii)                   Ribosomes

(iii)                 Aminoacyl-tRNA-synthetases

(iv)                 mRNA

(v)                   The growing peptide

(d)                   Analogously, transcription employs DNA, RNA polymerase, and a growing RNA transcript

(e)                    Like transcription, translation occurs in three basic steps

(i)                     Initiation

(ii)                   Elongation

(iii)                 Termination

(f)                     Note that much of translation is powered by the nucleoside triphosphate GTP (which you last saw during the Krebs cycle) rather than ATP

(g)                    Remember that the primary goal of translation is the synthesis of a polypeptide from mRNA-coded information

(h)                    Also, keep in mind that it is probably much easier to understand translation by following the figures in your text than from simply reading the text or these lecture notes

(i)                      See Figure, A summary of transcription and translation in a eukaryotic cell

(j)                      [translation RNA (Google Search)] [index]

(30) Transfer RNA (2) (see also transfer RNA and tRNA)

(a)                    Transfer RNAs are the translating units

(b)                    One side of the tRNA binds to a specific codon found on an mRNA

(c)                    The other side binds to a specific amino acid

(d)                   See Figure, Translation, the basic concept

The Genetic Code (supplemental table)

 

U

C

A

G

 

U

Phenylalanine

Serine

Tyrosine

Cysteine

U

C

Leucine

STOP

STOP

A

Tryptophan

G

C

Leucine

Proline

Histidine

Arginine

U

C

Glutamine

A

G

A

Isoleucine

Threonine

Asparagine

Serine

U

C

Lysine

Arginine

A

Methionine

G

G

Valine

Alanine

Aspartic Acid

Glycine

U

C

Glutamic Acid

A

G

(e)                    See Figure, The structure of transfer RNA (tRNA)

(f)                     [transfer RNA, tRNA (Google Search)] [index]

(31) Anticodon (see also anticodon)

(a)                    The region of the tRNA that binds to the mRNA codon is called the anticodon

(b)                   See Figure, Translation, the basic concept

(c)                    Note that the anticodon is more or less complementary to the mRNA codon in terms of base-pairing

(d)                   [anticodon (Google Search)] [index]

(32) Wobble (see also wobble)

(a)                    This complementarity between codon and anticodon is "more or less" because the third base of a codon tends to be ambiguously bound by the anticodon

(b)                    Note that much of the variation in the sequence of the codons specifying individual amino acids is found in the third base of the codon

(c)                    The anticodon third-base ambiguous binding is why redundant (i.e., synonymous) codons tend to vary at the third base

(d)                   This tendency of anticodons to bind codons varying in their third base is called wobble (see table to right)

(e)                    See Figure, The dictionary of the genetic code (to see how the third bases in codons tend to have a more-minor role in specifying the amino acid than the first two bases)

(f)                     See Figure, The structure of transfer RNA (tRNA) (note that it is the 5' base that is read ambiguously due to wobble)

(g)                    [wobble translation (Google Search)] [index]

(33) Aminoacyl-tRNA synthetases (see also aminoacyl tRNA synthase and aminoacyl tRNA)

(a)                    tRNAs employ their anticodons to bind specific codons found on mRNAs

(b)                    However, tRNAs are not responsible for specifying what amino acid they attach to

(c)                    Instead there exist enzymes that recognize specific tRNAs (often at the anticodons) and attach specific amino acids

(d)                   These enzymes are called aminoacyl-tRNA-synthetases

(e)                    (yes, it is a big word; sound it out as: amino-acyl-tRNA-syn-theh-tase)

(f)                     The cost of amino acid addition is one ATP

(g)                    See Figure, An aminoacyl-tRNA synthetase joins a specific amino acid to a tRNA

(h)                    There exist at least one aminoacyl-tRNA-synthetase for each amino acid (i.e., 20)

(i)                      [aminoacyl-tRNA synthetase (Google Search)] [index]

 

THE PROCESS OF TRANSLATION

 

(34) Ribosomes (A site, P site, E site) (see also ribosome, A site, P site, and E site)

(a)                    Ribosomes are the machines within which tRNAs function to read the mRNA code and translate that code into polypeptides

(b)                    Ribosomes consist of one large and one small subunit (both which are complexes of rRNA and many proteins)

(c)                    Ribosomes have three major binding sites, one each for

(i)                     The mRNA

(ii)                   The tRNA attached to the incoming amino acids (the A site)

(iii)                 The tRNA attached to the growing polypeptide (the P site)

(d)                   Ribosomes additionally have an "E site" from which tRNAs exit the ribosome

(e)                    See Figure, The anatomy of a functioning ribosome

(f)                     The ribosome's function is to catalyze the peptide bond formation between the polypeptide held at the P site to the incoming amino acid held at the A site

(g)                    [ribosome (Google Search)] [index]

(35) Initiation (see also translation initiation)

(a)                    Initiation of translation involves the binding of the Met-carrying tRNA to the AUG start codon found on the mRNA that in turn is bound to the small subunit of the ribosome

(b)                   See Figure, The initiation of translation

(c)                    Note that the mRNA is bound to the ribosome by a ribosome-recognition sequence found on the mRNA

(d)                   Note that the tRNA is found at what will be the P site

(e)                    The large ribosomal subunit then binds to the small subunit

(f)                     The above binding occurs at a cost of one GTP

(g)                    [translation elongation (Google Search)] [index]

(36) Elongation (2) (see also translation elongation)

(a)                    Elongation in translation is more complex than that of transcription because there are more players (e.g., tRNAs and ribosomes) and because the mRNA is read three nucleotides (one codon) at a time rather than only a single nucleotide (i.e., as in transcription)

(b)                    Charged tRNAs (i.e., ones to which an amino acid is bound) diffuse into the A site and only those that successfully interact with the mRNA codon stay there (this step actually requires energy to perform--two GTPs per amino acid added)

(c)                    A peptide bond is then formed between the incoming amino acid and the peptide held at the P site (this releases the peptide from the P-site located tRNA--no additional energy is required from that already stored in the various molecules involved)

(d)                   The mRNA is then translocated one codon forward so that the tRNA that had held only one amino acid in the A site, but now holds the growing polypeptide, is now found in the P site

(e)                    The translocation step requires one GTP

(f)                     See Figure, The elongation cycle of translation

(g)                    Note that the ribosome moves along the mRNA in the 5' --> 3' direction--the mRNA thus moves through the ribosome in the 3' --> 5' direction (i.e., the 5' end leads)

(h)                    [translation elongation (Google Search)] [index]

(37) Termination (see also translation termination and termination (molecular genetics))

(a)                    When the codon in the A site is a nonsense (stop) codon, no associated tRNA exists

(b)                    Instead release factors bind to the stop codon in the A site

(c)                    This causes the now-completed peptide to be hydrolyzed off of the P site tRNA

(d)                   In addition, the ribosome releases the mRNA and then separates into two subunits

(e)                    See Figure, The termination of translation

(f)                     [translation termination (Google Search)] [index]

 

POST-TRANSLATION PROCESSES

 

(38) Post-translational polypeptide modification (see also post-translational modification)

(a)                    "During and after its synthesis, a polypeptide chain begins to coil and fold spontaneously, forming a functional protein of specific conformation: A three-dimensional molecule with secondary and tertiary structures. A gene determines primary structure, and primary structure determines conformation."

(b)                    Posttranslational modifications of this folding polypeptide, however, can include

(i)                     Covalent attachment of sugars, lipids, phosphate groups, etc.

(ii)                   Removal of one or more leading (amino) end amino acids (e.g., Met)

(iii)                 Cleavage of polypeptide chain

(c)                    [post-translational modification, posttranslational modification (Google Search)] [index]

(39) Signal sequences (see also signal sequence)

(a)                    The targeting of proteins occurs during and after translation

(b)                    An amino-terminal amino acid sequence can play a role in protein targeting

(c)                    Such sequences are called signal sequences

(d)                   "Signal sequences function like ZIP codes, addressing proteins to certain locations in the cell."

(e)                    See Figure, The signal mechanisms for targeting proteins to the ER

(f)                     [signal sequence (Google Search)] [index]

 

MUTATION

 

(40) Mutation (see also mutation)

(a)                    A mutation is a replicable change in nucleotide sequence

(b)                    Contrast this with DNA damage which is a non-replicable alteration in DNA structure

(c)                    Mutations come in a variety of (often overlapping) categories including

(i)                     Point mutations

(ii)                   Silent mutations

(iii)                 Missense mutations

(iv)                 Nonsense mutations

(v)                   Insertions

(vi)                 Deletions

(vii)               Frameshift mutations

(d)                   [mutation (Google Search)] [index]

(41) Mutations are typically detrimental . . . (see also detrimental mutation, detrimental allele, deleterious allele, and lethal allele)

(a)                    Mutations represent a change in highly evolved information

(b)                    Typically changes to well functioning systems are detrimental, and mutations are no exception

(c)                    (i.e., mutations are the biological equivalent of a violation of the "If it ain't broke', don't fix it" axiom)

(d)                   [mutations detrimental, mutations bad (Google Search)] [index]

(42) ...but Mutations are the only way to change (see also beneficial mutation beneficial allele, neutral mutation, allele (neutral), and neutral variation)

(a)                    Despite the typically detrimental nature of mutations, they also represent the only way in which novel, beneficial information is typically introduced into a genetic system

(b)                    (the other way is horizontal transfer, i.e., from different species, and even then mutations still represent the ultimate source of information)

(c)                    Thus, while mutations typically are detrimental, from time to time a mutation actually increases the survival and reproductive potential of an organism

(43) Point mutation (see also point mutation)

(a)                    Mutations come in a number of "flavors", the easiest to envisage being the point mutation

(b)                    A point mutation is simply a change of one nucleotide in a base sequence to a different nucleotide (e.g., a change from A to G)

(c)                    See Figure, The molecular basis of sickle-cell disease: a point mutation

(d)                   Upon replication that change will be duplicated into the complementary strand of one of the daughter chromosomes

(e)                    [point mutation (Google Search)] [index]

(44) Silent mutation (see also silent mutation)

(a)                    Point mutations, even those occurring within exons, need not result in changes to amino-acid sequence

(b)                    Why? Recall that third base substitutions in codons frequently will not result in a change in the amino acid coded for

(c)                    [silent mutation (Google Search)] [index]

(45) Missense mutation (see also missense mutation)

(a)                    When a point mutation results in a change in amino acid, that mutation is termed a missense mutation

(b)                   See Figure, Categories and consequences of point mutations

(c)                    Note that missense mutations may or may not have significant impact on protein structure or function

(d)                   If the mutation occurs in a less crucial region of a polypeptide, or results in a change to a functionally similar amino acid, no significant impact may occur

(e)                    If the mutation occurs in the active site or other crucial region of the polypeptide, significant impact may occur

(f)                     Note that typically any impact will be detrimental

(g)                    [missense mutation (Google Search)] [index]

(46) Nonsense mutation (see also nonsense mutation)

(a)                    A nonsense mutation is a point mutation that results in a change from an amino acid-coding codon (a.k.a., a sense codon) to a stop codon (a.k.a., nonsense codon)

(b)                   See Figure, Categories and consequences of point mutations

(c)                    Note that nonsense mutations truncate polypeptides (i.e., shortens them)

(d)                   Note also that not all sense codons can be converted to a nonsense codon via only a single point mutation

(e)                    [nonsense mutation (Google Search)] [index]

(47) Insertion (see also insertion)

(a)                    An insertion increases the number of nucleotides in a sequence

(b)                    [insertion mutation (Google Search)] [index]

(48) Deletion (see also deletion)

(a)                    A deletion decreases the number of nucleotides in a sequence

(b)                    [deletion mutation (Google Search)] [index]

(49) Frameshift mutation (see also frameshift mutation)

(a)                    Insertions or deletions of more or less than multiples of three cause the most significant disruption

(b)                    Such changes are termed frameshift mutations because they change the sequence of the entire gene downstream of the mutation

(c)                    (i.e., they shift reading frames)

(d)                   See Figure, Categories and consequences of point mutations

(e)                    Frequently such changes result in the "formation" of an in-frame stop codon which serves to truncate the protein

(f)                     [frameshift mutation (Google Search)] [index]

 

CODA

 

(50) What is a gene? (see also what is a gene?)

(a)                    "Mendelian" (classical genetical) concept: Discrete unit of inheritance

(b)                    "Morgan" (chromosome theory) concept: Locus on a chromosome

(c)                    "Watson and Crick" (DNA structure) concept: sequence of nucleotides

(d)                   "Beadle and Tatum" I (biochemical) concept: one gene-one enzyme

(e)                    "Beadle and Tatum" II (biochemical) concept: one gene-one protein

(f)                     "Beadle and Tatum" III (biochemical) concept: one gene-one polypeptide

(g)                    "Modern" I (transcriptional) concept: one gene-one RNA

(h)                    "Modern" II (post-transcriptional) concept: one gene-more than one type of RNA (especially in eukaryotic systems)

(i)                      "Abedon" (pedagogical) concept: one gene-one exam question! (ha, ha)

 

VOCABULARY

 

(51) Vocabulary [index]

(a)                    A site

(b)                    AUG

(c)                    Aminoacyl-tRNA-synthetases

(d)                   Anticodon

(e)                    Central dogma of molecular genetics

(f)                     Codons

(g)                    Codons are a property of mRNA

(h)                    Codons don't overlap

(i)                      Deletion

(j)                      E site

(k)                    Elongation (1)

(l)                      Elongation (2)

(m)                  Eukaryotic segregation of transcription and translation

(n)                    Frameshift mutation

(o)                    Initiation

(p)                    Insertion

(q)                    Introns and exons

(r)                     Lack of ambiguity in the triplet code

(s)                     Messenger RNA

(t)                     Methionine

(u)                    Missense mutation

(v)                    Mutation

(w)                  mRNA

(x)                    mRNA processing

(y)                    Nonsense mutation

(z)                    One gene--one polypeptide hypothesis

(aa)                 P site

(bb)                Point mutation

(cc)                 Post-translational polypeptide modification

(dd)               Promoter binding

(ee)                 Reading frame

(ff)                  Redundancy of triplet code

(gg)                Ribosomal RNA

(hh)                Ribosomes

(ii)                    RNA

(jj)                    RNA polymerase

(kk)                rRNA

(ll)                    Signal sequences

(mm)            Silent mutation

(nn)                Spliceosome

(oo)                Start codon

(pp)                Stop codons

(qq)                Template strand

(rr)                   Termination

(ss)                  Termination of transcription

(tt)                   There is no punctuation between codons

(uu)                Transcription factor

(vv)                Transcription in detail

(ww)            Transcription--introduction

(xx)                Transfer RNA (1)

(yy)                Transfer RNA (2)

(zz)                 Translation in detail

(aaa)             Translation--introduction

(bbb)            tRNA

(ccc)             Universal triplet code

(ddd)          Uracil

(eee)             What is a gene

(fff)               Wobble

(52) Practice questions [index]

(a)                    What has a promoter, a nonsense codon, and a start codon?

(b)                    What is the primary enzyme involved in transcription?

(c)                    During translation, just prior to a subsequent elongation step, the two "business" ends of tRNA found in the A site are associated with __________ at one end and __________ at the other. (note: each blank may be filled with a reasonably large number of correct answers; the answer to neither is ribosome)

(d)                   The tendency of anticodons to bind codons varying in their third base is called __________.

(i)                     Wobble

(ii)                   Ambiguity

(iii)                 Redundancy

(iv)                 Versatility

(v)                   Termination

(vi)                 Elongation

(e)                    Describe the contents of the A site and the P site of a ribosome following initiation of translation but prior to the start of elongation. Be very specific in your description of the contents.

(f)                     Distinguish silent mutation from missense mutation.

(g)                    An insertion of how many nucleotides (> zero) would we predict would be minimally disruptive of gene product (polypeptide) function?

(h)                    A(n) __________ is a string of amino acids found at the amino end of a growing polypeptide which specifies the location in the cell to which the polypeptide should be transported.

(i)                      Name the three aspects of the central dogma (as classically defined) of molecular genetics (i.e., the names corresponding to DNA --> DNA, DNA --> RNA, and RNA --> protein information flow).

(j)                      Name the four nitrogenous bases found in RNA.

(k)                    How does the timing/physical location of transcription or translation differ between prokaryotes and eukaryotes?

(l)                      Name the nucleotide sequence of a single codon as well as the amino acid that codon specifies.

(m)                  Concerning the location of the start codon and the direction of travel of the RNA polymerase, approximately where is the transcription promoter found?

(n)                    Which of the following is not directly associated with a functioning (i.e., elongation stage) ribosome?

(i)                     Transfer RNA

(ii)                   Ribosomal RNA

(iii)                 Aminoacyl-tRNA-synthetases

(iv)                 Messenger RNA

(v)                   The growing peptide

(vi)                 All are directly associated

(o)                    What is the technical term used to describe the ability of some tRNAs to recognize more than one codon during translation, particularly their ability to recognize different third-base nucleotides?

(p)                    Describe the initiation of translation including as many relevant details as you can recall. That is, be as thorough and as detailed as you can. However, note that this question is not asking for a complete description of all of translation and I strongly encourage you to just describe the initiation of translation. Relative points will be gained for any relevant detail. Relative points will be lost for incorrect information, so don't BS! (All points are lost if you don't at least plausibly describe the initiation of translation.) Use (properly labeled) figures and diagrams if you like (though these are by no means required). Do try to write both neatly and articulately.

(q)                    A tRNA to which an amino acid has been attached is said to be __________.

(r)                     The last thing added to a peptide-tRNA complex during the termination of the ribosome-associated translation process is __________.

(s)                     What is a signal sequence?

(t)                     What is a point mutation?

(u)                    What is a nonsense mutation?

(v)                    What kind of mutations result in frame shifts ("frameshift mutation" is not an acceptable answer)?

(w)                  Polypeptides are not the products of all genes (rRNA is an example of a non-polypeptide gene product). However, for those genes whose ultimate products are polypeptides, how many different types of functional polypeptides does an individual gene typically produce?

(i)                     1

(ii)                   2

(iii)                 3

(iv)                 4

(v)                   5

(x)                    For what cellular process involving nucleic acid polymerization is only a single template strand typically involved?

(y)                    About 60% of the mass of ribosomes consists of what non-proteinaceous type of macromolecule? Please be specific.

(z)                    What cellular constituent in eukaryotes physically segregates transcription from translation? (no, mRNA is not the answer)

(aa)                 How many sense (i.e., amino-acid-coding) codons are there?

(i)                     20

(ii)                   32

(iii)                 58

(iv)                 61

(v)                   64

(bb)                What does a lack of codon ambiguity mean?

(cc)                 What is the significance of "AUG"?

(dd)               For a protein consisting a single 380 amino-acid-long polypeptide, how many nucleotides long is the reading frame that codes for this protein? Assumed no post-translational modification and don't worry about introns.

(ee)                 In transcription, incoming ribonucleoside triphosphates chemical react with what specific functional group found on the growing RNA transcript?

(ff)                  What do promoters promote?

(gg)                Which aspect of mRNAs is common (at various times in their processing and function) to both eukaryotes and most bacteria

(i)                     AUG

(ii)                   5' cap

(iii)                 Coupled transcription and translation

(iv)                 Introns

(v)                   Poly-A tail

(hh)                What RNA-containing nuclear structure is necessary for the creation of continuous reading frames in many eukaryotic mRNAs?

(ii)                    On what kind of molecule does one find anticodons?

(jj)                    What are the three substrates of aminoacyl-tRNA-synthases necessary for tRNA activation?

(kk)                What is a nonsense mutation?

(ll)                    Frameshift mutations can result from which of the following mutation types

(i)                     Deletion

(ii)                   Missense

(iii)                 Nonsense

(iv)                 Point

(v)                   Silent

(mm)            Why is the phrase "One gene-one enzyme" less correct than the phrase "One gene-one polypeptide"?

(nn)                Name the three classes (types) of RNAs typically produced by cells.

(oo)                Why is there no segregation of transcription from translation in prokaryotes?

(i)                     Binary fission vs. mitosis/meiosis

(ii)                   Circular vs. linear chromosomes

(iii)                 Different ribosome types

(iv)                 Lack vs. presence of nucleus

(v)                   Presence vs. absence of multigene mRNAs

(pp)                Besides DNA, on what specific type of molecule does one find codons?

(qq)                How many different stop codons are there?

(rr)                   What one enzyme is involved in DNA binding, elongation, and termination during gene expression?

(ss)                  Draw a cartoon of a gene showing the relative locations of the start codon, sense codons, stop codon, and the promoter?

(tt)                   On what kind of molecule does one find a 5' cap?

(uu)                What do aminoacyl-tRNA synthases do?

(vv)                To what do anticodons bind?

(ww)            Which of the following is least involved in elongation during translation?

(i)                     A site

(ii)                   Charged amino acids

(iii)                 Growing polypeptide

(iv)                 Helicase

(v)                   P site

(xx)                During translation elongation the growing polypeptide is transferred from a tRNA sitting in the P site to what? Be specific.

(yy)                A change of one nucleotide in a base sequence to a different nucleotide is called a __________ mutation.

(i)                     deletion

(ii)                   frameshift

(iii)                 insertion

(iv)                 nonsense

(v)                   point

(zz)                 What must a mutation accomplish to be termed a missense mutation?

(aaa)             Why is a deletion of more or less than multiples of three considered a frameshift while insertions or deletions that are in multiples of three not considered a frameshift?

(bbb)            What is the Central Dogma of molecular genetics?

(ccc)             What is the name of the nitrogenous base found in RNA but not in DNA?

(ddd)          The one gene-one enzyme hypothesis was subsequently modified to the one gene-one protein hypothesis and then to the one gene-one __________ hypothesis. Why?

(eee)             The molecular-genetic term for the polymerization of RNA (of specific sequence) is __________.

(fff)               What is the argument for why codons are not 2 nucleotides long nor 4 nucleotides long?

(ggg)            The start codon, AUG, codes for what amino acid?

(hhh)            How many different kinds of stop codons are there?

(iii)                  Where are promoters typically located vis--vis start codons?

(jjj)                  The addition of a 5' cap, a poly-A tail, and the removal of introns are all examples of mRNA __________.

(kkk)            In the maturation of most eukaryotic RNAs intervening sequences called __________ must be excised before translation may take place.

(lll)                  The three general steps of translation (as well as transcription), in order, are (i) initiation, (ii) __________, and (iii) __________.

(mmm)      Much of translation is powered by the nucleoside triphosphate __________, rather than ATP.

(nnn)            While mRNAs supply the information to ribosomes, within which the mRNA information is translated into amino-acid sequence information, the actually translating units are the __________.

(i)                     codons

(ii)                   mRNAs

(iii)                 rRNAs

(iv)                 spliceosomes

(v)                   tRNAs

(ooo)            The enzymes that add amino acids to tRNAs are called __________acyl-tRNA-_________.

(ppp)            The three tRNA-interacting sites in ribosomes are called, in order, the __________ site, the __________ site, and the __________ site.

(qqq)            Upon initiation of translation the Met tRNA can be found in the

(i)                     A site

(ii)                   E site

(iii)                 G site

(iv)                 M site

(v)                   P site

(rrr)                To effect translation termination release factors bind at the

(i)                     A site

(ii)                   E site

(iii)                 G site

(iv)                 M site

(v)                   P site

(sss)               Covalent attachment of sugars, lipids, phosphate groups, etc., removal of leading-end amino-acid groups, and cleavage of polypeptide chains are all examples of post-__________ polypeptide modification.

(ttt)                Which of the following is not (necessarily) a consequence of a point mutation

(i)                     Frameshift mutation

(ii)                   Missense mutation

(iii)                 Nonsense mutation

(iv)                 Silent mutation

(v)                   All of the above can result from point mutation

(uuu)            There are two general categories of frameshift mutations that distinguish these types of mutations from point mutations, particularly as they occur in other than multiples of three. What are these two non-point types of mutations that can give rise to frameshifts?

(vvv)            A nonsense mutation gives rise to what?

(www)      What is the significance of uracil to molecular genetics?

(xxx)            The DNA strand that provides the complementary __________ to RNA polymerization is called the __________ strand. (the same term fills both blanks)

(yyy)            If the RNA produced by transcription is to be used to code for the synthesis of specific proteins, then it is called __________ RNA.

(zzz)             In Eukaryotes transcription is said to be segregated from translation. What does that mean?

(aaaa)          What is a codon and where are they found?

(bbbb)        What does it mean that the triplet code is redundant but not ambiguous?

(cccc)          What is the significance of the codon AUG?

(dddd)      What fraction of codons specify amino acids?

(eeee)          What enzyme polymerizes transcription?

(ffff)            True or False, promoters are found downstream of the start codon.

(gggg)        Poly-A tails are added to what?

(hhhh)        True or False, an intron is removed in the course of mRNA maturation.

(iiii)                All of the following are directly involved in translation except __________.

(i)                     Aminoacyl-tRNAs

(ii)                   Elongation

(iii)                 rRNA

(iv)                 Termination of transcription

(v)                   tRNA

(jjjj)                Where are anticodons found?

(kkkk)        What are the three major tRNA binding sites found on ribosomes?

(llll)                The initiation step of translation is directly powered by the hydrolysis of __________.

(i)                     1 ATP

(ii)                   2 ATP

(iii)                 3 ATP

(iv)                 4 ATP

(v)                   None of the above

(mmmm)                        The ribosome separates into two subunits upon __________.

(nnnn)        What is the difference between a silent mutation and a missense mutation?

(oooo)        Under what circumstances would an insertion mutation not also be a frameshift mutation?

(pppp)        Place the following concepts of a gene in appropriate historical order:

(i)                     One gene-one enzyme

(ii)                   Locus on a chromosome

(iii)                 One gene-one RNA

(iv)                 One gene-one polypeptide

(v)                   One gene-one protein

(qqqq)        Nucleotide insertions into gene reading frames in multiples of what result the least disruption of gene activity?

(i)                     1

(ii)                   2

(iii)                 3

(iv)                 4

(v)                   5

(rrrr)              What sort of mutation always has the effect of truncating (i.e., shortening) the resulting polypeptide?

(ssss)            The amino acids sequence (primary structure) of a polypeptide determines its three-dimensional structure (i.e., its conformation). What determines a polypeptide's primary structure?

(tttt)              What role do release factors play in translation? Please be specific.

(uuuu)        Besides coding for the amino acid methionine (i.e., "Met"), what key role does the codon AUG play in translation?

(vvvv)        True or False, individual tRNA molecules are solely responsible for specifying what amino acid they attach to.

(wwww)                        Most eukaryotic genes do not exist as continuous reading frames. Instead, the sequences that ultimately will be stitched together to form the mRNA alternate with segments of RNA known as __________.

(i)                     3' GTP

(ii)                   Exons

(iii)                 Introns

(iv)                 Poly-A regions

(v)                   Spliceosomes

(xxxx)        What fraction of codons specify amino acids?

(yyyy)        What does it mean that codons are not ambiguous?

(53) Practice question answers [index]

(a)                    A gene/a reading frame

(b)                    RNA polymerase

(c)                    a codon (or anticodon); amino acid (or aminoacyl-tRNA-synthetase or growing polypeptide)

(d)                   i, wobble

(e)                    The A site is unoccupied and the P site is occupied with a tRNA which possesses the anticodon to AUG and is charged with the amino acid methionine

(f)                     A silent mutation is a point mutation which does not result in a change in the amino acid specified by the three nucleotides making up a codon (i.e., the mutation is to a synonymous codon). A missense mutation is a point mutation which does result in a change in the amino acid specified (i.e., the mutation is to a non-synonymous codon).

(g)                    3

(h)                    replication, transcription, translation.

(i)                      Guanine, cytosine, adenine, uracil.

(j)                      Eukaryotes transcribe DNA in the nucleus while prokaryotes transcribe DNA in the cytoplasm (since prokaryotes lack a nucleus).

(k)                    AUG, methionine (i.e., the start codon).

(l)                      upstream; before the start codon; in the 5' direction from the start codon as measured on the growing mRNA; in the 3' direction from the start codon as measured on the DNA template strand. Note that this location of the promoter results in transcription beginning before the start codon such that mRNAs do not begin directly with a start codon (though the reading frame does).

(m)                  (iii) aminoacyl-tRNA-synthetases activate tRNAs before the tRNAs interact with the ribosome.

(n)                    Wobble

(o)                    The translation initiation complex consists of the small ribosomal subunit, the mRNA (bound at its ribosome recognition sequence), the methionine-associated activated tRNA present in what will be the P site of the ribosome, one hydrolyzed GTP, and ultimately the addition of the large subunit.

(p)                    Charged.

(q)                    a molecule of water.

(r)                     it is a portion of a protein that targets the protein within the cell, e.g., for insertion into a membrane.

(s)                     a change in codon sequence at the DNA level.

(t)                     a mutation that converts a codon that specifies for an amino acid to one that specifies for a stop codon.

(u)                    deletions or insertions

(v)                    signal sequence

(w)                  (i) 1

(x)                    transcription

(y)                    rRNA

(z)                    nuclear membrane

(aa)                 61 (i.e., 64 -- three stop codons)

(bb)                it means that each codon specifies one and only one amino acid

(cc)                 AUG is the start codon

(dd)               (380 * 3) + 1 = 1143

(ee)                 the three-prime hydroxyl group (-OH) on the 3'-end nucleotide

(ff)                  promoters promote the initiation of transcription

(gg)                (i) AUG

(hh)                spliceosomes

(ii)                    anticodons are found on tRNAs (specifically on the anticodon loop); in this case "not specific enough" might be something like "associated with ribosomes during translation"; in this case "not specific enough" might be something like "associated with ribosomes during translation"

(jj)                    tRNA, amino acid, ATP

(kk)                A nonsense mutation is a point mutation that converts a sense codon into a stop codon

(ll)                    (i) deletion

(mm)            Because genes code for polypeptides while enzymes can consist of more than one polypeptide

(nn)                tRNA, mRNA, rRNA

(oo)                (iv) Lack vs. presence of nucleus; Prokaryotes don't have a nucleus and it is the nuclear membrane that segregates transcription from translation in eukaryotes

(pp)                One finds codons on mRNA

(qq)                There are three different stop codons

(rr)                   RNA polymerase

(ss)                  Promoter--start codon--sense codons--stop codon

(tt)                   mRNA following maturation in eukaryotes

(uu)                Aminoacyl-tRNA synthases add amino acids to tRNAs

(vv)                Anticodons bind to codons on mRNAs during translation

(ww)            (iv) Helicase (which is involved in replication, not translation

(xx)                The polypeptide is transferred to an amino acid attached to a tRNA sitting in the A site

(yy)                (v) point

(zz)                 The mutation must result in a change of amino acid in the protein product

(aaa)             Codons do not have punctuation so increasing or decreasing nucleotides in numbers other than multiples of three changes the reading frame of all downstream codons

(bbb)            DNA --> DNA = replication, DNA --> RNA = transcription, RNA --> protein = translation

(ccc)             Uracil

(ddd)          Polypeptide

(eee)             Transcription

(fff)               The number of combination of nucleotide with 2-nucleotide codons is less than 20 (24 = 16) while the number with four is much-much grater (24 = 4*64 = 256) than 20 (= the number of amino acids) thereby requiring perhaps too complex a translational machinery

(ggg)            Methionine (Met)

(hhh)            Three

(iii)                  At and before the start of reading sequences

(jjj)                  Processing

(kkk)            Introns

(lll)                  Elongation and termination

(mmm)      GTP

(nnn)            (v) tRNAs

(ooo)            Aminoacyl, synthetases

(ppp)            A, P, E

(qqq)            P site

(rrr)                A site

(sss)               Translational

(ttt)                (i) Frameshift mutation

(uuu)            Insertion and deletion

(vvv)            A stop codon; a truncated polypeptide

(www)      Uracil is the base employed by RNA in the place of the thymine employed by DNA

(xxx)            Template

(yyy)            Messenger (m)

(zzz)             It means that transcription occurs inside of the nucleus whereas translation occurs in the cytosol

(aaaa)          Codons are three-nucleotide stretches of sequence that are found on mRNAs and which code for amino acids in polypeptides

(bbbb)        It means that more than one codon can code for a given type of amino acid, but only one type of amino acid can be encoded by a given codon

(cccc)          AUG is the start codon, coding for methionine

(dddd)      61/64 codons specify amino acids

(eeee)          RNA polymerase

(ffff)            False (it is found upstream)

(gggg)        mRNA (in eukaryotes)

(hhhh)        True

(iiii)                (iv) Termination of transcription

(jjjj)                Anticodons are found on tRNAs

(kkkk)        A, P, E

(llll)                (v) None of the above (it is one GTP)

(mmmm)                        Termination of translation

(nnnn)        A missense but not a silent mutation results in the change of an amino acid in a polypeptide

(oooo)        If the insertion were multiples of three nucleotides long

(pppp)        (ii), (i), (v), (iv), (iii)

(qqqq)        (iii) 3

(rrrr)              Nonsense

(ssss)            A gene; a sequence of nucleotides

(tttt)              They are responsible for the termination of translation, taking the place of tRNAs when the codon being read is a stop codon.

(uuuu)        AUG is the start codon

(vvvv)        False

(wwww)                        (iii) Introns

(xxxx)        61/64

(yyyy)        Each codon specifies only one amino acid, not more than one.

 

Note that the questions from 2003 are missing from above. These can be found only on saved exams, including, presumably, the final.