Ch.17

Front 1

anti-

Back 1

= opposite

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exo-

Back 2

= out, outside

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intro-

Back 3

=within

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muta-

Back 4

= change

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-gen -

Back 5

= producing

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poly-

Back 6

=many

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trans-

Back 7

=across

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-script

Back 8

= write

Front 9

5' Cap (def.)

Back 9

The 5' end of a pre-mRNA molecule modified by theaddition of a cap of guanine nucleotide

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A site (def)

Back 10

Oneof a ribosome’s three binding sites for tRNA during translation. The A siteholds the tRNA carrying the next amino acid to be added to the polypeptidechain. (A stands for aminoacyl tRNA.)

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anticodon (Def)

Back 11

A specialized base triplet at one end of a tRNAmolecule that recognizes a particular complementary codon on an mRNA molecule.

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Base-pair substitution (def)

Back 12

A type of point mutation; the replacement of onenucleotide and its partner in the complementary DNA strand by another pair ofnucleotides

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Codon (def)

Back 13

Athree-nucleotide sequence of DNA or mRNA that specifies a particular amino acidor termination signal; the basic unit of the genetic code.

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Deletion (def)

Back 14

A mutational loss of one or more nucleotide pairs froma gene.

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E site (def)

Back 15

One of a ribosome’s three binding sites for tRNAduring translation. The E site is the place where discharged tRNAs leave theribosome. (E stands for exit.)

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Exon (def.)

Back 16

Acoding region of a eukaryotic gene.

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Frameshift mutation (def)

Back 17

Amutation occurring when the number of nucleotides inserted or deleted is not amultiple of three, resulting in the improper grouping of the followingnucleotides into codons.Insertion: A mutation involving the addition of one ormore nucleotide pairs to a gene.

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Intron (def)

Back 18

A noncoding, intervening sequence within a eukaryoticgene. ,

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Messenger RNA (mRNA) (def)

Back 19

Atype of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasmand specifies the primary structure of a protein.

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Missense mutation (def)

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Themost common type of mutation, a base-pair substitution in which the new codonmakes sense in that it still codes for an amino acid.

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Mutation (Def):

Back 21

A rare change in the DNA of a gene, ultimatelycreating genetic diversity.

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P site (def)

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Oneof a ribosome’s three binding sites for tRNA during translation. The P siteholds the tRNA carrying the growing polypeptide chain. (P stands for peptidyltRNA.)

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Point mutation (def)

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A change in a gene at a single nucleotide pair

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Poly-A tail (def)

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The modified end of the 3’ end of an mRNA moleculeconsisting of the addition of some 50 to 250 adenine nucleotides.

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Primary transcript (def)

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An initial RNA transcript; also called pre-mRNA whentranscribed from a protein-coding gene.

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Promoter (def)

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A specific nucleotide sequence in DNA that binds RNApolymerase and indicates where to start transcribing RNA

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Reading frame (def)

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The way a cell’s mRNA-translating machinery groups themRNA nucleotides into codons.

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Ribosomal RNA (rRNA) (def)

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The most abundant type of RNA, which together withproteins forms the structure of ribosomes.

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Ribosome (def)

Back 29

A cell organelle constructed in the nucleolus andfunctioning as the site of protein synthesis in the cytoplasm; consists of rRNAand protein molecules, which make up two subunits.

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RNA polymerase (def)

Back 30

An enzyme that links together the growing chain ofribonucleotides during transcription.

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RNA processing (def)

Back 31

Modification of RNA before it leaves the nucleus, aprocess unique to eukaryotes.

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RNA splicing (def)

Back 32

The removal of noncoding portions (introns) of the RNAmolecule after initial synthesis.

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TATA box (def)

Back 33

A promoter DNA sequence crucial in forming the transcriptioninitiation complex.

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Template strand (Def)

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TheDNA strand that provides the template for ordering the sequence of nucleotidesin an RNA transcript.

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Transcription factor (def)

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A regulatory protein that binds to DNA and stimulatestranscription of specific genes.

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Transcription initiation complex (def)

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The completed assembly of transcription factors andRNA polymerase bound to the promoter

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Transcription unit (def)

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: A region of aDNA molecule that is transcribed into an RNA molecule.

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Transfer RNA (tRNA) (def)

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An RNA molecule that functions as an interpreterbetween nucleic acid and protein language by picking up specific amino acidsand recognizing the appropriate codons in the mRNA.

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Translation (def)

Back 39

The synthesis of a polypeptide using the geneticinformation encoded in an mRNA molecule

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Triplet code (def)

Back 40

A set of three-nucleotide-long words that specify theamino acids for polypeptide chains.

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DNAprovides inherited genetic information that can:

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be reliablycopied and passed between generations

This informationis encoded in the sequence of DNA nucleotides

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Individual segments of DNA called genes provide:

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o the specificsequences that ultimately instruct the cell through gene expression tomanufacture particular RNA or polypeptides

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Thestrand of DNA used for a given gene is called the:

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template strand

The template strand’s complementary strand is calledthe non-template strand

Which strand is the template strand is dependent oneach individual gene

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Basepairs are bracketed in groups of 3 (triplet code) which are:

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codons

Codons must be kept in the same reading frame forproper gene expression

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Gene expressionhas 2 major steps:

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1.Transcription: Using a DNA template to provide the pattern to make a messenger, mRNAtranscript

2.Translation: Using the mRNA transcripts to assemble amino acids in the correct orderto make a polypeptide

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Universal GeneticCode:

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All organismsshare the same genetic code of 64 possible unique codons from the 4 nucleotidebases

61 of the 64 codefor amino acids, 3 are stop codons, one codon (AUG) is the start codon as wellas coding for an amino acid

No codon codesfor more than one amino acids but, for a given amino acid, there can be morethan one codon that codes for it

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Transciption:

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The promoterregion of a gene is a reliable sequence along the DNA template strand thatsignals where transcription will begin

A common promoterregion in eukaryotes is the TATA Box

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RNApolymerase is the enzyme responsible for:

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addingRNA nucleotides to the mRNA transcript

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RNApolymerase binds to thebody:

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promoter regionalong with several proteins collectively called transcription factors sotogether they are called the transcription initiation complex

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Thesection of DNA transcribed is the transcription unit which includes the:

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eventualcoding region along with many other additional nucleotides upstream anddownstream from the coding region of the gene

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Transcriptionproceeds in a 3 step process:

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1. Initiation

2. Elongation

3. Termination

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1. Initiation

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Matchingof the transcription initiation complex to the promoter region and separationof the DNA double strands to allow access

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2. Elongation:

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Addingof RNA nucleotides using the base pairing rules with U substituting for T onthe mRNA transcript

RNA nucleotidesare added to the 3’ end of the transcript

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3. Termination:

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ThemRNA transcript will be released from the DNA template strands at apre-determined sequence

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RNAprocessing:

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· Eukaryotes make apre-mRNA transcript during transcription that needs to be edited beforetranslation (Note: Prokaryotes do not have RNA processing and the transcribedmRNA is used immediately)

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The5’ end of the pre-mRNA receives a:

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a 5’ cap (Gnucleotide with 3 phosphate groups) and the 3’ end receives a long series of Anucleotides called the poly-A tail

Both structures serve to protect the mRNA transcriptas it moves from the nucleus to the cytoplasm and to help recognition andbinding of the mRNA to the ribosomes

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Certainregions in the coding segment called introns are:

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removed from thetranscript, leaving segments called exons that will be expressed duringtranslation

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Translationoccurs at:

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· the ribosomes,bound or free

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Ribosomesare made of:

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o 2 proteinsubunits (a large and small) + ribosomal or rRNA molecules

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Theinitiation of translation occurs when:

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mRNAtranscripts attach to the small subunit at the mRNA binding site

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Aminoacids are present in the:

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cytoplasm andenzymes called aminoacyl-tRNA synthases catalyze the attachment of each aminoacid to transfer, tRNA molecules

Each tRNA has an amino acid attachment site on one endand a region called the anticodon, which is a triplet of bases complementary tothe codon, that matches the amino acid that tRNA holds

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tRNA’sare matched to the codons along the:

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mRNAtranscript

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Initiationof translation begins when:

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the first tRNA (which holds methionine, Met) binds tothe start codon AUG on the mRNA

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Thisfirst tRNA docks at:

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aspecific place on the ribosome called the P site

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Onceit has docked, the large subunit joins to:

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the small subunitEnergy is needed in the form of GTP molecules

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Thenext tRNA will dock at a site called the:

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Asite using its anticodon to match with the next codon on the mRNA

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Thefirst amino acid (Met) will release from its tRNA and move over to the tRNA atthe A site, forming :

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a peptide bond with the next amino acid in the sequence

The start tRNA isnow empty and will move to the E or exit site of the ribosome and eventuallyreleased back out into the cytoplasm to find another Met molecule

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ThetRNA holding the now 2 amino acid long chain will move over to the:

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P site, leaving the A site free for the next tRNAbearing the next amino acid in the chain to join

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GTPmolecules are needed to

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providethe energy for this process

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Thepolypeptide chain continues to grow until:

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one of the 3 stop codons is reached on the mRNA

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Proteinscalled release factors bind to the stop codons and this signals the

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breaking apart ofthe ribosome subunits, release of the mRNA and completed polypeptide

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Thepolypeptide chain will undergo modification to form the:

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secondary,tertiary or possibly quaternary structure needed for a functional final protein

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Amutation is a change in the:

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DNA nucleotidesequence

Mutations can be spontaneous mistakes or caused byother agents called mutagens

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Apoint mutation is a :

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change in asingle base pair

The base may be substituted,an extra base inserted or one deleted

More than onebase may be affected however in mutations other than point; sometimes wholecodons are inserted or deleted

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Ifa base substitution alters the codon in a way that allows it to still code forthe same amino acid as the wild type, the mutation is:

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silent and has noeffect on the protein

This is possiblebecause of the redundancy in the genetic code

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Ifthe base substitution codes for a different codon than the wild type version,it is:

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a missense mutation

Depending on whatamino acid is altered and the location in the polypeptide chain of that aminoacid, the result to the protein is variable

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If thebase substitution creates a premature stop codon, the protein is:

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more likely to be negatively affected andnon-functional, again, dependent on where the mutation occurs in the sequence

This called anonsense mutation

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Insertionsand deletions of single bases have a far greater potential effect on theprotein than:

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substitutions asthey will cause a reading frame shift and all remaining codons will beincorrect

Insertions ordeletions of whole codons however may not have a great affect because therewill be no reading frame shift, just an extra or missing amino acid which canvary in affect

Front 79

Explain how RNA differs from DNA.

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Both are nucleic acids so their monomers are nucleotides. RNA nucleotides have a phosphategroup like DNA but the 5 carbon sugar is ribose in RNA unlike deoxyribose in DNA. Of thenitrogenous bases, RNA has adenine, cytosine and guanine but thymine is replaced by uracil.RNA is single stranded while DNA is double stranded. RNA is found in the nucleus but, unlikeDNA, is also found outside of the nucleus.

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Briefly explain how information flows from gene to protein.

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The sequence of nucleotides in DNA holds the instructions for making proteins but must first betranscribed into RNA nucleotides. RNA then takes the message out of the nucleus to theribosomes, the site of protein synthesis. At the ribosomes, RNA is translated into amino acidsto form a polypeptide that later folds to become a protein

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Distinguish between transcription and translation.

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Transcription is the copying of DNA nucleotides to RNA nucleotides. Translation is theconversion of RNA nucleotides (codons) into amino acids.

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Define codon and explain the relationship between the sequence of codons on mRNA and thesequence of amino acids in a polypeptide.

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A codon is a triplet of nucleotides. With 4 nitrogenous bases, there are 64 different possiblecodons. Every 3 DNA nucleotides is transcribed into a mRNA codon. Because there are only 20amino acids, more than one codon can code for a given amino acid but a codon can never betranslated into more than one amino acid. There is one codon that translate to the amino acidmethionine but is also the Start codon that signals the beginning of the translated region. Thereare also 3 Stop codons that signal the end of translation. The universal genetic codedesignates which codons translate to what amino acids.

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Explain the significance of the reading frame during translation.

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Is it very important to begin the bracketing of codons at the Start codon and keep the pattern ofthe next 3 nucleotides designated as the next codon. This is called the proper reading frame. Ifyou shift a nucleotide up or down or otherwise alter the reading frame, you will change theidentity of all the subsequent codons which will then translate into entirely different amino acidspossibly

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Explain the general process of transcription, including the three major steps of initiation, elongation,and termination.

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Initiation begins when RNA polymerase binds with a promoter region of DNA and the DNAunwinds. The polymerase begins to add RNA nucleotides that are base paired to the templatestrand of DNA. Elongation continues as the polymerase moves downstream, unwinding theDNA as it goes and adding RNA nucleotides in a 5’ to 3’ direction. The DNA will reform thedouble helix as the RNA polymerase passes. Termination occurs when the polymerase reachesthe terminator sequence and the RNA transcript is released and the polymerase drops off theDNA

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Explain how RNA is modified after transcription in eukaryotic cells.

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The primary mRNA transcript first gets a 5’ cap and a poly-A tail on the 3’ end which helpprotect the transcript from degradation as it moves from the nucleus to the ribosome. Regions of nucleotides called introns that will not be used for translation into amino acids are thenedited out and the exons or true coding regions are sealed back together.

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Describe the structure and functions of tRNA.

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Transfer RNA (tRNA) is the true translator for going between codons and amino acids. Thereare 45 different tRNA molecules in the cytoplasma. On one end, they have an attachment sitefor an amino acid. The other end has a special RNA nucleotide sequence called an anticodonthat can complementary base pair with the matching codons. There are 64 codons but only 45anticodons necessary due to the redundancy of the 3rd nucleotide in the codon sequence (aphenomenon called wobble).

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. Describe the structure and function of ribosomes

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Ribosomes are composed of 2 subunits (one large, one small) made in the nucleus in thespecial region called the nucleolus. The subunits are made of protein and ribosomal RNA(rRNA). The come out into the cytoplasm and assemble when a mRNA transcript arrives to betranslated. The ribosomes have 3 sites called the A, P and E site. As the mRNA transcriptmoves through the ribosome, the tRNA carrying the newest amino acid that will be added to thepolypeptide stand binds to the A site. The existing polypeptide strand is bound to the P site.This strand moves over to tRNA that is in the A site as a peptide bond is formed, joining the newamino acid. The tRNA that had contained the polypeptide strand is now discharged from the Esite.

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Describe the process of translation including initiation, elongation, and termination.

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Initiation brings together the mRNA transcript, the first tRNA carrying the first amino acid of thepolypeptide and the 2 subunits of the ribosomes. This establishes the reading frame from thispoint on. Elongation continues as new amino acids are added one by one to the growingpolypeptide strand as codon matching occurs between the codons on the mRNA and theincoming tRNA molecules. Termination occurs when one of the 3 Stop codons is encounteredand instead of an amino acid, a release factor binds to the Stop codon site and signals therelease of the polypeptide strand. The ribosomal subunits then break apart.

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Define point mutations. Distinguish between base-pair substitutions and base-pair insertions.Define missense and nonsense mutations.

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A point mutation is a single change in a nucleotide base. With a base pair substitution, thewrong base pair is present but the overall number of base pairs is correct. This change may ormay not have a significant effect on the protein made. If the change is in the 3rd base of acodon, because of redundancy in the genetic code, there will be no change in the amino acidtranslated and the protein will be the same. If the change is in the 1st or 2nd spot, the amino acidtranslated will be different. It depends on the particular protein and where the change occurs ifthis will greatly affect the protein. This type of change is called a missense mutation when anamino acid is coded for but just not the correct one. If the change causes a premature Stopcodon, this is a nonsense mutation and can have a dramatic effect on the protein. If the changeis an insertion of an extra base or the deletion of one, the reading frame will shift from that pointon and cause extensive missense or nonsense.