AP Bio Chapter 14

Describe the structure of a eukaryotic ribosome?

-Eukaryotic ribosomes slightly larger and differ from bacterial ribosomes in molecular composition -antibiotic drugs can inactivate bacterial ribosomes without inhibiting ability of eukaryote to make proteins

How does a prokaryotic ribosome differ from a eukaryotic ribosome? What is the medical significance of this difference?

-antibiotic drugs can inactivate bacterial ribosomes without inhibiting ability of eukaryote to make proteins

State the hypothesis formulated by George Beadle while studying eye color mutations in Drosophila

-each of the various mutations of affecting eye color blocks pigment synthesis at a specific step by preventing the production of the enzyme -showed that genes control the production of enzymes and that the enzymes are related to traits

Cite two significant findings that resulted from the research of Beadle and Tatum

-some proteins aren't enzymes (one gene-one) -proteins are composed of several polypeptides each of which has its own gene -metabolic defects are linked to defective genes

Describe at least three-types of post-translational modifications?

1) certain amino acids may be chemically modified by attachment of sugars, lipids, phosphate groups, etc 2)enzymes may remove 1 or more amino acids from leading amino end of the polypeptide chain 3) 2 or more polypeptides may come together, becoming subunits of protain that has quaternary structure

Much like transcription, we can divide translation into three stages. List them.

1) initiation 2)elongation 3)termination

What are three properties of RNA that allow it to function as an enzyme? 1. 2. 3.

1) it can form a 3-Dimensional structure because of its ability to base pair with itself 2)Some bases in RNA contain functional groups that participate in catalysis 3)Ability to Hydrogen bond with other nucleic acid molecules (RNA/DNA) adds specificity to catalytic activity

Let's now take a closer look at initiation. Read the paragraph titled "RNA Polymerase Binding and Initiation of Transcription" carefully. List three important facts about the promoter here. (1) (2) (3)

1) promoter of a gene includes within it the transcription start point 2) promoter typically extends several dozen of more nucleotide pairs upstream from the start point 3) RNA Polymerase binds in a precise location and orientation on the promoter

How many different aminoacyl-tRNA synthases are there?

20

How many nucleotides are required to code for these 20 amino acids.

3

How many codons are there above?

4

How many nucleotide bases are there? How many amino acids?

5, 20

What is a polyribosome?

A cluster of ribosomes translating the same mRNA, but positioned at different sites along the mRNA

Now it is time to put all of the elements of transcription together. Write an essay below to describe the process by which mRNA is formed. Use these terms correctly in your essay, and underline each one: TATA box, gene, terminator, promoter, elongation, 5' to 3', termination, initiation RNA, polymerase RNA nucleotides, template, start point, termination signal, and transcription factors.

A promoter, often including a TATA box in eukaryotes, establishes where RNA synthesis is initiated. Beginning at the start point on the template strand, RNA synthesis is catalyzed by RNA polymerase, which links together RNA nucleotides complementary to a DNA template strand. The RNA transcript runs 5' to 3', the reverse of the template. Transcription factors help eukaryotic RNA polymerase recognize promoter sequences, forming a transcription initiation complex. Transcription follows the same base-pairing rules as DNA replication, except that in RNA, uracil substitutes for thymine. The three stages of transcription are initiation, elongation, and termination. The mechanisms of termination are different in bacteria and eukaryotes. In bacteria, transcription proceeds through a terminator sequence in DNA. In eukaryotes, RNA pol II transcribes a specific signal sequence, which codes for a termination signal.

What is the start codon?

AUG

What revision of detail did this hypothesis undergo as more information was gained? Write this restatement and then highlight it, this is an important concept.

Because not all proteins are enzymes and because each proteins consists of two or more different polypeptide chains, each specified by its own gene, the hypothesis was revised and restated as one gene-one polypeptide hypothesis

Write the central dogma of molecular genetics, as proclaimed by Francis Crick:

DNA-->RNA-->Proteins

Now, summarize the events of elongation. Include these components: mRNA, A site, tRNA, codon, anticodon, ribozyme, P site, and E site. Again, the figure may help you.

First, the anticodon of an incoming aminoacyl tRNA base-pairs with the complementary mRNA codon in the A site. Hydrolysis of GTP increases the accuracy and efficiency of this step. Although not shown, many different aminoacyl tRNAs are present, but only the one with the appropriate anticodon will bind and allow the cycle to progress. Second, an rRNA molecule of the large ribosomal subunit catalyzes the formation of a peptide bond between the amino group of the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site. This step removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site. Finally, the ribosome translocates the tRNA in the A site to the P site. At the same time, the empty tRNA in the P site is moved to the E site, where it is released. The mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site.

What are three important functions of the 5 cap and poly A tail?

First, they seem to facilitate the export of the mature mRNA from the nucleus. Second, they help protect the mRNA from degradation by hydrolytic enzymes. Third, they help ribosomes attach to the 5' end of the mRNA once the mRNA reaches the cytoplasm.

Which situation did Archibald Garrod suggest caused inborn errors of metabolism?

Garrod suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions. A person's inability to make a particular enzyme.

Distinguish between introns and exons, perhaps it will help to remember that exons are expressed.

Introns-noncoding segments of nucleic acid that lie b/w coding regions intervening sequences Exons-segments of nucleic acid that are eventually expressed by being translated into amino acid sequences?

Why is the genetic code redundant but not ambigous?

It is redundant because it can many codon pairs can pair for the same amino acid, but 2 amino acids can not pair with 1 codon.

Explain the process of a specific amino acid being joined to a tRNA. Be sure to use the words amino-acyl tRNA synthetase, ATP, amino acid, and tRNA.

Linkage of the tRNA and amino acid is an endergonic process that occurs at the expense of ATP. The ATP loses two phosphate groups, becoming AMP.

What is always the first amino acid in the new polypeptide?

Met

Which organism did Beadle and Tatum use in their research?_________ How did this organism's nutritional requirements facilitate this research?

Neurospora has modest food requirements and can grow in a laboratory on a simple solution. the mold cells use their metabolic pathways to produce all other molecules they need. -identifies mutants were unable to survive on minimal solution because they were unable to synthesize essential molecules.

Descibe Nirenberg's experiments in which he identified the first codon?

Nirenburg synthesized an artificial mRNA by linking identical RNA nucleotides containing uracil as their base

What are the monomers of DNA and RNA? Of Proteins?

Nucleotides, and amino acids

Explain how proteins are targeted for the ER.

Polypeptide synthesis begins on a free ribosome in the cytosol. An SRP binds to the signal peptide, halting synthesis momentarily. The SRP binds to a receptor protein in the ER membrane. This receptor is part of a protein complex (a translocation complex) that has a membrane pore and a signal-cleaving enzyme. The SRP leaves, and polypeptide synthesis resumes, with simultaneous translocation across the membrane. (The signal peptide stays attached to the translocation complex.) The signal-cleaving enzyme cuts off the signal peptide. Finally, the rest of the completed polypeptide leaves the ribosome and folds into its final conformation.

Which enzyme, DNA Poly III, or RNA polymerase does not require an RNA primer?

RNA Polymerase

Name the enzyme that uses the DNA template strand to transcribe a new mRNA strand

RNA synthesis catalyzed by RNA polymerase which pries the DNA strands apart and hooks together the RNA nucleotides

From the first paragraph in this section, find three ways in which RNA differs from DNA.

Rna is single stranded, It has Uracil not Thymine, and Ribose is present not Deoxyribose

What is the consequence of alternative spicing of identical mRNA transcripts?

Some genes can encode more than one kind of polypeptide depending on which segments are treated as exons during RNA splicing - alternative splicing because of alternative splicing # of different proteins an organism can produce is greater than its gene number

DNA is double stranded, but for each protein, only one of these two strands is used to produce an mRNA transcript. What is the coding strand called?

Template strand

What commonly held idea was rendered obsolete by the discovery of ribozymes?

The idea that all biological catalysts are proteins

Summarize the events of initiation. Include these components, small ribosomal subunits, large ribosmal subunits, mRNA, initatior codon, tRNA, Met, initiation complex, P site, and GTP.

The initiation stage of translation brings together mRNA, a tRNA bearing the first amino acid of the polypeptide, and the two subunits of a ribosome. First, a small ribosomal subunit binds to a molecule of mRNA. In a bacterial cell, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon. An initiator tRNA with the anticodon UAC base-pairs with the start codon, AUG. This tRNA carries the amino acid methionine. The arrival of a large ribosomal subunit completes the initiation complex. Proteins called initiation factors are required to bring all the translation components together. Hydrolysis of GTP provides the energy for the assembly. The initiator tRNA is in the P site; the A site is available to the tRNA bearing the next amino acid.

Explain the functions of the A, P, and E sites on a ribosome?

The peptidyl-tRNA binding site holds the tRNA carrying the growing polypeptide chain, while the aminoacyl-tRNA binding site holds the tRNA carrying the next amino acid to be added to the chain. Discharged tRNAs leave the ribosome from the exit site

Here is a short DNA template. Below it, assemble the complementary mRNA strand. 3'A C G A C C A G T A A A 5' How many codons are there above?

UGCUGGUCAUUU

What was the first codon-amino acid pair to be identified?

UUU-Phe

How were Neurospora spores treated to increase the mutation rates?

X-Rays

Use figure 14.9 in your text to explain the three stages of initation.

a DNA sequence in eukaryiotic promoters crucial in forming the transcription initiation complex -name comes from Thymine and Adenine which make it up

What is the TATA box? How did it get it's name?

a DNA sequence in eukaryiotic promoters crucial in forming the transcription initiation complex -name comes from Thymine and Adenine which make it up

What is a gene? It used to be simply stated that one gene codes for one polypeptide. That definition has now been modified. Write below the broader molecular definition in use today.

a DNA sequence that codes for a specific polypeptide chain

Describe two important ways in which bacterial and eukaryotic gene expression differ

a bacterial cell ensures a streamlinal operation in the absence of a nucleus it can simultaneously transcribe and translate the same gene. the eukaryotic cell's nuclear envelope segregates transcription from translation and provides a compartment for extensive RNA processing

What is a ribozyme?

an RNA molecule that functions as an enzyme such as an intron that catalyzes its own removal during RNA splicing

Describe the action of different types of chemcial mutagens?

base analogs are chemcials that are similar to normal DNA bases but pair incorrectly during DNA replication. some other chemical mutagens interfere with correct DNA replication by inserting themselves into the DNA and distorting the double helix

What strategy did Beadle and Tatum adopt to test this hypothesis.

bombarded bread mold Neurospora with X-Rays and then looks amoung survivors for mutants that differ in their nutritional needs form the wild type bread mold

Three types of RNA are needed for protein synthesis. Complete the chart below. Description Function mRNA tRNA rRNA

carries genetic material from the DNA to the protein synthesizing machinery of cell transfers amino acids from cytoplasmic pool of amino acids to a growing polypeptide in a ribosome (ribosomal RNA) together with proteins ; make up ribosomes ; most abundant type of RNA

Define a mutation in terms of molecular genetics?

changes to the genetic information of a cell or virus

Define point-mutations?

chemical changes in a single base pair of a gene

Describe one example Garrod used to illustrate his hypothesis

ex: hereditary condition called alkaptonuria where urine is black because it contains the chemical alkapton which darken upon exposure to air. Most people have an enzyme that metabolizes alkapton, whereas people with alkaptonuria have inherited an inability to make that anzyme. -linking gemes to enzymes require understanding that cells synthesize and degrade molecules in a series of steps, a metabolic pathway

What are some of the things that will result in a final-form functional protein?

folding, chemical modification of amino acids, enzymatic removal, rearrangement

What are frameshit mutations, Identify two mechanisms by which frameshifts may occur?

insertion or deletion or nucleotides that alter the frame of the genetic message, the triplet groupings of bases on mRNA that is read during translation. base pair substitutions and base pair insertions or deletions

What is an anticodon?

nucleotide triplet at one end of a tRNA molecule that base - pairs with a particular complementary codon on an mRNA molecule

What are the two categories of mutagens?

physical and chemical

In eukaryotes, what is the pre-mRNA called?

primary transcript

What is a release factor? By what mechanism is termination acomplished?

protein shaped like an aminoacyl tRNA, which binds directly to the stop codon in the A site through hydrolyzation , releasing polypeptide through exit tunnel of ribosome's large subunit

Explain the concept of reading frame.

reading frame is the grouping of ribonucleotides used by the translation machinery during polypeptide synthesis

What is a transcription unit?

region of DNA that is transcribed into an RNA molecule

You will be introduced to a number of small RNA's in this course. What type is the RNA in snRNP.

small nuclear RNA

Study the figure and text carefully to explain how the splice sites are recognized.

snRNAs, part of the spliceosome complex, recognize specific nucleotide sequences on the intron and catalyze the process of intron removal excellent ex of catalytic functions in mRNA

What are snRNP? What two types of molecules make up a snRNP?

snRNPs are small nuclear ribonucleoproteins made up of RNA and protein molecules

tRNA has two attachment sites. What binds at each site? Know where the sites are and what attatches?

specific anticodon binds at one end of tRNA and corresponding amino acids at other end formed by covalent bonds --hydrogen bonds hold shape of tRNA

What is the difference between missense and nonsense mutations?

substitutions which change one amino acid to another one point mutations changes codon for an amino acid into a stop codon and causes translation to be stopped prematurely

Define each of these processes that are essential to the formation of a protein- Transcription Translation

synthesis of RNA using DNA template, mRNA takes instructions from DNA to ribosom where protein can be made DNA --> RNA produces mRNA synthesis of RNA under DNA direction

RNA processing occurs in eukaryotic cells. The primary transcipt is altered at both ends, and sections in the middle are removed. a. What happens at the 5 end. b. What happens at the 3 end.

the 5 end-receives a modified nucleotide 5' cap the 3 end -recieves a poly-A tail

What compromises a transcription initation complex?

the completed assembly of transcritpion factors and RNA polymerase bound to a promoter

What is gene expression?

the process by which DNA directs protein synthesis

Complete the following table to summarize each processes. Template Product Synthesized Location Transciption Translation

the synthesis of a polypeptide using genetic info encoded in an mRNA molecule change of "language" from nucleotides in amino acids DNA -->RNA-->Nucleus mRNA-->Polypeptide-->Cytoplasm

Scientists expected to find one aminoacyltRNA per codon, but far fewer have been discovered. How does wobble explain this?

wobble is flexibility in base pairing rules where the nucleotide at 5' end of tRNA anticodon form hydrogen bond with more than one kind of base in 3' end of a codon. flexibility explains why there are only 45 tRNAs