question

What is gene expression?

answer

The process by which DNA directs the synthesis of proteins (or sometimes just RNA's).

question

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

answer

that some people are unable to make a particular enzyme to metabolize certain things.

question

Describe one example Garrod used to illustrate his hypothesis:

answer

Alkaptonuria: most people have an enzyme to metabolize alkapton, but people who have inherited an inability to do so have black urine b/c of the presence of alkapton.

question

State the hypothesis formulated by George Beadle while styuding eye color mutations in drosophila:

answer

Each of the various mutations affecting eye color blocks pigment synthesis at a specific step, by preventing the production of the enzyme that catalyzes that step.

question

What strategy did Beadle and Tatum adopt to test the hypothesis George Beadle made about eye color mutations in drosophila?

answer

They experimented on neuspora, which only need a minimal food supply. After mutating some of them with xrays, some couldn't survive on minimal since their enzymes couldn't synthesize needed molecules from that food. Complete growth medium allowed them to survive though. (Their natural food with lots added.)

question

How did Beadle and Tatum figure out what mutant was defective in what area?

answer

If several identical mutants were put in different solutions, and one of these was Arginine and that was the only one that survived, the mutant must have been defective in making arginine since that's the one that survived.

question

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

answer

1. The function of a gene is to dictate the production of a specific enzyme 2. Not all proteins are enzymes

question

What is the hypothesis of gene expression?

answer

one gene -> one polypeptide. Many eukaryotic genes can code for a set of related proteins though, called alternative splicing. And many genes code for RNAs that don't become proteins.

question

What are three ways that RNA differs from DNA

answer

1. It contains ribose instead of deoxyribose 2.it has uracil instead of thymine 3. it's usually one stranded instead of double stranded.

question

What are the monomers of DNA, RNA or proteins?

answer

DNA + RNA = the 4 types of nucleotides (U or T) Proteins= amino acids

question

Define the process of transcription

answer

DNA is used as a template to make a complementary sequence of mRNA

question

Define the process of translation

answer

synthesis of a polypeptide under the direction of mRNA. Translates codons to amino acids at ribosomes

question

where does translation occur in a eukaryotic cell

answer

the cytoplasm

question

in eukaryotes, what is the pre-mRNA called?

answer

the primary transcript. It's only called this in the nucleus, before modification.

question

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

answer

DNA -> RNA -> Protein.

question

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

answer

4, 20

question

how many nucleotides are required to code for these 20 amino acids?

answer

4, in triplet arrangements (4^3 = 64 unique triplets)

question

how many codons are there?

answer

4^3 = 64. 300 codons in an mRNA -> 100 polypeptides in the amino acid

question

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?

answer

the template strand, since it gives the pattern/template for the sequence of nucleotides in an RNA transcript. Either strand can be a template for different genes at different times.

question

What are codons?

answer

the mRNA base triplets

question

Describe nirenberg's experiment in which he identified the first codon:

answer

he synthesized an artificial mRNA by linking identical RNA nucleotides containing uracil at their base: one codon in repetition: UUU.

question

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

answer

UUU -> Phe

question

of the 64 possible codons, how many code for amino acids, and what are the rest

answer

61. UAA, UAG, and UGA are stop signals

question

what is the start codon?

answer

Aug -> met

question

wht is the genetic code said to be redundant but not ambiguous?

answer

both GAA and GAG specify glutamic acid (redundancy for less harmful mutations) neither specifies any other amino acid (no ambiguity for no mix-ups).

question

Explain the concept of reading frame

answer

reading symbols of a language in the correct groupings

question

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

answer

RNA polymerase, assembles RNA in 5' -> 3'

question

Both DNA polymerase III and RNA polymerase can assemble a new polynucleotide only in the 5' ->3' direction. Which enzyme, DNA pol III or RNA pol doesn't need a primer to begin synthesis?

answer

RNA pol doesn't need a primer

question

What is a transcription unit?

answer

the stretch of DNA that's transcribed into an RNA (from promoter to terminator sequence)

question

What are the 3 stages of transcription?

answer

1. Initiation: After RNA pol binds to the promoter, the DNA strands unwind, and the pol initiates RNA syn at the start point on the template strand. 2. Elongation: The polymerase moves downstream, unwinding the DNA + elongating the RNA transcript 5' -> 3'. In the wake of transcription, the DNA strands re-form a double helix. 3. Termination: Eventually, the RNA transcript is released, and the polymerase detaches from the DNA.

question

How many RNA pol do bacteria/euk have

answer

bacteria = 1 eukaryotes= 3

question

List 3 important facts about the promoter:

answer

1. The transcription start point (the nucleotide where RNA synthesis begins) is included in the promoter 2. Determines which of the two strands are used as the template 3. needs transcription factors (in eukaryotes) to mediate the binding of RNA pol + initiation of transcription.

question

What are the 3 stages of initiation?

answer

1. The eukaryotic promoter includes a nucleotide sequence containing TATA about 25 nucleotides upstream from the start point. 2. one or a few transcription factors recognize the TATA box and bind to the DNA so that RNA pol II can do so. 3. Additional transcription factors bind to the DNA along with RNA pol II, forming the transcription initiation complex. The DNA double helix then unwinds, and RNA syn beings at the start point on the template strand.

question

What is the TATA box?

answer

a crucial promoter DNA sequence.

question

What comprises a transcription initiation complex?

answer

the complex of transcription factors and RNA pol II bound to the promoter.

question

RNA processing happens only in ______ cells. what is it in one sentence.

answer

eukaryotic cells. the primary transcript is altered at both ends and sections in the middle are removed.

question

What happens at the 5' end of the primary transcript in RNA processing?

answer

it receives a 5' cap, where a form of guanine modified to have 3 phosphates on it is added after the first 20-40 nucleotides.

question

What happens at the 3' end of the primary transcript in RNA processing?

answer

An enzyme adds 50-250 adenine nucleotides, forming a poly-A tail.

question

what are 3 important functions of the 5' cap and the poly-A tail?

answer

1. The seem to help facilitate the export of the mature mRNA from the nucleus 2. They protect the mRNA from degradation by hydrolytic enzymes 3. They help ribosomes attach to the 5' end of the mRNA once it reaches the cytoplasm.

question

What are UTR's?

answer

untranslated regions: parts of mRNA that won't be translated to protein but have functions like ribosome binding. located at the 5' and 3' ends.

question

Distinguish between introns and exons:

answer

Introns are noncoding segments of nucleic acid between coding regions. Exons are expressed regions that exit the nucleus.

question

Eukaryotic Termination:

answer

RNA pol II transcribes the polyadenylation (PD) signal sequence, which codes for a PD signal in the pre-mRNA. Then 10-35 nucleotides downstream, associated proteins with the growing RNA cut it free from the pol. The pol continues transcribing though for 100s of nucleotides past termination. This extra RNA is then digested by an enzyme that moves along the pre-mRNA until it reaches the pol, then the pol falls off and transcription is terminated.

question

What are snRNPs? what two types of molecules make up snurps?

answer

small nuclear ribonucleoproteins are proteins in the nucleus that recognize the splice sites at each end of an intron (short nucleotide sequences). Made up of RNA & protein molecules.

question

What type of RNA is in a snRNP?

answer

small nuclear RNA about 150 nucleotides long

question

Snurps band together in little snurp groups to form spliceosomes. How do spliceosomes work?

answer

spliceosomes interact with certain sites along an intron, releasing it and joining the exons that were around it. They catalyze this process, participate in spliceosome assembly, and splice site recognition.

question

List the 3 steps of modifying a pre-mRNA:

answer

1. snRNPs and other proteins together form a spliceosome on a pre-mRNA molecule containing introns and exons. 2. Within the spliceosome, snRNPs base pair with nucleotides at specific sites along the intron. 3. The spliceosome cuts out the intron and at the same time splices the exons together. The spliceosome then comes apart itself and releases the only-exon mRNA.

question

Explain hwo splice sites are recognized:

answer

the RNA parts of snRNP base-pair to specific sites along an intron.

question

What are ribozymes?

answer

RNA molecules that function as enzymes. In some organisms, RNA splicing can occur without any other proteins or RNAs: the intron acts as its own excisor.

question

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

answer

that all biological enzymes were proteins. Actually RNA can be enzymes/catalysts too.

question

What are the 3 properties of RNA that allow it to function as an enzyme?

answer

1. Since RNA is single-stranded, a region of an RNA molecule may base-pair with a complementary region in the same molecule, giving it a 3D shape that's specific. This is essential for its catalytic function. 2. Like amino acids in an enzymatic protein, some of the bases in RNA contain functional groups that may participate in catalysis. 3. It's able to H bond with other nucleic acids (RNA/DNA), which adds specificity to its catalytic activity. (ex: base pairing in mRNA & spliceosomes).

question

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

answer

A single gene can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA processing.

question

What is an anticodon?

answer

a nucleotide triplet at the bottom of the tRNA that base pairs to the codon of the mRNA so the amino acid can detach.

question

Description & Function of mRNA:

answer

Messenger RNA: modified single strand chain of nucleotides that are complementary to DNA. Carries the message of genes, of what proteins to make

question

Description & Function of tRNA:

answer

a tRNA has an anticodon one one end and an amino acid on the other end. Functions to transfer amino acids from the cytoplasm to the mRNA, at the ribosome.

question

Description & Function of rRNA:

answer

ribsosomal RNA: molecules that make up a ribosome, where mRNA's message is translated to amino acids.

question

Exon shuffling:

answer

introns increase the probability of beneficial cross-overs between the exons of alleles by not interrupting coding sequences. Either allelic or nonallelic shuffling can lead to new proteins with new functions.

question

Where is tRNA made and where are the bonds it makes

answer

Hbonds between base pairs of itself (in the T), and Hbonds anticodon to codon.

question

How many different aminoacyl-tRNA sythetases are there, and what are they?

answer

20, one for each amino acid. They are a group of related enzymes that facilitate the correct matching up of tRNA and amino acids.

question

What is wobble?

answer

Wobble explains why the synonymous codons for a given amino acid can differ in their third base, but usually not in their other bases

question

Explain the process of a specific amino acid being joined to a tRNA.

answer

1. Active site of aminoacyl-tRNA synthetase binds the amino acid and ATP. 2. ATP loses two P groups and joins amino acid to AMP. 3. Appropriate tRNA covalently bonds to an amino acid, displacing AMP. 4. The tRNA charged with amino acid is released by the enzyme.

question

Describe the structure of a eukaryotic ribosome and how it's made:

answer

In the nucleus, rRNA genes on the chromosomal DNA are transcribed, and the RNA is processed and assembled with proteins from the cytoplasm. The resulting ribsomal subunits are then exported to cytoplasm. In both bacterial and eukaryotic ribosomes, large & small subunits join only when they attach to an mRNA. 2/3 of the mass of a ribosome consists of rRNAs.

question

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

answer

Pro: smaller, 3 rRNA mc's. Euk: larger, 4 rRNA mc's. Certain antibiotic drugs can inactivate bacterial ribosomes without inhibiting the ability of euk ribo's to make proteins. used to combat infections.

question

Explain the functions of the APE sites.

answer

A site holds the tRNA carrying the next amino acid to be added to the chain. P site (start site) holds the tRNA carrying the growing polypeptide chain. E site is where discharged tRNAs exit the ribosome.

question

3 stages of translation:

answer

1. Initiation: Initiation factors bring together mRNA and tRNA carrying 1st amino acid met. 2. Elongation: Amino acids are added one by one to the preceding amino acid. Stimulated by elongation factors. 3. Termination: UAG, UAA, or UGA codes for a stop signal and release factor binds.

question

Summary of initiation:

answer

1. Small ribosomal subunit binds to mRNA, and initiator tRNA with the anticodon UAC base pairs with the start codon AUG, carrying the amino acid met. 2. Large RS binds to complete the complex, using GTP. Initiation factor proteins bring all the components together.

question

Is a ribosome an enzyme?

answer

Yes, it's a big ribozyme since it's the catalyst of peptide bond formation.

question

Summary of Elongation:

answer

1. Codon Recognition: The tRNA anticodon base-pairs with the mRNA codon in the A site. Hydrolysis of GTP here increases the efficiency and accuracy of this step. 2. Peptide bond formation: the large ribosomal subunit catalyzes the formation of a peptide bond between the new amino acid in the A site the growing polypeptide in the P site. This removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site. 3. Translocation: The ribosome moves 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 to go find another amino acid. The mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site.

question

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

answer

A protein that binds directly to the stop codon in the A site. Causes the addition of an H20 mc instead of an amino acid. This hydrolyzes the bond between the completed polypeptide and the tRNA on the P site, releasing the polypeptide through the E site of the ribosome. Requires the hydrolysis of two more GTP molecules.

question

What is a polyribosome?

answer

string of ribosomes all translating the same mRNA at the same time allow many copies of the polypeptide to be made more quickly.

question

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

answer

protein folding due to primary structure & amino acid interactions, which sometimes occur in chaperonins, determine shape and function. Post-translational modifications: attachments (sugars, phosphates) or removal (of 1 or more amino acids) have to occur sometimes for the protein to function in the cell.

question

Example of 2 proteins being edited to result in a final-form functional protein:

answer

1. sometimes a polypeptide is enzymatically cleaved= insulin. 2. or brought together: hemoglobin

question

List 5 types of post-translational modifications:

answer

1. amino acid removal from the end of the polypeptide chain 2. chain enzymatically cleaved into pieces 3. cut out central & reattach other parts (insulin) 4. attach two or more separate polypeptides (hemoglobin) 5. add sugars, phosphates, lipids, etc.

question

Define a mutation in terms of molecular genetics:

answer

changes to the genetic information of a cell or virus. Responsible for the huge diversity of genes among organisms.

question

Define point mutations:

answer

chemical changes in a single base pair of a gene.

question

What are frameshift mutations:

answer

insertions or deletions of base pairs that cause the whole later sequence to be off, shifted by one or more. Easier to catch than substitutions.

question

Explain how proteins are targeted for the ER (6 steps)

answer

1. polypeptide synthesis begins on a free ribosome in the cytosol. 2. Signal recognition particle (SRP) binds to signal peptide (end of polypeptide) momentarily halting synthesis. 3. SRP binds to a receptor protein in the ER membrane. This is part of the T complex that has a membrane pore and a signal-cleaving enzyme. 4. The SRP leaves and polypeptide synthesis resumes, with simulaneous translocation across the ER membrane. 5. signal cleaving enzyme cuts off the signal peptide 6. The rest of the completed polypeptide leaves the ribosome and is processed in the ER.

question

Where does polypeptide synthesis take place/

answer

always in the cytosol unless it has a signal peptide, which sends the protein to the ER. signal peptide has to be recognized first though by the SRP, then it brings the ribosome to a receptor protein built into the ER membrane (part of translocation complex).

question

What is the difference between a nonsense and missence mutation?

answer

Nonsense causes translation to be terminated too early, so the protein is cut short. Nearly all of these lead to non-functional proteins. Missense

question

Identify two mechanisms by which frameshifts may occur.

answer

Insertion and deletion. Occurs whenever the nucleotides deleted or inserted aren't in multiples of 3. All downstream will be incorrectly grouped into the wrong codons.

question

How can a base pair substitution result in a silent mutation?

answer

ex: if CCG mutated to CCA, its corresponding \"anticondon would change from GG C to GG U, but ti would still attach the same amino acid, glycine at the right location int he protein. silent mutations don't affect the organism

question

What are the two categories of mutagens?

answer

(physical and chemical agents that interact with DNA in ways to cause mutations) Physical ex: x rays Chemical ex: 1. base analogs: normal DNA bases that pair incorrectly in DNA replication 2. Insertions distort the double helix 3.Some cause chemical changes to distort their pairing properties.

question

Describe 2 important ways in which bacterial and eukaryotic genes differ:

answer

1. Initiation & termination of translation is different 2. Bacteria have no compartmental organization so transcription and translation can occur at the same time

question

What is a gene? Write the more accurate version of 'one gene codes for one polypeptide.'

answer

A gene is a region of DNA that can be expressed to produce a final functional product that is either an RNA or a polypeptide

question

Summarize 'From Gene to Protein' (6 steps)

answer

1. RNA is transcribed from DNA to template 2. In eukaryotes, the pre-mRNA is spliced and modified to produce mRNA which moves from the nucleus to the cytoplasm 3. mRNA leaves the nucleus and attaches to a ribosome 4.Each amino acid attaches to its proper tRNA with the help of enzyme + ATP 5. A succession of tRNAs add their amino acids to the pp chain as the mRNA is moved through the ribosome one codon at a time. 6. Polypeptide is released either for more modification or finished!

Chapter 17: From Gene to Protein

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