Chapter 15 Facts - Genetics, A Conceptual Approach, V.3 By Benjamin A. Pierce

Front 1

Describe Neurospora, and the medium it can grow on.

Back 1

Neurospora is haploid and lets recessive mutation be observed easily. It grows on minimal medium, which only contains inorganic salts, nitrogen, a carbon source like sucrose, and biotin.

Front 2

What can happen if Neurospora mutates?

Back 2

Mutations that occur might disrupt fungal growth by destroying Neurospora’s ability to make one or more essential molecules.

Front 3

What happens to the Neurospora mutants (auxotrophs)?

Back 3

The Neurospora mutants (auxotrophs) won’t grow on a minimal medium, but they can grow on a medium that gives them the nutrients they can’t make themselves.

Front 4

What is the "one gene, one enzyme" hypothesis?

Back 4

The one gene, one enzyme hypothesis states that genes function by encoding enzymes, and each gene codes for a separate enzyme.

Front 5

What is the basic structure of a protein?

Back 5

All proteins are made of amino acids that are linked end to end.

Front 6

What is the common structure of the 20 common amino acids?

Back 6

The 20 common amino acids have a similar structure: a central carbon atom bound to an amino group, a hydrogen atom, a carboxyl group, and an R (radical) group that is different for each amino acid.

Front 7

Describe how amino acids are joined and what they make.

Back 7

The amino acids in proteins are joined by peptide bonds to form polypeptide chains, and a protein is made of one or more polypeptide chains. The primary protein structure is the sequence of amino acids.

Front 8

Define and describe codons.

Back 8

The basic unit of the genetic code is a codon, a set of three nucleotide bases that code for one amino acid. Each position in the codon can contain one of four bases: A, G, C, or U (T instead of U in bacteria). There are 64 possible codons.

Front 9

Describe stop codons.

Back 9

Three of the 64 codons are stop codons, which end translation.

Front 10

Describe sense codons.

Back 10

The other 61 codons that are not stop codons are sense codons, and they code for amino acids.

Front 11

What is the degenerate code?

Back 11

Since the code contains more information than needed to specify amino acids, it is called a degenerate code; when amino acids can be made by more than one codon. Only tryptophan and methionine have one codon.

Front 12

What are synonymous codons?

Back 12

Synonymous codons are different codons that make the same amino acid.

Front 13

Define and describe adaptor molecules.

Back 13

tRNAs are adaptor molecules, and they bind to specific amino acids and deliver them to the ribosome where they are made into polypeptide chains. Each type of tRNA attaches to one type of amino acid.

Front 14

Describe isoaccepting tRNAs.

Back 14

Isoaccepting tRNAs are different tRNAs that accept the same amino acid but that have different anticodons.

Front 15

What is the initiation codon, and what is its job?

Back 15

The initiation codon sets the reading frame. It is the first codon of the mRNA to make an amino acid; it normally an AUG (GUG and UUG are rare), which means that the first amino acid is always a methionine.

Front 16

What does the initiation codon code for in bacteria?

Back 16

In bacterial cells, AUG codes for a modified methionine called N-formylmethionine, and all proteins in bacteria begin with it. Sometimes the formyl group or the entire amino acid is removed after the protein is made. When the AUG isn’t a start codon, it codes for normal methionine.

Front 17

What are the termination codons, and what are their jobs?

Back 17

The termination codon signals the end of the protein. There are three termination codons: UAA, UAG, and UGA. They don’t code for amino acids, so they are also called stop codons, termination codons, or nonsense codons.

Front 18

Why can't stop codons bind with tRNAs?

Back 18

Because no tRNA molecule has an anticodon that can pair with a stop codon, so they end translation.

Front 19

What is translation and where does it happen?

Back 19

Translation is when amino acids are made into proteins. It happens on ribosomes.

Front 20

What is the generally overview of what happens in translation?

Back 20

A ribosome attaches near the 5’ end of an mRNA strand and goes towards the 3’ end and translates codons as it goes. Synthesis starts at the amino end of the protein, and the protein is elongated when new amino acids are added to the carboxyl end.

Front 21

What types of interactions occur in protein synthesis?

Back 21

Protein synthesis includes many RNA-RNA interactions. The interactions include reactions between the mRNA and the rRNA that hold the mRNA in the ribosome, interactions between the codon on the mRNA and the anticodon on the tRNA, and the interactions between the tRNA and the rRNAs on the ribosome.

Front 22

What are the four stages of protein synthesis?

Back 22

Protein synthesis has four stages: tRNA charging, initiation, elongation, and termination.

Front 23

Describe tRNA charging.

Back 23

tRNA charging is the first step of protein synthesis, when the amino acids bind to the tRNAs.

Front 24

Describe tRNAs, and how they attach to amino acids.

Back 24

Each tRNA is specific for one amino acid. They all have the sequence CCA at their 3’ ends, and the carboxyl group (COO-) of the amino acid is attached to the adenine nucleotide at the end of the tRNA.

Front 25

Describe aminoacyl-tRNA synthetases.

Back 25

Aminoacyl-tRNA synthetases are the key to the specificity between amino acids and tRNAs. A cell has 20 different ones, one for each amino acid. Each aminoacyl-tRNA synthetase recognizes one amino acid (based on shape, size, and R group), and the tRNA that accepts the amino acid.

Front 26

What is the basic reaction of tRNA charging?

Back 26

tRNA charging requires energy, which is given by ATP (amino acid + tRNA + ATP --> aminoacyl-tRNA + AMP + PPi).

Front 27

Why are errors so rare in tRNA charging?

Back 27

Errors in tRNA charging are rare (1 in 10,000-1 in 100,000 reactions). This is due to the proofreading that happens, which detects and removes incorrectly paired amino acids form the tRNAs.

Front 28

What is initiation?

Back 28

Initiation is the second step of protein synthesis, when the parts needed for translation are assembled at the ribosome.

Front 29

What are the parts needed for initiation to occur?

Back 29

The parts needed for translation are (1) mRNA, (2) the small and large ribosomal subunits, (3) a set of three proteins called initiation factors, (4) initiator tRNA with an N-formylmethionine attached (fMet-tRNAfmet), and (5) GTP (guanosine triphosphate).

Front 30

What are the three major steps of initiation?

Back 30

Initiation has three major steps: (1) mRNA binds to the small ribosomal subunit; (2) initiator tRNA binds to the mRNA through base pairing between the codon and the anticodon; (3) the large ribosome joins the initiation complex.

Front 31

Describe the basic structure of a ribosome.

Back 31

A ribosome has two subunits: the small 30S subunit and the large 50S subunit (in bacteria).

Front 32

When can an mRNA bind to the ribosome, and how?

Back 32

An mRNA molecule can only bind to the small ribosomal subunit when the subunits are separate. Initiation factor 3 (IF-3) binds to the small subunit of the ribosome and prevents the large one from binding during initiation.

Front 33

Describe the Shine-Dalgarno consensus sequence in relation to ribosome (the second step of initiation)?

Back 33

The Shine-Dalgarno consensus sequence is complementary to the nucleotide sequence at the 3’ end of 16S rRNA (part of the small subunit). The nucleotides in the SD sequence pair with the complements in the 16s rRNA and let the small ribosomal subunit attach to the mRNA and position the ribosome over the initiation codon.

Front 34

What happens after the Shine-Dalgarno sequence nucleotides base pair to their complements, and what is required here (the third step of initiation)?

Back 34

The 30S initiation complex is formed. The initiator tRNA (fMet-tRNAfmet) attaches to the initiation codon, which requires initiation factor 2 (IF-2), and forms a complex with GTP. Here, the initiation complex made of (1) the small ribosomal subunit, (2) the mRNA, (3) the initiator tRNA with the amino acid, (4) one GTP molecule, and (5) several initiation factors.

Front 35

What happens after the 30S initiation complex is formed (the fourth and final step of initiation)?

Back 35

In the final initiation step, the 70S initiation complex is made. IF-3 dissociates from the small subunit and lets the large subunit join the complex. The GTP (provided by IF-2) is hydrolyzes to GDP, and IF-1 and IF-2 leave.

Front 36

Describe the interaction of proteins that attach to the poly(A) tail, and the following action.

Back 36

Proteins that attach to the poly(A) tail interact with proteins that bind to the 5’ cap, which enhances the binding of the small ribosomal subunit to the 5’ end of the mRNA, so the poly(A) tail helps to initiate translation. mRNA bends backwards and makes a circular structure here.

Front 37

Describe elongation.

Back 37

Elongation is the third step of protein synthesis, when amino acids are joined one at a time to the growing polypeptide chain.

Front 38

What does elongation require?

Back 38

Elongation requires (1) the 70s complex, (2) tRNAs with their amino acids, (3) elongation factors, and (4) GTP.

Front 39

Name and describe the three site of the ribosome.

Back 39

A ribosome has three sites that tRNAs can occupy: the A site (aminoacyl), the P site (peptidyl), and the E site (exit), in the order EPA (but the tRNAs travel APE). The initiator tRNA starts in the P site, but all other tRNAs start in the A site.

Front 40

What does the ribosome look like after initiation? What is in the sites?

Back 40

After initiation, the ribosome is attached to mRNA, the fMet-tRNAfmet is over the AUG start codon in the P site, and the A site is empty.

Front 41

What is the first step of elongation?

Back 41

First, a charged tRNA binds to the A site when elongation factor Tu (EF-Tu) joins GTP and forms a three-part complex with the charged tRNA, which enters the A site of the ribosome. Once the complex is in the A site, GTP cleaves to GDP, and EF-Tu-GDP complex is released. Then, elongation factor Ts (EF-Ts) regenerates EF-Tu-GDP to EF-Tu-GTP.

Front 42

What is the second step of elongation, after EF-Ts regenerates the EF-Tu-GDP complex to EF-Tu-GTP?

Back 42

In the second step of elongation, a peptide bond forms between the amino acids that are attached to tRNAs in the P and A sites. When this peptide bond forms it releases the amino acid in the P site from its tRNA.

Front 43

What is the third step of elongation, after the peptide bond formation releases the amino acid in the P site from its tRNA?

Back 43

The third step of elongation is translocation, where the ribosome moves down the mRNA in the 5’-->3’ direction. This puts the ribosome over the next codon and needs elongation factor G (EF-G) and GTP to happen. Then the ribosome shifts, so that the tRNA in the P site is now in the E site, and from there it will go into the cytoplasm to get recharged with another amino acid.

Front 44

What happens after translocation? What do the ribosome sites look like?

Back 44

After translocation, the A site is empty and ready to get another tRNA specified by the next codon. Throughout the cycle, the polypeptide chain stays attached to the tRNA in the P site.

Front 45

What is termination?

Back 45

Termination is the fourth and final step of protein synthesis, when synthesis stops at the termination codon and the translation parts are released from the ribosome.

Front 46

What happens to the A site in termination?

Back 46

No tRNA enters the A site when a stop codon is found, since there are no tRNAs with anticodons complementary to a stop codon.

Front 47

What happens in termination, now that the A site is empty?

Back 47

Since the A site is empty after a stop codon, proteins called release factors bind to the ribosome. E. coli has three release factors: RF1, RF2 and RF3. In eukaryotic cells there are two release factors, eRF1 (recognizes all three stop codons) and eRF2 (binds GTP and stimulates the release of the polypeptide from the ribosome).

Front 48

What are polyribosomes, and how are they made?

Back 48

Polyribosomes are mRNAs with several ribosomes attached, and they are made when mRNA molecules are translated at the same time by multiple ribosomes.

Front 49

In a polyribosome, what is successively happening?

Back 49

In a polyribosome, each ribosome successively attaches to the ribosome-binding site at the 5’ end of the mRNA and moves towards the 3’ end. The polypeptide associated with each ribosome gets longer as the ribosome moves along the mRNA.