Gene Expression:From Gene to Protein

In a research article about Alkaptonuria published in 1902, Garrod suggested that humans inherit two "characters" (alleles) for a particular enzyme and that both parents must contribute a faulty version for the offspring to have Alkaptonuria. Today, would this disorder be called dominant or recessive?

What polypeptide product would you expect from a poly-G mRNA that is 30 nucleotides long?

The template strand of a gene contains the sequence 3’-TTCAGTCGT-5’. Imagine that the non-template plate sequence was transcribed instead of the template sequence. Draw the mRNA sequence and translate it using Figure 17.6. (Be sure to pay attention to the 5’ and 3’ ends.) Predict how well the protein synthesized from the non-template strands would function, if at all.

What is a promoter? Is it located at the upstream or downstream end of a transcription unit?

What enables RNA polymerase to start transcribing a gene at the right place on the DNA in a bacterial cell? In a eukaryotic cell?

Suppose X-rays caused a sequence change in the TATA box of a particular gene's promoter. How would that affect the transcription of the gene? (See Figure17.9)

There are about 20,000 human protein-coding genes. How can human cells make 75,000-100,000 different proteins?

How is RNA splicing similar to how you would watch a recorded television show? What would introns be?

What would be the effect of treating cells with an agent that removed the cap from mRNAs?

In the sequence logo (bottom, left), the horizontal axis shows the primary sequence of the DNA by nucleotide position. Letters for each base are stacked on top of each other according to their relative frequency at that position among the aligned sequences, with the most common base as largest letter at the top of the stack. The height of each letter represents the relative frequency of that base at that position. (a) In the sequence alignment, count the number of each base at position-9 and order them from the most to least frequent. Compare this to the size and placement of each base -9 in the logo. (b) Do the same for position 0 and 1. 

The height of a stack letters in a logo indicates the predictive power of the stack (determined statistically). If the stack is tall, we can be more confident in predicting what base will be in that position of a new sequence is added to the logo. For example, at position2 in the sequence alignment, all 10 sequences have a G: the probability of finding a G there in a new sequence is very high, as is the stack in the sequence logo. For short stacks, the bases all have about the same frequency, so it’s hard to predict would be at those positions. (a) Looking at the sequence logo, which two positions have the most predictable bases? What bases do you predict would be at those positions in a newly sequenced gene? (b) Which 12 positions have the least predictable bases? How do you know? How does this reflect the relative frequencies of the base shown at these positions in the sequence alignment? Use the two leftmost positions of the 12 as examples in your answer. 

In the actual experiment, the researchers used 149 sequences to build their sequence logo, which is shown below. There is a stack at each position, even if short, because the sequence logo includes more data. (a) Which three positions in this sequence logo have the most predictable bases? Name the most frequent base at each. (b) Which four positions have the least predictable bases? How can you tell?

(a) Based on the logo, what five adjacent base positions in the 5' UTR region are most likely involved in ribosome binding? Explain. (b) What is represented by the bases in positions 0-2?

What two processes ensure that the correct amino acid is added to a growing polypeptide chain?

Describe how a polypeptide to be secreted reaches the endomembrane system. 

Draw a tRNA with the anticodon 3’-CGU-5’. What two different codons could it bind to? Draw each codon on an mRNA, labeling all 5’ and 3’ ends, the tRNA, and the amino acid it carries.

In eukaryotic cells, mRNAs have been found to have a circular arrangement in which proteins hold the poly-A tail near the 5’ cap. How might this increase translation efficiency?

What happens when one nucleotide pair is lost from the middle of the coding sequence of a gene?

Individuals heterozygous for the sickle-cell allele are generally healthy but show phenotypic effects of the allele under some circumstances (see Figure 14.17). Explain in terms of gene expression.

The template strand of a gene includes this sequence:

3’-TACTTGTCCGATATC-5’. It is mutated to 

3’-TACTTGTCCAATATC-5’. For both wild-type and mutant sequences, draw the double-stranded DNA, the resulting mRNA, and the amino acid sequence each encodes. What is the effect of the mutation on the amino acid sequence?

In eukaryotic cells, transcription cannot begin until

1. the two DNA strands have completely separated and exposed the promoter.

2. several transcription factors have bound to the promoter.

3. the 5’caps are removed from the mRNA

4. the DNA introns are removed from the mRNA.

Which of the following is not true of a codon?

1. It may code for the same amino acid as another codon.

2. It never codes for more than one amino acid.

3. It extends from one end of a tRNA molecule

4. It is the basic unit of the genetic code.

The anticodon of a particular tRNA molecule is:

1. complementary to the corresponding mRNA codon.

2. complementary to the corresponding triplet in rRNA.

3. the part of tRNA that bonds to a specific amino acid.

4. catalytic, making the tRNA a ribozyme.

Which of the following is not true of RNA processing?

1. Exons are cut out before mRNA leaves the nucleus.

2. Nucleotides may be added at both ends of the RNA.

3. Ribozymes may function in RNA splicing.

4. RNA splicing can be catalyzed by spliceosomes.

Which component is not directly involved in translation?

1. GTP

2. DNA

3. tRNA

4. ribosomes

Using Figure 17.6, identify a 5’– 3’ sequence of nucleotides in the DNA template strand for an mRNA coding for the polypeptide sequence Phe-Pro-Lys. 

(A) 5’-UUUCCCAAA-3’

(B) 5’-GAACCCCTT-3’

(C) 5’-CTTCGGGAA-3’

(D) 5’-AAACCCUUU-3’

Which of the following mutations would be most likely to have a harmful effect on an organism?

1.  a deletion of three nucleotides near the middle of a gene

2. a single nucleotide deletion in the middle of an intron

3. a single nucleotide deletion near the end of the coding sequence

4.  a single nucleotide insertion downstream of, and close to, the start of the coding sequence.

Would the coupling of the processes shown in Figure 17.24 be found in a eukaryotic cell? Explain why or why not. 

Complete the following table:

Most amino acids are coded for by a set of similar codons (see Figure17.6). Propose at least one evolutionary explanation to account for this pattern.

Knowing that the genetic code is almost universal, a scientist uses molecular biological methods to insert the human β-globin gene(shown in Figure17.12) into bacterial cells, hoping the cell will express it and synthesize functional β-globin protein. Instead, the protein produced is non-functional and contains fewer amino acids than does β-globin made by a eukaryotic cell. Explain why.

Evolution accounts for the unity and diversity of life, and the continuity of life is based on heritable information in the form of DNA. In a short essay (100-150words), discuss how the fidelity with which DNA is inherited is related to the processes of evolution. (Review the discussion of proofreading and DNA repair in Concept 16.2)

Some mutations result in proteins that function well at one temperature but are non-functional at a different (usually higher) temperature. Siamese cats have a "temperature-sensitive" mutation in a gene encoding an enzyme that makes dark pigment in the fur. The mutation results in the breed's distinctive point markings and lighter body color (see the photo). Using this information and what you learned in the chapter, explain the pattern of the cat's fur pigmentation.