Central dogma and proteins

Assignment

Audesirk, Audesirk & Byers Chapter 10

Today's musical selection
Lewis Lee Attack of the killer tomatoes

Central Dogma of cell biology (review)

Figure 10.3
DNA
transcription
RNA
translation
protein
(reverse transctiption, using reverse transcriptase enzyme, in AIDS-causing retrovirus HIV)
As you will eventually see, there is more to it than this, like RNA processing,

Genetic code (partly a review)

Table 10-3
3 letter code for aa's (codons)
Note, with 20 amino acids, and 4 x 4 x 4 = 64 codons, there is redundancy, called "degeneracy."
For instance, (top left) for phenylalanine, code can be UUU or UUC.
(It is interesting to contemplate that if a mutation converted UUU to UUC or vice versa, the amino acid would still be the same.)
There are 3 stop codons
Methionine is the start codon

Study question: Is this code for RNA or DNA?
Answer: RNA (You can tell when you notice that U is one of the four bases specified)

Figure 10-9
combining the information from the last 2 figures, here is a diagram of what nucleotide sequences might be for DNA and RNA and the amino acid sequence would be.
(It is interesting to contemplate that only one of the two DNA strands would work, the "template DNA strand" or the sense strand [the other being "the complementary DNA strand" or the antisense strand])

Example: Hemoglobin

Table 10-4
On the topic of mutations, consider that if CTT changes to CAT, Glu -> Val, the sickle cell anemia mutation.
When one amino acid is changed to another, this is a missense mutation.

Mutations

(1) change base in degenerate 3rd position - no effect
(2) change a base that matters - "missense" - the protein will have a different amino acid
(3) change base so that there is a stop codon - "nonsense" the protein will not be full length
(4) insertion or deletion - many amino acid changes and/or premature stop
To understand this last point, I introduce the expression "open reading frame;" even though you could conceivably start anywhere, only if you start in right place (the right one of 3 nucleotides) for a normal (non-mutant) gene will the reading proceed for a reasonable distance without hitting a stop codon.

Transcription and translation

Figure 10-4a
RNA polymerase makes mRNA
(I'll say more about the "promoter" later)

Figure 10-5
What transcription looks like

Translation
In general, there are 3 RNA's, t (transfer), m (messenger), and r (ribosomal).
(1) Ribosome is the machinery, and it is big.
(2) mRNA codes for the protein.
(3) Many different tRNA's read (by base pairing, using the anticodon) each codon and carry one amino acid to the growing peptide chain.

Figure 10-8 (I will show Fig. 10-8 b, f, and i)
step by step, peptide is elongated, aminoacyl tRNA (tRNA with amino acid hooked to it) brings in amino acid.
eventually, when one of the 3 stop codons is encountered, the protein is released.

Question: What is a gene?

One theoretical answer: The DNA sequence that codes for one protein.
But: In eukaryotes there is way too much DNA.
Explanations:
(1) There are extra stretches of DNA interspersed in the coding sequence.
(That will be one topic we cover here.)
(2) There are places between "genes," some of which regulate the genes because of:

The need for gene regulation

In multicellular eukaryotic organism,
(1) ALL CELLS HAVE SAME GENES
(2) CELLS ARE DIFFERENT BECAUSE OF WHICH GENES ARE EXPRESSED
(but this can be fairly permanent, development gene regulation)

Prokaryote example, the lac operon

Figure 10-10
(relates to fundamental topic of gene regulation) lac operon - genes for enzymes for metabolism of lactose, the disaccharide in milk. When lactose is present, allolactose pulls repressor off of operator so that RNA polymerase can move from promoter to make mRNA for genes (lacZ, lacY and lacA) that code for their respective enzymes (beta-galactosidase, permease and transacetylase, enzymes for lactose metabolism. The bacterium "does not bother" making lactose metabolizing enzymes unless lactose (the sugar in milk) is present. Note that one mRNA is for 3 proteins, never the case in eukaryotes.

The 1965 Nobel Prize was shared by FRANÇOIS JACOB and JACUES MONOD who established the operon model.

Lactose digestion in humans

Box on p. 113
(also reference in digestion chapter
All infants can digest lactose, obviously
There is a racial difference in whether adults have lactase.
Blacks and Asians are likely to be lactose intolerant
Caucasians are usually lactose tolerant
Europeans evolved with dairy husbandry

Eukaryotic gene structure and RNA processing

Figure 10-7
RNA polymerase II makes "pre-mRNA"
methylated G nucleotide - at 5' cap
extra copied after end of gene is not capped, degraded
poly-A tail 100-200 residues of adenylic acid
site shows where end of gene transcription should be.
primary transcript
Exons are spliced together and form the coding sequence, and introns are spliced out.

Question: Is this splicing useful in any way? (other than to get rid of junk DNA)
Answer: Different exons can be spliced together (for instance in different tissues) to make several different proteins from the same gene.

Promoting gene action

Note that there are places "upstream" of the "gene" (coding sequence), the promoter, where transcription factors (proteins) bind to notify RNA polymerase to do its job. Since the 1980's, there has been a lot of interest in "promoter bashing," determining properties of the transcription factors and the DNA sequences they interact with. Here is where many hormones and signaling pathways determine a cell's specifics

Questions used in 2007 and 2008 related to this outline

Ribosomes might be situated (A-where?) and serve (B-what function?).
(a) A in the nucleus; B to store genetic information.
(b) A in the Golgi apparatus; B to deliver energy.
*(c) A in the rough endoplasmic reticulum; B to synthesize proteins.
(d) A in the microsomal fraction; B to mediate transcription.
(e) A in the intercalated disk; B to carry the genetic code for each protein.

A poly-A tail characterizes
(a) the intron.
*(b) mRNA.
(c) the operator.
(d) methionine.
(e) the anticodon.

In eukaryotes, what gets spliced to what?
(a) The promoter to the coding sequence.
(b) The lacZ, LacY and LacA genes.
(c) The template and complementary DNA strands.
(d) Jacob to Monod.
*(e) One exon to another.

An amino acid can be coded for by more than one codon. What is this called?
(a) Heterozygosity
*(b) Degeneracy
(c) Nondisjunction
(d) Translation
(e) Nonsense mutations

The tRNA molecule for which amino acid binds to the start codon during translation?
(a) Tyrosine
(b) Glucose
(c) Arginine
(d) Glycine
*(e) Methionine

Humans only have a fraction of their DNA that codes for proteins. Where is this? (a) in ribosomes
(b) in operators
(c) in promoters
(d) in introns
*(e) in exons

What factor accounts for the variety of cell types in different tissues?
(a) Some cells are homozygous, others are heterozygous.
(b) Different cells have different subsets of genes.
*(c) Different genes are expressed.
(d) Different cells contain different sets of chromosomes.
(e) Some mRNAs are translated; others are not.

The codons on the table for the genetic code are triplets from
(a) the template DNA strand.
(b) the sense DNA strand.
(c) the complementary DNA strand.
*(d) mRNA.
(e) the RNA sequence of ribosomal RNA (rRNA)

What would happen if a codon for an amino acid were mutated into a stop codon?
(a) Lactose intolerance would result.
(b) There would be a missense mutation.
*(c) The growing peptide would be ejected from the ribosome prematurely.
(d) Not much since the change would be in the third base.
(e) People would suffer from sickle cell anemia.

In the lac operon, RNA polymerase would be blocked if (what) were present?
*(a) The repressor.
(b) Introns.
(c) The operator.
(d) The promoter.
(e) Lactose.

DNA polymerase had already duplicated the DNA to make two identical copies of all the genetic material. Where are these two copies?
(a) in the two kinetochores
(b) in the two centrioles
*(c) in the two sister chromatids
(d) in the two homologues
(e) one in the autosome, the other in the sex chromosome
Which of the following is TRUE of the genetic information in the cells of your body?
A) Different kinds of cells contain different genetic information.
B) Each type of cell contains only the genetic information it needs to be that type of cell.
*C) The genetic information in all somatic cells (this excludes gametes) is identical.
D) Growth, development, and differentiation result from mutations in DNA.
E) Meiosis ensures that each somatic cell will be different.

The number of consecutive mRNA bases needed to specify one amino acid is
*A) 3.
B) 4.
C) 20.
D) 64.
E) many more than any of the above numbers .

"Val is substituted in place of Glu in the sixth position of the beta chain of hemoglobin."
A) This a nonsense mutation.
B) This could only happen if the deletion of one base pair offset the open reading frame.
C) This is because of regulation of the lac operon.
*D) This is a result of a mutation in DNA that causes sickle cell anemia.
E) This is because of degeneracy in the genetic code.

The number of different possible codons is
A) 3.
B) 4.
C) 20.
*D) 64.
E) way higher than any of the above numbers.

"Splicing" is a term applied to
A) the polycistronic (multi-gene) mRNA of bacteria.
*B) putting together exons to make mRNA from pre-mRNA.
C) the release of mRNA from DNA when the RNA polymerase reaches the end of the gene.
D) what happens at the ribosome when a stop codon is encountered.
E) regulating which genes are expressed in different cells.

What would happen if the complementary DNA strand were transcribed into mRNA instead of the template strand?
A) It seems to me it ought to work if RNA polymerase just went the other way along the DNA double helix.
B) That is precisely what happens in the checkpoint letting cells in G0 go on into prophase.
C) That is precisely what the cause of missense mutations is.
D) Lactose would be bound to the repressor.
*E) A ridiculous mRNA would be made and the translation machinery would encounter stop codons.

All of the following occur during DNA replication EXCEPT
A) separation of parental DNA strands.
B) use of parental DNA as a template.
*C) translation into RNA.
D) synthesis of a new strand to make double-stranded DNA.
E) use of DNA polymerase.

When comparing DNA and RNA, we find
A) RNA has the sugar deoxyribose while DNA has no sugar.
B) DNA is a chain of nucleotides while RNA is a chain of amino acids.
C) DNA is used for translation while RNA is used for transformation.
*D) adenine pairs with different bases in DNA and RNA.
E) cytosine pairs with different bases in DNA and RNA.

Questions used in 2002 relating to this outline (and other outlines)

The central dogma of cell biology
(a) postulates that protein is transcribed directly from DNA.
*(b) runs in reverse with the virus that causes AIDS.
(c) applies to how one DNA strand has the information to synthesize the other strand.
(d) states that amino acid sequences are translated into nucleotide sequences.
(e) explains the plasmid.

Introns
(a) are "jumping genes" with inverted repeats at their ends.
(b) are the type of virus that "eat" bacteria.
(c) are only found in prokaryotes.
*(d) are the parts of eukaryotic pre-mRNA that are spliced out to make mRNA.
(e) cause mad cow disease.

In prokaryotes, transcription
(a) makes a molecule with introns and exons.
(b) makes proteins.
(c) makes transcription factors.
*(d) makes mRNA.
(e) takes place in the nucleus.

Anticodon is a term applied to
(a) ribosomal subunits.
(b) the DNA template.
*(c) aminoacyl-tRNA.
(d) the exon.
(e) the poly-A tail.

Reverse transcriptase would work on [A] to form [B].
(a) [A] bacteria; [B] bacteriophage
(b) [A] pre-mRNA; [B] mRNA
(c) [A] mRNA; [B] protein
(d) [A] DNA; [B] PCR reaction products
*(e) [A] RNA; [B] DNA

If the sequences of bases along the template strand of DNA is A-G-A-T, what is the sequence along the mRNA strand?
(a) A-G-A-T
*(b) U-C-U-A
(c) A-T-C-T
(d) A-G-A-U
(e) U-A-G-A

Sickle cell anemia is a
*(a) missense mutation.
(b) nonsense mutation.
(c) frameshift.
(d) thymine dimer.
(e) result of telomerase.

The codes for leucine include CUU, CUC, CUA, and CUG. A nucleotide substitution in the third position of the codon would
*(a) have no effect on the final protein.
(b) have no effect on the exact mRNA sequence.
(c) cause the protein synthesis to stop prematurely.
(d) not even change which tRNA molecule recognizes the codon.
(e) result in an amino acid substitution.

Which enzyme is the hallmark of HIV (human immunodeficiency virus) that causes AIDS (acquired immunodeficiency virus)?
(a) primase.
(b) nuclease.
(c) telomerase.
(d) hemoglobin.
*(e) reverse transcriptase.

Codons such as CUG would be found
*(a) on the mRNA.
(b) on an antibody.
(c) in the restriction endonuclease.
(d) on the ribosome.
(e) on the template DNA.

Nonsense mutations are
(a) codons changed to start.
*(b) codons changed to stop.
(c) codons changed to codons for another amino acid.
(d) mutations in the position that defines degeneracy of DNA.
(e) jumping genes.

One thing that is unique to gene transcription in bacteria is
*(a) several enzymes might be coded for by one mRNA.
(b) introns are spliced out.
(c) there is processing of a pre-mRNA to mRNA before mRNA leaves the nucleus.
(d) genetic information is carried by RNA that is transcribed to DNA.
(e) the hereditary information is carried by proteins.

The genetic code for Met (the amino acid methionine), AUG, is unique because
(a) it is a DNA sequence.
(b) it is the sort of palindrome that is cut by a restriction enzyme.
(c) it is also the binding site for a helix turn helix molecule.
*(d) it is also the start codon.
(e) it is also the stop codon.

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