Chapter 2

Question 1

Protein

Answer 1

-a molecule composed of one or more long chains of amino acids occurring in a specific sequence or order.
-This very specific sequence is coded for by the sequence of DNA within the gene for that protein.
-Thus, the purpose of a gene is to provide directions for assembling (synthesizing) a very specific protein.
-All hormones, enzymes, growth facrors, and other protein-based chemicals needed for normal human physiologic function are protein gene products that are produced when the correct genes are activated and expressed.

Question 2

Protein synthesis

Answer 2

-the selective activation of a gene, eventually resulting in the production of me appropriate protein.
-For this reason, proteins are called gene products.
-Each gene provides me code for making one specific protein.

Question 3

Gene expression

Answer 3

The activation of a gene, leading to its transcription and translation and, ultimately to the synthesis of a specific protein.

Question 4

Protein synthesis
Transcription and translation

Answer 4

Figure 2-1

Question 5

Structure of a protein

Answer 5

-The basic structure of a protein is its amino acid sequence. -The 20 different amino acids are commonly called the building blocks of life.
- the sequencing order of me amino acids is what makes one protein different in structure and function from anomer protein. If one amino acid is out of order or completely deleted from the sequence, thr protein will be affected and may not perform its function well.
-the order of the amino acids is critical for the final function of any protein, and even one amino acid change can alter the protein’s function.

Question 6

Table DNA Triplets and RNA Codons for the 20 Amino Acids

Question 7

DNA triplets

Answer 7

-Each amino acid has at least one specific code within the DNA
-these codes are each three nucleotide bases long and are called DNA triplets.
-For example, the final active form of beta globin has 146 amino acids. Thus, the minimum number of bases needed in the gene for beta globin is 438 (3 bases per amino acid multiplied by 146 amino acids).
-[The gene for beta globin (the HBB gene) is located on the short arm (p arm) of chromosome II. The synthesis of beta globin occurs only in immature RBCs, although the HBB gene is present in the nucleus of every cell. This means that the HBB gene is part of every cell’s genome, and beta globin is part of the cellular proteome for RBCs. Synthesis of beta globin, just like for any protein, involves the processes of transcription, translation, and protein modification.]

Question 8

Transcription

Answer 8

-Transcription is the process of making a strand of ribonucleic acid (RNA) that contains the same amino acid codes as the DNA sequence of the gene for the protein needed.
-This phase of protein synthesis takes place completely within the nucleus.

Question 9

DNA coding regions

Answer 9

-Examining DNA reveals DNA coding regions separated by noncoding regions.
-DNA coding regions contain many genes, and the sequences of these genes are largely the same from one person to another.
-For example, the gene for insulin has the same DNA sequence in all healthy humans.

Question 10

DNA noncoding regions

Answer 10

• sections of DNA that contain multiple repeat sequences that are not genes or parts of genes and that do not code for specific proteins.
  -These noncoding regions, sometimes called redundant DNA or desert DNA, make up about 95% of nuclear DNA.
  -These regions vary from one person to another and are used to identify the DNA from a specific individual.
  -The noncoding regions of DNA influence how genes are expressed, but not all of their functions are yet understood.

Question 11

Difference between DNA synthesis and protein synthesis

Answer 11

-During DNA replication, both double strands of all the DNA within one cell are entirely copied, resulting in two new strands of DNA.
- Key difference: Extent of the process.
- DNA replication copies both double strands resulting in two new complete strands.
- Protein synthesis only involves the gene-containing DNA segment.
- A segment of one DNA strand is transcribed into RNA.

Question 12

Protein Synthesis Process

Answer 12

-In protein synthesis, only the area of DNA that contains the actual “recipe” for the protein is read (transcribed), and a complementary strand of RNA is synthesized.
-RNA is a single strand of nitrogenous bases constructed during transcription from a segment of DNA containing the template for a specific protein.
-Several types of RNA exist, and the ultimate purpose of all types is to ensure that the information held in the genes reaches cell areas where formation of the actual proteins needed for normal human funcrion can occur.
-In this sense, RNA is a molecular interpreter of the DNA information stored in the genes.
-Newly transcribed RNA functions as the initial pattern for protein synthesis.

Question 13

RNA and DNA differences

Answer 13

-RNA is very similar to DNA, with a few differences.
-First, functional RNA is single stranded (ss) rather than double stranded (ds).
-The sugar component of RNA is ribose rather than deoxyribose, which just means that it contains one more oxygen molecule than does the sugar in DNA.
-Another difference is that RNA does not contain the pyrimidine base thymine.
The base uracil is used in place of thymine.
-It is a pyrimidine base almost identical to thymine except that uracil does not contain the methyl group (CH3) that thymine has (Fig. 2-3).
-However, this difference is important because molecules in the nucleus that contain a methyl group remain trapped inside the nucleus.
-Because the remaining phases of protein synthesis occur outside the nucleus, the newly transcribed RNA must be able to exit the nucleus.

Question 14

Sense Versus Antisense

Answer 14

-Some of the same enzymes involved in DNA synthesis assist in the loosening and unwinding of the DNA coding region that contains the beta globin gene.
-Once this DNA is loosened and unwound, the two strands are slightly separated into a sense strand and an anti sense strand (Fig.2-5).
-After the strands are slightly separated, an enzyme known as RNA polymerase II reads and then transcribes the gene sequence on the anti sense strand of DNA (template strand), resulting in the formation of a complementary strand of RNA that will have exactly the same amino acid codes as the gene in the sense strand.
-Thus, the antisense strand is the “template” used to direct RNA synthesis.
-The DNA information is transcribed using the bases adenine, guanine, cytosine, and uracil into a single RNA strand that amino acid codes identical to the gene (see Fig. 2-5).
-Because this RNA is used as a recipe to direct the building of the actual protein coded for by the gene, it is known as messengerRNA, or mRNA.
-The instructions in the gene have now been converted into RNA codons by the process of transcription of the template (antisense) strand (Fig. 2-6).

Question 15

DNA sense strand

Answer 15

-The DNA sense strand, also known as sense DNA, contains the actual gene-coding sequence for the protein to be synthesized

Question 16

DNA antisense strand

Answer 16

-The DNA antisense strand, also known as antisense DNA, contains the complementary base sequence to this gene, not the gene itself.

Question 17

Starting and Stopping

Answer 17

• DNA contains start and stop codes for RNA synthesis.
• Start signal is upstream from gene triplets that code for specific amino acid.
• It can be over 100 base pairs upstream.
• These regions are known as promoter regions for RNA synthesis (term is different when ref. to cancer .
• A common promoter sequence is the TATA box (cont. many thymine and adenine).
• downstream from the gene, there are transcription stop signals.
• They halt DNA-to-RNA codon transcription.
• A poly-A tail is added to the RNA, known as polyadenylation.
• Poly-A tail has mainly adenine and isn’t part of the protein.

Question 18

Codon

Answer 18

-A codon is a specific RNA base sequence containing the complementary code to each amino acid’s DNA triplet.
-For example, the DNA triplet for the amino acid methionine is TAC-thymine, adenine, and cytosine (see Table 2-1).
-Remember that RNA contains uracil instead of thymine. Thus, everywhere an adenine is positioned in the gene’s DNA, a uracil is positioned in the complementary strand of RNA.
-This makes the RNA codon for methionine AUG-adenine. uracil. and guanine.

Question 19

Exons

Answer 19

The sectional parts of the gene that actually belong in the gene are known as exons (for expressed sequences).

Question 20

Introns

Answer 20

The additional sequences that do not code for part of that protein are introns (for interoening sequences).

Question 21

Posttranscriptional Modification

Answer 21

-Once the gene has been initially transcribed into mRNA, the RNA must be further processed to its mature form through posttranscriptional modification.
-This is a process that eliminates the introns before the mRNA can be translated and used to direct the precise synthesis of the protein coded for by the gene (Fig. 2-7).
-Removing the introns and conneccing the exons is known as RNA splicing.
-After the initial mRNA transcript has been processed and the introns eliminated, the mature mRNA is moved out from the cell nucleus into the cytoplasm, where actual translation into a protein occurs.

Question 22

RNA splicing

Answer 22

Removing the inrrons and conneccing the exons is known as RNA spLicing.

Question 23

Translation

Answer 23

-Translation is the process of using a mature mRNA molecule as the directions for placing amino acids in the correct sequence to synthesize a protein. This energy-requiring activity involves the interaction of amino acids and mRNA along with two other types of RNA: transfer RNA (tRNA) and ribosomal RNA (rRNA).
-Translation occurs in the cytoplasm.
-If chromosomes are the recipes in a cookbook, consider the cytoplasm to be the “kitchen,” where all the ingredients and the appliances for cooking are available for translating the transcribed recipe into an actual product (such as chocolate chip cookies).

Question 24

Transfer RNA

Answer 24

-Transfer RNA molecules are specialized carrier molecules that can move an amino acid into position to be incorporated correctly into a growing peptide chain during protein synthesis.
-For each of the 61 codons specifying individual amino acids, a separate tRNA molecule binds to each individual codon. (Keep in mind that the remaining codons code for a Stop signal and not an amino acid.)
-Each type of tRNA can carry and transfer only one specific amino acid.
-For example, alanine tRNAs attach to and transfer only the amino acid alanine, whereas valine tRNAs attach to and transfer only the amino acid valine.
-The tRNAs have an upside- down, three-leaf-clover appearance, with two important areas for protein synthesis: the amino acid attachment site and the anticodon (Fig. 2-8).

Question 25

Transfer RNA
Anticodon

Answer 25

• Amino acids attach to specific tRNAs via the amino acid attachment site.
• The tRNA’s anticodon determines which amino acid it carries, matching the amino acid codon.
• An anticodon is the complementary code to an amino acid codon.
• Example: Methionine (AUG codon) pairs with UAC anticodon on its specific tRNA.
• Each tRNA only binds and carries its complementary amino acid.
• Thus, each amino acid has dedicated tRNAs; some amino acids have multiple codons and anticodons.

Question 26

Ribosome

Answer 26

• Ribosomes decode mRNA and ensures proper placement of amino acids to the growing peptide chain during protein synthesis.
• They consist of two subunits with some RNA.
• These subunits combine around mRNA for translation.
• Ribosomes are nonspecific (translate any mature mRNA in the cytoplasm as long as it’s present.)

Question 27

Starting and Stopping

Answer 27

• Mature mRNA reaches the cytoplasm
• rRNAs (with appropriate amino acids attached) and activated ribosomes are needed for translation.
• The start signal prompts ribosomes to decode mRNA from 5’ to 3’.
• different tRNAs try to deliver amino acids, only the specific correct one will unload.
• tRNA exits after transferring its amino acid.
• Ribosomes continue protein synthesis until stop signal.
• The stop signal causes ribosomes to split into two subunits, releasing the protein.
• Protein synthesis is efficient, allowing multiple translations from one mRNA.
• Multiple ribosomal complexes initiate translation as the first one moves down from the start signal.b

Question 28

MicroRNA (miRNA)

Answer 28

• another way of regulating gene expression post-transcription is by microRNAs (miRNA).
• MiRNA is a small noncoding RNA that acts on RNA level.
• These 20-25 base RNAs bind to specific (targeted) mRNA making them partially double stranded, inhibiting translation.
• miRNA also accelerates mRNA degradation.
• Prevents excessive protein production even when gene transcription overproduces specific mRNA.
• Crucial for cell cycle control, cell differentiation, viral replication, and metabolic pathways.

Question 29

[Post translational Modification]
Primary structure

Answer 29

-Getting the right amino acids in the right order through translation is the protein’s primary structure.
-However, most proteins are not in their final forms for active function when they are first synthesized and thus require post translational modification.
-This is the further processing of the newly translated primary protein Structure into the secondary and tertiary structures (and sometimes even a quaternary structure) needed to make it fully functional.
-Although further processing leads to these formations, correct secondary, tertiary, and quaternary protein forms all depend on an accurate primary structure.

Question 30

[Post translational Modification]
Secondary protein structure

Answer 30

• Secondary protein structure: Twisting of primary structure.
• Interaction of nearby amino acids.
• Sequence stays the same.
• Adds 3D depth as parts project differently.

Question 31

[Post translational Modification]

Tertiary structure
Quaternary structure

Answer 31

-Tertiary structure is the folding of the linear structure and occurs as the result of remote amino acids interacting with each other.
-These interactions allow parts of the linear structure to draw closer together in some areas and have greater distances in other areas.
-Folding often creates a “pocket” within the protein that becomes an “active site,” able to interact with other structures or substances.
-Folding in some proteins is enhanced when “bridges” are formed that connect distant amino acids. The most common bridges are formed by linking two sulfide molecules (known as disulfide bridges).
-Some proteins are active after proper folding into the tertiary structure; others require associations with additional protein molecules to be active.
-For example, one tertiary beta globin molecule cannot carry oxygen. It must associate properly with another beta globin molecule, two alpha globin molecules, and a heme molecule to form the oxygen-carrying compound hemoglobin.
-Thus, a protein’s quaternary structure is its needed association with one or more specific ocher proteins for effective functioning.

Question 32

[Post translational Modification]

Additional Modification

Answer 32

-Some amino acids may need to be removed to activate a protein.
-For example, the protein insulin is first translated into a “preprohormone” that contains more than the 51 amino acids that compose active insulin.
-The pre part of the preprohormone is a signaling peptide that is removed in the endoplasmic reticulum shortly after insulin is translated, converting it to a prohormone that contains 84 amino acids. (The 33-amino-acid pro part of the prohormone is later removed in the liver right before active insulin is present in the blood and binds to its membrane receptor.)
-Another type of posttranslational modification involves adding other substances to the protein to make it functional. These other substances may include various types of sugar molecules, lipid molecules, or additional peptides.
-Once again, the proper order of amino acids in the primary structure is important for these other substances to be correctly attached in order to result in the most functional form of a protein.
-One common way of processing proteins synthesized in one cell for use in other body areas involves packaging the new protein within a secretory vesicle in the Golgi apparatus of the cell.
-This processing surrounds the new protein with plasma membrane components that allow the vesicle to fuse with the cell’s plasma membrane.
-After the vesicle membrane fuses with the cell’s plasma membrane, the vesicle opens on the outer aspect of the cell, and the newly synthesized and processed protein is released into the circulatory system. Once in the blood, the protein can travel to other body areas for final function.

Question 33

Mutation

Answer 33

-A mutation is an alteration in the base sequence of DNA or RNA.
-Although mutations can occur anywhere in the DNA or RNA, they are most noticed when they occur in a gene-coding region.
-When a mutation becomes a permanent part of one cell’s DNA, it can be passed on to or inherited by other generations of cells.

Question 34

Somatic mutations

Answer 34

-Mutations that occur after birth in general body cells (somatic cells) are known as somatic mutations.
-Because these mutations are present only in a person’s somatic cells, somatic mutations cannot be passed on to offspring.
-One problem associated with somatic mutations is an increased risk for cancer in cells with such mutations.

Question 35

Germline mutations

Answer 35

-Germline mutations occur in germ cells (sex cells, sperm, or ova) and can be passed on to offspring (children) at conception.
-When a child inherits a germline mutation, each of that child’s cells contains the mutated DNA, including the child’s sex cells.
-This means that the mutation can be passed to many generations as long as the mutation does not interfere with the person’s fertility.

Question 36

Point mutations

Answer 36

-Point mutations are substitutions of one base for another and can occur in DNA or RNA.
-This type of change does not result in an extra base or a lost base, just a substitution.
-Thus, the DNA triplets remain intact, although one may be incorrect. This change may or may not alter amino acid position or protein synthesis, depending on where it occurs.
-When a single point mutation occurs in a DNA coding region or in mature RNA, the result can change one amino acid in the protein’s primary structure, with a resulting change in protein function, but it also may have little or no effect.
-When a point mutation has little or no effect on a protein’s function, it is known as a benign mutation or a normal variation.

Question 37

Silent Point Mutations

Answer 37

• Point mutations in gene-coding regions vary in impact.
• A mutation might have no, mild, or major effects on protein synthesis.
• If the mutation occurs in the third base of a triplet, the resulting RNA codon still codes for the same amino acid.
• This is called a silent point mutation.
  (Fig. 2-10).

Question 38

Missense Point Mutations

Answer 38

-A point mutation that does change the amino acid sequence is a missensepoint mutation and does affect protein function, usually reducing it to some extent (see Fig. 2-10).
-Some missense point mutations reduce protein function only slightly, and others cause a more profound change in protein function.

Question 39

Nonsense Point Mutations

Answer 39

-A point mutation that results in an inappropriate placement of a Stop signal is known as a nonsense point mutation, which has a negative effect on protein function.
-This type of mutation, also shown in Figure 2-10, prevents the completion of a protein.
-The protein may not be synthesized at all if the stop signal is present early in the reading sequence.
-If it is present later in the sequence, protein synthesis stops prematurely and results in a short, or truncated, protein that usually has little, if any, function.

Question 40

Single-Nucleotide Polymorphisms

Answer 40

• Most people share the same DNA sequences for most genes.
  -The most common known sequence of a gene in a population is known as the wild-type sequence rather than the normal sequence.
• Some genes have minor variations in specific populations.
• These variations often result from missense point mutations.
• They’re called single-nucleotide polymorphisms (SNPs).
• Example: Cytochrome P450 enzyme system.
• This system includes a 10-gene family with subsets.
• The genes in this family all have names that begin with CYP.
• Variations in these genes affect protein function, making some more active and others less active than “wild-type” .
• function of the proteins produced by these genes is crucial in drug metabolism.

Question 41

Frameshift Mutations

Answer 41

-Frameshift mutations are disruptions of the DNA reading frame from having one base or a number of bases that are not multiples of three added or deleted. (A frameshift mutation involving only one base is a specific type of point mutation.)
-When this type of mutation occurs in gene-coding regions, it always disrupts the reading frame from the start of the mutation to the end of the gene.
-The result is complete alteration of amino acid position and prevention of synthesis of a functional protein.
-A normal protein cannot be made from a gene with a frameshift mutation.

Question 42

Mutational Events

Answer 42

-Mutations can occur at any generic level and in any genetic process.
-Thus, mutations can involve individual nucleotides, DNA segments, genes, RNA, chromosomes, or the genome, and they can occur in any step of the various processes involved in DNA replication, cell division, and protein synthesis. -Some known causes of mutations include the following:
• Spontaneous DNA replication error
• Poor DNA repair function
• Exposure to environmental mutagens (biological, chemical, physical, viral)

Question 43

Mutagen

Answer 43

-A mutagen is any substance or event that can inflict temporary or permanent changes in the normal DNA sequence.

Question 44

Summary pt 1.

Answer 44

-Protein synthesis is an essential process for all life-forms. It is complex and requires precision in all steps for proper outcomes.
-Changes in protein synthesis are a common factor in many health problems.
-These changes can occur as the result of somatic cell mutations, which are a problem only for the person who developed the mutation.
-Protein synthesis changes also can occur from germline mutations and thus may be inherited.
-Specific health problems associated with changes in protein synthesis form the foundation of the clinically focused chapters of this text.

• All hormones, enzymes, growth factors, and other protein-based chemicals needed for normal human physiologic function are protein gene products that are produced when the correct genes are activated and expressed.
• The sequencing order of the amino acids is what makes one protein different in Structure and function from another protein.
• Only about 5% of nuclear DNA contains gene-coding regions, and these are largely the same from one person to another.
• DNA noncoding regions are different from one person to another, even between identical twins.
• DNA sequences are read from the 5’ to the 3’ direction.
• The transcription phase of protein synthesis takes place completely within the nucleus.
• The DNA antisense strand is read by RNA polymerase to make a complementary mRNA strand during
transcription.
• DNA sequences of one gene are in pieces within a coding region and are separated by areas of DNA that are not part of that gene.

Question 45

Summary pt 2.

Answer 45

• RNA is single stranded (ss) and serves as the interpreter of information stored within the genes of DNA.
• RNA contains the base uracil in place of thymine.
• When messenger RNA is first constructed, it contains segments of the gene to be expressed (exons), as
well as noncoding segments (inrrons).
• Introns must be removed from mRNA before protein synthesis can occur properly.
• The translation phase of protein synthesis takes place in the cytoplasm, often in an organelle known as the endoplasmic reticulum.
• Translation requires sufficient amounts of amino acids, ribosomes, mRNA, and tRNAs.
• Each tRNA is specific for only one amino acid and can be used more than once.
• Each mRNA is translated multiple times for as long as it is present.
• Molecules known as microRNA can regulate the translation of mRNA by either binding to it so that
translation does not occur or by increasing the rate at which mRNA molecules are degraded.
• The initial translation that produces a peptide with all the amino acids in the correct order is a protein’s primary structure.
• Further modification of a protein’s primary structure is needed for function.
• Although DNA synthesis is a process with high fidelity, errors do occur.
• Mutations can involve individual nucleotides, DNA segments, genes, RNA, chromosomes, and genomes
and can occur during any step in DNA replication, cell division, and protein synthesis.
• Not all mutations have deleterious results.
• A new somatic cell mutation cannot be inherited by offspring.
• Germline mutations occur in sex cells and can be inherited by offspring.
• A silent point mutation does not change protein function, a missense point mutation usually reduces protein function, and a nonsense mutation often eliminates protein function.
• A normal protein cannot be made from a gene with a frameshift mutation.
• Many cellular repair mechanisms exist to correct mutations or prevent them from becoming permanent.

Question 46

1. Which structure serves as an interpreter of DNA information stored in the genes?
   a. cRNA
   b. mRNA
   c. microRNA
   d. ribosomal RNA

Answer 46

b. mRNA

Question 47

2. Why is it useful for mRNAs to have only a short life span?
   a. Energy is conserved by avoiding mRNA maintenance activity.
   b. Their components can be reassembled into new mRNAs.
   c. Protein synthesis can be more tighcly controlled.
   d. The precision of RNA maturation is increased.

Answer 47

c. Protein synthesis can be more tightly controlled.

Question 48

3. Which statement regarding the tertiary structure of a protein is true?
   a. It is direccly coded for within the gene.
   b. It is created by remote amino acids interacting for protein folding.
   c. It requires assembly with other additional proteins for final activity.
   d. It makes the protein resistant to external mutagens and other mutational events.

Answer 48

b. It is created by remote amino acids interacting for protein folding.

Question 49

4. A strand of recently transcribed mRNA contains the following components: exon (I), intron (2), intron (3), exon (4), intron (5). Which sequence represents the mature mRNA?
   a. 1,4
   b. 2,3,5
   c. 2,3,4
   d. 1,2,3,4,5

Answer 49

a. 1,4

Question 50

5. How does microRNA (miRNA) disrupt protein synthesis?
   a. By competing with mRNA for ribosomal attachment
   b. By inhibiting amino acid detachment from [RNAs
   c. By covering translational scan signals on mRNA
   d. By binding to mRNA, preventing translation

Answer 50

d. By binding to mRNA, preventing translation

Question 51

6. What would be the effect on protein synthesis if the DNA sense strand were used as the template for transcription into RNA?
   a. Improper placement of introns
   b. Increased rate of mRNA degradation
   c. Incorrect translation of the gene product
   d. Inability of translation to recognize stop signals

Answer 51

c. Incorrect translation of the gene product

Question 52

7. What is the expected result of a “missense” point mutation?
   a. Replacement of one amino acid with another in the final gene product
   b. Total disruption of the gene reading frame and no production of protein
   c. Replacement of an amino acid codon with a “stop” codon, resulting in a truncated protein product
   d. No change in amino acid sequence and no change in the composition of the protein product

Answer 52

a. Replacement of one amino acid with another in the final gene product.

Question 53

Transcription

Answer 53

●The process of making a strand of RNA that is complementary to the DNA sequence that contains the gene for the protein needed

Question 54

RNA Codons for Individual Amino Acids

Answer 54

Ala GCU, GCC, GCA, GCG
Lys AAA, AAG
Phe UUU, UUC
Ser UCU, UCG, UCA, UCC
Val GUU, GUC, GUA, GUG
Start AUG
Stop UAA, UAG, UGA