DNA Transcription and Translation Standards

Name______Date:______Period:____ DNA Transcription and Translation Standards 1d. Students know the central dogma of molecular biology outlines the flow of information from transcription of ribonucleic acid (RNA) in the nucleus to translation of proteins on ribosomes in the cytoplasm.

4a. Students know the general pathway by which ribosomes synthesize proteins, using tRNAs to translate genetic information in mRNA.

DNA, which is found in the nucleus of eukaryotes, contains the genetic information for encoding proteins. The DNA sequence specifying a specific protein is copied (transcribed) into messenger RNA (mRNA), which then carries this message out of the nucleus to the ribosomes located in the cytoplasm. The mRNA message is then translated, or converted, into the protein originally coded for by the DNA. CENTRAL DOGMA

Transcription can be explained easily in 4 quick steps. Step 1: DNA unwinds/"unzips" as the Hydrogen Bonds Break. Step 2: The free nucleotides of the RNA, pair with complementary DNA bases. As in DNA replication, DNA is read from 3' → 5' during transcription. The complementary RNA is created from the 5' → 3' direction. In eukaryotes, RNA polymerase, and therefore the initiation of transcription, requires the presence of a core promoter sequence in the DNA. Step 3: RNA sugar-phosphate backbone forms. (Aided by RNA Polymerase.) Step 4: Hydrogen bonds of the untwisted RNA+DNA "ladder" break, then the RNA leaves the nucleus through the small nuclear pores. This then goes to the cytoplasm to continue on to protein processing.

DNA does not leave the cell nucleus, but messenger RNA (mRNA), complementary to DNA is transcribed to carry encoded information from DNA to the ribosomes (rRNA and protein) (transcription) in the cytoplasm. The ribosomes translate mRNAs to make protein. Freely floating amino acids within the cytoplasm are bonded to specific transfer RNAs (tRNAs) that then transport the amino acid to the mRNA now located on the ribosome. As a ribosome moves along the mRNA strand, each mRNA codon, or sequence of three nucleotides specifying the insertion of a particular amino acid, is paired in sequence with the anticodon

Biology Standard 4a-4c 1 of the tRNA that recognizes the sequence. Each amino acid is added, in turn, to the growing polypeptide at the specified position. Vocabulary

1. mRNA

2. protein [polypeptide chain]

3. amino acid

4. transcription

5. translation

6. Central Dogma of Molecular Biology

7. Ribosomes

8. Codons

9. RNA polymerase

10. Anticodon

11. tRNA

12. start codons

13. stop codons

Explain in your own words how to read the genetic code

Biology Standard 4a-4c 2 4b. Students know how to apply the genetic coding rules to predict the sequence of amino acids from a sequence of codons in RNA.

The sequence of amino acids in protein is provided by the genetic information found in DNA.  In prokaryotes, mRNA transcripts of a coding sequence are copied from the DNA as a single contiguous sequence.  In eukaryotes, the initial RNA transcript, while in the nucleus, is composed of exons, sequences of nucleotides that carry useful information for protein synthesis, and introns, sequences that do not. Before leaving the nucleus, the initial transcript is processed to remove introns and splice exons together. This splicing activity is also called ligation and uses a ligase enzyme. The processed transcript, then properly called mRNA and carrying the appropriate codon sequence for a protein, is transported from the nucleus to the ribosome for translation.

RNA processing is to generate a mature mRNA (for protein genes) or a functional tRNA or rRNA from the primary transcript. Biology Standard 4a-4c 3 Processing of pre-mRNA involves the following steps:

 Capping - add 7-methylguanylate (m7G) to the 5' end.  Polyadenylation - add a poly-A tail to the 3' end.  Splicing - remove introns and join exons.

In your own words describe three ways that the initial RNA transcript is processed before moving to the cytoplasm.

Vocabulary

1. Initial mRNA

2. transcript

3. Introns

4. Exons

5. Excised

6. Ligated

7. Ligase

8. Processed transcript

4c. Students know how mutations in the DNA sequence of a gene may or may not affect the expression of the gene or the sequence of amino acids in the encoded protein.

Mutations are permanent changes in the sequence of nitrogen containing bases in. Mutations occur when base pairs are incorrectly matched (e.g., A bonded to C rather than A bonded to T) and can, but usually do not, improve the product coded by the gene. Inserting or deleting base pairs in an existing gene can cause a mutation by changing the codon reading frame used by a ribosome. Mutations that occur in somatic, or nongerm, cells are often not detected because they cannot be passed on to offspring. They may, however, give rise to cancer or other undesirable cellular changes. Mutations in the germline can produce functionally different proteins that cause such genetic diseases as Tay-Sachs, sickle cell anemia, and Duchenne muscular dystrophy.

Types of mutation Biology Standard 4a-4c 4 Point mutaton Frameshift mutation Insertion Deletion Substitution

Somatic mutation

Germ cell mutation

Tay-Sachs disease is a rare inherited disorder1 that progressively destroys nerve cells (neurons) in the brain and spinal cord. The most common form of Tay-Sachs disease becomes apparent in infancy. Infants with this disorder typically appear normal until the age of 3 to 6 months, when their development slows and muscles used for movement weaken. As the disease progresses, children with Tay-Sachs disease experience seizures, vision and hearing loss, intellectual disability, and paralysis. An eye abnormality called a cherry-red spot, which can be identified with an eye examination, is characteristic of this disorder. Children with this severe infantile form of Tay-Sachs disease usually live only into early childhood.

Other forms of Tay-Sachs disease are very rare. Signs and symptoms can appear in childhood, adolescence, or adulthood and are usually milder than those seen with the infantile form. Characteristic features include muscle weakness, loss of muscle coordination (ataxia) and other problems with movement, speech problems, and mental illness. These signs and symptoms vary widely among people with late-onset forms of Tay-Sachs disease.

Tay-Sachs disease is very rare in the general population. The genetic mutations that cause this disease are more common in people of Ashkenazi (eastern and central European) Jewish heritage than in those with other backgrounds. The mutations responsible for this disease are also more common in certain French- Canadian communities of Quebec, the Old Order Amish community in Pennsylvania, and the Cajun population of Louisiana.

Mutations in the HEXA gene cause Tay-Sachs disease. The HEXA gene provides instructions for making part of an enzyme called beta-hexosaminidase A, which plays a critical role in the brain and spinal cord. This enzyme is located in lysosomes, which are structures in cells that break down toxic substances and act as recycling centers. Within lysosomes, beta-hexosaminidase A helps break down a fatty substance called

1 http://ghr.nlm.nih.gov/condition/tay-sachs-disease Biology Standard 4a-4c 5 GM2 ganglioside. Progressive damage caused by the buildup of GM2 ganglioside leads to the destruction of these neurons, which causes the signs and symptoms of Tay-Sachs disease.

Because Tay-Sachs disease impairs the function of a lysosomal enzyme and involves the buildup of GM2 ganglioside, this condition is sometimes referred to as a lysosomal storage disorder or a GM2- gangliosidosis.

Sickle cell anemia2 is an inherited blood disorder characterized primarily by chronic anemia and periodic episodes of pain. The underlying problem involves hemoglobin, a component of red blood cells. Hemoglobin molecules in each red blood cell carry oxygen from the lungs to body organs and tissues and bring carbon dioxide back to the lungs. In sickle cell anemia, the hemoglobin is defective. After hemoglobin molecules give up their oxygen, some may cluster together and form long, rod-like structures. These structures cause red blood cells to become stiff and assume a sickle shape. Unlike normal red cells, which are usually smooth and donut-shaped, sickled red cells cannot squeeze through small blood vessels. Instead, they stack up and cause blockages that deprive organs and tissues of oxygen-carrying blood. This process produces periodic episodes of pain and ultimately can damage tissues and vital organs and lead to other serious medical problems. Sometimes pain lasts only a few hours; sometimes it lasts several weeks, requiring hospitalization. Pain is the principal symptom of sickle cell anemia in both children and adults. Normal red blood cells live about 120 days in the bloodstream, but sickled red cells die after about 10 to 20 days. Because they cannot be replaced fast enough, the blood is chronically short of red blood cells, a condition called anemia. Sickle cell anemia Inheritance Sickle cell anemia is an autosomal recessive genetic disorder caused by a defect in the HBB gene, which codes for hemoglobin. The presence of two defective genes (SS) is needed for sickle cell anemia. Sickle cell anemia Incidence Sickle cell anemia affects millions throughout the world. It is particularly common among people whose ancestors come from sub-Saharan Africa; Spanish-speaking regions (South America, Cuba, Central America); Saudi Arabia; India; and Mediterranean countries such as Turkey, Greece, and Italy. In the Unites States, it affects around 72,000 people, most of whose ancestors come from Africa. The disease occurs in about 1 in every 500 African-American births and 1 in every 1000 to 1400 Hispanic-American births.

Duchenne Muscular dystrophy3 is a genetic conditions characterized by progressive muscle weakness and wasting (atrophy). The Duchenne muscular dystrophy primarily affect the skeletal muscles, which are used for movement, and the muscles of the heart. These conditions occur much more frequently in males than in females. Duchenne and Becker muscular dystrophies together affect 1 in 3,500 to 5,000 newborn males. Between 400 and 600 boys in the United States are born with these conditions each year. Females are rarely affected by these forms of muscular dystrophy.

2 http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/sca.shtml 3 http://ghr.nlm.nih.gov/condition/duchenne-and-becker-muscular-dystrophy Biology Standard 4a-4c 6 Mutations in the DMD gene cause Duchenne and Becker muscular dystrophy. The DMD gene provides instructions for making a protein called dystrophin. This protein helps stabilize and protect muscle fibers and may play a role in chemical signaling within cells. Mutations in the DMD gene alter the structure or function of dystrophin, or prevent any functional dystrophin from being produced. Muscle cells without this protein become damaged as muscles repeatedly contract and relax with use. The damaged fibers weaken and die over time, leading to the muscle weakness and heart problems characteristic of Duchenne and Becker muscular dystrophies.

This condition is inherited in an X-linked recessive pattern. A condition is considered X-linked if the mutated gene that causes the disorder is located on the X chromosome, one of the two sex chromosomes. In males (who have only one X chromosome), one altered copy of the gene in each cell is sufficient to cause the condition. In females (who have two X chromosomes), a mutation must be present in both copies of the gene to cause the disorder. Males are affected by X-linked recessive disorders much more frequently than females. A striking characteristic of X-linked inheritance is that fathers cannot pass X-linked traits to their sons.

PRACTICE QUESTIONS

1. A scientist analyzed the base composition present in a certain cell. He generated the incomplete data shown on the table below: What would be the expected % Thymine content of the cell? a. 13% c. 28% b. 14% d. 56%

2. Some events that place during the synthesis of a specific protein are listed below: (A) Messenger RNA attaches to a ribosome (B) DNA serves as a template for RNA production (C) Transfer RNA bonds to a specific codon (D) Amino acids are bonded together (E) RNA moves from the nucleus to the cytoplasm

The correct order of these events is a. B→E→A→C→D c. B→C→E→D→A b. D→A→E→C→B d. C→B→A→E→D

3. Which of the following relationships is the most similar to the relationship below? nucleotide: DNA a. amino acid : protein b. codons : tRNA c. mRNA : anticodons d. carbohydrate : glucose

Biology Standard 4a-4c 7 4. A segment of a DNA strand has the following bases: TAC GAT. What is the complementary strand of DNA? a. UAG CAU c. AUG CUA b. TAG CAT d. ATG CTA

5. What is the complementary messenger-RNA sequence for the DNA sequence shown below?

a. C-A-A-G-G-U b. G-T-T-C-C-A c. G-U-U-C-C-A d. C-A-A-G-G-T

6. Chromosomal mutations occurring in gametes of humans can affect the appearance of offspring because a. many traits are usually affected b. only one trait is usually affected c. these mutations usually speed up embryonic development d. these mutations usually result in sex-linked Traits

7. One similarity between DNA and messengerRNA molecules is that they both contain a. the same sugar b. genetic codes based on sequences of bases c. a nitrogenous base known as uracil d. double-stranded polymers 8. Given: A DNA template strand with the nucleotide sequence 3′–ATTGCGTAC–5′. The RNA transcribed from this template strand will have the nucleotide sequence: (a) 5′–AUUGCGUAC–3′, (b) 3′–AUUGCGUAC–5′, (c) 5′–UAACGCAUG–3′, (d) 3′–UAACGCAUG–5′, (e) 5′–TAACGCATG–3′.

9. The replacement of a DNA nucleotide pair with a different nucleotide pair is called a(an): (a) insertion mutation, (b) deletion mutation, (c) thymine dimer mutation, (d) frameshift mutation, (e) substitution mutation.

10. The protein subunits of the protein shell that encloses the viral genome are called: (a) capsomeres, (b) capsids, (c) envelopes, (d) histones, (e) centromeres.

11. Bacteria do not have: (a) ribosomes, (b) a plasma membrane, (c) a true nucleus, (d) a genome, (e) choices “a”, “b”, and “c” are correct, but choice “d” is not correct. Biology Standard 4a-4c 8 12. A DNA nucleotide is composed of: (a) a nitrogenous base, (b) the sugar ribose, (c) a phosphate, (d) all of the above choices, “a”, “b”, and “c”, are correct, (e) choices “a” and “c” are both correct, but choice “b” is not correct.

13. In an experiment we discussed in lecture, bacteria were cultured for several generations in a medium containing heavy nitrogen (N15). They were then transferred to a medium containing light nitrogen (N14) and DNA was extracted from some of the cells and centrifuged after one replication cycle and extracted from other cells and centrifuged after two replication cycles. This experiment proved that: (a) DNA is the genetic material, (b) DNA replication is conservative, (c) DNA replication is semiconservative, (d) DNA replication is dispersive,

14. In DNA replication, a lagging strand is synthesized: (a) continuously in the 3′ to 5′ direction as a series of Okazaki fragments, (b) continuously in the 5′ to 3′ direction as a series of Okazaki fragments, (c) discontinuously in the 3′ to 5′ direction as a series of Okazaki fragments, (d) discontinuously in the 5′ to 3′ direction as a series of Okazaki fragments, (e) choices “a” and “c” are both correct, but choices “b” and “d” are not correct.

15. Molecules of DNA are composed of long chains of a. amino acids c. monosaccharides b. fatty acids d. nucleotides 16. The primary function of DNA is to a. make proteins b. store and transmit genetic information c. control chemical processes within cells d. prevent mutations 17. A nucleotide consists of a. a sugar, a protein, and adenine b. a sugar, an amino acid, and a starch c. a sugar, a phosphate group, and a nitrogen-containing base d. a starch, a phosphate group, and a nitrogen-containing base 18. The part of the molecule for which deoxyribonucleic acid is named is the a. phosphate group c. nitrogen base b. sugar d. none of the above 19. Purines and pyrimidines are a. bases found in amino acids b. able to replace phosphate groups from defective DNA c. names of specific types of DNA molecules d. bases found in nucleotides 20. The scientists credited with determining the structure of DNA are a. Avery and Chargaff c. Mendel and Griffith b. Hershey and Chase d. Watson and Crick 21. The base-pairing rules state that the following are base pairs in DNA: Biology Standard 4a-4c 9 a. adenine - thymine; guanine – cytosine b. adenine - thymine; uracil – cytosine c. adenine - guanine; thymine – cytosine d. uracil - thymine; guanine – cytosine 22. ATTG : TAAC :: a. AAAT : TTTG c. GTCC : CAGG b. TCGG : AGAT d. CGAA : TGCG 23. The enzymes responsible for adding nucleotides to the exposed DNA template bases are called a. Replicases b. Helicases c. DNA polymerases d. Nucleotidases 24. All of the following are TRUE about the structure of DNA except a. every DNA nucleotide contains a sugar, a phosphate group, and a base b. short strands of DNA are contained in chromosomes inside the nucleus of a cell c. DNA consists of two strands of nucleotides joined by hydrogen bonds d. the long strands of nucleotides are twisted into a double helix

25. The function of rRNA is to a. synthesize DNA c. form ribosomes b. synthesize mRNA d. transfer amino acids to ribosomes

26. Which of the following types of RNA carries the instructions for making proteins? a. mRNA c. tRNA b. rRNA d. all of the above

27. RNA differs from DNA in that RNA a. is sometimes single-stranded c. contains the nitrogen base uracil b. contains a different sugar molecule d. all of the above

28. Which of the following is NOT found in RNA? a. Adenine c. Thymine b. Cytosine d. guanine

29. In RNA molecules, adenine is complementary to a. cytosine c. thymine b. guanine d. uracil

30. Given the following strand of mRNA, identify the strand of DNA from which it was made mRNA: CUCAAGUGCUUC a. CUCAAGUGCUUC c. GAGTTCACGAAG b. GAGUUCACGAAG d. AGACCTGTAGGA

31. Each nucleotide triplet in mRNA that specifies a particular amino acid is called a(n) a. Mutagen c. Anticodon b. Codon d. exon

32. codon: nucleotides:: a. ribosomes : binding sites c. RNA : bases b. ribosome : DNA molecules d. DNA : bases

Biology Standard 4a-4c 10 33. During a.transcriptionproteins are synthesized c. RNA is produced b. DNA is replicated d. translation occurs

34. Transcription proceeds when RNA polymerase a. attaches to a ribosome b. binds to a strand of DNA c. binds to a strand of RNA d. attaches to a promoter molecule 35. Given the following sequence of mRNA, what series of amino acids are coded for? mRNA: CUCAAGUGCUUC

a. Ser - Tyr - Arg – Gly b. Val - Asp - Pro – His c. Leu - Lys - Cys – Phe d. Pro - Glu - Leu - Val 36. For the same mRNA sequence as in question 35, the anticodons for the codons in the mRNA are a. GAG - UUC - ACG – AAG b. GAG - TTC - ACG – AAG c. CUC - GAA - CGU – CUU d. CUU - CGU - GAA - CUC 37. Given the following sequence of amino acids, use the genetic code table to determine the DNA sequence that codes for the amino acids. amino acid sequence: tyrosine - proline - aspartic acid - isoleucine - cysteine a. AUGGGUCUAUAUACG b. ATGGGTCTATATACG c. GCAAACTCGCGCGTA d. ATAGGGCTTTAAACA 38. codons : mRNA :: a. anticodons : tRNA b. triplets : DNA c. rRNA : ribosomes d. all of the above 39. The codon AUG, which codes for the amino acid methionine, also serves as a. a lac operon c. a stop codon b. a start codon d. a promoter 40. The codons UAA, UAG, and UGA all code for a. Arginine c. Phenylalanine b. Threonine d. stop codons 41. With the exception of tryptophan, each amino acid is coded for by more than one codon. This is called a. Translation c. Redundancy b. Reversal d. sequentialism 42. The fact that the genetic code is almost universal in living organisms is considered to be evidence that all organisms a. are evolutionarily related b. are genetically identical c. have the same sequence of anticodons d. none of the above 43. Anticodons are found on Biology Standard 4a-4c 11 a. rRNA c. DNA b. mRNA d. tRNA 44. The entire genetic code consists of ____ amino acids and ____ codons. a. 20, 20 c. 30, 60 b. 20, 64 d. 30, 72 45. Given the original DNA strand below what would the final polypeptide chain be?

i. ile-stop c. met-pro-trp-gly-arg-leu-stop ii. met-ile-gln-val-stop d. ile-gln-val-val-stop

46. Which relationship is most similar to the relationship below? tRNA : ribosome a. baker : pie c. key : lock b. delivery truck : factory d. book : publisher

The human DNA is up to 80 million base pair long in a chromosome. Thus, the DNA is unwound at multiple places along its length and DNA replication steps are carried out simultaneously at many places.

Fact File: The human DNA is copied at about 50 base pairs per second. The multiple location of DNA replication process takes about 1 hour to complete. If this were not the case, then it would take about a month to finish replicating the entire DNA strand!

The DNA replication process is almost error free with the help of DNA polymerase and other simple DNA replication enzymes, that proofread the nucleotides being added to the strand. If the nucleotides are not found to be complementary, then they are removed and a new nucleotide is synthesized. Thus, creating an error free DNA strand.

Fact File: A billion nucleotides have less than one mistakes. This means that copying 100 dictionaries with 1000 pages word to word, page to page and symbol to symbol, with only one mistake!

In 1950, Erwin Chargaff and colleagues examined the chemical composition of DNA and demonstrated that the amount of adenine always equals that of thymine, and the amount of guanine always equals that of cytosine. This observation became known as Chargaff's rule. a. Based on the structure of DNA, explain the basis of Chargaff's rule.(Why is the amount of adenine and thymine always equal?)

Biology Standard 4a-4c 12 b. The diagram below represents a single-stranded segment of DNA. Write the complementary DNA strand that would form from this strand during replication. Use the letters A, C, G, and T to designate the bases: A = adenine; C = cytosine; G = guanine; T = thymine.

c. Why is Chargaff's rule so important to DNA's ability to replicate itself accurately?

Biology Standard 4a-4c 13