From Gene to Protein.

From Gene to Protein

How does a chemical control so much?
DNA, genes, chromosomes How does a chemical control so much?

Intro to DNA Video

Review of ch 16 Vocabulary: 1. DNA /double helix, 2. Nucleosome

Griffith’s experiment 1928: transformation
Showed that “something” changed the non virulent bacteria into virulent!

Frederick Griffith--Discovery of the Transforming Principle (Video Clip)

Avery 1944 To show that it was DNA and not protein that transformed the bacteria…

Hershey and Chase 1952 Convinced people that DNA not protein contained the genetic material. Radioactive Sulfur found in protein only and radioactive phosphorus, found in DNA only was inserted into bacteria using viruses that infect bacteria called bacteriophages that had been labeled with the radioactive elements. Radioactivity showed the protein remained outside the bacteria and could not cause the transformations!

Franklin 1952 Rosalind Franklind and Wilkins X ray diffraction pictures helped determind the shape of DNA

Erwin Chargaff 1950 He found that when he analyze DNA, the amount of Adenine always equaled the amount of Thymine and the amount of Guanine equaled the amount of cytosine.

Watson and Crick 1953 Determined the basic structure of DNA. Antiparallel sides of deoxyribose sugar and phosphate with nitrogen bases paired A-T and C-G, (with the help of Chargaffs research)

How does DNA replicate? 1. Before replication can occur, the length of the DNA double helix about to be copied must be unwound. DNA helicase

2. the two strands must be separated, much like the two sides of a zipper, by breaking the weak hydrogen bonds that link the paired bases. 3. Once the DNA strands have been unwound, they must be held apart to expose the bases so that new nucleotide partners can hydrogen-bond to them.

4. The enzyme DNA polymerase III then moves along the exposed DNA strand, joining newly arrived nucleotides into a new DNA strand that is complementary to the template

Animation of replication

DNA replication Video

Vocabulary: 1. mRNA 2. rRNA 3. tRNA 4. Transcription 5. RNA polymerase
6. Intron 7. Exon 8. Codon 9. Translation

DNA Deoxyribo Nucleic Acid

Answers 1. Proteins are chains of linked amino acids that have been folded into compact shapes. Some proteins play important roles as enzymes. Other proteins are structural components of cells and tissues. 2. Ribosomes are structures built of proteins and RNA that serve as assembly sites for protein synthesis.

3. DNA is an extremely long, linear molecule containing many genes; genes are relatively short segments of DNA that code for protein or RNA. 4. DNA is made of two strands of complementary nucleotides and contains the four bases adenine, thymine, cytosine, and guanine. DNA contains the sugar deoxyribose and serves to store the complete set of an organism’s genetic material. 5. In DNA, adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C).

General Vocabulary 1. gene 2. chromosome 3. chromosomal mutation
4. codon 5. double helix 6. frameshift mutation 7. messenger RNA mRNA 8. monosomy 9. mutation 10. nitrogen base 11. nondisjunction 12. point mutation 13. replication 14. ribosomal RNA rRNA 15. transcription 16. transfer RNA tRNA 17. translation 18. trisomy 19. anticodon 20. protein

The instructions for building a protein are found in a gene and are “rewritten” to a molecule of RNA during transcription. The RNA is then “deciphered” during translation

Making a protein DNA is found in the nucleus.
The proteins are made on a ribosome from amino acids found in the cytoplasm. The instructions must get from the nucleus to the ribosome…

Start and stop codes on the DNA define where one gene starts and ends.
The DNA has to be un wound and un zipped for this process to work, just like in DNA synthesis. Some sections of DNA will be used more often then others.

1. What is gene expression?

Gene expression is the process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs enzyme like RNA’s This expression happens in two stages: transcription and translation

2. What situation did A. Garrod suggest caused inborn errors in metabolism?

A person’s inability to make a particular enzyme.

3. Describe one example Garrod used to illustrate his hypothesis.

Garrod gave as one example the hereditary condition called alkaptonuria. In this disorder, the urine is black because it contains the chemical alkapton, which darkens upon exposure to air. Garrod reasoned that most people have an enzyme that metabolizes alkapton, whereas people with alkaptonuria have inherited an inability to make that enzyme.

4. State the hypothesis formulated by George Beadle while studying eye color mutations in
Drosophila.

The hypothesis stated that in Drosophila, each of the various mutations affecting eye color blocks pigment synthesis at a specific step by preventing production of the enzyme that catalyzes that step. He showed that the genes control the production of enzymes and that the enzymes are related to traits! Often these occur in a series of steps and if one is missing the entire process can be altered!

5. What strategy did Beadle and Tatum adopt to test this hypothesis?

Beadle and Tatum bombarded the bread mold Neurospora with X-rays, and then looked among the survivors for mutants that differ in their nutritional needs from the wild-type bread mold.

6. Which organism did Beadle and Tatum use in their research?

Neurospora. MOLD!

How did this organism’s nutritional requirements facilitate this research?

Wild-type Neurospora has modest food requirements
Wild-type Neurospora has modest food requirements. It can grow in the laboratory on a simple solution of inorganic salts, glucose, and the vitamin biotin, and incorporated into agar, a support medium. From this minimal medium, the mold cells use their metabolic pathways to produce all other molecules they need. Beadle and Tatum identified mutants that could not survive on minimal medium, apparently because they were unable to synthesize certain essential molecules

7. How were Neurospora spores treated to increase the mutation rate?

Neurospora spores were treated with X-rays to increase the mutation rate.

Wild can grow on any thing
Mutant: can’t grow Gene A Gene B Gene C

9. Cite two significant findings that resulted from the research of Beadle and Tatum.

1. that metabolic defects are linked to defective genes,
2. support for the one gene–one enzyme hypothesis

10. What revision of detail (but not of basic principle) did this hypothesis undergo as more information was gained? Write this restatement and then box or highlight it. This is an important concept! .

Because not all proteins are enzymes, and because each protein consists of two or more different polypeptide chains, each specified by its own gene, the hypothesis was revised. Beadle and Tatum’s idea was restated as the one gene–one polypeptide hypothesis

Best current gene definition!
a DNA sequence that is expressed to form a functional product: either RNA or polypeptide

DNA and RNA Sugars ribose and deoxy ribose are different!

RNA has the nitrogenous base uracil rather than thymine.

An RNA molecule usually consists of a single strand rather than DNA’s double strand

11. From the first paragraph in this section, find three ways in which RNA differs from DNA.

1. RNA contains ribose instead of deoxyribose as its sugar.
2. RNA has the nitrogenous base uracil rather than thymine. 3. An RNA molecule usually consists of a single strand rather than DNA’s double strand

12. What are the monomers of DNA and RNA
12. What are the monomers of DNA and RNA? The four types of nucleotides, which differ in their nitrogenous bases are the monomers of DNA and RNA. Of proteins? Amino acids are the monomers of proteins

DNA to mRNA The synthesis of RNA using a DNA template
Transcription step 1 DNA to mRNA The synthesis of RNA using a DNA template A copy of the instructions found on the DNA is made using messenger RNA. The job of the mRNA is to take the instructions to the ribosome where the protein can be made!

DNA to mRNA If the DNA reads… DNA AAT CCT GGG CCC
Then what will the complementary m RNA read? Remember that RNA had uracil instead of thymine, but all other nitrogen bases are the same.

transcription DNA AAT CCT GGG CCC mRNA UUA GGA CCC GGG
This is called the complementary strand and goes out into the cytoplasm to find a ribosome….

Transcription

RNA polymerase is the enzyme that helps this reaction occur!
From Genes to Proteins . The RNA is complementary to the gene, and the RNA nucleotides are put together with the help of RNA polymerase. This process is very similar to DNA replication except only one side is copied and with RNA nucleotides instead of DNA. RNA polymerase is the enzyme that helps this reaction occur!

Translation: turning the code into a protein
The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of “language” from nucleotides to amino acids. When the mRNA gets to a ribosome, the 2 parts of the ribosome assemble on top of it.

There is a start code on the mRNA
AUG the RNA bases will be read as 3 together (in triplets) from the 5’ to the 3’ direction. Each triplet makes up a codon.

Transfer RNA or tRNA tRNA is the translator – each tRNA molecule carries one of the 20 amino acids attached to its 3’ end. About midway along the sequence of nucleotides in tRNA are 3 bases that are complementary to the codon – this base sequence in tRNA is called the anti-codon.

The anticodon matches with the codon bringing with it the amino acid = translation into a polypeptide

13. Define each of these processes that are essential to the formation of a protein:
Transcription: translation:

transcription: The synthesis of RNA using a DNA template
translation: The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of “language” from nucleotides to amino acids.

14. Complete the following table to summarize each process.

15. In eukaryotes, what is the pre-mRNA called?

Primary transcript

16. Write the central dogma of molecular genetics, as proclaimed by Francis Crick, in the box below.

DNA  RNA  Protein

17. How many nucleotide bases are there? How many amino acids?

4 bases 20 amino acids

18. How many nucleotides are required to code for these 20 amino acids?

19. So, the language of DNA is a triplet code
19. So, the language of DNA is a triplet code. How many unique triplets exist?

20. DNA is double-stranded, but for each protein, only one of these two strands is used to produce an mRNA transcript. What is the coding strand called?

Template strand

21. Here is a short DNA template
21. Here is a short DNA template. Below it, assemble the complementary mRNA strand. 3'A C G A C C A G T A A A 5'

3'A C G A C C A G T A A A 5' 5' U G C U G G U C A U U U 3'

3'A C G A C C A G T A A A 5' 5' U G C U G G U C A U U U 3' 22. How many codons are there above? Label one codon.

4 3'A C G A C C A G T A A A 5' 5' U G C U G G U C A U U U 3'

23. Describe Nirenberg’s experiment in which he identified the first codon.

Nirenberg synthesized an artificial mRNA by linking identical RNA nucleotides containing uracil as their base. uuuuuuuuuuuuuuuuuuuuuuuu

24. What was the first codon–amino acid pair to be identified?
UUU (poly-U)-phenylalanine

25. Of the 64 possible codons, how many code for amino acids? 61

Ribosomes Amino acids are physically linked together to form proteins on the ribosomes, which are located throughout the cytoplasm. Ribosomes are complex structures composed of proteins and rRNA.

The start codon always has the sequence 5’-AUG-3’.
The ribosome subunits will come together at the start codon and a tRNA with the anti-codon 3’-UAC-5’ will enter the ribosome and will H bond with the codon on the mRNA. This tRNA will be carrying the amino acid methionine (or formylmethionine in Bacteria).

26. What event is coded for by UAA, UAG, and UGA?
Stop

27. What is the start codon? AUG

28. Why is the genetic code said to be redundant but not ambiguous?

Although more than one codon may specify a particular amino acid, neither codon specifies any other amino acid.

A second tRNA carrying a second amino acid will enter the ribosome and if the anti-codon complements the codon then the mRNA and tRNA will base pair. In the ribosome these first 2 tRNA come side-by-side so that the amino acids they carry will form a peptide bond between them.

Then the entire ribosome will move along the mRNA by 3 bases (1 codon), a third tRNA with an anti-codon complementary to this codon and a third amino acid will enter the ribosome. Another peptide bond links the 3rd amino acid to the 2nd amino acid, and so a polypeptide (protein) forms.

For some codons there is no amino acid-carrying tRNA with a complementary anti-codon (stop codons). When the ribosome comes across these codons, no tRNA enters the ribosome and so the process of translation will stop and protein is released from the ribosome.

Overview of Protein Synthesis

Many ribosomes can translate a piece of mRNA at the same time!

During translation, the mRNA molecule binds to a ribosome, and tRNAs carry amino acids to the ribosome according to the codons on the mRNA.

29. Explain the concept of reading frame.

On an mRNA, the reading frame is the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis.

30. Now here is an important idea: DNA is DNA is DNA
30. Now here is an important idea: DNA is DNA is DNA. By this we mean that the code is nearly universal, and because of this, jellyfish genes can be inserted into pigs, or firefly genes can make a tobacco plant glow. Enjoy a look at Figure 17.6 in your text and no question to answer here! What does this tell you about all organisms? A gene from an organism can theoretically be expressed by any other organism.

Concept 17.2 Transcription is the DNA-directed synthesis of RNA: A closer look
What evidence makes scientist believe RNA may have evolved before DNA? DNA polymerase uses a primer, usually made of RNA.

31. Name the enzyme that uses the DNA template strand to transcribe a new mRNA strand.

32. Recall from Chapter 16 that DNA polymerase III adds new nucleotides to the template DNA strand to assemble each new strand of DNA. Both enzymes can assemble a new polynucleotide only in the 5' direction. Which enzyme, DNA polymerase III or RNA polymerase, does not require a primer to begin synthesis?

RNA polymerase

33. What is a transcription unit?

A transcription unit is a region of DNA that is transcribed into an RNA molecule.

34. Figure 17. 7 in your text will require a bit of study
34. Figure 17.7 in your text will require a bit of study. Use it to label the following elements on the figure below: promoter, RNA polymerase, transcription unit, DNA template, nontemplate DNA, and RNA transcript. Then, to the right of the figure, name the three stages of transcription and briefly describe each stage.

Promoter, RNA polymerase initiation
Unwound DNA RNA transcript elongation Termination Completed RNA Non template DNA Template DNA

35. Let’s now take a closer look at initiation
35. Let’s now take a closer look at initiation. Read the paragraph titled “RNA Polymerase Binding and Initiation of Transcription” carefully. List three important facts about the promoter here. .

1. Promoter of a gene includes within it the transcription start point.
2. Promoter typically extends several dozen of more nucleotide pairs upstream from the start point. 3. RNA polymerase binds in a precise location and orientation on the promoter

36. Use Figure 17.8 in your text to label the following elements of the figure that follows: TATA box, RNA polymerase II, transcription factors, template DNA strand, start point, 5' and 3', and mRNA transcript. To the right of the figure, explain the three stages of initiation that are shown.

TATA A sequence of nucleotides about 25 nucleotides up from the start point is called the TATA box and is important is binding the RNA polymerase and starting the initiation of transcription.

Transcription factors
Protein-protein interactions are necessary for the complex to occur and the process to work properly! Several proteins must bind to the DNA before the RNA polymerase can bind in the correct position. These are transcription factors.

Transcription factors

Transcription initiation complex
Along with the RNA polymerase II a complex forms and un winds the DNA so that the process of RNA synthesis can begin

36. Use Figure 17.8 in your text to label the following elements of the figure that follows: TATA box, RNA polymerase II, transcription factors, template DNA strand, start point, 5' and 3', and mRNA transcript. To the right of the figure, explain the three stages of initiation that are shown.

37. What is the TATA box? How do you think it got this name?

The TATA box is a DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex. The name TATA box is from the thymine (T) and adenine (A) that make it up.

38. What comprises a transcription initiation complex?

The completed assembly of transcription factors and RNA polymerase bound to a promoter

39. Now it is time to put all of the elements of transcription together. Write an essay below to describe the process by which mRNA is formed. Use these terms correctly in your essay, and highlight (orunderline) each one: TATA box, gene, terminator, promoter, elongation, 5' to 3', termination,initiation RNA, polymerase RNA nucleotides, template, start point, termination signal, and transcription factors. This essay is typical of what you might be asked to write on the AP Biology exam.

Concept 17.3 Eukaryotic cells modify RNA after transcription

40. RNA processing occurs only in eukaryotic cells
40. RNA processing occurs only in eukaryotic cells. The primary transcript is altered at both ends, and sections in the middle are removed. a. What happens at the 5' end?

The 5' end is synthesized first; it receives a 5' cap, a modified form of a guanine (G) nucleotide added onto the 5' end after transcription of the first 20–40 nucleotides.

b. What happens at the 3' end?

The 3' end of the pre-mRNA molecule is also modified before the mRNA exits the nucleus. An enzyme adds 50–250 more adenine (A) nucleotides, forming a poly-A tail.

41. What are three important functions of the 5' cap and poly-A tail?

1. They seem to facilitate the export of mature mRNA from the nucleus.
2. They help protect the mRNA from degradation by hydrolytic enzymes. 3. They help ribosomes attach to the 5' end of the mRNA once the mRNA reaches the cytoplasm.

Many eukaryotic genes are interrupted by segments of DNA that do not code for proteins; these segments are called introns. The segments of DNA that are expressed are called exons.

After transcription, the introns are cut out, and the exons are joined
After transcription, the introns are cut out, and the exons are joined. The exons are then translated.

42. Distinguish between introns and exons
42. Distinguish between introns and exons. Perhaps it will help to remember this: Exons are expressed.

Introns are the noncoding segments of nucleic acid that lie between coding regions, also called intervening sequences Exons are the segments of nucleic acid that are eventually expressed by being translated into amino acid sequences.

43. On the following figure label: pre-mRNA, 5' cap, poly-A tail, introns, and exons.

44. What are snRNPs? What two types of molecules make up a snurp?

snRNPs are small nuclear ribonucleoproteins
snRNPs are small nuclear ribonucleoproteins. snRNPs are made up of RNA and protein molecules.

45. You will be introduced to a number of small RNAs in this course
45. You will be introduced to a number of small RNAs in this course. What type is the RNA in a snRNP? Small nuclear RNA

46. Snurps band together in little snurp groups to form spliceosomes
46. Snurps band together in little snurp groups to form spliceosomes. How do spliceosomes work?

The spliceosome interacts with certain sites along an intron, releasing the intron, which is rapidly degraded, and joining together two exons that flanked the intron.

The idea that all biological catalysts are proteins
These will not be covered on the test!!! 47. On the figure below, label the following: pre-mRNA, snRNPs, snRNA, protein, spliceosomes, intron, and other proteins. See page 335 of your text for the labeled figure. 48. Study the figure and text carefully to explain how the splice sites are recognized. snRNAs, part of the spliceosome complex, recognize specific nucleotide sequences on the intron and catalyze the process of intron removal. This is an excellent example of catalytic function in snRNA. 49. What is a ribozyme? An RNA molecule that functions as an enzyme, such as an intron that catalyzes its own removal during RNA splicing 50. What commonly held idea was rendered obsolete by the discovery of ribozymes? The idea that all biological catalysts are proteins

51. What are three properties of RNA that allow it to function as an enzyme?

a. Because RNA is single-stranded, a region of an RNA molecule may base-pair with a complementary region elsewhere in the same molecule, which gives the molecule a particular three-dimensional structure. A specific structure is essential to the catalytic function of ribozymes, just as it is for enzymatic proteins. b. Like certain amino acids in an enzymatic protein, some of the bases in RNA contain functional groups that may participate in catalysis. c. This ability of RNA to hydrogen-bond with other nucleic acid molecules (either RNA or DNA) adds specificity to its catalytic activity

Each codon specifies an amino acid. Codons are found on the mRNA
They are made of 3 nitrogen bases. They are complementary to the original DNA and exactly like the “other side of the strand that was copied. The anticodon ( found on tRNA) is complementary to the codon.

The amino acids are joined to form a protein
The amino acids are joined to form a protein. The genetic code (codons) used by most organisms to translate mRNA is nearly universal. This shows a link between living things!!!

54. What is an anticodon?

A nucleotide triplet at one end of a tRNA molecule that base-pairs with a particular complementary codon on an mRNA molecule

55. Transfer RNA has two attachment sites. What binds at each site
55. Transfer RNA has two attachment sites. What binds at each site? Sketch tRNA to indicate the two attachment sites, and note where complementary base pairing and hydrogen bonding occur to give it shape.

A specific anticodon binds at one end of tRNA, and a corresponding amino acid at the other end. By covalent bonds! Hydrogen bonds hold the shape of the tRNA

Omit these! 56. How many different aminoacyl-tRNA synthetases are there? 20 57. Scientists expected to find one aminoacyl-tRNA synthetase per codon, but far fewer have been discovered. How does wobble explain this? Wobble is flexibility in the base-pairing rules in which the nucleotide at the 5' end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3' end) of a codon. This flexibility explains why there are only about 45 tRNAs. 58. Use the following figure to explain the process of a specific amino acid being joined to a tRNA. Also add these labels: aminoacyl-tRNA synthetase, ATP, amino acid, and tRNA.

59. Describe the structure of a eukaryotic ribosome.

A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more rRNAs.

60. How does a prokaryotic ribosome differ from a eukaryotic ribosome
60. How does a prokaryotic ribosome differ from a eukaryotic ribosome? What is the medical significance of this difference? .

Eukaryotic ribosomes are slightly larger in structure and differ somewhat from bacterial ribosomes in their molecular composition. Certain antibiotic drugs can inactivate bacterial ribosomes without inhibiting the ability of eukaryotic ribosomes to make proteins. These drugs, including tetracycline and streptomycin, are used to combat bacterial infections

61. On the following figure, label the large subunit, small subunit, A, P, and E sites, mRNA binding site. To the right of the figure, explain the functions of the A, P, and E sites.

62. Much like transcription, we can divide translation into three stages. List them.
a. initiation b. elongation c. termination

63. Summarize the events of initiation
63. Summarize the events of initiation. Include these components: small ribosomal subunit, large ribosomal subunit, mRNA, initiator codon, tRNA, Met, initiation complex, P site, and GTP. See page 339 in your text for the labeled figure.

A small ribosomal subunit binds to a molecule of mRNA
A small ribosomal subunit binds to a molecule of mRNA. In a bacterial cell, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon.

An initiator tRNA, within the anticodon UAC, base-pairs with the start codon, AUG. This tRNA carries the amino acid methionine (Met). The arrival of a large ribosomal subunit completes the initiative complex.

Proteins called initiation factors are required to bring all the translation components together. Hydrolysis of GTP provides the energy for the assembly. The initiator tRNA is in the P site; the A site is available to the tRNA bearing the next amino acid

64. What is always the first amino acid in the new polypeptide?

64. What is always the first amino acid in the new polypeptide
64. What is always the first amino acid in the new polypeptide? methionine

65. Now, summarize the events of elongation
65. Now, summarize the events of elongation. Include these components: mRNA, A site, tRNA, codon, anticodon, ribozyme, P site, and E site.

The anticodon of an incoming aminoacyl tRNA base-pairs with the complementary mRNA codon in the A site. Hydrolysis of GTP increases the accuracy and efficiency of this step.

An rRNA molecule of the large ribosomal subunit catalyzes the formation of a peptide bond between the amino group of the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site. This step removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site.

The ribosome translocates the tRNA in the A site to the P site
The ribosome translocates the tRNA in the A site to the P site. At the same time, the empty tRNA in the P site is moved to the E site, where it is released. The mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site

66. What is a release factor
66. What is a release factor? By what mechanism is termination accomplished?

A release factor is a protein shaped like an aminoacyl tRNA, which binds directly to the stop codon in the A site. Hydrolyzation is the mechanism by which termination is accomplished, releasing the polypeptide through the exit tunnel of the ribosome’s large subunit.

67. What is a polyribosome?

A polyribosome is a group of several ribosomes attached to, and translating, the same messenger RNA molecule.

68. What are some of the things that will result in a final-form functional protein?

Modifications of a protein after translation include protein folding, chemical modification of amino acids, enzymatic removal or rearrangement of amino acids, or the formation of quaternary level proteins as in the case of hemoglobin.

69. Describe at least three types of post-translational modifications.

1. Certain amino acids may be chemically modified by the attachment of sugars, lipids, phosphate groups, or other additions. 2. Enzymes may remove one or more amino acids from the leading (amino) end of the polypeptide chain. 3. Two or more polypeptides that are synthesized separately may come together, becoming the subunits of a protein that has quaternary structure.

70. Use the following figure to explain how proteins are targeted for the ER.
See page 343 in your text for the labeled figure. ER golgi export

Polypeptide synthesis begins on a free ribosome in the cytosol
Polypeptide synthesis begins on a free ribosome in the cytosol. An SRP binds to a receptor protein in the ER membrane. This receptor is part of a protein complex that has a membrane pore and asignal-cleaving enzyme. The SRP leaves, and the polypeptide synthesis resumes, with simultaneous translocation across the membrane. The signal-cleaving enzyme cuts off the signal polypeptide. The rest of the completed polypeptide leaves the ribosome and folds into its final conformation.

Essay Explain the process of making a protein from start to finish.
Make sure your steps are in the correct sequence. Add as many details as possible. Name the processes and the enzymes. The more items listed, the more points. Do not contradict yourself.

Exchange papers Check to see if all of the parts are there and they are in order. Give a point for each of the items included in the paper. Count up the points. Give the paper back to the owner… How did you do?

Things that should be in the answer:
1. Starts in the nucleus with the DNA gene. 2. DNA to mRNA is called transcription 3. RNA polymerase is the enzyme that unzips and transcribes DNA to RNA. 4. Complimentary bases A-U, T-A, C-G, G-C ( no Thymine in RNA) 5. mRNA goes out of nucleus to the cytoplasm to find a ribosome. 6. Ribosome matches mRNA to tRNA 7. mRNA has the codon 8. codon is a set of 3 nitrogen bases that codes for an amino acid. 9. tRNA has the anti codon on one end 10. tRNA has the amino acid on the other end 11. ribosome has an A and a P site 12. amino acids bond together with peptide bonds to form proteins 13. The part of the process that occurs on the ribosome is called translation

Concept 17.5 Mutations of one or a few nucleotides can affect protein structure and function

mutations

frameshift Can cause the most problems if near the start of a sequence!

71. Define a mutation in terms of molecular genetics.
A change in the nucleotide sequence of an organism’s DNA or in the DNA or RNA of a virus .

72. Define point mutations.
A point mutation is a change in a single nucleotide pair of a gene.

73. What are frameshift mutations?
A frameshift mutation is a mutation occurring when nucleotides are inserted in or deleted from a gene and the number inserted or deleted is not a multiple of three, resulting in the improper grouping of the subsequent nucleotides into codons

74. Identify two mechanisms by which frameshifts may occur.

Insertion and deletion

75. What is the difference between a nonsense and missense mutation?

A nonsense mutation changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein. A missense mutation is a nucleotide-pair substitution that results in a codon that codes for a different amino acid.

76. How can a nucleotide-pair substitution result in a silent mutation?
A change in the nucleotide pair may transform one codon into another that is translated into the same amino acid. This mutation has no observable effect on the phenotype.

77. What are the two categories of mutagens?
Physical and chemical

78. Describe the action of different types of chemical mutagens.
1. Chemicals that are similar to normal DNA nucleotides but that pair incorrectly during DNA replication 2. Chemicals that interfere with correct DNA replication by inserting themselves into the DNA and distorting the double helix 3. Chemicals that cause chemical changes in bases that change their pairing properties

mutations Mutations can be selected for or against based on their ability to help an organism survive. The TATA box seems to have survived mutation, thus it has had mutations over time occur to it, but they must have been selected against and therefore been removed allowing it to remain intact!

79. Describe two important ways in which bacterial and eukaryotic gene expression differ.

1. Transcription is terminated differently in bacteria and eukaryotes.
2. In the absence of a nucleus, bacterial cells can simultaneously transcribe and translate the same gene, and the newly made protein can quickly diffuse to its site of function. The eukaryotic cell’s nuclear envelope segregates transcription from translation and provides a compartment for extensive RNA processing. This processing state includes additional steps whose regulation can help coordinate the eukaryotic cell’s elaborate activities.

80. What is a gene?

It used to be simply stated that one gene codes for one polypeptide.
That definition has now been modified. Write below the broader molecular definition in use today. A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule

Tell the story!

Prokaryotic Translation can begin while transcription is still in progress.

Chapter 17 AP guidelines Transcription:
c. Genetic information flows from a sequence of nucleotides in a gene to a sequence of amino acids in a protein.

1. The enzyme RNA-polymerase reads the DNA molecule in the 3' to 5' direction and synthesizes complementary mRNA molecules that determine the order of amino acids in the polypeptide. 2. In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications. To foster student understanding of this concept, instructors can choose an illustrative example such as: Addition of a poly-A tail Addition of a GTP cap Excision of introns

Translation: 3. Translation of the mRNA occurs in the cytoplasm on the ribosome.

4. In prokaryotic organisms, transcription is coupled to translation of the message.

5. Translation involves energy and many steps, including initiation, elongation and termination. The salient features include The mRNA interacts with the rRNA of the ribosome to initiate translation at the (start) codon. The sequence of nucleotides on the mRNA is read in triplets called codons. Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many amino acids have more than one codon. tRNA brings the correct amino acid to the correct place on the mRNA. The amino acid is transferred to the growing peptide chain. The process continues along the mRNA until a “stop” codon is reached. The process terminates by release of the newly synthesized peptide/protein.

d. Phenotypes are determined through protein activities.
To foster student understanding of this concept, instructors can choose an illustrative example such as: Enzymatic reactions Transport by proteins Synthesis Degradation

3B Structure and function in biology result from the presence of genetic information and the correct expression of this information. The expression of the genetic material controls cell products and these products determine the metabolism and nature of the cell. Most cells within an organism have the same set of genetic instructions, but the differential expression of specific genes determines the specialization of cells. Some genes are continually expressed, while others are regulated allowing for more efficient use metabolically.

Gene expression is controlled by environmental signals and developmental cascades that involve both regulatory and structural genes. A variety of different gene regulatory systems are found in nature. Two of the best studied are the inducible and the repressible regulatory systems ( operons) in bacteria and several regulatory pathways that are conserved across the phyla use a combination of positive and negative regulatory motifs.

In eukaryotes, gene regulation and expression are more complex and involve many factors, including a suite of regulatory molecules. Multicellular organisms have developmental pathways from zygote to adult, yet all cells in the organism start with the same complement of DNA. The developmental sequences are predominately determined and programmed by differential gene expression. Which gene gets expressed and the level of expression are determined by both internal and external signals. In Multicellular organisms, cell to cell interactions and cell to cell signaling via small molecules modulate and control gene expression and cell function. For example, morphogens help to determine spatial development and hormones can influence cell metabolism.

Developmental gene sequences have an evolutionary origin and are conserved across species, for example, HOX genes are present in genome sequences from Drosophila to humans. Errors in changes in regulation of genes involved in development often lead to severe, detrimental and even bizarre consequences.

Enduring understanding 3
Enduring understanding 3.A: Heritable information provides for continuity of life. Essential knowledge 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information. (phenotypes and proteins) d. Phenotypes are determined through protein activities. To foster student understanding of this concept, instructors can choose an illustrative example such as: Enzymatic reactions Transport by proteins Synthesis Degradation

Learning Objectives: LO 3.3 The student is able to describe representations and models that illustrate how genetic information is copied for transmission between generations. [See SP 1.2] LO 3.4 The student is able to describe representations and models illustrating how genetic information is translated into polypeptides. [See SP 1.2]

LO 3.5 The student can justify the claim that humans can manipulate heritable information by identifying at least two commonly used technologies. [See SP 6.4] LO 3.6 The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression. [See SP 6.4]

Enduring understanding 3
Enduring understanding 3.C: The processing of genetic information is imperfect and is a source of genetic variation.

Essential knowledge 3.C.1:
Changes in genotype can result in changes in phenotype. a. Alterations in a DNA sequence can lead to changes in the type or amount of the protein produced and the consequent phenotype. [See also 3.A.1]

Evidence of student learning is a demonstrated understanding of the following:
1. DNA mutations can be positive, negative or neutral based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein. b. Errors in DNA replication or DNA repair mechanisms, and external factors, including radiation and reactive chemicals, can cause random changes, e.g., mutations in the DNA.

d. Changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction can be selected by environmental conditions. [See also 1.A.2, 1.C.3] .

To foster student understanding of this concept, instructors can choose an illustrative example such as: Antibiotic resistance mutations Pesticide resistance mutations Sickle cell disorder and heterozygote advantage Evidence of student learning is a demonstrated understanding of the following: Selection results in evolutionary change

Learning Objectives: LO 3.24 The student is able to predict how a change in genotype, when expressed as a phenotype, provides a variation that can be subject to natural selection. [See SP 6.4, 7.2] LO 3.25 The student can create a visual representation to illustrate how changes in a DNA nucleotide sequence can result in a change in the polypeptide produced. [See SP 1.1] LO 3.26 The student is able to explain the connection between genetic variations in organisms and phenotypic variations in populations. [See SP 7.2]

Essential knowledge 3.C.2:
Biological systems have multiple processes that increase genetic variation. a. The imperfect nature of DNA replication and repair increases variation. b. The horizontal acquisitions of genetic information primarily in prokaryotes via transformation (uptake of naked DNA), transduction (viral transmission of genetic information), conjugation (cell-to-cell transfer) and transposition (movement of DNA segments within and between DNA molecules) increase variation. [See also 1.B.3]

Learning Objectives: LO 3.27 The student is able to compare and contrast processes by which genetic variation is produced and maintained in organisms from multiple domains. [See SP 7.2] LO 3.28 The student is able to construct an explanation of the multiple processes that increase variation within a population. [See SP 6.2]

Evidence of student learning is a demonstrated understanding of the following:
1. Whether or not a mutation is detrimental, beneficial or neutral depends on the environmental context. Mutations are the primary source of genetic variation.

Chapter 18 Gene regulation and Mutation Vocabulary: 1. Gene regulation
2. Operon

Gene Regulation and Structure
Prokaryotic and eukaryotic cells are able to control which genes are expressed and which are not, depending on the cell’s needs. In prokaryotes, gene expression is regulated by operons. Gene expression is switched off when repressor proteins block RNA polymerase from transcribing a gene.

Lac operon: the operon that controls the production of lactose metabolism enzymes.

In eukaryotes, an enhancer must be activated for a eukaryotic gene to be expressed. Transcription factors initiate transcription by binding to enhancers and to RNA polymerases. Repressors are proteins that bind to the operon and physically block RNA polymerase from producing mRNA

Mutations are changes in DNA
Mutations are changes in DNA. Gene alterations are mutations that change a gene. These mutations can involve a change in a single nucleotide or an entire gene.

What is transcription? When mRNA copies the DNA in the nucleus Where in the cell does transcription take place? In the nucleus What is translation? _ when the mRNA is de coded by a tRNA matching its anticodons to the codon and putting the correct amino acid into place on the ribosome. What are the types of RNA and their roles in this process? 1. mRNA makes the copy of DNA and takes it to the ribosome 2. tRNA transfers the a.a to the protein by matching up with the codon on the mRNA 3. rRNA part of the ribosome that brings together the mRNA and the tRNA

What is a gene? A sequence of DNA that codes for a polypeptide or a protein or RNA What are alleles? Forms of a gene How does the information in the DNA eventually get to become the protein or polypeptide? The instructions in the DNA are transcribed by the mRNA and taken to a ribosome in the cytoplasm where the codon is matched with an anticodons on a tRNA. The amino acid attached the the tRNA is added to the chain as the sequence on the mRNA is translated into the protein.

SC.912.L Explain how and why the genetic code is universal and is common to almost all organisms. 1. What are the 4 basic nitrogen bases found in DNA? Cytosine, adenine, thymine and guanine 2. How many bases make a codon? 3, what do they code for? an amino acid Proteins and amino acids and genetic codes are similar in most all eukaryotic organisms, this shows a link between all organisms. The degree of similarity can be seen by matching the DNA of different organisms. 3. Are the codes from one organism to another similar? yes. What does this tell you about organisms? All organisms are genetically similar in the DNA code

Section 4 Gene regulation and Mutation
SC.912.L Explain how mutations in the DNA sequence may or may not result in phenotypic change. Explain how mutations in gametes may result in phenotypic changes in offspring. How are bacteria able to regulate genes? Operons, such as the lac operon How do eukaryotes regulate the transcription of genes? Gene regulation What is a mutation? A permanent change in the cell’s DNA 4. What are several types of mutations? Point mutation, insertion, deletion, frame shift Why are frameshift mutations some of the most serious? they cause the entire sequence of codes to be incorrectly read. Can mutations that occur in body cells, somatic cells, be passed on to offspring? No

In what type of cells must the mutations occur in order for the mutation to be inherited?
Gametes 7. Are all mutations bad? No SC.912.L Describe how mutation and genetic recombination increase genetic variation. Describe how mutation and genetic recombination increase genetic variation. What is genetic variation? Differences in the genetic material from generation to generation 2. If no mutations occur, will there be variations? yes What are other ways genes recombine? Crossing over 3. Is genetic variation a positive thing for species survival? Yes, it provides new traits that may allow a species to survive better in its environment.

Animations links

Review 1. How was DNA determined to be the genetic material and not protein? Discuss the process that was needed. You do not need to remember the specific details of the experiments but do need to explain the process that was used in more general terms. ( 2 pts) 2. Describe the basic process of DNA replication. Name the major enzymes needed in the process. Use your vocabulary terms in the process of your explanation. ( 5pts) 3. Explain how proteins are made in the process of gene expression or protein synthesis. You will receive points for each detail that you correctly describe in the proper order, so include as much detail as you can. Start in the nucleus… ( 10 pts) there may be bonus points for extra information given.

What does DNA do? It contains all of the instructions to make the proteins living things need for life!

How can all of that information fit into a single cell?
DNA is a long chemical molecule with only 4 different nucleotides. It is the sequence of these nucleotides that makes each organism different.

A-T-C-C-G-G-G-A-G This little piece of DNA had three codes: ATC CGG
GAC

The alphabet of life A T C G

In triplets or codons The order of the bases makes all of the difference!!! Change one letter and it is totally different. Just like EAT is not the same as TEA Same letters, different order= new meaning!!

DNA Replication When new cells are made, DNA must make a copy of it self. This process is called DNA replication.

First the DNA “unzips” down the center

Nucleotides floating free in the cell bond in the open spaces.

The original molecule serves as a pattern for the new
The new strand is called complementary to the old one.

Translation How to “translate” the code into proteins

DNA is in the nucleus Messenger RNA comes into the nucleus and makes a copy of the section of DNA needed. DNA unzips the section and RNA nucleotides copy the DNA The mRNA takes the message out to the cytoplasm RNA polymerase is the enzyme that does this!

Ribosomal RNA Reads the code by matching up with the messenger RNA and connecting the correct transfer RNA to the mRNA

Transfer RNA has the anticodon
mRNA has the codon These match up like the strands of DNA.

tRNA Each tRNA has an amino acid attached to it

rRNA Ribosomal RNA “reads” the codon and attaches the correct anticodon. The amino acids attached to the tRNA get bonded together to form a protein.

There are start and stop codes.
There are even enzymes that look for mistakes and make corrections. Bu sometimes mistakes happen…

MUTATIONS A change in DNA

Point mutations A single base pair is changed. THE DOG BIT THE CAT
THE DOG BIT THE CAR Only one letter is different yet….

Frame shift Mutation A single base is added or deleted
This causes the entire line to be read differently!!! CCG AAU GGU ADD ONE C AND CCG AAU GGU READS CCC GAA UGG U

CHROMOSOMAL MUTATIONS
Parts of chromosomes break off Join to the wrong chromosome Chromosomes do not separate correctly during meiosis: non disjunction

Trisomy monosomy Three where there should be two Or
One where there should be two.

From Gene to Protein.

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