Topic 3: Chemistry of Life - DNA

Topic 3: Chemistry of Life - DNA

Topic 3: Chemistry of Life - DNA

3.3 DNA Structure

• Sugar/Phosphate group = sides of the DNA ladder or backbone

• Nitrogenous Bases = rungs of the DNA ladder

3.3 DNA Structure

• Covalent bonds hold together the sugar of one nucleotide, to the phosphate group of another nucleotide.

• The backbone/sides of the ladder are alternating sugar/phosphates.

• Remember covalent bonds are STRONG, sides of the double helix are never broken!

3.3 DNA Structure• Hydrogen bonds hold together the

complementary nitrogenous bases (rungs of the ladder)

• Remember hydrogen bonds are WEAK, our body needs to separate the DNA double helix in DNA replication (S phase of Interphase)

• A = T and G = C

3.3 DNA Structure

3.3 DNA Structure• Draw and label a simple diagram of the

molecular structure of DNA:

3.3 DNA Structure

• James Watson and Francis Crick: 2 British men credited for discovering the double helix shape of DNA and later awarded a Nobel Prize.

• Not so fast! They would never have received the prize without Rosalind Franklin's help!

3.3 DNA Structure• Rosalind was not aware there

was a race for the DNA structure, and gladly showed Watson her DNA photograph - which was the key he was missing to finally publish a paper on the double helix.

• Rosalind died in 1958 at the age of 30, and Watson and Crick received the Nobel Prize in 1962

• Would Rosalind have had a share in the Nobel Prize had she not died so young?

• Many say no, she was snubbed out of the prize because she was looking for help and confidence on her work within the scientific community rather than out for glory like Watson and Crick.

• She died so young because photographing DNA can take up to 100 hours of radiation exposure per picture - she was around radiation all the time and never protected herself.

• She passed away from ovarian cancer.

• Homework:

• Examine the table below. Compare the amounts of adenine, guanine, cytosine, and thymine found in the DNA of each of the cells studied.

Percent of Each Base in DNA Samples

Source of Sample A G C T

Human Liver 30.3 19.5 19.9 30.3

Human Blood Cell 30.9 19.9 19.8 29.4

Salmon Sperm 27.8 22.2 22.6 27.5

Yeast 31.7 18.2 17.4 32.6

• 1. Compare the amounts of A, T, G and C in each kind of DNA. Why do you think the relative amounts are so similar in human liver and human blood cells?

• 2. How do the relative amounts of each base in salmon sperm compare with the relative amounts of each base in yeast?

• 3. What fact can you state about the overall composition of DNA, regardless of its source?

3.4 DNA Replication

★Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by formation of the new complementary strands of DNA polymerase.

★Explain the significance of complementary base pairing in the conservation of the base sequence of DNA

★ State that DNA replication is semi-conservative.

3.4 DNA Replication

• Before a cell divides (mitosis), it needs to make a complete set of genetic instructions (DNA) for each new cell.

• S phase/Interphase = DNA Synthesis

• The time where DNA is doubled, otherwise known as DNA Replication

• This occurs in the nucleus.

• Remember, mitosis produces 2 IDENTICAL daughter cells.

DNA Synthesis/Replication

3.4 DNA Replication

• DNA Replication Step by Step Details:

• 1. Unzip the 2 strands.

• DNA Helicase (an enzyme) moves along the double helix, unwinding and separating the 2 strands.

• The weak hydrogen bonds that hold the bases together are broken.

3.4 DNA Replication• 2. The unpaired nucleotides are exposed

and each single strand now acts as an "old" template to form a new complementary strand.

• Free nucleotides move into place (A=T, G=C)

• 3. DNA Polymerase is the enzyme that binds the new nucleotides to the old strands.

• Two new DNA molecules are rewound, each forming a new double helix.

3.3 DNA Structure

★Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate

★State the names of the 4 bases in DNA

★Outline how DNA nucleotides are linked together by covalent bonds into a single strand.

3.3 DNA Structure

★Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds.

★Draw and label a simple diagram of the molecular structure of DNA

3.3 DNA Structure

• DNA (Deoxyribonucleic Acid) molecules make up the genetic material of all living organisms.

• DNA is an extremely long molecule - if uncoiled, the DNA in all the cells in your body would stretch 10 billion miles, from here to Pluto and back!

• This long chain of DNA is made up of many subunits called nucleotides.

3.3 DNA Structure

• Although DNA is the genetic material of living organisms and is therefore immensely important, it is made of relatively simple subunits.

• These subunits, if you get down to the smallest parts, are made of Hydrogen, Carbon, Oxygen, Nitrogen.

• HCON=4 most common elements in all living things, now you know why!

3.3 DNA Structure• Nucleotides are the building blocks

(monomers) of nucleic acids (polymers)

• Nucleotide:

• 1. Sugar (deoxyribose)

• 2. Phosphate group

• 3. Nitrogenous base (Adenine, Thymine, Guanine, Cytosine) - A, T, G or C

3.3 DNA Structure

• Classwork/Homework Monday 2/4:

• 1. What does DNA strand for and why?

• 2. Where are covalent bonds and hydrogen bonds located in DNA?

• 3. If there were 6 guanines in a strand of 30, how many C? T? A?

3.3 DNA Structure

• DNA is a twisted ladder, known as a double helix.

• Two DNA strands make up the double helix, running in opposite directions of each other.

• The 2 strands are held together by base pairs that are complimentary to each other.

3.3 DNA Structure

• DNA is a twisted ladder, known as a double helix.

• Two DNA strands make up the double helix, running in opposite directions of each other (antiparallel)

• The 2 strands are held together by base pairs that are complimentary to each other.

3.4 DNA Replication

• The two new DNA strands produced are absolutely identical to the original strand because of complementary base pairing.

• DNA replication is semi-conservative.

• Each new set of DNA has one old strand and one new strand.

• This ensures each new cell has an exact copy of the genetic instructions.

3.5 DNA Transcription and Translation

★Compare the structure of RNA and DNA

★Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase.

★ Describe the genetic code in terms of codons composed of triplets of bases.

★Explain the process of translation, leading to polypeptide formation.

3.5 DNA Transcription and Translation

★Explain the process of translation, leading to polypeptide formation (include the roles of mRNA, tRNA, codons, anticodons, ribosomes and amino acids).

★Discuss the relationship between one gene and one polypeptide.

• The main role of DNA is to direct the activities of the cell.

• It does this by controlling the proteins that the cell produces.

• Enzymes, hormones and many other important biochemical molecules are proteins, which control what the cell becomes, what it synthesizes and how it functions.

3.5 DNA Transcription and Translation

3.5 DNA Transcription and Translation

• Protein synthesis has 2 steps:

• 1. Transcription (in nucleus)

• 2. Translation (in cytoplasm)

• The sections of DNA that code for specific proteins are known as genes.

• Genes have specific sequences of bases in sets of three, called triplets (called it a codon freshman year)

• Some triplets control where transcription and translation start and end.

3.5 DNA Transcription and Translation

• Before DNA can be coded into a protein, there is an intermediate molecule (or middle man) that needs to be produced called messenger RNA (mRNA)

• RNA = Ribonucleic Acid

• Obviously Deoxyribonucleic Acid looks a lot like Ribonucleic Acid - that's because it is! Except with a couple differences...

3.5 DNA Transcription and Translation

DNA RNA

Sugar: Deoxyribose, 5 carbon

Sugar: Ribose, 5 carbon

Bases: A, G, C, TBases: A, G, C, U (uracil

instead of thymine)

Molecule: Double Stranded

Molecule: Single Stranded

3.5 DNA Transcription and Translation• First stage of protein synthesis: TRANSCRIPTION

• Let's sum up transcription before we break it down:

• Transcription= to make an mRNA molecule

• Transcription Details:

• 1. DNA is unzipped by the enzyme RNA polymerase

• a. Transcription begins just like replication - DNA double helix unzips, separating the 2 strands

3.5 DNA Transcription and Translation

• b. But now the enzyme doing the unzipping is called RNA polymerase.

• 2. Free RNA nucleotides move into place along one of the 2 DNA strands.

• a. These RNA nucleotides have a ribose sugar, phosphate, and A, G, C or U.

• b. A Thymine on the DNA strand will bind with the new Uracil of a RNA nucleotide

3.5 DNA Transcription and Translation

• 3. RNA polymerase puts the free RNA nucleotides in the right place using complimentary base pairing.

• a. RNA polymerase does double duty in transcription - unzips DNA and attaches new RNA nucleotides to the DNA strand.

• b. A=U, G=C

• c. The end product (mRNA) is only single stranded, so RNA nucleotides will only bind to one DNA strand, not both!

3.5 DNA Transcription and Translation

• d. The new strand of mRNA is much shorter than the DNA molecule because it is just a copy of one section of the DNA - a gene.

• 4. mRNA separates from the DNA strand

• a. DNA double helix is zipped up again by RNA polymerase.

• b. mRNA moves through the nuclear envelope pores into the cytoplasm (to await translation)

• c. mRNA needs to be single stranded to fit through those nuclear pores!

3.5 DNA Transcription and Translation

• Second stage of protein synthesis: TRANSLATION

• Let's sum up translation before we break it down:

• Translation= a polypeptide (several polypeptide chains make a protein)

• Translation Details:

• 1. Triplet or Codon: sequence of 3 bases

• a. IB uses both terms.

3.5 DNA Transcription and Translation

• b. Each triplet corresponds to a specific amino acid.

• c. The order of the triplet determines which amino acid is picked.

• d. Triplets are only on the mRNA, so to determine which specific amino acid it codes for, look on the codon chart.

• e. Several amino acids chained together makes a polypeptide chain (end product of translation!)

3.5 DNA Transcription and Translation

• 2. Translation is carried out in the cytoplasm by ribosomes and transfer RNA (tRNA)

• a. The ribosome binds to the mRNA - where it reads AUG (only start codoc)

• b. Ribosome draws in the appropriate tRNA based on its anticodon.

• The tRNA anticodon is the exact opposite of the mRNA codon/triplet.

• EX: mRNA = AUG, tRNA = UAC, brings amino acid Methionine

3.5 DNA Transcription and Translation

• DNA: TAC GCA CCC ACA GTA TTT ATT

• mRNA:

• Amino acid chain:

3.5 DNA Transcription and Translation

• DNA: TAC AAC GTA CGG GTA CAC ACU

• mRNA:

• tRNA:

• Amino acid chain:

3.5 DNA Transcription and Translation• c. Only 2 tRNA molecules

fit onto the ribosome at once. Each tRNA carries with it a specific amino acid.

• The anticodon of the tRNA binds to the mRNA codon with hydrogen bonds (weak bonds because they will be broken quickly)

3.5 DNA Transcription and Translation

• 3. A peptide bond forms between the two amino acids they carry to form a dipeptide.

• a. Once a dipeptide has been formed, the first tRNA molecule detaches from both the amino acid and the ribosome.

• b. The ribosome moves along the mRNA to read the next codon.

3.5 DNA Transcription and Translation

• 4. This process is repeated over and over again until a polypeptide is formed.

• The dipeptide is only 2 amino acids, but an amino acid chain is also known as a polypeptide because of the many peptide bonds between amino acids.

• What stops translation is when the ribosome reads one of 3 stop codons on the mRNA.

• 5. After reaching a stop codon, the polypeptide falls off, and floats freely in the cytoplasm until it is needed to make a larger protein.

3.5 DNA Transcription and Translation

★Discuss the relationship between one gene and one polypeptide.

3.5 DNA Transcription and Translation

• In the 1940s, scientists proposed that each gene was responsible for the production of one protein.

• Later, the hypothesis was modified to state that one gene produces one polypeptide (because proteins have several polypeptides)

• Today, it is generally agreed that each gene does code for a single polypeptide (although there are exceptions)

3.5 DNA Transcription and Translation

• Exceptions to the one gene=one polypeptide rule:

• EX: Some DNA sequences/genes just act as regulators of transcription or translation.

• EX: Some DNA sequences/genes code for mRNA or tRNA, not polypeptides.

• 1. The following diagram shows a short stretch of DNA. What bases are indicated by labels Y and Z?

• Answer: B, thymine and guanine

Y Z

A. thymine adenine

B. thymine guanine

C. uracil guanine

D. uracil adenine

• 2. The percentage of thymine in the DNA of an organism is approximately 30%. What is the percentage of guanine?

• A. 70%

• B. 30%

• C. 40%

• D. 20%

• Answer: D, 20%

• 3. The diagram below represents part of the DNA molecule. What are the parts labelled in I, II and III?

• Answer: C

I II IIIA. hydrogen bond base deoxyriboseB. hydrogen bond deoxyribose phosphate

groupC. covalent bond base deoxyriboseD. covalent bond deoxyribose phosphate

group

• 4. Which molecule is found in both DNA and RNA?

• A. Ribose

• B. Uracil

• C. Phosphate

• D. Amino acid

• C, phosphate

• 5. What is a codon?

• A. A sequence of nucleotides on rRNA that corresponds to an amino acid.

• B. A sequence of nucleotides on mRNA that corresponds to an amino acid.

• C. A sequence of nucleotides on tRNA that corresponds to an amino acid.

• D. A sequence of nucleotides on DNA that corresponds to an amino acid.

• Answer: B, on mRNA

• 6. Which enzyme catalyzes the elongation of the new DNA strand?

• A. RNA polymerase

• B. Helicase

• C. DNA polymerase

• D. Ligase

• Answer: C, DNA polymerase

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Synthesis of new strand

• 7. If mRNA has a codon CAU, what is the corresponding anticodon on the tRNA molecule?

• A. CAT

• B. GUA

• C. CAU

• D. GTA

• Answer: B

• 8. Which molecules form the nucleotide marked in the diagram?

• A. phosphate, deoxyribose, nitrogenous base

• B. phosphorus, ribose, nitrogenous base

• C. phosphorus, deoxyribose and guanine

• D. phosphate, ribose, guanosine

• Answer: A

• 9. What happens during translation?

• A. Copying of DNA to produce DNA

• B. Copying of DNA to produce mRNA

• C. Copying of DNA to produce tRNA

• D. Polypeptide synthesis

• Answer: D, making polypeptides

• 10. What sequence of processes is carried out by the structure labelled X during translation?

• A. Combining with an amino acid and then binding to an anticodon.

• B. Binding to an anticodon and then combining with an amino acid.

• C. Binding to a codon and then combining with an amino acid.

• D. Combining with an amino acid and then binding to a codon.

• Answer: D

• 11. What enzyme is used in transcription but not in translation?

• A. DNA polymerase

• B. Helicase

• C. Protease

• D. RNA polymerase

• D, RNA polymerase

• 12. A certain gene in a bacterium codes for a polypeptide that is 120 amino acids long. How many nucleotides are needed in the mRNA to code for this polypeptide?

• A. 30

• B. 40

• C. 360

• D. 480

• C, 360

• 13. The graph below shows the effect of temperature on the separation of the strands in DNA to form single strands. The temperature at which 50% of the DNA is single stranded is called the melting temperature (Tm)

• 13. What do the results show?

• A. When the temperature reaches 85°C there are no more double-stranded DNA molecules.

• B. When the temperature reaches 85°C the DNA strands start separating rapidly.

• C. A Tm of 85°C means that DNA is not stable at room temperature (25°C)

• D. The separation of the DNA strands is directly proportional to the increase in temperature.

• Answer: B

• 14. The base ratios in the DNA and RNA for an onion are given below. What is the reason for the difference between these figures?

• A. DNA is only found in the nucleus but RNA is found throughout the cell.

• B. DNA is made entirely of double helix but RNA is not.

• C. In DNA, bases A and T are complementary but in RNA, bases A and C are complementary.

• D. RNA comes in three forms but DNA only comes in one form.

• Answer: B

Bases A % B % C % T %

DNA 31.8 18.4 18.2 31.3 Bases A % B % C % T %

RNA 24.9 29.8 24.7 20.6

• 15. What is replicated by a semi-conservative process?

• A. Messenger RNA (mRNA) only

• B. Messenger RNA (mRNA) and transfer RNA (tRNA) only

• C. Messenger RNA (mRNA), transfer RNA (tRNA) and DNA only

• D. DNA only

• Answer: D, DNA only

• 16. The strand on the DNA molecule coding for 3 codons of a gene is TATCGCACG What are the anticodons of the three tRNA molecules that correspond to this sequence?

• A. UAU, CGC, ACG

• B. ATA, GCG, TGC

• C. AUA, GCG, UGC

• D. TAT, CGC, ACG

• Answer: A

• 17. The diagram shows part of a molecule produced by replication of DNA. What is the significance of the shaded and the unshaded regions?

• A. The shaded parts are DNA and the unshaded parts are mRNA

• B. The shaded parts contain adenine and thymine and the unshaded parts contain guanine and cytosine.

• C. The shaded part is a codon and the unshaded part is an anticodon.

• D. One of the parts has been newly synthesized and the other was part of a pre-existing DNA molecule

• Answer: D

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• 18. In some people, hemoglobin always contains the amino acid valine in place of glutamic acid at one position in the protein. What is the cause of this?

• A. An error in transcription of the hemoglobin gene

• B. An error in translation of the mRNA

• C. Lack of glutamic acid in the diet

• D. A base substitution in the hemoglobin gene

• Answer: D, base substitution

• 19. What is the sequence of the amino acids that is being translated from the following mRNA sequence?

• AUGGGUGCUUAUUGGUAA

• A. Met-Cys-Ser-Tyr-Trp

• B. Met-Pro-Arg-Ile-Thr

• C. Met-Gly-Ala-Tyr-Trp

• D. Met-Gly-Tyr-Ala-Thr

• Answer: C

First baseSecond base in codon

Third basein codon U C A G in codon

U Phe Ser Tyr Cys U

Phe Ser Tyr Cys C

Leu Ser — — A

Leu Ser — Trp G

C Leu Pro His Arg U

Leu Pro His Arg C

Leu Pro Gln Arg A

Leu Pro Gln Arg G

A Ile Thr Asn Ser U

Ile Thr Asn Ser C

Ile Thr Lys Arg A

Met Thr Lys Arg G

G Val Ala Asp Gly U

Val Ala Asp Gly C

Val Ala Glu Gly A

Val Ala Glu Gly G