1. Warm-up 4/9/12 Proteins What are proteins composed of? (building blocks) Name one function of proteins

2. DNA Unit Answers

3. Sec. 12.1 DNA Basics

4. 1. Draw a nucleotide. What are the four different bases they can contain? P-S-AP = Phosphate P-S-TS = Deoxyribose Sugar P-S-GA, T, G, C = Nitrogenous Base P-S-C

5. 2. Draw a DNA molecule with one strand having the sequence GATTACA. Label the phosphate, deoxyribose sugar, bases, hydrogen bonds, 5’ ends, and 3’ ends. 5’3’ P- S – G --------- C – S- P P – S- A --------- T- S -P P- S- T --------- A- S - P P – S- T --------- A- S - P P - S – A --------- T- S - P P – S- C --------- G -S - P P- S -A --------- T – S- P Hydrogen Bond 3’5’

6. 3. Why are DNA strands called anti- parallel? DNA strands are called ‘anti-parallel’ because one strand is built in the 5’ to 3’ direction, and the other is in the 3’ and 5’ direction. They are mirror images of each other, flipped upside down.

7. 4. Describe the scientific contributions that each scientist(s) made to the discovery of DNA: Chargaff: Chargaff’s rule states that in any DNA strand, the percentage of A’s and T’s will be equal, and the percentage of G’s and C’s will be equal. Franklin: took the first photo of double helix using x-ray crystallography Watson and Crick: discovered the double helix shape

8. Sec. 12.2 DNA Replication

9. 1. What is the purpose of a chromosome? The purpose of our 46 chromosomes is to package a meter of DNA into a microscopic nucleus.

10. 2. How many chromosomes are in each human cell? 46

11. 3. When is DNA replicated (doubled)? In S Phase of the Cell Cycle. We double our DNA when we need to make new cells, because every cell needs the same 46 chromosomes.

12. 4. Draw and explain the process of DNA replication, including all three enzymes involved, the 5’ and 3’ ends of each strand involved, and origins of replication. a. an enzyme, helicase, unwinds the DNA strands by breaking the hydrogen bonds. RNA polymerase lays down a RNA primer as the point of origin. b. DNA polymerase builds a new strand for original strand one. Creating a continuous strand called the leading strand c. DNA polymerase builds a new strand for original strand two. Creating a disconituous strand in the opposite direction called the lagging strand. d. an enzyme, ligase, joins together the fragments to create a complete strand. Lagging Strand Leading Strand

13. 5. Why is one strand built without interruption while the other is built in small segments? To ensure that the strands are built correctly and in the correct direction. Lagging strand is built the opposite way and proofreads along the way

14. 6. What is the finished product of DNA replication? Two identical strands of DNA- each one with an original strand and copy built by DNA Polymerase.

15. Sec. 12.3 Transcription and Translation

16. 1. Complete DNA mRNA Proteins (made of amino acids)

17. 2. Why is an mRNA copy of DNA necessary? The directions for making proteins are contained in DNA, and the machinery is the ribosome. DNA can’t leave the nucleus to get to the ribosome, so the mRNA acts as a messenger of information to the ribosome.

18. 3. What are the three major differences between RNA and DNA? 1. RNA is single stranded; DNA is double stranded 2. RNA has ribose sugar; DNA has deoxyribose sugar 3. RNA contains the base uracil (U) in place of thymine (T), found only in DNA

19. 4. Draw and explain the process of transcription, including the two steps. Step One: RNA Polymerase (an enzyme) breaks the DNA strands apart by breaking the hydrogen bonds Step Two: RNA Polymerase builds a single, complimentary mRNA strand using one of the DNA strands Step Three: The mRNA leaves the nucleus and the DNA winds back up

20. 5. If a DNA strand has the sequence ACATTACGG, what would the mRNA copy be? UGUAAUGCC

21. 6. Where does transcription occur? nucleus

22. 7. Draw and explain the three major steps of translation, including mRNA, ribosome, rRNA, codon, tRNA, anti- codon, amino acid, and protein. 1. mRNA leaves the nucleus and binds to a ribosome 2. rRNA on the ribosome grabs the mRNA and begins reading it three letters at a time (one codon at a time) 3. tRNA with the exact anti-codon lands on a segment of mRNA and drops off the amino acid it is carrying. That segment of mRNA is pulled through, and another tRNA lands on an mRNA codon and drops off its amino acid. The amino acids link together to form a protein.

23. 8. If a DNA strand has the sequence TACCCCAAAACT, what would the mRNA codons and tRNA anti-codons be? What amino acids are made from this sequence? mRNA codons: AUG GGG UUU UGA tRNA anti-codons: UAC CCC AAA ACU amino acids (based on mRNA): Methionine (start), Glycine, Phenylalanine, Stop

24. 9. Where does translation occur? At a ribosome in the cytoplasm

25. 12.4 Mutations

26. 1. What are three causes of DNA mutations? 1. DNA is copied incorrectly by DNA polymerase in DNA replication 2. DNA is copied incorrectly by RNA polymerase in transcription 3. Outside radiation (i.e. UV rays) damage DNA strands

27. 2. Define substitution, and give an example of a disease caused by it. Substitution is when a letter is put in place of the letter that is supposed to be there. Ex.: if DNA is supposed to be AATG, it is accidentally made as ATTG. Disease Example: Sickle Cell Anemia

28. 3. Define insertion and deletion and be able to recognize them. Why are they considered ‘frameshift mutations?’ Why are they more disruptive to proteins than a substitution? Insertion is when an extra letter is put into a DNA strand, and deletion is when a letter is removed. Each three letters of DNA makes an mRNA codon, which codes for a particular amino acid (see section 12.3). By adding or deleting a letter, the DNA code is off by one letter, making each mRNA codon and amino acid incorrect. The reading frame of DNA is shifted one letter, called a ‘frameshift mutation’. This is very serious because it creates entire proteins that are wrong, not just one amino acid that is wrong within a protein.

29. 4. What is the difference between a gene mutation and a chromosomal mutation? A gene mutation is a change in the DNA sequence (letters) in a small segment of DNA. A chromosomal mutation is a change in an entire chromosome, which contains millions of letters. Chromosomal mutations usually result in death.

30. 5. How can DNA mutations benefit populations? DNA mutations can create physical characteristics that are beneficial to individuals. For example, Sickle Cell Anemia actually protects African populations from malaria, as the protist Plasmodium cannot infect a sickle shaped cell.

31. Special Topic: Gel Electrophoresis

32. 1. What two properties determine which way molecules travel in gel electrophoresis? Electrical charge and size

33. 2. In the gel below, which molecule fragment is the largest? Smallest? Which molecules are positively charged? Negatively charged? Molecules that are negatively charged go towards the positive end; those that are positively charged go to the negative end. The smallest molecules travel the farthest. Molecule E is the largest Molecule D is the smallest Molecule A, C are negatively charged Molecule B, D, E are positively charged