NUCLEIC ACID & PROTEINS

1. NUCLEIC ACID & PROTEINS IB HL #1

2. DNA STRUCTURE & REPLICATION • At one end of each strand of DNA is a phosphate linked to • carbon atom “# 5” of deoxyribose. This is the 5’ terminal. • It has a phosphate attached & nothing more. • Adjacent nucleotides are linked by a bond between the • phosphate group of one nucleotide and the carbon atom • “# 3” of the other nucleotide. • At one end of each strand is a hydroxyl group attached to • carbon atom “3” of deoxyribose. This is the 3’ terminal.

3. Hydrogen bonds link the bases. Two bonds form between • adenine and thymine and three bonds between guanine • and cytosine. • Two of the bases in DNA are purines: adenine and guanine. • They have two rings in their molecules. • Two of the bases in DNA are pyrimidines: Cytosine and • thymine. They have one ring in their molecule. • Only a purine plus a pyrimidine will fit in the space • between the sugar-phosphate backbones.

4. The two strands of DNA have their 3’ and 5’ terminals • at opposite ends …. they are anti parallel.

5. DNA IN EUKARYOTES AND PROKARYOTES All eukaryotes and prokaryotes use DNA as their genetic material and use the same genetic code, but there are differences in the way that DNA is used. 1. • In eukaryotes the DNA is associated with proteins to • form nucleosomes. • A nucleosome consists of DNA wrapped around eight • histone protein molecules & held together by another • histone protein. Nucleosomes have two functions: • They help to super coil the chromosomes B. They help regulate transcription

6. In prokaryotes the DNA is naked. • The DNA consists of single copy genes that are transcribed & • translated without modification.

7. DEOXYNUCLEOSIDES • The cell produces many free deoxynucleoside triphosphates for DNA replication. A nucleotide consist of a sugar, a phosphate & a base A nucleoside is just a deoxyribose + a base. So a deoxynucleoside triphosphateis a deoxynucleoside with three phosphates.

8. The abbreviation for deoxynucleoside triphosphate is dNTP. The abbreviation for a nucleoside triphosphate ( ribose instead of dexoyribose is NTP. dNTPs are used to synthesize DNA NTPs are used to synthesize RNA When these molecules are added to the DNA or RNA chain the two end phosphates are chopped off.

9. Nuclear DNA can be divided into two types: 1. Unique or single – copy DNA 55 to 95% of the DNA in eukaryotes consists of a sequences called genes that only have a single copy. These form the proteins (polypeptides) used by the cell. 2. Repetitive sequences (satellite DNA) 5 to 45% of DNA in eukaryotes consists of repetitive bases sequences 5 to 300 bases long, which are not translated. These sequences can be repeated up to 10,000 times. their function is not clear.

10. Prokaryotes do not usually have repetitive sequences.

11. There are two requirements for building a DNA chain! 1. The chain must be built in a 5’ to 3’ direction 2. The chain must grow toward the replication fork

12. ENZYMES USED IN DNA REPLICATION FUNCTION • Adds deoxynucleoside triphosphates to the 3’ end. • Joins the Okazaki fragments together

13. The leading strand is the new strand that is made (synthesized) in the same direction as the unzipping The lagging strand is the new strand that is made (synthesized) in the opposite direction to the unzipping. It is made by joining Okazaki fragments.

14. DNA REPLICATION • The cell produces many free nucleoside triphosphates • for DNA replication. Two of the phosphates are removed • during replication. 2. Helicase unwinds the DNA at the replication fork by breaking the hydrogen bonds between the bases. ATP is required

15. 3. DNA polymerase III adds deoxynucleosides in 5’ to 3’ direction. On the 3’ to 5’ strand it moves in the same direction as the replication fork, close to helicase. On the other strand it moves in the opposite direction.

16. 4. RNA primase adds a short length of RNA attached by a base pairing to the template strands (the original strands of DNA.) This forms an RNA primer, allowing DNA polymerase to bind and begin replication

17. 5. On the chain that runs 5’ to 3’, DNA polymerase III starts replication next to the RNA primer and adds deoxynucleosides triphosphates in a 5’ to 3’ direction. The DNA polymerase therefore moves away from the replication fork on the strand, but the chain grows toward the fork

18. 6. Short lengths of DNA are formed between RNA primers on the lagging strand, called Okazaki fragments (small bits or fragments of DNA)

19. 7. DNA polymerase I removes the RNA primer and replaces it with DNA . A nick is left where two nucleotides are still unconnected.

20. 8. DNA ligase seals up the nick by making another sugar-phosphate bond.

21. At the end of replication the parent DNA molecule produces two daughter DNA molecules Each daughter DNA has oneoldstrand that belongs to the parent DNA and one new strand This method of DNA replication is called semiconservative replication

22. Replication of DNA begins at special initiation points. …… eukaryotes have many of these initiation points along each chromosome. …… prokaryoteshave one

23. The strands in the double helix are antiparallel. • The sugar-phosphate backbones run in opposite directions. • Each DNA strand has a 3’ end with a free hydroxyl group attached to deoxyribose and a 5’ end with a free phosphate group attached to deoxyribose. • The 5’ -> 3’ direction of one strand runs counter to the 3’ -> 5’ direction of the other strand.

24. The other parental strand (5’->3’ into the fork), the lagging strand, is copied away from the fork in short segments (Okazaki fragments). • Okazaki fragments, each about 100-200 nucleotides, are joined by DNA ligase to form the sugar-phosphate backbone of a single DNA strand.

25. To summarize, at the replication fork, the leading stand is copied continuously into the fork from a single primer. • The lagging strand is copied away from the fork in short segments, each requiring a new primer.

26. Many genes in eukaryotes contain non-coding sequences that are transcribed but not translated called introns. Introns are found in newly transcribed mRNA, but are removed. Mature mRNA does not contain introns. The sequences not removed are called exons. Prokaryotes do not usually have introns in their genes.

27. STOP