DNA

2.6.1 The nucleic acids DNA and RNA are polymers of nucleotides Nucleic acids  first discovered in material extracted from the nucleus  2 types  DNA  RNA

Nucleotides  Monomers of nucleic acids  Composed of 3 parts  5-Carbon sugars (pentose sugar)  Phosphate group (acidic, negatively charged)  Nitrogen containing base (1 or 2 rings)  The nitrogen base and the phosphate group are linked to the pentose sugar by covalent bonds

 Formation of nucleic acid  Covalent bonds are formed between the phosphate of one nucleotide and the sugar of the next (creating a strong backbone of sugar and phosphate group)  There are 4 bases, so there are 4 different types of nucleotides that can be linked in any sequence  **Any sequence is possible in DNA and RNA. This is the key to DNA acting as a store for genetic information.

2.6.2 DNA differs from RNA in the number of strands present, the base composition, and the type of pentose There are 3 major differences between DNA and RNA 1. Pentose sugars DNA-deoxyribose sugar RNA-ribose sugar 2. Number of polymers of nucleotides (strands) DNA- 2 strands RNA- 1 strand 3. Nitrogen bases DNA- A, T, G, C RNA- A, U, G, C

S2.6.1 Drawing simple diagrams of the structure of the single nucleotides of DNA and RNA, using circles, pentagons, and rectangles to represent phosphates, pentoses, and bases. Covered in class; diagram should look like this.

2.6.3 DNA is a double helix made of 2 antiparallel strands of nucleotides linked by hydrogen bonding between complimentary base pairs  Each strand is a chain of nucleotides linked by covalent bonds  The 2 strands are parallel, but run in opposite directions: antiparallel (one runs 5’ to 3’, the other runs 3’ to 5’)  The two strands are wound together to form a double helix  The strands are held together by hydrogen bonds between their bases  Complimentary base pairing: A-T (linked with 2 hydrogen bonds) G-C (linked with 3 hydrogen bonds)

A2.6.1 Crick and Watson’s discovery of the structure of DNA using model making.  Watson and Crick used evidence to develop possible structures for DNA and then tested their theories by building models.  1 st model- triple helix, bases on the outside, magnesium holding the strands together. This was falsified for 2 reasons.  Ratio of adenine to thymine was not 1:1 (as discovered by Chargaff)  It required too much magnesium as identified by Franklin

2 nd model-  Base Pairs  Watson and Crick had to take into account Chargaff’s findings that the amount of adenine bases equal the amount of thymine bases, and the amount of guanine equals the amount of cytosine.  They cut cardboard models of the nitrogen bases and showed that base pairs could be formed, with hydrogen bonds linking them.  Antiparallel strands  Based on setbacks from first model and Xray diffraction patterns, they knew DNA must be a double helix  They realized that the 2 strands had to run in opposite directions in order to fit together (antiparallel)  They built a model to scale and quickly convinced all who saw it.  The model also suggested a mechanism for copying DNA and led to the realization that the genetic code must consist of triplets of bases.

2.7 and 7.1 (HL) DNA Replication

2.7.1 The replication of DNA is semi-conservative and depends on complimentary base pairing.  As a cell prepares to divide, the 2 strands of a DNA double helix separate, each serving as a template for a new strand.  New strands are formed by adding nucleotides, one by one, resulting in 2 DNA molecules each composed of an original strand and a newly synthesized strand  semi-conservative replication

2.7.2 Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds. Helicase unwinds and separates the DNA strands by breaking hydrogen bonds. Helicase consists of 6 globular polypeptides arranged in a donut shape. One strand goes through the center and the other strand is on the outside. Energy from ATP is used to move helicase along the strand, breaking hydrogen bonds.

2.7.3 DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as a template. DNA polymerase moves along template strand, adding complimentary base pairs to form a new DNA strand. -Adds one nucleotide at a time -only adds nucleotides to the 3’ end of the previous nucleotide -hydrogen bonds form between the complimentary bases -covalent bonds form between the phosphate group of the free nucleotide and the C3 on the sugar at the existing end of the new strand.

7.1.1 nucleosomes help to supercoil the DNA.  Nucleosomes are formed by wrapping DNA around 8 different histone proteins.  Each nucleosome is composed of eight histone proteins bundled tightly together at the center (in purple) and encircled by two loops of DNA (in orange)  Nucleosomes are coiled together and then stacked on top of each other, forming chromatin.  Nucleosomes protect DNA and allow it to be packaged in the nucleus.  na-packaging na-packaging

 Nucleosomes help to supercoil the DNA  Supercoiling- when a DNA strand has been wound back on itself multiple times so that the molecule becomes compacted  DNA needs to be supercoiled because  Cells need to package 6 ft (2 m) of DNA (nucleus is about 10 µm wide. It is essential to pack genetic material into the nucleus.  To organize DNA  To control DNA expression (supercoiled DNA can’t be transcribed)  To protect DNA

S7.1.1 Utilization of molecular visualization software to analyze the association between protein and DNA within the nucleosome.  Use the link provided to use the Jmol visualization and answer the following questions.  1. Identify the 2 copies of each histone protein. This can be done by locating the tail of each protein.  2. Suggest how the positive charges help to form the nucleosome (with the negatively charged DNA molecule)  eId=1AOI&bionumber=1

7.1.2 DNA structure suggested a mechanism for DNA replication  Complimentary base pairing imply a method for replication. Evidence that supports complimentary base pairing:  X-ray diffraction- helix is tightly packed and regular, so purines (A & G) must pair with pyrimidines (C & T)  Electrical charges of adenine and thymine are compatible and opposite, allowing 2 hydrogen bonds to form between them  Pairing of cytosine and guanine allows for 3 hydrogen bonds to form between them.

7.1.3 DNA polymerase can only add nucleotides to the 3’ end of a primer.

7.1.4 DNA replication is continuous on the leading strand and discontinuous on the lagging strand.  Refer to in-class notes and previous slide for further explanation.

7.1.5 DNA replication is carried out by a complex system of enzymes  Know the function of:  Helicase  DNA gyrase  Single stranded binding proteins  DNA primase (primase)  DNA polymerase III  DNA polymerase I

7.1.6 Some regions of DNA do not code for proteins but have other important functions.  DNA is the blue print for the production of polypeptides. However, only some of the DNA sequences code for the production of polypeptides. These are called coding sequences (genes)  The non-coding DNA is still important to organisms for many reasons Some serve as a guide in producing tRNA and rRNA Some regulate gene expression, such as enhancers or silencers Introns are segments of DNA within a gene, but not included in the final polypeptide product

 Repetitive sequences are common within the genome (nearly 60% of human DNA consists of repetitive sequences)  Ex. telomeres, found on the ends of chromosomes. During replication, DNA polymerase can’t continue all the way to the end of the chromosome. The telomeres provide a buffer region so that no essential DNA is left off during replication. This non-coding, repetitive region gets shorter with each DNA replication, but sacrificing the repetitive sequence serves a protective function.

A7.1.2 Use of nucleotides containing dideoxyribonucleic acid to stop DNA replication in preparation of samples for base sequencing.  Watch the following video for a brief overview.  method-of-DNA-sequencing-3D-animation-with- narration.html