DNA Study Guide - Nucleic Acids PDF

# HL - 06 - Study Guide for Unit 6 (Nucleic Acids) ## Ver 2.0 ### 1. DNA (deoxyribonucleic acid) - contains all the genetic information for an organism to develop, function and reproduce. - is a nucleic acid, a polymer (polynucleotide) made of repeating nucleotide units. - Each nucleotide contains:...

# HL - 06 - Study Guide for Unit 6 (Nucleic Acids) ## Ver 2.0 ### 1. DNA (deoxyribonucleic acid) - contains all the genetic information for an organism to develop, function and reproduce. - is a nucleic acid, a polymer (polynucleotide) made of repeating nucleotide units. - Each nucleotide contains: - A pentose sugar - Phosphate - One nitrogenous base - The bases in DNA are adenine (A), guanine (G), cytosine (C) or thymine (T). - The bases in RNA are adenine (A), guanine (G), cytosine (C) or uracil (U). - C, U, and T are single ring bases belonging to the pyrimidines while A and G are double ring bases belonging to the purines. - The pentose sugar in DNA is deoxyribose, and in RNA it is ribose. - DNA has the shape of a double helix. - The sugars and phosphates alternate on the sides of the molecule with the bases in the middle occurring in complementary pairs or base pairs. - A always with T - G always with C. - The bases are held together by hydrogen bonds. - Bases attach to the sugars of the sugar-phosphate backbone. - The two strands of the DNA molecule are antiparallel and this directionality is designated as running 5'-->3' on both sides. - The "3" and "5" numbers refer to the carbon number in the deoxyribose sugars. - RNA also has a sugar-phosphate backbone with 5' and 3' ends. ### 2. Molecular Structures - You are required to know the molecular structures for deoxyribose, ribose as well as a nucleotide, DNA and RNA. - You may be asked to draw one or more of these five molecules. You don't have to label the carbon numbers. - Be prepared to compare (sameness and similarities) and contrast (differences) DNA and RNA molecules. ### 3 Parts of a Nucleotide - A nucleotide contains three parts: a phosphate group, a pentose sugar, and a nitrogenous base. - The structure of a nucleotide is shown in the image. ### 3. Watson and Crick - Watson and Crick were the first to publish the correct structure of DNA. - They used essential data determined by Rosalind Franklin. - There were several important experiments and discoveries about DNA that helped make possible the work of Franklin, Crick, Watson and other scientists in pursuit of DNA's structure and function. - Two of the key experiments were: - **Chargaff's Rule:** - Erwin Chargaff discovered that in DNA the amount of guanine is equal to the amount of cytosine. - Likewise, the amount of adenine is equal to the amount of thymine. - This means there is a 1:1 ratio of purine and pyrimidine bases. - The rule applies to dsDNA but not to ssDNA or molecules of RNA. - **Hershey-Chase Experiment**: - The Hershey-Chase experiment proved that DNA was the genetic material of life. - They used E. coli bacteria and bacteriophage viruses (or just "phages") that only infect bacteria. - Viruses have a protein shell called a capsid and inside the capsid is their genetic material. - The T2 phages they used carry DNA. - The viruses inject their DNA into the bacteria to infect them but their protein capsids stay on the outside. - Inside the bacteria, the viral DNA is expressed and the host cell makes new viral capsid proteins and replicates the viral DNA. - The cell bursts open to spill out 100s to 1000s of new viruses. - Hershey and Chase also used radioisotopes of sulfur (35S) and phosphorus (32P). - Sulfur is found in some amino acids and therefore is in proteins but there is no sulfur in DNA. - Phosphorus is in the phosphate groups of DNA but there is no phosphorus in proteins. - 35S can be used to track protein and 32P can be used to track DNA. - When isotopes of elements are used to track molecules, those molecules are said to be "radiolabeled". - It was known at the time that viruses inject their genetic material into their host cell and that the protein shell stays on the outside. - They ran two experiments: - **Experiment 1: Testing Proteins** - Found that proteins were not the genetic material. - **Experiment 2: Testing DNA** - Found that DNA was the genetic material. ### 4. DNA Replication - The IB wants you to know how this process works in prokaryotes (bacteria) but it's very similar to how eukaryotes replicate their DNA. - Prokaryotic DNA replication starts at a single origin (starting place) and there opens a replication bubble. - Enzymes read the parent strand and construct the daughter strand. - Replication continues bidirectionally until the entire loop is replicated and they separate into two new daughter molecules of DNA. - This process is semi-conservative meaning each new DNA molecule is 50/50 new and original DNA. - You need to know the steps of the DNA replication process. - **Overview** - The process involves the enzymes helicase, primase, DNA polymerase III, DNA polymerase I and DNA ligase. - **Helicase** - Breaks the hydrogen bonds holding the bases together. - **Single-stranded binding proteins** - Keep the strands from reforming the hydrogen bonds long enough for DNA polymerase III to begin copying. - **Primase** - Puts RNA primers on the parental DNA. - **DNA polymerase III** - The main enzyme to copy the DNA code. It must have a free 3' end of an RNA primer to attach to the DNA and begin copying the code. It copies DNA in the 5' to 3' direction. - **Leading strand** - DNA polymerase III copying in the 5' to 3' direction is the same direction as the overall direction of replication in the fork. - **Lagging strand** - DNA polymerase III is copying in the opposite direction as the overall direction of replication. - **DNA polymerase I** - Replaces RNA primers with DNA. - **DNA ligase** - Completes the final covalent bond in the sugar-phosphate backbone. - The fragments of daughter DNA are called Okazaki fragments. - The artwork illustrates the individual roles of the enzymes but these enzymes in actuality are joined together in a cluster called a replisome. ### 5. Proofreading - DNA polymerase III also has a proofreading role in DNA replication. - It can detect an error, remove the incorrect nucleotide and replace it with the correct one. ### 6. Genes - Genes are coding segments of DNA on chromosomes. - Genes code for proteins but there are some sections of DNA that code for a variety of RNA molecules. - The genome is called the transcriptome. - Examples include: - messenger RNA (mRNA) - transfer RNA (tRNA) - ribosomal RNA (rRNA) - These sections code for RNA molecules but are not considered to be "coding DNA". - Only about 1.5% of the entire genome are coding genes and 98.5% is "noncoding DNA". - The ends of linear eukaryotic chromosomes, called telomeres, are also noncoding DNA. - The telomeres can not be fully replicated during DNA replication so with each cycle of replication, the chromosomes shorten a very small amount. ### 7. DNA Packing - DNA exists in the nucleus of eukaryotes as highly-organized chromosomes in different levels of organization sometimes called "packing". - At all levels of packing, DNA is associated with proteins, and this DNA proteins is called chromatin. - The first level of packing is DNA looped twice around nucleosomes. - Each nucleosome is made of eight histone proteins. - Each histone is globular-shaped with a small "tail" sticking out. - Another protein, the H1 protein, helps hold the DNA to the nucleosome. - There is a small gap before DNA loops around the next nucleosome.. - DNA looped around a series of nucleosomes resembles a beaded necklace or beads on a string. ### 8. Protein Synthesis - When the expressed gene is for a protein, that process is called protein synthesis. - Protein synthesis occurs in two stages: - Transcription - Translation. - **Transcription** is the process of first transcribing a copy of the gene into a molecule of messenger RNA (mRNA). - Transcription takes place in the nucleus, then the mRNA molecule leaves the nucleus to the cytoplasm. - **Translation** is the process of translating the mRNA (with the help of transfer RNA (tRNA)) into a protein at a ribosome in the cytoplasm. - A reminder that small proteins (less than 50 amino acids) are called peptides and large proteins are called polypeptides. ### 9. - **Transcription Starting Point** - A gene on a chromosome begins with a start codon and ends with a stop codon. - **Promoter Region** - Between the codons are alternating segments of coding DNA called exons and noncoding DNA called introns. Upstream from the start codon is the promoter region that has an important role in the initiation of transcription. - **Transcription Factors** - Before transcription can begin a set of proteins called transcription factors bind to the promoter region upstream from the gene. In eukaryotes, the promoter region usually begins with the DNA bases TATA and is thus sometimes called the "TATA box". - **RNA Polymerase II** - The transcription factors must be in place in order for RNA polymerase II enzyme to begin transcribing. Once in place, the RNA polymerase II is able to break the hydrogen bonds between the DNA bases and begins transcribing the template strand of DNA and assembling a molecule of messenger RNA (mRNA) in the 5' to 3' direction. The actual starting place of transcription is slightly upstream from the start codon. The transcription factors fall away, no longer needed. - **Pre-mRNA or Immature mRNA** - RNA polymerase II continues transcribing, adding new RNA nucleotides to the free 3' end of the growing mRNA molecule until it goes past the stop codon then falls away and the mRNA molecule is released. Please recall that thymine is not used in RNA so the base uracil is found in the mRNA. At this stage the mRNA is sometimes called "pre-mRNA" or "immature mRNA" because it has not been processed yet. ### 10. mRNA Processing - **5' Cap** - The immature mRNA will next undergo its first post-transcriptional modification. To the 5' end is added a molecule of guanosine triphosphate (GTP), called the 5' cap.. - **Poly-A Tail** - To the 3' end a segment of DNA with about 50 to 250 adenine bases is added, called the "poly-A tail". - **Spliceosomes** - Both the 5' cap and poly-A tail stabilize the ends of the mRNA molecule, protect it from digestion by cellular enzymes, help route it to other parts of the cell and encourage further modification. The introns are removed by structures called spliceosomes in a process called RNA processing. ### 11. Translation - **tRNA** - Translation requires molecules of transfer RNA (tRNA) and ribosomes. tRNA molecules are folded RNA that carry amino acids to the ribosomes during translation. On a tRNA are three base pairs, the anticodon, that match a specific mRNA codon. Opposite of the anticodon is the amino acid binding site. Each tRNA can carry only one amino acid at a time, and because its anticodon can only match one codon, this ensures the correct amino acid is delivered to the ribosome. - **Ribosomes** - Ribosomes are tiny structures made of protein and folded RNA (rRNA). The ribosome has a small subunit and a large subunit. Inside the ribosome are three tRNA binding sites: The E, P and A sites. During translation, the ribosome slides along the mRNA molecule. Multiple ribosomes can be translating the same mRNA at the same time. The ribosomes of prokaryotes and eukaryotes differ slightly in the sizes of their large small subunits. - **Prokaryotes** - Small subunit: 30S, Large subunit: 50S, Both subunits: 70S. - **Eukaryotes** - Small subunit: 40S, Large subunit: 60S, Both subunits: 80S. ### 12. Translation Events - Translation happens at ribosomes in the cytoplasm. - Proteins are made at ribosomes on the nuclear membrane or the rough endoplasmic reticulum, those proteins are typically made for secretion. - Proteins made at free ribosomes in the cytosol are typically kept within the cell. ### 13. Genetic Code - The genetic code is read in triplets where every three bases on mRNA is a codon. - You must know how to use an mRNA codon chart (either rectangle version or wheel version). - For example, the codon AUG codes for the amino acid methionine. - There are 20 amino acids but 64 codons. - Three codons are stop codons, so among the 61 codons for amino acids there is degeneracy (redundancy). - For example, there are six codons for leucine. - Only two amino acids have a single codon. ### 14. Initiation - To initiate (begin) translation, the small ribosomal subunit binds to the mRNA upstream from the start codon near the 5' cap until the AUG start codon is found. - Next, the first tRNA with the anticodon UAC and carrying methionine binds to the start codon then the large subunit of the ribosome binds to the small subunit, putting the first tRNA in the P site. ### 15. Elongation - The next tRNA with the anticodon matching the second codon after the start codon, binds to the mRNA in the A site of the ribosome. - The first amino acid (methionine) is linked with the second, forming a peptide bond between them, then the ribosome slides to put the third codon in the A site. - The second tRNA is now in the P site and the first tRNA exits the ribosome from the E site. - One by one, tRNA molecules with the matching anticodons bind to mRNA codons and the polypeptide is constructed by joining amino acids by peptide bonds until the stop codon is reached. ### 16. Termination - When a stop codon is reached, a release factor will bind to the A site, and the polypeptide will be released from the ribosome. ### 17. Condensation - To remind you from Unit 01, the formation of peptide bonds is an example of a condensation reaction. ### 18. Gene Regulation - Again, when a gene is expressed to make a protein, the processes of transcription and translation together is called protein synthesis. - There are many ways to modify this process. - In general, the term gene regulation refers to any measure used by the cell to promote or suppress gene expression or alter the final protein product. - Gene regulation may happen before, during or after transcription and translation. - The IB wants you to know a few examples: - **Pre-transcriptional gene regulation:** - For some genes, there are segments of DNA called enhancers that work with proteins called activators that interact with the promoter region and transcription factors to promote transcription. - Acetyl groups and methyl groups can be added to the proteins of histones in the DNA packing to affect gene expression. Acetylated genes have loosened DNA packing to promote gene expression and methylated genes are the opposite: They are more tightly packed to prevent gene expression. DNA itself can also be methylated, having the same effect to suppress gene expression. - **Post-transcriptional gene regulation:** - The addition of the 5' cap and poly-A tail (mentioned earlier in this document) is considered to be a form of gene regulation. - Eukaryotic genes have introns and these must be removed from the pre-mRNA in a process called RNA processing. While still in the nucleus, specialized molecules recognize the introns, remove them, then join the exons together to form mature mRNA ready for translation in the cytoplasm at a ribosome. - In some cases, eukaryotic cells can rearrange, duplicate or leave out exons (exon skipping) from the mature mRNA so that different versions of proteins from the same gene can be made. This is called alternative RNA processing and it explains why from a human genome of about 20,000 genes we have over 100,000 proteins in our proteome. For example, one tropomyosin gene can be alternatively spliced using exon skipping to form different proteins found in muscle, brain and connective tissues. - **Translational gene regulation:** - During translation, at some point the cell will no longer want to synthesize the protein and a common way for the cell to stop translation is by mRNA degradation. The poly-A tail will be shortened by enzymes that remove some of the adenine bases. The 5' cap can also be removed. Both these disrupt the stability of the mRNA molecule, inhibiting the binding of ribosomes to the molecule and thus stopping protein synthesis. - **Post-translational gene regulation:** - Proteins after translation can be modified in many ways. One example is the production of insulin in the body. The initial protein translated is called preproinsulin, but to become insulin, it must have a signaling sequence removed, then undergo a re-folding to have the A and B chains form disulfide bridges. At this point it is called proinsulin. Then the C-chain is removed and then the hormone is finished. - Amino acids are recycled from proteins that are damaged or no longer needed. These proteins are tagged with ubiquitin molecules that cause the unwanted proteins to be degraded by proteasomes. The proteasome is a large protein complex that breaks down the protein back into amino acids and smaller peptides. ### 19. Gene Expression - Gene expression in some cases can be affected by external factors, coming from outside the cell. - For example, a hormone like testosterone or estrogen is released into the bloodstream and it circulates throughout the body. - On the target cells and tissues, the hormone enters, binds to its receptor and the complex initiates gene expression by serving as a transcription factor. - The gene cannot be expressed in the absence of the hormone + receptor. This study guide was written and compiled by Mr. Roth for his current biology classes only. It was created for your use as a resource to do well on assignments and exams. This study guide is not to be downloaded, printed, screenshotted or otherwise reproduced and given to anyone without permission. This includes, but is not limited to, other ISM students, ISM staff, parents, siblings, or tutors.