Exam 3 Study Guide PDF

EXAM 3 STUDY GUIDE DNA STRUCTURE: -Know what a nucleotide is Building block of nucleic acids like DNA and RNA – has a nitrogenous base, sugar molecule and phosphate group. - Know the difference between a nucleotide and a nucleoside Nucleotide has one or more phosphate groups attached to a nucleosid...

EXAM 3 STUDY GUIDE DNA STRUCTURE: -Know what a nucleotide is Building block of nucleic acids like DNA and RNA – has a nitrogenous base, sugar molecule and phosphate group. - Know the difference between a nucleotide and a nucleoside Nucleotide has one or more phosphate groups attached to a nucleoside. Nucleoside – made up of a nitrogenous base and a five-carbon sugar. Nucleotide – made up of a nucleoside and one or more phosphate groups – gives it a negative charge making them hydrophilic – able to interact with water. -Know the names of the nitrogenous bases (A,G,C,T,U) Adenine, Thymine, Cytosine, Guanine, in RNA thymine is replaced by Uracil. -Know which nitrogenous bases are classified as purines and pyrimidines A and G = purines C, T and U = pyrimidines -Know the structure of the pentose sugar for both the ribose and deoxyribose - Deoxyribose has less oxygen than ribose. -Know the difference between ribose and deoxyribose Ribose has (-OH) on the second carbon atom in its sugar ring, while deoxyribose has a hydrogen atom at that same position. Deoxyribose – missing an oxygen atom compared to ribose. -Know what carbon the nitrogenous base comes off of, the hydrogen atom, the OH group, and the phosphate group Nitrogenous base always attaches to the 1’ carbon of the sugar molecule. Nitrogenous bases – attached to 1’ Carbon. Phosphate group – attached to the 5’ carbon. Hydroxyl Group (OH) – found on the 3’ carbon. -Know that it's the Phosphodiesterase (Covalent Bond) between the phosphate group and the OH group -Know that there are 2 hydrogen bonds between A & T and 3 hydrogen bonds between C & G -Know that the phosphate group is negatively charged, this allows it to interact with the histone proteins -Know the two forms of chromatin (Euchromatin, Heterochromatin) how are they different 2 Forms of Chromatin – Euchromatin and Heterochromatin Heterochromatin – tightly packed Euchromatin – loose, relaxed. - Know what it means that DNA is semi-conservative When DNA replicates, each new double helix is composed of one strand from the original DNA molecule and one newly synthesized strand, essentially conserving half of the original DNA molecule in each new copy. -Know what it means when we say DNA is anti-parallel Lines up 5’ -3’ to 3’ – 5’ DNA REPLICATION -Know what stage DNA replication occurs in Interphase -Know that the origin of replication is the area that is rich in A-T nucleotides. You can have multiple origins of replication going on. -Know that the pre-replication protein complex will come into the origin of replication and begin recruiting additional enzymes and proteins -Know what the single strand binding protein does Keeps DNA strands separate. -Know what nucleases do Breaks down nucleotides. -Know the function of helicase Splits DNA -Know the function of topoisomerase and its two domains DNA - binding/cleavage domain responsible for recognizing and cutting the DNA, and the ATPase domain which is necessary for the energy-dependent strand passage in type II topoisomerases, allowing one DNA duplex to pass through another. -Know how topoisomerase can be used to trat cancer Enzyme is a target of potent anti-cancer drugs such as etoposide, which trap the protein when it is bound to broken DNA and thus turn Topo II into a DNA-damaging toxin. -Know the difference between the leading and lagging strand Leading Strand – synthesized in a continuous manner, whereas. Lagging Strand – requires primase that makes RNA primers that are extended by the DNA polymerase to form Okazaki fragments – short DNA fragments that are processed to produce a continuous DNA strand. -Know the function of primase Synthesizing short RNA sequences called primers, which act as a starting point for DNA synthesis by DNA polymerase; Primes the DNA strand by providing a necessary initial point for new nucleotide addition, as DNA polymerases can only add nucleotides to an existing strand. -Know the function of DNA Polymerase 3 Synthesizing new DNA strands during DNA replication – building the leading and lagging strands of DNA by adding nucleotides to the growing chain at the replication fork. -Know that primase enables the DNA Polymerase 3 to make DNA -Know what Okazaki fragments are and how they are formed Short pieces of DNA formed during the discontinuous synthesis of the lagging strand during DNA replication. They are created because DNA polymerase can only add nucleotides in the 5’ to 3’ direction, causing the lagging strand to be synthesized in short fragments that are later joined together by DNA ligase. -Know the function of DNA Polymerase 1 Functions to remove RNA primers from the DNA strand during replication and fill in the gaps left behind, essentially acting as a “repair” enzyme by replacing RNA primers with DNA nucleotides during the process of DNA replication; it is particularly important in joining Okazaki fragments on the lagging strand. -Know that all of these enzymes will Read in a 3’-→5’ direction. Synthesize in a 5’-→ 3’ direction. Proofread in a 3’-→ 5’ direction. CELL CYCLE Know all the stages of mitosis and what occurs in each phase. Interphase – cell spends most of its time. S phase is where DNA replication is occurring Prophase – chromatin condenses, get rid of nuclear envelope, centrioles appear on the outside of the cell and nucleolus disappears. Prometaphase – nuclear envelope breaks down, kinetochores form – chromosomes attach to the mitotic spindle. Metaphase - Cells are arranged on metaphase place, getting to read to be pulled apart, line up in the middle. Anaphase – chromosomes get pulled apart, move to opposite poles of the cell. Telophase – chromosomes decondense, and new nuclear membranes from around each set. Cytokinesis – cytoplasm divides, forming two genetically identical daughter cells. TRANSCRIPTION Process in which a segment of DNA is copied into RNA by the enzyme RNA polymerase. This is the first step in the expression of genes and leads to production of proteins. Steps: Initiation, Elongation, and Termination. TRANSLATION Process by which mRNA (messenger RNA) produced during transcription is decoded to synthesize a specific protein. It occurs in the ribosome, which acts as the molecular machinery that reads the mRNA sequence and assembles the corresponding amino acids into plypeptide chain. The second major step in Gene Expression. MUTATION & CANCER Know what oncogenes are – mutated genes that can cause cancer by causing cells to grow and divide uncontrollably. Know what tumor-suppressor genes are – Genes that regulate cell growth and division, and can prevent the development of cancer. Know the function of p53 – regulates cell division and DNA repair. Know what CDK & Cyclins do for the cell cycle – regulates progression of the cell cycle by phosphorylating specific target proteins at different phases, essentially acting as “switches” that allow the cell to move from one stage to the next. Cyclins activate CDK’s by binding them, making them functional enzymes that can then trigger the necessary events for cell cycle progression. How do oncogenes lead to cancer development – when a proto-oncogene is mutated, changing it into an oncogene and causing the cell to divide and multiply uncontrollably. Know the general definition of what cancer is – disease that occurs when cells in the body grow and spread uncontrollably. Know basically how cancer develops and spreads – spreads by breaking away from the original tumor and travelling to other parts of the body MEIOSIS Know the phases of meiosis (We will go over these in the coming days) Meiosis I reduces a diploid cell to a haploid cell by separating homologous chromosomes. Meiosis II produces 4 haploid cells from the two haploid cells produce in meiosis I. Prophase I Metaphase I Anaphase I Telophase I Metaphase II Anaphase II