Biology Past Paper (September 2024) PDF

SEPTEMBER 4,6,10 Subject on breast cancer September 4, 2024 Chapter 2 - The Chemical Basis of Life I: Atoms, Molecules, and Water Subatomic particles(Protons, Electrons and Neutrons) # of electrons and protons are equal with exception of ions ON EXAM!!!(Multiple Choice) - Which of t...

SEPTEMBER 4,6,10 Subject on breast cancer September 4, 2024 Chapter 2 - The Chemical Basis of Life I: Atoms, Molecules, and Water Subatomic particles(Protons, Electrons and Neutrons) # of electrons and protons are equal with exception of ions ON EXAM!!!(Multiple Choice) - Which of the following is a subatomic particle? Figure 2.1 Isotopes Have same # of protons in nuclei and position in periodic table but differ due to different # of neutrons changing atomic mass Ex. Hydrogen, tritium, deuterium Radioisotopes - Used in radiotherapy Where are particles located(don’t worry too much but worry about electrons) There are orbitals(forget about quantum #’s) An electron orbital can be considered as 3-D region where there is a 95% probability Orbitals Different cells and orbitals have different energy levels An electron orbital is depicted as 3D region Valence electrons An electron pair consists of 2 electrons that occupy the same orbital it can be considered stable Atom is very happy if electrons are paired Chapter 2 - The Chemical Basis of Life I: Atoms, Molecules, and Water SEPTEMBER 4,6,10 2.1 Atoms Matter is anything that has mass and occupies space (composed of atoms) Molecules are 2 or atoms bonded together Atoms are composed of subatomic particles - Each atom is called an element (a pure substance made of 1 kind of atom) - # subatomic particles: protons, neutrons, electrons - Protons and neutrons are found in atomic nucleus Electrons occupy orbitals around and atom’s nucleus - An orbital is a region of space surrounding the nucleus - Orbitals are found within electron shells/energy levels - Octet rule (2,8,8) Each atom has diff. # of protons (atomic #) Atomic mass indicates an atom’s mass relative to the mass of other atoms Isotopes - Differ in # of neutrons - Unstable isotopes are called radioisotopes (emit radiation as they decay) Mass of organism is mostly O, C, H, N - Other important elements are called mineral elements (1%) - Also contain trace elements like iron (.01%) Bonds + Molecules - Compound refers to molecule composed of two or more elements (H2O) - Covalent bond is when two atoms share electrons REMEMBER - Sometimes double bonds occur Nonpolar or Polar Covalent bonds: Sharing of e- - Electronegativity of an atom is ability to attract electrons - Nonpolar is 6 O2+ 12 NADPH + 18 ATP Calvin Cycle (In Stroma)  Uses CO2, ATP and NADPH to make carbs (glucose) RuBisCo enzyme RuBP ribose phosphate ( five atoms of carbon and a phosphate group on each end) It takes six turns of the calvin cycle to make one carb molecule(one for each CO2 molecule fixed) The remaining G3P molecules regenerate RuBP 2 G2P creates one glucose which comes form 6 turns of the calvin cycle CO2 + NADPH + ATP → CH2O + NADP+ + ADP + Pi (6 Remember Stroma Thylakoid membrane PS II (P680) & PS I (P700) - DON’T need to know specific components of electron transport chain Electron goes through cytochrome complex Water splits at PSII to make O2 12 H2O + NADP+ + 18 ADP + 18 Pi + light and chlorophyll —> 6 O2+ 12 NADPH + 18 ATP Calvin cycle - 6 Carbons, 5 carbons, 3 Carbons Slides Questions How many ATP’s are required to make glucose 18 Atp’s are required (6 cycles) What is the donor for electrons in PS2 P680`  Mendelian Patterns of Inheritance What is a gene? A gene is the basic physical and functional unit of heredity. Genes specify traits or characters Genes are made up of DNA and are located in chromosomes Some genes act as instructions to make molecules called proteins which are needed for the body to function. However most genes do not code for proteins but for RNA(final product) We now know that the human genome contains over 8000 genes and from those about 19,900 genes are used to produce proteins. Inheritance: acquisition of traits by their transmission from parents to offspring Chromosomes are threadlike structures made of protein and a single molecule of DNA that serve to carry the genomic information from cell to cell In plants and animals (including humans), chromosomes reside in the nucleus of cells’ Humans have 22 pairs of numbered chromosomes (autosomes) and one pair of sex chromosomes (X,X or XY) for a total of 46 A sex chromosome is a type of chromosome involved in sex determination Humans and most other mammals have two sex chromosomes X and Y that in combination determine the sex of an individual Females have two X chromosomes in their cells while males have X and one Y Each pair contains two chromosomes, one coming from each parent which means that children inherit half of their chromosomes from their mother and half from their father. Inheritance: The acquisition of traits by their transmission from parent to offspring. Typically, humans have two copies of each gene (homologous pair), one inherited from each parent, except for the mitochondrial genes and sex chromosomes (from mother). Many genes are identical in all humans, but some genes are slightly different in DNA sequence and/or function. Forms of the same gene with differences in their sequence of DNA bases are called alleles. These small differences contribute to each person's unique physical features. If the 2 alleles are identical in diploids there are called homozygous for that gene. If the 2 alleles are not identical in diploids there are called heterozygous for that gene. The "genotype" is an organism's full hereditary information. The "phenotype" is an organism's actual observed properties, such as morphology, development, or  behavior. This distinction is fundamental in the study of inheritance of traits and their evolution. The terms dominant and recessive describe the inheritance patterns of certain traits. That is, they describe how likely it is for a certain phenotype to pass from parent offspring. A dominant allele produces a dominant phenotype in individuals who have one copy of the allele, which can come from just one parent. For a recessive allele to produce a recessive phenotype, the individual must have two copies, one from each parent. Mendel’s Law of Segregation Experiment P generation (crossed dominant and recessive) P1 generation (gamete) F1 generation (Dominant traits) F2 generation (Dominant and recessive traits) Law: The two alleles of a gene separate (segregate) from each other during the process that gives rise to gametes so every gamete receives only one allele Mendel's law of segregation Gametes are specialized sex cells responsible for transmitting genetic information Gametes contain only half the genetic material of a diploid, complete, organism (Le., haploid) The two alleles of a gene separate (segregate) from each other during the process that gives rise to gametes, so every gamete receives only one allele, (at random) Mendel's law of segregation (and dominance) Single factor crosses A monohybrid cross is one in which both parents are heterozygous for a Human Traits Determined (maybe) by Single Genes Earlobes: - Dominant allele (E): Results in free-hanging earlobes. - Recessive allele (e): Causes attached earlobes. PTC Tasting: - Tasting allele (dominant): About 75% of people can taste PTC. Only one copy of the tasting allele is enough to taste it. - Non-tasting allele (recessive): Non-tasters have two copies of the non-tasting allele. Freckles:  - Controlled by MC1R gene: Freckles follow a dominant inheritance pattern, meaning if parents have freckles, their children likely will too. Tongue Curling: - It was thought to be controlled by a single gene, but studies suggest environmental factors play a role. Around 70% of identical twins share this trait. Red/Green Colorblindness: - X-linked recessive trait: More common in males (1 in 12) than females (1 in 250) due to its location on the X chromosome. Pigmented Iris (Eye Color): - B allele (dominant): Brown eyes. - b allele (recessive): Blue eyes. This simple model works in most cases, with additional influence from the OCA2 gene for blue eyes. Blue or brown describes only a portion of eye colour There are intermediate variations of green and hazel, as well as albino eyes, which lack pigment entirely-all examples for which the simple Mendelian model does not apply. Geneticist Victor McKusick stated, "The early view that bilue is a simple recessive has been repeatedly shown to be wrong by observation of brown-eyed offspring of two blue-eyed parenta" We now know that eye colour is actually a complex genetic trait, involving interaction of some major genes and many minor genes. This Mendelian-Complex genetic explanation for eye colour also crosses over into the genetics of many other eye diseases such as age related macular degeneration and glaucoma. Many people can look at the eye colours in their own families and draw their own pedigrees to see how the Mendelian model applies Punnett Squares The punnett square is a table in which all the possible outcomes for a genetic cross between two individuals with known genotypes are given. Allows to determine relative proportions of genotypes and phenotypes of offspring Testcross TT or tt To determine if organism is with dominant phenotype 2 factor cross Two traits or characters: more than one gene Mendel's law of independent assortment the alleles of two or more genes get assorted into gametes independent of each other  Every possible combination of alleles for every gene is equally likely to occur. Pefigree Analysis Squares = males Circles = females Black & white = heterozygous (carrier) Black = affected individual Used to determine cystic fibrosis (CFTR - recessive) Huntington’s disease is caused by dominant trait Sex-linked Hemophilia (recessive in X) NOT ON EXAM Genetic Mechanism Accounting for Mendel’s Law of Segregation and independent assortment Locus is singular & Locci is plural Summary What is a gene? Gene: unit of heredity made of DNA, located in chromosomes Controls traits or characteristics Can provide instructions to make proteins or RNA*** Human genome has over 8000 genes Around 19,900 genes are used to produce proteins Inheritance Inheritance: The transmission of traits from parents to offspring. Chromosomes: Threadlike structures made of protein and DNA, carrying genetic information from cell to cell. In plants and animals, chromosomes reside in the nucleus. Humans have 46 chromosomes in total: 22 pairs of autosomes and 1 pair of sex chromosomes (XX for females, XY for males). Sex chromosomes: X and Y chromosomes that determine the sex of an individual. - Females: XX - Males: XY Children inherit half of their chromosomes from each parent.  Humans have two copies of each gene (homologous pair), except for mitochondrial genes and sex chromosomes. Alleles: Different forms of the same gene, causing variations in traits. Homozygous: Two identical alleles for a gene. Heterozygous: Two different alleles for a gene. Genotype: An organism's full hereditary information, the genes. Phenotype: The observed traits, like appearance or behavior. Dominant allele: Produces a dominant trait with just one copy from either parent. Recessive allele: Requires two copies (one from each parent) to show the recessive trait. Mendelian Inheritance patterns and Molecular Basis 1. Simple Mendelian Inheritance - Pattern: Traits are determined by a dominant/recessive allele pair on autosomes. The dominant allele masks the recessive allele. 2. X-Linked Inheritance - Pattern: Traits determined by genes on the X chromosome. Males (with only one X chromosome) often show recessive X-linked traits more than females. - Molecular Basis: Females with one recessive allele can still produce the dominant trait, but males with a recessive allele don't have a second X to provide a dominant allele, so they express the recessive trait. 3. Incomplete Dominance - Pattern: The heterozygote shows an intermediate phenotype, such as pink flowers from a cross of red and white flowered plants. Molecular Basis: 50% of the functional protein leads to a mix of traits, resulting in the intermediate phenotype. 4. Codominance - Pattern: Both alleles are expressed simultaneously, as seen in ABO blood types (A and B are both expressed in AB blood). 5. Epistasis - Pattern: One gene's alleles mask the effects of another gene. - Molecular Basis: Two genes are needed for a particular phenotype. If one gene loses function, it alters the overall phenotype. 6. Continuous Variation - Pattern: Offspring display a continuous range of phenotypes. Mendel’s Law of Segregation  P generation (crossed dominant and recessive) P1 generation (gamete) F1 generation (Dominant traits) F2 generation (Dominant and recessive traits) Checklist Mendelian genes Chromosomes Allele Mendelian inheritance Diploid Haploid Homozygous Heterozygous Evolution Phenotypes Genotypes Dominance Genetics Punnett Square Slides  Chapter 16: The Eukaryotic Cell Cycle, Mitosis, and Meiosis DNA Parts Chromatids Euchromatin Heterochromatin Chromatin Centromere Test of Karyotypes Karyotypes: individual set of chromosomes Can only show the karyotype of the cells are constantly dividing How many copies of a gene? 4 copies EXAM Eukaryotic Cell Cycle Phases: G1, S, G2, M (PMAT) Starts at a phase of G0 - Where majority of cells are - Not dividing - Stem Cells & Cancer cells only divide - Body is made up of 100 trillion cells (1014) Starts with G1 - Ex: 3 pairs of chromosomes (6 total) - Lot of proteins made for S phase - Originally began with 2 copies for 1 gene S Phase - Chromosme doubles - 4 copies of gene G2 Phase - Prepare the cell to divide - Nucleus begins to disappear Mitosis  - If animal, lose nuclear membrane - Chromosome is going to line up in plane - Chromatid is going to split to 2 daughter cells Summary - Start of with 3 pairs of each - Duplicates & divides into 2 daughter cells - End with same thing Cancer - P53 Cyclins & Cyclin Dependent Kinases Control Progression through the cycle Cyclins & Cyclin Dependent Kinases (CDK) work together to activate protein, after approved, destroy themselves Only if perfect able to pass through cycle A kinase is a type of protein that modifies proteins Checkpoints: ensure proper things are done at each cycle Exam: know what their job is and what they are used for Summary Cell enters cycle Eachchromosme is replicated Last picture only exists at metaphase of mitosis Mitotic Spindle Apparatus Structure responsible for organizing and sorting eukaryotic chromosomes during cell division Microtubule protein fibers - Attach to little structures associated with centromere (kinetochore) - A pair of kinetochores for every centromeres Centrosome is going to replicate - Move to poles of cell Mitosis (Sorting Process)  Interphase (not part of mitosis): - Check if nuclear envelope is intact - Chromosomes are replicated Prophase - Nuclear envelope begins to disintegrate - Spindle starts to form - Don’t worry about nucleolus Prometaphase - See centrosomes move to poles - Creates mitotic spindle - Chromatids attached to spindle - No nuclear envelope Metaphase - Chromatids are aligned along the plate Anaphase - Two sister chromatids are split to both ends of the poles Telophase & Cytokinesis - Starts to pinch inwards - Break the cell in half - End up with two daughter cells Mitosis in Animals and Plants Mitosis in Bacteria In bacteria is called Binary fission  Meiosis (Gametes) Crossing Over Form Synapsis Bivalent forms Information gets exchanged from chromosome (rearrange from dad and mom) If synapsis is stopped, you are going to be sterile Crossing over is called Chiasma Ex. Allows you to not stuck with same genes for every generation (good & bad gene from dad) ***Cells replicate during S Phase 1 cell produce 4 eggs Diploid cell becomes haploid Meiosis 1 (Separates Homologous Chromosomes) Meiosis 2 (Separates Sister Chromatids) Tetrad Figure 16.13 from Textbook Exam Pay attention to difference between mitosis and meiosis  Mendel’s Allele Segregation Caused by meiosis Understanding from above helps learn this concept Different allele segregate Mendel didn’t know how they separate allele Law of Independent Assortment Starts with genotype of heterozygous Cell can take two different paths Important Terms Ploidy: # of sets of chromosome you have (n) - Haploid: 1 set (n) - Diploid: 2 set (2n) - Triploid: 3 sets (3n) - Polyploid: 4 or more Euploidy: referred to an organism that has correct amount of chromosomes Aneuploidy: referred to an organism that doesn’t have correct amount of chromosomes - Monosomy: have only one out of two chromosomes in a pair  - Trisomy: have three out of two chromosomes in a pair Nondisjunction: problem in meiosis Aneuploidies of the Sex Chromosome Morphology of Chromosomes Know which are short are long arms Multiple Choice Question Don't Memorize the syndromes Prof said he could give xo, yo which is viable Which are associated with which chromosomes (patu’s, edwards, down) Which ones are x related and which ones are autosomal Checklist Chromatin Chromatids Eukaryotic cell cycle - Sister chromatids - G1, S, G2, M - Check points Mitotic cell division Meiosis SUMMARY OF MITOSIS Interphase Long strings of DNA (Chromatin) Centrosome duplication occurs DNA replicates itself Prophase Chromatin condenses to form chromosomes Duplicates (chromatids) stay attached at centromere Nuclear envelope disintegrate  Centrosomes move to ends of poles, leaving behind ropes (proteins) called microtubules Metaphase Chromosomes line up in middle Anaphase Motor proteins pull hard to poles Ana = back Telophase Cell structures reconstructed (nuclear membrane, nucleoli form) Chromatids from back into chromatin Cytokinesis Cell movement Cells separate SUMMARY OF MEIOSIS Meiosis 1 1. P1 DNA is in form of chromosome (chromatids) Crossover and Homologous recombination (trade sections of DNA - allele) - Allows for natural selection - So offspring will not get all bad genes - 23rd pair doesn’t do recombination if you are male 2. M1 Line up with homologous pair in middle Homologous pair gets pulled apart 3. A1 Same thing, pulled apart into poles 4. T1 Nuclear membrane forms and splits End up with 2 haploid cells (23 double chromosomes - cytokinesis) Meiosis 2 1. P1 DNA clumps again into chromosomes 2. M1 Moved to middle of cell 3. A1 Chromatids separated apart 4. T1 Nuclear membrane forms and splits End up with 4 cells with 23 chromosomes each  Half are girls, half for boys For girls - 3 polar bodies created, one egg only made  Chapter 5: Membrane Structure, Synthesis, and Transport Tile During a routine screening as a newborn. Emily was diagnosed as having cystic fibrosis (CF) As she has grown up, hei symptoms have included a persistent cough, lung infections, and poor weight gain due to blockages in the tubes that carry digestive enzymes from her pancreas to the small intestine. CF is a genetic disease caused by a mutation via gene called CFTR. which encodes a protein named the cystic brass conductance transmembrane (regulator). Emily inherited a faulty copy of the CFTR gene from both of her parents. By comparison, each of Emily's parents has one fully functional copy of the CFTR gene and one faulty copy Both of them passed the faulty copy to Emily Because each parent has one fully functional CFTR gene, they do not have disease symptoms Membranes The endoplasmic reticulum (ER) is a type of organelle made up of two subunits - rough endoplasmic reticulum (RER) , and smooth endoplasmic reticulum (SER) ,. The endoplasmic reticulum is found in most eukaryotic cells and forms an interconnected network of flattened, membrane-enclosed sacs known as cisternae (in the RER), and tubular structures in the SER. The membranes of the ER are continuous with the outer nuclear membrane. The endoplasmic reticulum is not found in red blood cells, or spermatozoa. Important topics Membrane structure and function Fluidity of membranes Synthesis Membrane transport Biological membrane Any membrane made by living cells; can be the plasma membrane or an internal membrane that surrounds an organelle. Plasma membrane The biological membrane that separates the internal contents of a cell from its external environment Phospholipid bilayer The basic framework of a biological membrane, consisting of two layers of phospholipids Types of membrane proteins Approximately 20-30% of All Genes Encode Transmembrane Proteins transmembrane protein - has one or more regions that are physically embedded in the hydrophobic interior of a membrane's phospholipid bilayer. lipid-anchored protein - is attached to the membrane via a lipid molecule. peripheral membrane protein - Is noncovalently bound to a region of an integral membrane protein that projects out from the membrane or noncovalently bound to the polar head group of a phospholipid. Membrane Damage  Aspirin + ibuprofen + tylenol (everytime you take this you interfere with a pathway) - You damage a membrane of a cell through trauma, etc. - Membrane phospholipids are cleaved - ASK ABOUT CYCLOOXYGENASE (make really bad signals) What more beneficial for patients with arthritis and vascular disease Cyclooxygenase Membranes are Semi Fluid Factors affecting membrane fluidity - length of phospholipid tails - Double bonds in phospholipid tails - Cholesterol - more fluid = (kinks - double bonds) - Less fluidity if single bonds - Double bonds in lipid tails causes it to be less mobility - If in hot temperatures, want less mobility Cholesterol Is the principle sterol of all animal cells Is an essential structural and signaling component of animal cell membranes High temperature cause it to more solid Cold temperatures cause it to be more fluid Synthesis of Membrane Phospholipids (phosphatidylcholines) in the SER membrane Take two fatty acids and attache the CoA enzyme Through enzymatic action, it's going to insert itself in the smooth ER Active Transport Uses ATP Most Transmembrane Proteins are First Inserted Into the ER Membrane Have a special amino acid (signal) to enter Whole bunch of hydrophobic amino acids Membrane Resident Molecules Glycosylation: the covalent attachment of a carbohydrate to a protein, RNA or lipid, producing a glycoprotein, glycoRNA or glycolipid, respectively Glycosylation The attachment of carbs to protein occurs in the ER and Golgi Apparatus Glycolipid: A lipid that has carbs attached to it Glycoprotein: a protein that has a carb attached to it Mucus is an example of glycoprotein and glycolipid abo blood group is determined by the congregation of sugar residues in membrane lipids of RBC Protein modifications MEMORIZE ALL THE THREE COLUMNS Know 3 letters code, kinases (phosphates) Glycosylation: attachment of prot, lipid, RNA onto carb for membrane attachment - covalent bond formation Membrane Transport Phospholipid bilayer is a barrier to the simple diffusion of hydrophobic solutes Simple Diffusion: ions (polar) Facilitated diffusion: aid of a transport protein, high [] to low [] Factors Affecting Permeability of Membrane by Solutes Size: Small solutes cross bilayers faster than larger ones. Polarity: Nonpolar solutes cross bilayers faster than polar ones. Charge: Noncharged solutes cross bilayers faster than charged ones. Concentration: The rate of movement of a solute across a membrane will be higher when its concentration is higher. GRADIENT = high [] to low [] Low to high uses ATP Transmembrane gradient or concentration gradient A situation in which the concentration all a solute is higher on one side eff a membrane than on the other Electrochemical Gradient A dual gradient across a membrane, having both electrical and chemical components determines the direction in which ions will move Osmosis is the movement of water across a membrane to balance solute concentrations If solute cannot readily move across membrane, water will do so and tend to balance solute concentrations Membrane Transport by Proteins Facilitated diffusion (no energy input) Channels Transporters Channels provide open passageways for solute movement channel A transmembrane protein that forms an open passageway for the facilitated diffusion of ions or molecules across a membrane. gated A property of many channels that allows them to open and close to control the movement of solutes across a membrane Transporters bind their solutes and undergo conformational changes transporter A transmembrane protein that binds a solute and undergoes a conformational change to allow the movement of the solute across a membrane; also called a carrier. Types of Transporters Active Transport In Movement of Solutes Against a Gradient Types of active transport. (a) During primary active transport, a pump directly uses energy, in this case from ATP, to transport a solute against a concentration gradient. The pump shown here uses ATP to establish an H+ electrochemical gradient. (b) Secondary active transport via a symporter involves the use of this gradient to drive the active transport of a solute, such as sucrose. Osmosis Water diffuse through a membrane form an area with more water to an area of less water If the solutes cannot move, water movement can make the cell shrink or swell as water leaves or enter the cell Osmosis in Animal cells Animals cells must maintain a balance between extracellular and intracellular solute concentration to maintain their size and shape Crenation: shrinkage of cells in a hypertonic solution Osmotic cycle: swelling and bursting of a cell in a hypotonic solution Osmosis in Plant Cells A cell wall prevents major changes in cell size If a cell take up a small amount of water the cell wall prevents osmotic lysis from occurring Plasmolysis: plasma membrane pulls away from the cell wall (when water exits the cell) Transporters Also known as carriers Conformational change transports solute across membrane Principal pathway for uptake of organic molecules, such as sugars, amino acids and nucleotides Transporter Types (Goes With Gradients) Uniporter - Single molecule or ion Symporter or Cotransporter - Two or more ions or molecules transported in same direction Antiporter - Two or more ions or molecules transported in opposite direction Active Transport Movement of a solute across a membrane against its gradient from a region of low to high concentration Energetically unfavorable and requires the input of energy - Primary active transport uses a pump and requires energy to transport solute - Secondary active transport uses a pre existing gradient to drive transport ATP-Driven Ion Pumps Generation Electrochemical Gradients Na/K-ATPase Actively transports Na and K' against their gradients using the energy from ATP hydrolysis 3Na are exported for every 2K imported into cell - Antiporter - ions move in opposite directions - Electrogenic pump - exports one net positive (+) charge lon pumps play the primary role in the formation and maintenance of lon electrochemical gradients that drive many important cellular functions Exocytosis and endocytosis  Used to transport large molecules such as proteins and polysaccharides involve packaging the transported substance into a membrane vesicle or vacuole Exocytosis (out of cell) Material inside the cell packaged into vesicles and excreted into the extracellular medium Endocytosis Plasma membrane invaginates (folds inward) to form a vesicle that brings substances into the cell Three types of endocytosis: 1. Receptor-mediated endocytosis- receptor in the plasma membrane is specific for a given cargo, s vesicle forms to transport cargo into the cell 2. Pinocytosis-membrane vesicles form from the plasma membrane to allow cells to internalize the extracellular fluid 3. Phagocytosis-an enormous membrane vesicle forms to engulf a large particle such as a bacterium  Chapter 11: Nucleic Acid Structure, DNA Replication, and Chromosome Structure Nucleotides 3 components: sugar, phosphate group and base sugar - 1’ = nitrogenous base (EXAM) - 2’ = DNA has no hydroxyl group on 2 carbon, RNA does + Exam: what is important of the 2’ position of a nucleotide + b/c distinguishes between building blocks of DNA & RNA - 3’ = - 5’ = phosphate group Joined By phosphodiester bond DNA RNA Sugar: Deoxyribonucleotide (not Sugar: Ribonucleotide nucleotides) * sugar is fundamentally different The Bases Just the name of the base —> Nucleotides (base + sugar + phosphate) - ATP (Adenosine triphosphate) - ADP Nucleosides (base + sugar)  Pay attention to ribonucleosides Remember name of base, ribonucleoside and add deoxy (if dna)  It’s dTMP b/c thymine is only present in DNA You never have deoxyuridine. Bonds between base and sugar is glycosidic bond EXAM: deoxythymidine monophosphate & deoxycytidine triphosphate Phosphodiester bond (nucleic acids together) Always 3’ has phosphate where hydroxy was DNA & RNA sequence is always 5’ to 3’  Always extend 3’ hydroxy Polymerase and ligase Role of deoxyribonucleoside triphosphate Deoxynucleoside triphosphate Polymerase breaks covalent bond to release pyrophosphate (two phosphates) that provide energy to connect nucleotides Watson-crick base pairing A pairs with T C pairs with g DNA Are antiparallel 5’ to 3’ Exam Write down complement of a strand Example: AATCC Answer: TTAGG First/reverse complement means 5’ to 3’ Compliment means 3’ to 5’ Question: 5’-ATGC-3’ - Reverse complementary is GCAT and compliment is TACG Chargaff’s Rule State that in the ds DNA of any species and any organism the amount of guanine should be equal to the amount of cytosine and the amount of adenine should be equal to the amount of thymine AT/GC rule Refers to the phenomenon that an adenine (A) in one DNA strand always hydrogen-bonds with a thymine (T) in the opposite strand and a guanine (G) in one strand always hydrogen-bonds with a cytosine © in the opposite strand  2 hydrogen bonds between A - T, 3 hydrogen bonds between G-C EXAM: if there is 30% A, how much of other will there be Adding methyl Methylation and ethylation of nucleotides happen very often with smoking Happens when you are exposed to smoke Don’t worry about this: you get abduct if you eat burnt meat If you have a pollutant changes base pairing (G will pair with T instead of C), causing a mutation Major and Minor Grooves Groves are received in the space filling model Major grooves - Proteins bind to affect gene expression Minor grooves - Narrower Semiconservative Mechanism Whenever you see ssDna means single stranded Whenever you see dsDNA means double-stranded DNA Replication The two parental strands separate and serve as template strands New nucleotides must obey AT/GC rule End result: two new double helices with same base sequence as original Replicated DNA molecules retain the same info as the original molecule Major Mechanism of DNA Replication Origin oof replication provides an opening called a replication bubble that forms two replication forks DNA replication proceeds outward from frocks - bidirectional replication Bacteria have single origin of replication Eukaryotes have multiple origins of replication Proteins necessary for DNA replication Dna helicase - Binds to dna and travels 5’ to 3’ using ATP to separate strand and move fork forward DNA topoisomerase - Relieves additional coiling ahead of replication fork Single-strand binding proteins  - Keep parental strands open to act as templates Role of DNA polymerase Dna polymerase - Covalently links nucleotides - Resembles a human hand with the DNA threaded through it - Deoxynucleotide triphosphates hydrogen bond to exposed bases in the template strand - DIrection for DNA: Only extend (builds) 3’ hydroxy, never extend 5’ phosphate Primer - EXAM: goes from 5’ to 3’ Features of DNA polymerase DNA polymerase cannot begin synthesis on care template strand, need 3’ OH Requires a primer to get started Dna primase makes the primer from RNA The rna primer is removed and replaced with DNA later DNA polymerase only works 5’ to 3’ (extends at 3’) Comparison of leading and lagging Strands Leading strand - Dna synthesized in as one long molecule - DNA primase makes a single Rna primer - DNA polymerase adds nucleotides in a 5’ to 3’ direction as it slides forward Lagging strand - Dna synthesized 5’ to 3’ but as okazaki fragments - Okasaki fragments consist of RNA primers plus DNA In both strands - RNA primers are removed by DNA polymerase and replaced with DNA - DNA ligase joins adjacent DNA fragments  Exonuclease (not just remove primers but fixes mistakes) & ligase creates phosphodiester bonds & ATP DNA polymerase in bacteria Bacteria use two different DNA polymerases for DNA replication DNA Polymerase III adds nucleotides in the 5’ to 3’ direction on the growing chain  Has a subunit called the clamp protein that allows the enzyme to slide along the template strand without falling off - called processivity DNA polymerase I: digests linkages between nucleotides in each RNA primer nucleotides in each RNA primer in a 5’ to 3’ direction and fills in the vacant region with DNA LEVEL OF DETAIL FOR EXAM DNA replication is very accurate In bacterial DNA replication only 1 mistake per 100 million nucleotides is made Three mechanisms for accuracy: H Bonding between A & T, and between G & C is more stable than mismatched combinations Active site of DNA polymerase is unlikely to form bonds if pairs mismatched Dna polymerase can proofread to remove mismatched pairs - DNA polymerase backs up and digests linkages DP III: multiple subunits resp for majority of rep DP I - single subunit rapidly removes DNA primers and fills in DNA DP II, IV and V - DNA Repair and can replicate damaged dna DP I and II stall DNA damage PRIMASE IN BACTERIA: DnaG Remember delta and axela and gamma ***Memorize carbon number of sugar (1’ to 5’) - Remember numbering Chapter 11: Nucleic Acid Structure, DNA Replication, and Chromosome Structure Nucleotides Components: Each nucleotide consists of three parts: ○ Sugar (Deoxyribose in DNA, Ribose in RNA) ○ Phosphate group ○ Nitrogenous base (A, T, C, G in DNA; A, U, C, G in RNA) Important Carbon Positions on Sugar: ○ 1’: Where the nitrogenous base attaches. ○ 2’: Differentiates DNA and RNA: DNA: Lacks a hydroxyl group (-OH) at the 2’ position. RNA: Has a hydroxyl group at the 2’ position. ○ 5’: Attached to the phosphate group. ○ 3’: Key attachment point during polymerization; where the next nucleotide attaches. Bond Types: ○ Phosphodiester bond: Links nucleotides between the 3’ and 5’ carbons. ○ Glycosidic bond: Connects the sugar to the nitrogenous base. Polymerase and Ligase Polymerase: ○ Function: Responsible for synthesizing DNA by adding nucleotides to the growing strand. ○ Mechanism: Breaks a covalent bond in deoxynucleoside triphosphates, releasing pyrophosphate (two phosphates) to provide the energy needed for bonding nucleotides together. Ligase: ○ Function: Seals nicks in the DNA backbone by forming phosphodiester bonds. ○ Role in Replication: Essential for connecting Okazaki fragments on the lagging strand, ensuring the continuity of the DNA strand. DNA Structure and Base Pairing  Watson-Crick Base Pairing: ○ Pairs: Adenine (A) pairs with Thymine (T); Guanine (G) pairs with Cytosine (C). ○ Hydrogen Bonds: A-T: Forms 2 hydrogen bonds. G-C: Forms 3 hydrogen bonds, making this pair more stable. Antiparallel Orientation: DNA strands run in opposite directions, labeled 5’ to 3’. Chargaff’s Rule and the AT/GC Rule Chargaff’s Rule: In double-stranded DNA, the amount of adenine equals thymine, and the amount of guanine equals cytosine. ○ Example Calculation: If there is 30% adenine, then thymine is also 30%, and guanine and cytosine each make up 20%. AT/GC Rule: Adenine always pairs with thymine, and guanine always pairs with cytosine, maintaining the DNA structure. Additional Notes Methylation: Often occurs with exposure to smoke or pollutants, potentially causing mutations by altering base pairing (e.g., G might pair with T instead of C). Complementary Sequences: ○ 5’ to 3’: Example, the original strand "AATCC" has a complementary strand "TTAGG".