Biology 3341 EXAM 1 Review PDF

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This document contains notes and practice exam questions taken from lectures 1-4, and lectures 5-7 material is only the practice questions. This document was made by me to study for Dr. Feng's BIOL 3341 exam....

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BIOLOGY 3341 EXAM 1 REVIEW: LECTURES 1-7 LECTURE 1: OVERVIEW AND INTRODUCTION  Smallest unit of the human genome is the DNA nucleotide. o Consists of A SUGAR, A PHOSPHATE GROUP, AND A NITROGENOUS BASE  The 4 Nitrogenous Bases: o Adenine, Thymine, Guanine, Cytosine  SUGAR creates the backbones.  3 Hydrogen bonds pair Cytosine and Guanine.  2 Hydrogen bonds pair Adenine and Thymine.  Each cell contains 3 BILLION DNA base pairs, and it spans 2 meters in length.  All human genomes are 99.9% alike, but the 0.1% that is different contains 3 MILLION DIFFERENCES.  Variants: Differences in DNA sequence.  SNV: A single nucleotide variant o The definition of SNV stands for single nucleotide variation, which means at one base there is a difference. This definition does not imply any kind of how often this variation occurs, just that there is at this particular nucleotide a difference. For example: ATG -> CTG has an SNV at A -> C

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o However, a SNP or single nucleotide polymorphism does imply that there is an implication how often this variation occurs. This means that there is an inherit implication when someone refers to a SNP that this variation is common (at least 1% of population). This means that it isn’t just a fluke that we are seeing this variation, but is an observation seen more often than a few individuals. This implies there might be something important at that location. 23andMe performs SNP (Single Nucleotide Polymorphism) sequencing. DNA and Chromatin o Form of chromatin and chromosomes depending on the stage of the cell cycle. o BASIC UNIT OF CHROMOSOMES IS THE NUCLEOSOME.  Composed of HISTONES and DNA o DNA has a double-helix structure. o A gene is a region of DNA that encodes a function. o THERE ARE 20,000 GENES IN THE HUMAN GENOME, which is LESS THAN 2% OF THE GENOME. o Gene: A region of DNA that encodes a protein’s function. Central Dogma o DNA cannot produce proteins directly, so RNA aids in this. o Transcription: Process of creating RNA from DNA.

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Translation: Process of creating PROTEIN from RNA. DNA Replication: Making a new copy of DNA. COVID and AIDS carry reverse transcriptase, making DNA from RNA. TRANSCRIPTION TAKES PLACE IN THE NUCLEUS. TRANSLATION TAKES PLACE IN THE CYTOPLASM. DNA REPLICATION TAKES PLACE IN THE NUCLEUS. Transcription factors make up most of gene factors (12%).

Red Blood Cells DO NOT contain a nucleus. Human blood lymphocytes: o DNA is in the form of chromatin. Euchromatin: o Lightly packed. o Enriched in GENES. o 92% OF THE HUMAN GENOME. o Involved in TRANSCRIPTION. Heterochromatin: o Tightly packed. o Enriched in repetitive, non-coding DNA folded by histones. o Located in the PERINUCLEAR REGION of the nucleus (perimeter). o Very few genes are located in heterochromatin.

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NUCLEOLUS o FUNCTION IS TO PRODUCE RIBOSOMES. o Involved in ribosomal biogenesis. o Participates in gene transcription and gene splicing. o In cancer cells, nucleoli are much larger than normal cells because they need more proteins to proliferate.  Heart disease is the number one cause of death in the US, Cancer is number two, Car Accidents number three, Chronic Lower Respiratory Disease number four, Stroke is number five, Alzheimer’s, Diabetes, Flu/Pneumonia, Septicemia. o COVID-19 IS NOW NUMBER THREE. LECTURE 2: CELL STRUCTURE AND FUNCTIONS (BOOK PAGES 18-26)  “Cell” named by Robert Hooke in 1665 by examining thin slices of cork under his microscope.  CELL THEORY 1. All living organisms are composed of one or more cells. 2. Cells are the smallest, most basic units of life. 3. Cells may only arise of pre-existing cells and cannot be created from non-living material. 4. Cells pass on the genetic material during replication in the form of DNA. 5. The cells of all organisms are chemically similar. 6. Cells are responsible for energy flow and metabolism.  Cell Cryopreservation o Liquid nitrogen tanks (-196C) used to freeze and preserve cells. After cells frozen in cryovials, they’re placed in the tank. o Cells are still able to show activity 30 years inside the tank.  Application of Cryopreservation o Semen, embryos, oocytes, ovarian tissues, testicular tissue, and umbilical cord blood.

o Cord blood has high amounts of stem cells. Stem cells have high differentiation potential and can be used to replace damaged cells if the child it came from develops diseases in the future.  The Option of Disease Treatment Using Cord Blood: o FDA has cleared 80 diseases of the blood and immune system to be treated with cord blood. o Blood diseases (leukemia), cancers, immune system disorders, metabolic disorders, solid tumors (neuroblastoma), bone marrow failure. o Best way to use cord blood if it’s from the umbilical cord of the person who needs it in order to reduce rejection.  Cryonics- Store Bodies for Future Use o Freeze whole dead bodies. o No successful results, but provides hope that resurrection is possible.  Journal called CELL ranked first overall in the category of highest impact journals (ALL FIELDS OF SCIENCE) over 1995-2005 with an average of 161.2 citations per paper.  Best way to find out if a journal is reliable or not is to look at its impact factor which is calculated by the number of times it is used as a citation.  In 2019, CELL ranked 1st out of 298 journals in Biochemistry and Molecular Biology in impact factor.  MORE THAN 200 TYPES OF CELLS IN THE HUMAN BODY, AND A TOTAL OF ABOUT 37 TRILLION CELLS IN THE HUMAN BODY.  Cell Structure Reflects Function o The basic structural and functional unit in ALL organisms (including humans) is the cell. o Although they look different, structurally they’re very similar. o ALL EUKARYOTIC CELLS HAVE:  Plasma membrane  Cytoplasm  Membranous organelles  Membrane-bound nucleus  The Chemistry of Cells o Cells are constructed from four classes of MACROMOLECULES.  CARBOHYDRATES-simple sugars and phospholipids  LIPIDS-fats and oils, phospholipids, and steroids  PROTEINS-polymers of amino acids  NUCLEIC ACIDS-polymers of nucleotides  A Human Cell *RECOGNIZE ORGANELLES AND REMEMBER THEIR FUNCTIONS FOR EXAMS* **REFER TO TABLES BELOW

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VIDEO ABOUT CELLS o All cells have 3 things the same:  Plasma membrane  Cytoplasm  DNA o Organelle means “little organ.” o Cell maintains shape through the cytoskeleton made of microfilaments which are made of protein and microtubules which are thin, hollow tubes. o Animal cells NEVER have a cell wall. o Cilia help move things (like mucus) in body in the lungs, respiratory tract, and middle ear. o Flagella aid in locomotion of the cell.  Only human cell with a flagellum is the sperm cell.

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The Plasma Membrane o The biological barrier that separates the inside of the cell from the outside of the cell. o Consists of phospholipid bilayer o Cholesterol in the membrane maintains the integrity and fluidity of the plasma membrane.  The HIGHER the CHOLESTEROL level the LOWER the FLUIDITY and MORE RIGID THE CELL MEMBRANE would be. o Contains proteins responsible for various biological activities. o Many membrane proteins are glycolated-meaning they have a carbohydrate chain.  Carbohydrates are important for cell-cell recognition in eukaryotic cells. They’re located on the SURFACE of the cell where they recognize other cells and share information. Phospholipids o HydroPHILIC head and hydroPHOBIC tails.

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The tails face each other, and the heads face the inside and outside of the cell.

o The HYDROPHOBICITY of the TAILS PLAYS an IMPORTANT ROLE IN STRUCTURE DETERMINATION in almost all biological molecules. Functions of Proteins in the Cell Membrane o Receptors: Send chemical signals in which cells interact.  Example: Epinephrine can’t get inside the target cells by passing diffusion, it can only bind to surface proteins (receptors).  NORMALLY FOR ONE SPECIFIC MESSENGER.

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o Enzyme: Assists in production of secondary messenger or break down hormones and other single molecules once their task is done.  NORMALLY BIND TO ONE SPECIFIC MESSENGER. o Ion Channels: Trans-membrane proteins open and close with pores that permit H2O and liquified ions to go through the membrane.  Some channels are constantly open.  Others, like gated ion channels, only open and close in different situations. o Cell-Identity Markers: Glycoproteins that distinguish body’s own cells from foreign cells.  Have carbohydrate chain attached. o Cell-Adhesion Molecule (CAM): Proteins located on the cell surface involved in binding with other cells or with the extracellular matrix (ECM) in the process called cell adhesion.  CAMs help cells stick to each other and to their surroundings.  Binds to the CAM of another cell and is important for forming cell-cell adhesion molecules. Endoplasmic Reticulum o System of cytoplasmic membranes arranged into sheets and channels. o Found in the cytoplasm in eukaryotic cells. o Synthesize and transport gene products. o Rough Endoplasmic Reticulum (rER) has ribosomes attached on the outside, but the Smooth Endoplasmic Reticulum (sER) does not. o Translation of RNA to proteins ONLY OCCURS IN THE CYTOPLASM. o Gene products: proteins, amino acids, and polypeptides. Endoplasmic Reticulum in Unactivated vs. Activated B Cells o Functionally, the activated B cells make antibodies (a type of protein). o Unactivated B cells DO NOT make antibodies.  WHY? 1. Activated B cells contain much MORE endoplasmic reticulum, which is needed for antibody translation. 2. An activated B cell contains a LARGE area of euchromatin, which is enriched in genes, indicating genes are actively transcribing in the nucleus to support proliferation of the B cell and to make protein (antibodies). Golgi Complex and Lysosomes o Lysosomes are the garbage cleaners of cells and contains an abundance of digestive enzymes.  Digestive enzymes are synthesized in the ribosomes attached to the Endoplasmic Reticulum, they’re internalized and engulfed by the Golgi. o The Golgi modifies and packages the enzymes.  The lysosomes pinch off the end of the Golgi membrane in the cytoplasm to create a vesicle containing the enzymes and infuse and digest the

contents of the vesicle and parts of the plasma membrane that have entered the cytoplasm. 

Mitochondria o POWERHOUSE OF THE CELL. o Provides energy to all kinds of cellular activities in the form of ATP (Adenine Triphosphate). o ONLY EXISTS IN THE CYTOPLASM. o Have double membranes.  The Nucleus o The Nuclear Envelope KEEPS DNA INSIDE OF THE NUCLEUS for protection from surrounding substances in the cytoplasm.  The nuclear envelope consists of TWO DOUBLE-LAYERED membranes.  Inner membrane faces the nucleoplasm.  Outer membrane faces the cytoplasm. o Nuclear Pores are protein complexes that span the nuclear envelope and allow for the transport of molecules across the nuclear envelope.  RNA and ribosomal proteins move FROM the NUCLEUS TO the CYTOPLASM.  Proteins such as DNA Polymerases, like carbohydrates, are signaling molecules and lipids that need to move from the cytoplasm into the nucleus. o The Nucleolus makes RIBOSOMES o No matter how crowded it is, DNA stays INSIDE the nucleus as chromatin. However, if the cells are moved to the MITOTIC stage, we cannot see chromatin anymore-we now see chromosomes.  Karyotype o THE NUMBER AND APPEARANCE OF CHROMOSOMES IN THE NUCLEUS OF A EUKARYOTIC CELL.  Human Karyotype: 23 pairs; 46 chromosomes. Half from the mother and half from the father. o Can tell you a lot of genetic information. o Female: Two (X) chromosomes. o Male: One (X) and one (Y) chromosome.  (Y) chromosome is SMALLER than the (X) chromosome.  Slide of male karyotype in lecture slide reveals Trisomy-21 (Down Syndrome). *WHERE CAN DNA BE FOUND IN A HUMAN CELL? *  IN THE NUCLEUS AND IN THE MITOCHONDRIA o Nuclear DNA (genomic DNA)  Has MORE than 3 BILLION base pairs  Around 20,000 GENES in the form of:  Chromatin  Chromosomes

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o Mitochondrial DNA (mtDNA)  16,569 base pairs  37 GENES  MATERNAL Inherited: Inherited from mother  Structure is double-stranded and CIRCULAR  Because mitochondria are ONLY in the CYTOPLASM, when the sperm and egg fuse and become a zygote, the sperm contributes its nucleus but barely any cytoplasm. The mitochondria in SPERM are usually DESTROYED by the egg cell AFTER fertilization.  The egg cell is the BIGGEST human cell at about 20X larger than sperm and provides almost ALL cytoplasmic materials-including the mitochondria. Other Functional Structures in Human Cells? o PHASE OPERATION  Liquid-Liquid Phase Separation (LLPS): The phenomenon in which solutes spontaneously separate into a demixed liquid phase suspended with the bulk of solvent. (Think of this demixed liquid phase suspended in this solvent like oil and water; oil is less dense than water, so it floats on top, just like the demixed liquid in the solvent). Dynamic Fluid Droplets Demix From Surrounding Nucleoplasm/Cytoplasm for Specific Functions o There are organelles, or subcellular structures, that do not have the membrane structure but can hold their specific components: 1. Nucleoli: Produce ribosomal proteins and RNA 2. Cajal Bodies (CB’s): Sites for assembly and/or posttranscriptional modification of the splicing machinery of the nucleus. 3. Histone Locus Body (HLB): Process histone pre-mRNAs. 4. Paraspeckles: Nuclear retention of mRNA.  Can hold mRNAs from nuclear export. Liquid-Liquid Phase Transition in Disease  HAS BEEN LINKED TO MANY NEURODEGENERATIVE DISEASES o Amyotrophic Lateral Sclerosis (ALS)  Progressive neurodegenerative disease that affects nerve cells in the brain and spinal cord.  Paralyzes muscles, and death occurs within 3-5 years after symptoms begin, but some people have lived 10+ years. Video on Liquid-Liquid Phase Transition in ALS o Proteins in organelles in the cell have to be able to slide around over each other for Liquid-Liquid Phase Separation (LLPS).  What proteins have this behavior? 1. PRION-LIKE domains associated with age-related diseases, but in healthy cells they’re found in membraneless compartments. o FUS protein is implicated in ALS  Liquid Criteria:

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Keep round shape 1. Ability to move around and rearrange (molecules in liquid droplets). 2. Liquid droplets that come close together, fuse, and become one large droplet.  FUS droplets met all criteria  In the test tube, the mutated FUS protein reacted the same as healthy FUS protein.  FUS formed solid aggregates after aging in the test tube in the mutant. o AGING = LIQUID TO SOLID PHASE TRANSITION o Liquid state  non-physiological aggregate o Aberrant Phase Transition  Protein aggregation is also seen in Alzheimer’s, Huntington’s, and Parkinson’s Liquid-Liquid Phase Transmission in ALS

o Aging is a crucial factor to trigger ALS. o This shows only one possible mechanism on how ALS develops.  Online Mendelian Inheritance in Man (OMIM) o Continuously updated catalog of HUMAN GENES and GENETIC DISORDERS and TRAITS, with particular focus on the GENE-PHENOTYPE relationship. o As of February 12, 2017, approximately 8,425 of 23,000 entries in OMIM represented GENES of which were related to known phenotypes. LECTURE 3: CELL CYCLE AND MITOSIS (CH 2.4-2.5 P 26-30 & CH 12.1-12.6 P 262-270)  Chromatin and Chromosome o DNA can exist in 2 forms: chromatin and chromosomes.  A chromosome is a more condensed form of chromatin  Chromosomes have an X-shaped structure:

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Mitosis of a Living Cell o Chromatin:  UNWOUND DNA  FOUND IN NON-DIVIDING CELLS o Chromosomes:  TIGHTLY PACKED DNA  FOUND ONLY DURING CELL DIVISION (IN DIVIDING CELLS) Two Types of Cell Division o Mitosis: 1 (2n) cell  2 (2n) daughter cells  1 DIPLOID  2 DIPLOID  Cell growth, repair, asexual division o Meiosis: 1 (2n) cell  4 (1n) daughter cells (gametes)  1 DIPLOID  4 HAPLOID  Sexual reproduction (sperm and egg)  Genetic information of sperm and egg combine to become 2n (Diploid) again Cell Cycle o To prepare for cell division, the cell will go through a series of events to accumulate enough materials and get ready for division. o There are 4 main phases in 1 cell cycle:  G1  S  G2

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Phases of the Cell Cycle o G0: NO DNA replication or cell division o G1: LONGEST PHASE; making of organelles, increase in cell size (growth) o S: DNA replication; COMPLETE duplication of DNA o G2: Relatively short; continues to make organelles, increase in cell size (growth); getting cell committed (ready) for upcoming mitosis. o M: Mitosis; SHORTEST PHASE; PMAT: Prophase, Metaphase, Anaphase, Telophase.  Because scientists can clearly see chromosomes in mitosis, based on the shapes or the changes in the cell, the mitosis can be further divided into 4 subphases (PMAT). Cell Cycle VIDEO o Interphase (Growth):  During G1, or first growth phase, normal cell functions occur as well as growth.  In S Phase, DNA replicates, producing 2 COPIES of each chromosome.  During G2, the cell continues to prepare for mitosis and cell division. o Mitosis:  Mitosis, or M Phase, has 4 stages. Prophase, Metaphase, Anaphase, and Telophase.  During PROPHASE, the chromosomes become visible and condensed, becoming thicker and shorter. Each identical copy of a single chromosome is called a SISTER CHROMATID. The nuclear envelope breaks down and spindle fibers form as microtubules grow out of the centrioles that move to opposite poles of the cell.  During METAPHASE, the double-stranded chromosomes line up along the equator of the cell. The spindle is now fully formed, and the microtubules attach to each sister chromatid at the centromere of each chromosome.  ANAPHASE begins when the sister chromatids of each chromosome begin to SEPARATE. The centromere that holds sister chromatids together

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divides and the chromosomes move away from each other along its spindle fiber.  In TELOPHASE, the two groups of chromosomes reach the opposite ends of the cell. As a new nuclear envelope starts to form around each group, the chromosomes uncoil, and the spindles disappear. o Cytokinesis:  The division of the cytoplasm and organelles is called cytokinesis, or the C phase.  ENDS MITOSIS  The result of mitosis and cytokinesis is the formation of two genetically identical cells, called daughter cells. Four Phases of Mitosis o PMAT (Prophase, Metaphase, Anaphase, and Telophase) 1. Prophase = Prepare: Cell prepares for mitosis 2. Metaphase= Middle: Chromosomes align in the middle of the cell 3. Anaphase= Apart: Centromere splits and sister chromatids are pulled apart by microtubules to the opposite poles of the cell. 4. Telophase= Two: Two daughter cells are reformed with separate nuclei Cytokinesis Divides the Cytoplasm o ENDS MITOSIS o Cleavage furrow divides the cytoplasm equally into 2 daughter cells. o Organelles are distributed to the daughter cells. Identify the Mitotic Stages of the Cells

1: Prophase; 2: Metaphase; 3. Anaphase; 4: Telophase Tools to Study Cell Cycle o Flow Cytometry  Used to detect cell cycle

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Machine is able to make measure of cells in solution

o (Image on left): DNA in cell is stained with fluorescent dye, therefor as long as one cell passes the laser, the machine gives a count. o (Image on right): S Phase cells accumulate in area between G! and G2/M Phase.  Why does G1 have highest count? BECAUSE MOST CELLS SPEND THE LONGEST TIME IN G1 PHASE (1/2 of cell cycle); M is 1 out of 24 hours (estimate).  USUALLY TWO PEAKS ARE OBSERVED.  Peak 1 is usually cells in G1 Phase  Peak 2 is usually cells in G2 Phase or M Phase Flow Cytometry Examples

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Control of the Cell Cycle by Cyclins Cyclin E: G1/S Phase cyclin. Cyclin D: Present throughout WHOLE cell cycle.

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o Cyclins are a family of regulatory proteins that control the progression o...