biol 200 final exam crash course

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BIOL 200 FINAL EXAM CRASH COURSE

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Table of Contents

Table of Contents ....................................................................................................................................... 1 Notes about the Exam .............................................................................................................................. 3 Notes about the BYC Crash Course Booklet ................................................................................... 3 Unit 1: Cell Organelles and Microscopy ........................................................................................... 4 Cell Organization ................................................................................................................................... 4 Microscopy ............................................................................................................................................... 6 BYC Concept Check ............................................................................................................................... 8 BYC Exam Practice Questions ....................................................................................................... 11 Unit 2: Biological Membranes ........................................................................................................... 13 The Lipid Bilayer ................................................................................................................................ 13 Proteins .................................................................................................................................................. 16 Membrane Proteins .......................................................................................................................... 17 BYC Concept Check ............................................................................................................................ 19 BYC Exam Practice Questions ....................................................................................................... 23 Unit 3: Nuclei Chromatin ..................................................................................................................... 25 The Interphase Nucleus .................................................................................................................. 25 Nucleic Acid Review ......................................................................................................................... 27 Chromosomes and Chromatin ...................................................................................................... 29 BYC Concept Check ............................................................................................................................ 31 BYC Exam Practice Questions ....................................................................................................... 34 Unit 4: From Gene to Protein ............................................................................................................. 36 Transcription ....................................................................................................................................... 36 RNA Processing ................................................................................................................................... 40 Translation............................................................................................................................................ 43 BYC Concept Check ............................................................................................................................ 45 BYC Exam Practice Questions ....................................................................................................... 49 Unit 5: Endomembrane System ........................................................................................................ 51 Overview (Protein Targeting) ...................................................................................................... 51 Targeting to ER ................................................................................................................................... 52 Vesicle Transport ............................................................................................................................... 55 Secretory Pathway ............................................................................................................................ 58 Endocytic Pathway ............................................................................................................................ 60 © Copyright 2015 by Beat Your Course Inc. All Rights Reserved. No part of this publication may be reproduced or transmitted in any form or by any means, or sorted in a data base or retrieval system, without the prior written permission of Beat Your Course Inc.



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BYC Concept Check ............................................................................................................................ 63 BYC Exam Practice Questions ....................................................................................................... 66 Unit 6: Mitochondria and Chloroplast ........................................................................................... 69 Mitochondria and Chloroplasts as Symbionts ....................................................................... 69 Mitochondria ....................................................................................................................................... 71 Chloroplasts ......................................................................................................................................... 74 BYC Concept Check ............................................................................................................................ 79 BYC Exam Practice Questions ....................................................................................................... 82 Unit 7: Cytoskeleton .............................................................................................................................. 84 Cytoskeleton ........................................................................................................................................ 84 BYC Concept Check ............................................................................................................................ 98 BYC Exam Practice Questions ..................................................................................................... 101 Unit 8: Cell Cycle and Mitosis ........................................................................................................... 105 Cell Cycle and Checkpoints .......................................................................................................... 105 CDK-Cyclin .......................................................................................................................................... 107 Mitosis and Cell Division ............................................................................................................... 113 BYC Concept Check .......................................................................................................................... 118 BYC Exam Practice Questions ..................................................................................................... 121 Comprehensive Exam Practice Questions ................................................................................. 124 BYC Practice Final #1 .......................................................................................................................... 130 BYC Practice Final #2 .......................................................................................................................... 138 Codon Table ............................................................................................................................................ 145 Extra Page 1 ............................................................................................................................................. 146 Extra Page 2 ............................................................................................................................................. 147 Extra Page 3 ............................................................................................................................................. 148



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Notes about the Exam BIOL200 exams are oftentimes tricky. The professors do not intend to trick the students, but the question are laid out in a manner which is unfamiliar to the students. Midterms are short and thus are a test of speed and accuracy. The exams generally begin with some vague and confusing microscopy questions in order to catch students off guard immediately. Some students make the mistake of spending all their time on these microscopy questions. DO NOT DO THIS as it will waste valuable time and the questions are not worth many marks. The microscopy section is often followed by a few multiple choice questions, some of which will be straightforward, but some of them follow the structure of “Of the following 5 items, which are true of _____”. These cause students to pause and panic. The reason these questions are used and why they are often difficult is because they require the students to be confident in their knowledge. The questions often have very subtle changes from the facts, adding to the difficulty. Finally, there are one or two questions regarding experimental evidence or experimental design. These are the most difficult questions and the questions worth the most marks. The wording of the question will be quite long and somewhat complex. Therefore, it is advisable to make notes while reading. Read the question carefully two times. DO NOT get into the habit of rereading the question each time you need information, as this will waste a ton of time. Generally, they will not introduce any complicated techniques, but be aware that they may explain a simple, but new, technique and expect students to understand the data produced. Ultimately, BIOL200 is designed to get students to think critically and discern what the questions ask. Given the proper preparation, students should have no trouble attaining a high grade.

Notes about the BYC Crash Course Booklet This booklet is designed as a study guide which explains most of the theory in the course. It omits materials covered in pre-requisite classes and assumes prior general knowledge which is required for understanding some of the concepts presented. Brief reviews are given for extremely relevant topics (i.e. amino acids, nucleotides). The material presented is generally presented with images (Taken from various sources) as a study aid to help those who are visual learners and to make clear complex content. The crash course booklet has many questions which aim to emulate questions and topics which may be covered in the final, but BYC has no insider knowledge of what will actually appear on the exam. The concept check questions are essentially the same in this booklet as the midterm booklet because they are simply there to ensure the main concepts of each section are understood. It is my personal hope that this booklet helps each student in attendance to fully understand and appreciate the beauty of biology and biochemistry and for each student to achieve academic success.





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BIOL200: Fundamentals of Cell Biology Unit 1: Cell Organelles and Microscopy All relevant readings can be found in Essential Cell Biology by Alberts et al. Unit 1 Cell Organization Microscopy



2nd Edition

3rd Edition

Chapter 1

Chapter 1

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4th Edition Chapter 1 1-36 Panel 1-1



Cell Organization −

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Cells – Small, membrane-enclosed units, filled with chemicals in an aqueous solution, which have the unique ability to grow and divide o Cells are the fundamental units of life (Nothing smaller is considered living) § Cell Theory: All living cells are formed from division of pre-existing cells o Cells can vary in size (µm), shape, and, subsequently, function § Variance of cells can arise from mutations (Evolution) or different expression of genes (See “From Gene to Protein” for details) o Cells contain fundamentally similar internal chemistry § Central Dogma of Molecular Biology: DNA à RNA à Protein Cytosol – Aqueous gel which is not contained within any intracellular membrane; the site of many crucial chemical reactions Organelles – Specialized subunit of a cell which carries out a specific function; generally separated (or enclosed) by one or more membranes o Nucleus – The most prominent organelle in eukaryotic cells; it is enclosed by a double-membrane (Nuclear envelope) and contains the genetic information o Mitochondria – The ‘powerhouse’ organelle found in most eukaryotic cells; it is enclosed by an inner and outer membrane and produces ATP § Contains its own genetic information, separate from the nucleus o Chloroplast – Large green organelles found in plants and algae; it is enclosed by an inner and outer membrane and makes sugar by harnessing light energy § Contains its own genetic information, separate from the nucleus o Endoplasmic Reticulum (ER) – Irregular set of interconnected spaces separated by a membrane; it is the site at which components for cell membranes and other exported products are made o Golgi Apparatus – A stack of flattened, membrane-enclosed sacs which package and modify products of the ER o Lysosomes – Small membrane-enclosed organelles which are responsible for intracellular digestion o Peroxisomes – Small membrane-enclosed vesicles in which reactions involving hydrogen peroxide (H2O2) and detoxification occur

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Cytoskeleton – A dynamic network of protein filaments within the cytoplasm which controls a cells mechanical strength, shape, and movement o Microfilaments (Actin Filaments) – Thinnest filaments which consist of actin o Intermediate Filaments – Intermediate in thickness between microfilaments and microtubules; they serve to strengthen the cell o Microtubules – The largest filaments which consist of tubulin



Modified from Essential Cell Biology (© Garland Science 2014)

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Microscopy Magnification and Resolution

1. Magnification – Enlarging the appearance of an object 2. Resolution – Describes the ability of an apparatus to distinguish between two points a. Resolution ∝

" #$%&'(&%







Light Microscopy – Microscopy which uses white light to illuminate specimens o Transmitted Light Microscopy – External source of light passes through specimen § Bright Field – Direct light passing through (Simplest) § Dark Field – Light source is aligned such that directly transmitted light (Through the specimen; unscattered) is minimized; only scattered light is observed § Phase Contrast – Specimens have a light halo; no preparation required Increase contrast for § Differential Interference Contrast (DIC) – Images look 3-Dimensional UNSTAINED samples (Raised) o Emitted Light Microscopy – External light is used to excite photons on the specimen, causing light emission § Epifluorescence – Excitatory light causes fluorescence of the entire specimen § Confocal – Allows focus on a single plane, reducing noise from planes above and below the desired plane (Optical slicing) −



Fluorescence Dyes

1. Direct Staining – Using dyes (Fluorochromes) which bind directly to the region of interest; works with membranes, nucleus (DNA), mitochondria, and cytoskeleton 2. Indirect Staining (Immunofluorescence) – Using a primary antibody which binds the target followed by a secondary antibody (With the dye) which binds the primary antibody 3. GFP-Tagging – Introduction of the GFP gene to the gene of interest







Electron Microscopy (EM) – Microscopy which uses electrons as a source of illumination o Transmission Electron Microscopy (TEM) – An electron beam passes through the specimen (Similar to light microscopy) o Scanning Electron Microscopy (SEM) – An electron beam is scanned across the surface of a specimen coated with a very thin layer of a heavy metal (i.e. gold), leading to electron emission, leading to a 3D image of the surface

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7 Resolution

Advantages

Limitations



Comparison of Microscopy Light TEM ~200nm (except confocal) 0.2nm Living Cells Colour (If stained) High resolution and detail Whole Tissues (Usually Stained) Samples are Dead No Colour Low resolution (Due to Difficult to know 3D wave-like nature of light) structures (Cross-section) Complex preparation





SEM 0.2nm 3D View of the Surface

Samples are Dead No Colour

Relative Size Structure Cell Nucleus Mitochondria Chloroplast Endoplasmic Reticulum Golgi Apparatus Lysosome Peroxisome



Size Range 10~100µm 3~10µm 0.5~3.0µm ~5.0µm 10~20µm 20~25µm 0.2~1µm 0.2~1µm



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BYC Concept Check 1. Consider the following: i. Cow ii. Virus iii. Neurons iv. Tree v. Proteins vi. Bacteria vii. Lysosome



Which are considered living and which are not considered living? Why?

2. What is the central dogma of molecular biology? Why is this such an important concept?

3. What is cell theory?





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4. Describe five (5) eukaryotic organelles and their basic function

5. Explain the structure-function relationship of the mitochondria (Specifically its inner membrane)

6. Explain the structure-function relationship of the endoplasmic reticulum





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7. Briefly describe three methods to dye cells for fluorescence microscopy.

8. Compare and contrast light microscopy and electron microscopy, including the advantages and limitations of both.

9. List the following in order of largest to smallest: a. Peroxisome b. Human c. Cell Nucleus d. Nucleolus e. Lung





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BYC Exam Practice Questions 1. For the following images, indicate the type of microscopy (TEM, SEM, or Light Microscopy) and a description of the micrograph.

a. Microscopy: Description:



b. Microscopy: Description:



c. Microscopy: Description:





Modified from Essential Cell Biology (© Garland Science 2014)







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2. A scientist at a big pharmaceutical company is testing a new drug which supposedly increases the production of creatine. Its primary target is to athletes who wish to enhance their performance without being detected. The supervisor is suspicious of this drug and wants to observe its effects on a living cell. What approach would you use? Explore the pros and cons.







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