Cell Biology Final Exam Study Guide PDF

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Study Guide for Cell Biology Final 1 Study Guide for Final Date of Exam: Friday, December 14, 2018 at 10:30am Chapter 1: A Preview of the Cell ASSIGNMENT: IT’S A CELL WORLD AFTER ALL!! Read pages 1-17 in your textbook. Answer the questions which follow in the lecture guide. 1. CELL BIOLOGY: What is it? 2. THE DISCOVERY OF CELLS: Who is credited with the discovery of cells? When? How? 3. THE CELL THEORY: a. What are the three basic tenets of the cell theory? i. All organisms consist of one or more cells. ii. The cell is the basic unit of structure for all organisms. iii. All cells arise only from preexisting cells. b. Name the scientists who contributed to the cell theory. i. Schwann c. When was the cell theory first proposed? i. 1839 4. Examine the cell biology timeline on the next page. a. How old is modern cell biology? i. Around 75 years old b. Describe the 3 disciplines that “intertwined” to create modern cell biology. i. Biochemistry ii. Cytology iii. Genetics 5. What is a hypothesis? A null hypothesis? a. Hypothesis – a tentative explanation that can be tested experimentally or via further observation b. Null hypothesis – rephrasing the hypothesis as its opposite and seek to prove the latter 6. Cell biology is not a collection of facts but a process of discovery. Outline the basic approach used in a well-designed, controlled experiment. 7. Cell biologists typically study cellular processes in “model systems” that includes cell culture (cells grown in a laboratory) and model organisms. a. What is a HeLa cell? What are the advantages of this cell line? What are the ethical issues surrounding their use? b. Name 6 common model organisms used in cell biology and provide some examples of what we have learned from them. See Figure 1-9 on page 15. c. Chapter 1 introduces some important terms and concepts. What do the following mean? i. In vitro ii. In vivo iii. In silico

Study Guide for Cell Biology Final 2 Chapter 2: Chemistry of the Cell - 5 Important Principles Essential for Us to Understand - Importance of Carbon - Importance of Water - Importance of Selectively Permeable Membranes - Importance of Synthesis of Carbon Containing Polymers - Importance of Self Assembly - Review of Chemical Principles - Atomic Structure - Down to the atom - Covalent Bonds - Electrons are shared - Polar – electrons are not shared equally - Non-polar – electrons are shared equally - Non-Covalent Bonds - Ionic bonds – driven by charge - Hydrogen bonds – the bond between hydrogen and another atom - Van Der Waals forces – attractive forces between 2 molecules - Hydrophobic interactions – don’t want to be near water - Importance of Carbon - The carbon atom has a valence of 4 - Most likely to form covalent bonds with one another and with oxygen, hydrogen, nitrogen and sulfur - Carbon chains can branch - Can form double and triple bonds and rings - Bond Polarity - Electrons are not shared equally among atoms - Result from a high electronegativity of oxygen and sulfur compared to carbon and hydrogen - Have water solubility compared to C-C or C-H bonds, in which electrons are shared equally

Study Guide for Cell Biology Final 3 - Functional Groups Chemical Hydroxyl Group -OH added to a Structure carbon chain

Name of Compound

Alcohol (specific names usually end in -ol)

Example

Ethanol

Functional Properties

Chemical Group Structure

-Polar -Can form hydrogen bonds -Can dissolve in water

Carboxyl

Amino

C=O

OH-C=O or -COOH

-NH2

Carboxylic acids, or organic acids

Amines

Acetic acid

Glycine

-Has acidic properties -Found in cells that are ionized -Polar and charged

-Acts as a base -ionized with a charge of 1+ -Keeps a positive charge

-Ketones if in the middle of a carbon chain -Aldehydes if at the end of a carbon chain Acetone, the simplest ketone Propanal, an aldehyde -Can have same chemical makeup but different properties -Found in sugars

Sulfhydryl

Phosphate

Methyl

-SH or -HS

-OPO32Organic phosphates Glycerol phosphate -Contributes negative charge to molecule -Has potential to react with water -Backbone of phospholipids -Huge part of DNA

-CH3 Methylated compounds

Name of Compound

Thiols

Example

Cysteine

Functional Properties

-Two sulfhydryl bonds can react called “crosslinking” -Holds a protein together

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Carbonyl

Importance of Water - Universal solvent - Stabilizes muscles and bones - Maintains body temperature - Creates lots of hydrogen bonds - Oxygen forms 2 H-bonds - Hydrogen can only form 1 H-bond

5-methyl cytidine -Affects gene expression -Can affect sex hormone shape and function -Modifies genes and DNA -Nonpolar

Study Guide for Cell Biology Final 4

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- Driven by charge - Closer to ionic bonds than covalent - Weak bonds - Strong only due to QUANTITY of bonds - Between multiple water molecules Synthesis of Carbon Containing Biological Polymers - Monomer vs. Polymer - Most cellular structures are made of ordered arrays of linear polymers called MACROMOLECULES - Important macromolecules in the cell include PROTEINS, NUCLEIC ACIDS, and POLYSACCHARIDES - LIPIDS share some features of macromolecules, but are synthesized somewhat differently - Not a traditional macromolecule - Dehydration Synthesis - Removal of water for the building of macromolecules (polymers) - Hydrolysis - Addition of water to break polymers apart Denaturation and Renaturation - The unfolding of polypeptides, denaturation, leads to a loss of biological activity - When denatured proteins are returned to conditions in which the native conformation is stable, they may undergo renaturation, a refolding into the correct conformation - Often renaturation is associated with the return of the protein function, but NOT ALWAYS - Denature = uncoils; loses its function - Degrade = break polymers

Study Guide for Cell Biology Final 5 Chapter 3: Macromolecules of the Cell - Amino Acids and Proteins - Nucleic Acids, DNA and RNA - Polysaccharides - Lipids - Steroids - Terpenes - Building Macromolecules from Small Building Blocks Table 3-1 Common Small Molecules in Cells Kind of Molecules

Number Present

Amino acids

20

Aromatic bases

5

Sugars

Varies

Number of Molecules See list in Table 3-2 Adenine Cytosine Guanine Thymine Uracil Ribose Deoxyribose Glucose

Lipids -

Varies

Fatty acids

Role in Cell

Figure Number for Structures

Monomeric units of all proteins

3-2

Components of nucleic acids

3-15

Component of RNA Component of DNA Energy metabolism; component of starch and glycogen Components of phospholipids and membranes

3-15 3-24 3-27a

Cholesterol 3-27e Proteins - Classes (Functions) of Proteins - Transport - Enzymes - Regulation - Structure - Storage - Movement/Mobility - Defense - Receptors - Signaling - Monomeric Structure - Central carbon - Carboxyl group to make it an acid - Amino group - Hydrogen atom - R group that determines the kind of amino acid - Proteins can exist at the physiological pH because they are charged and ionized - Stereoisomers

Study Guide for Cell Biology Final 6

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- L-amino acids and D-amino acids are mirror images of each other - L-amino acids make up all proteins Amino Acids - Non-Polar R Groups - Glycine - Alanine - Valine - Leucine - Isoleucine - Methionine - Phenylalanine - Tryptophan - Proline - Contain little oxygen and nitrogen - Polar/Uncharged R Groups - Serine - Threonine - Cysteine - Tyrosine - Asparagine - Glutamine - Lots of oxygen and nitrogen with some sulfur - Polar/Charged R Groups - Aspartate - Glutamate - Lysine - Arginine - Histidine - Lots of carboxyl and amino groups Building a Polymer of Amino Acids - The unfolding of polypeptides, denaturation, leads to the loss of biological activity. - When denatured proteins are returned to conditions in which the native conformation is stable, they may undergo renaturation, a refolding into the correct conformation. - Often renaturation is associated with the return of the protein function, but NOT ALWAYS

Study Guide for Cell Biology Final 7

Table 3-2 Amino Acid

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Abbrev. for Amino Acids 3-Letter 1-Letter Abbrev. Abbrev. Ala A Arg R Asn N Asp D Cys C Glu E Gln Q Gly G His H Ile I Leu L Lys K Met M Phe F Pro P Ser S Thr T Trp W Tyr Y Val V

Alanine Arginine Asparagine Aspartate Cysteine Glutamate Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine Hierarchal Protein Structure - Primary structure = amino acid sequence - Secondary structure = local folding of polypeptide - Describes local regions of structure that result from H-bonds between NH and CO groups along the polypeptide backbone - Two major patterns - Alpha helix - Beta sheet - Tertiary structure = three-dimensional conformation - Quaternary structure = interactions between monomeric proteins to form a multimeric unit - Certain AA tend to form alpha helices whereas others tend to form beta sheets - PROLINE cannot form hydrogen bonds and tends to disrupt alpha helix structures by introducing a bend in the helix Motifs - Repetitive and commonly found - Certain combinations of alpha helices and beta sheets have been identified in many proteins - These units of secondary structure consist of short stretches of alpha helices and beta sheets and are called MOTIFS - Examples include…

Study Guide for Cell Biology Final 8

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- Beta-alpha-beta - Hairpin loop - Helix-turn-helix Tertiary Structure - Reflects the unique aspect of the amino acid sequence because it depends on interactions of the R groups - Neither repetitive nor easy to predict - Due to the factors involved - Results from the sum of hydrophobic residues avoiding water, hydrophilic residues interacting with water, the repulsion of similarly charged residues, and attraction between oppositely charged residues - Drive overall structure Native Conformation - Most stable possible 3D structure of a particular polypeptide - Proteins can be divided into two broad categories - Fibrous - Long fibers - Very repetitive - Extensive regions of secondary structure - i.e. keratin, fibrous proteins in silk, collagen, elastin - Globular - Dense, randomly folded - Less repetitive - Most proteins are globular - Each has its own unique tertiary structure - May be mainly alpha helical, mainly beta sheet or a mixture of both Domain = combination of tertiary structures Motif = combination of secondary structures Quaternary Structure - Multiple polypeptide chains - Concerned with subunit interactions and assembly - Driven by specific R groups - Applies specifically to multimeric proteins - Some have multiple subunits - Bonds and forces are the same as in tertiary structure - Formation is usually, but NOT ALWAYS, spontaneous - Molecular chaperones are sometimes required to assist Higher Levels of Assembly - Possible in the case of proteins that are organized into multiprotein complexes - Each protein may be involved sequentially in a common multistep process - i.e. pyruvate dehydrogenase complex, in which 3 enzymes and 5 other proteins form a multi-enzyme complex Protein Folding - Linear peptide - Very disordered

Study Guide for Cell Biology Final 9 - High entropy Native form - Lowest free energy - Spontaneous folding - Fold without assistance from chaperones - Chaperone mediated protein folding - Requires assistance to form into native structures - Importance of self-assembly - PROTEIN SEQUENCE IS DRIVING OVERALL STRUCTURE Nucleic Acids - RNA and DNA each consist of only 4 different types of nucleotides - Each nucleotide consists of a 5-carbon sugar, a phosphate group and an aromatic base - Each base is either a PURINE or a PYRIMIDINE - Purines = adenine and guanine - Pyrimidines = thymine, cytosine, and uracil (in RNA) - Nucleotides have different names depending on how many phosphate groups are attached - Adenosine = aromatic base and sugar - Adenosine monophosphate (AMP) = aromatic base, sugar and 1 phosphate group - Adenosine diphosphate (ADP) = aromatic base, sugar and 2 phosphate group - Adenosine triphosphate (ATP) = aromatic base, sugar and 3 phosphate group - Polymers are RNA and DNA - Linear polymers of nucleotides linked by a 3’5’ phosphodiester bridge - Polynucleotides have a 5’ phosphate group at one end and a 3’ hydroxyl group at the other - Complementary Base Pairing - Adenine bonds with thymine (uracil in RNA) - Guanine bonds with cytosine - Fundamental property of nucleic acids - Essential property for DNA structure, some RNA structure, replication and transcription processes - DNA Structure - Francis Crick and James Watson postulated the double helix structure of DNA in 1953. - The structure accounted for the known physical and chemical properties of DNA - Suggested a mechanism for DNA replication - The double helix consists of two anti-parallel and complementary strands of DNA twisted around a common axis to form a right-handed spiral structure - Beta-DNA; the main form in cells - RNA Structure -

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Study Guide for Cell Biology Final 10 -

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RNA is normally single stranded There can be secondary structures formed depending on the bases present in the molecule i.e. tRNA Polysaccharides - Long chain polymers of sugars and sugar derivatives - Usually consist of a single kind of repeating unit, or sometimes alternating pattern of two kinds of sugars - Short polymers are sometimes attached to cell surface proteins - OLIGOSACCHARIDES - Monomeric Units (Monosaccharides) - Repeating units of polysaccharides are monosaccharides - A sugar may be an aldehyde (ALDOSUGARS) with a terminal carbonyl group or ketone (KETOSUGARS) with an internal carbonyl group - Common Monosaccharides - The single most common monosaccharide is the aldohexose D-glucose - The formula n(CH2O) is common for sugars and led to the general term carbohydrate - For every molecule of CO2 incorporated into a sugar, one water molecule is consumed - The carbons of glucose are numbered from the more oxidized (carbonyl) end - Monosaccharides Isomers - The formation of a ring by D-glucose can result in two alternative forms - These depend on the spatial orientation of the hydroxyl group on carbon number 1 - These forms are designated alpha (hydroxyl group downward) and beta (hydroxyl group upward) - Disaccharide Linkages - The linkage of disaccharides is a glycosidic bond, formed between two monosaccharides by the elimination of water - Glycosidic bonds involving the alpha form of glucose are alpha-glycosidic bonds - Glycosidic bonds involving the beta form of glucose are beta-glycosidic bonds - Polysaccharides - Storage or structure - The most familiar storage of polysaccharides are STARCH in plant cells and GLYCOGEN in animals cells and bacteria - Both consist of alpha D-glucose units - Starch - Glucose reserve commonly found in plant tissue - Occurs in both as unbranched amylose (10-30%) and branched amylopectin (70-90%) - Amylopectin have alpha branches once every 12-25 units and longer side chains than glycogen - Starch is stored as starch grains within the plastids

Study Guide for Cell Biology Final 11 -

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Chloroplasts, the sites of carbon fixation and sugar synthesis in photosynthesis - Amyloplasts, which are specialized for starch storage Structural Polysaccharides - The best-known structural polysaccharide is the cellulose found in plant cell walls - Cellulose in composed of beta-D-glucose - Mammals cannot digest cellulose - Do not have the enzyme to break down - Cows and sheep have microflora to break down cellulose - Also in fungus but with different bonds - The cellulose of fungal cell walls differs from that of plants and may contain either beta (1-4) or beta (1-3) linkages - Bacterial cell walls contain two kinds of sugars GlcNAc (Nacetylglucosamine) and MurNAc (N-acetylmuramic acid) - Both are derivatives of beta-glucosamine and are linked alternately in cell walls Chitin - Consists of GlcNAc units only - Found in exoskeletons of insects, crustacean shells, and fungal cell walls

Lipids - NOT A POLYMER! - Function to… - Store energy - Make up membranes - Signal within the cell - 6 different kinds… - Fatty acids - Triacylglycerols - Phospholipids - Glycolipids - Steroids - Terpenes - Fatty acids - Components of several other kinds of lipids - Long amphipathic, unbranched hydrocarbon chain with a carboxyl group at one end - The polar carboxyl group is the “head” and the nonpolar hydrocarbon chain is the “tail” - In saturated fatty acids, each carbon atom in the chain is bonded to the maximum number of hydrogens - These have long straight chains that pack together - Unsaturated fatty acids have one or more double bonds, so they have bends in the chains and pack less tightly together - Less hydrogen - Triacylglycerols: Triglycerides

Study Guide for Cell Biology Final 12 -

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Consist of a glycerol molecule with 3 fatty acids attached to it Glycerol is a 3-carbon alcohol with a hydroxyl group on each carbon Fatty acids are linked to glycerol, one at a time, by ester bonds, formed by the removal of water - The main function is energy storage - Contain mostly saturated fats - Usually solid at room temperature - Unsaturated fats are usually liquid at room temperature Phospholipids - Important to membrane structure due to their amphipathic nature - Can be divided into phosphoglycerides or sphingolipids, depending on their chemistry Phosphoglycerides - PREDOMINANT phospholipids in most membranes - Composed of 2-fatty acids, 1 phosphate group, and 1 glycerol - Have a small hydrophilic alcohol linked to the phosphate Sphingolipids - Based on sphingosine - Long hydrocarbon chain with a single site of unsaturation near the polar end - Can form an amide bond with a long-chain fatty acid to make a ceramide - Used for cell signaling Glycolipids - Contain a carbohydrate instead of a phospholipid - Often derivatives of sphingosine and glycerol - Carb groups attached to a glycolipid may be 1-6 sugar units - Occur largely on the outer surface of the plasma membrane Steroids - Derivatives of a 4-ringed hydrocarbon skeleton - Nonpolar and hydrophobic - Differ based on positions of double bonds and functional groups - Cholesterol is the most common in animal cells - Insoluble and found in plasma membranes - Starting material for synthesis of steroid hormones, which include male and female sex hormones, glucocorticoids, and mineralocorticoids - Stigmasterol and sitosterol are most common in plant cells - Ergosterol is most common in fungal cells Terpenes - Synthesized from the 5-carbon isoprene - Sometimes called isoprenoids - Joined in various combinations to produce substances like vitamin A and carotenoid pigments - Dolichols are involved in activating sugar compounds - Coenzyme Q and plastoquinone act as electron carriers - Polyisoprenoids are found in the cell membranes of Arch

Study Guide for Cell Biology Final 13 Chapter 4: Cells and Organelles - A Tour of the Cell - Cells come in various sizes and shapes - Some of the smallest bacteria are about 0.2-0.3 micrometers in diameter - Some highly elongated nerve cells may extend a meter or more - Despite the extremes, cells in general fall into predictable SIZE RANGES - Why are cells so small? - How things get around in the cell/diffusion is easier - Easier to get rid of wastes - Keeps the molecules concentrate...