Chapter 1: Biochemistry and the Unity of Life

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What three naturally occurring elements make up 98% of the atoms in an organism?
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-oxygen -hydrogen -carbon
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What has been referred to as the “matrix of life?”
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-water –>all life requires water
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What are most large molecules in living systems made up of?
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-carbon
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What do biological fuels react with oxygen to produce?
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-carbon dioxide and water
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Compare the strength of carbon-carbon bonds to silicon silicon bonds?
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-carbon-carbon bonds are much stronger than silicon-silicon bonds
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What two important consequences does this difference in bond strength have?
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1. large molecules can be built with the use of carbon-carbon bonds as the backbone because of stability of these bonds 2. more energy is released when carbon-carbon bonds undergo combustion than when silicon reacts with oxygen
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Carbon dioxide is readily soluble in water and can exist as a gas. What benefit does this offer?
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-it can remain in biochemical circulation, given off by one tissue or organism to be used by another tissue or organism
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Other than carbon, hydrogen, and oxygen, what three other elements have essential roles in living systems?
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-nitrogen -phosphorus -sulfer
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What percentage of humans are comprised of hydrogen?
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-63%
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What percentage of humans are comprised of oxygen?
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-25.5%
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What percentage of humans are comprised of carbon?
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-9.5%
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What are the four major classes of biomolecules?
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-proteins -nucleic acids -lipids -carbohydrates
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How many amino acids are there?
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-20
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What are amino acids linked by?
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-peptide bonds
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List 6 functions of proteins in the body.
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1. signal molecules 2. receptors for signal molecules 3. play structural roles 4. allow mobility 5. provide defenses agains environmental dangers 6. act as catalysts/enzymes
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What is the primary function of nucleic acids in the cell?
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-to store and transfer information
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What are nucleic acids constructed from?
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-nucleotides
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What are the three components of every nucleotide?
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1. five-carbon sugar 2. base (a heterocyclic ring) 3. at least one phoshoryl group
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What are the two types of nucleic acid?
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1. deoxyribonucleic acid (DNA) 2. ribonucleic acid (RNA)
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2WHat is the specific role of DNA?
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-to store genetic information
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What are the four deoxyribonucleotides that comprise DNA?
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1. adenine (A) 2. cytosine (C) 3. guanine (G) 4. thymine (T)
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What is the role of mRNA?
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-serves as a template for the synthesis of proteins
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Describe how RNA is different from DNA?
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-the base thymine (T) is replaced by the base uracil (U) -the sugar component of the ribonucleotides contains an additional hydroxyl (-OH) group
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Compare the size of lipids to the size of proteins and nucleic acids?
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-lipids are much smaller –>proteins and nucleic acids can have molecular weights of thousands to million, whereas a typical lipid has a molecular weight of 1300
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What is a key characteristic of many biochemically important lipids?
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-their dual chemical nature –>part of the molecule is hydrophilic and part is hydrophobic
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List three important functions of lipids.
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1. form barriers/membranes 2. store energy 3. act as signal molecules
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What are two important functions of carbohydrates?
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1. fuel source 2. sites of cell-to-cell interaction
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What is the most common carbohydrate fuel?
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-glucose
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What is glucose stored in animals as?
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-glycogen
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What does glycogen consist of?
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-many glucose molecules linke end to end and having occasional branches
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How many different types of carbohydrates are there?
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-thousands!
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What is the “central dogma”?
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-information flows from DNA to RNA and then to protein
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What is a genome?
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-the entirety of an organism’s hereditary information
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What is this information packaged into?
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-discrete units called genes
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What is the process of copying the genome called?
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-replication
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What enzymes catalyze the replication process?
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-a group of enzymes collectively called “DNA polymerase”
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What occurs during transcription?
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-DNA is copied into mRNA
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What enzyme catalyzes the transcription process?
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-RNA polymerase
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True or fals: every cell in a human body has the DNA information that encodes the instructions to make all tissues.
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-true
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What defines the function of a cell or tissue?
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-selective expression of DNA
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What occurs during translation?
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-information is translated from mRNA/nucleic acid to protein –>genetic information is rendered into a functional form
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Where does translation take place?
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-on large macromolecular complexes called ribosomes
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What do ribosomes consist of?
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-RNA and protein
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What is the basic unit of life?
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-the cell
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What is every cell delineated by?
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-a membrane that is comprised of a lipid bilayer
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Describe the lipid bilayer.
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-hydrophobic chains interact with each other -hydrophilic head groups interact with the environment
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What are the two basic types of cells?
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-eukaryotic cells -prokaryotic cells
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What is the main difference between the two?
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-the existence of membrane-enclosed compartments in eukaryotes and the absence of such compartments in prokaryotes
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List the four layers that surround every prokaryote, starting with the outermost layer.
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1. outer membrane 2. periplasmic space 3. cell wall 4. inner (plasma) membrane
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What two biochemical features minimally constitute a cell?
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1. barrier that separates the cell from its environment–plasma membrane 2. inside that is chemically different from the environment and that accommodates the biochemistry of living–cytoplasm
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What confers the selective permeability of the plasma membrane?
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-plasma proteins
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What two major processed to plasma proteins facilitate?
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1. the entrance of fuels and building blocks into the cell 2. the transduction of information from the extracellular space into the cell
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What is the plasma membrane of a plant itself surrounded by?
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-a cell wall
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What is the cell wall largely constructed from?
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-cellulose
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What is cellulose?
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-a long, linear polymer of glucose molecules
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In many eukaryotes, the cytoskeleton is a network of what three kinds of protein fibers?
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1. actin filaments 2. intermediate filaments 3. microtubules
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What is a key difference between eukaryotic cells and prokaryotic cells?
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-the presence of organelles
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What is the largest organelle in eukaryotes?
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-the nucleus
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What role does the nucleus play in the cell?
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-it houses the organism’s genome
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How many membranes surround the nucleus?
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-two
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How many membranes surround mitochondria?
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-two
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What are the names of these two membranes?
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-the outer mitochondrial membrane -the inner mitochondrial membrane
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What is the space between the two known as?
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-the intermembrane space
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In mitochondria, fuel molecules undergo __________ into __________ and __________ with the generation of __________.
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In mitochondria, fuel molecules undergo COMBUSTION into CARBON DIOXIDE and WATER with the generation of ATP.
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Approximately _____% of the energy used by a typical cell is produced in the mitochondria.
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Approximately 90% of the energy used by a typical cell is produced in the mitochondria.
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What double-membrane bound organelle is only found in plant cells?
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-chloroplast
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What occurs within chloroplasts?
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-the conversion of sunlight into chemical energy/photosynthesis
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What are the two types of endoplasmic reticulum?
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-smooth ER (no ribosomes) -rough ER (has ribosomes)
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What is the most notable role of the smooth ER?
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-processing of exogenous chemicals
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What are exogenous chemicals?
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-chemicals originating outside of the cell, such as drugs
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Where do biochemical reactions take place inside the ER?
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-on the cytoplasmic surfaces of the sacs -in their interiors/lumens
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Ribosomes are attached to what parts of rough ER?
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-the cytoplasmic side
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Free ribosomes synthesize proteins that are used in what location?
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-inside the cell
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Ribosomes attached to the rough ER synthesize proteins that are used in what location?
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-either inserted into cellular membranes or secreted from teh cell
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Proteins synthesized on the rough ER are transported into ______ ______ ______ ______ ______ ______ during the process of translation.
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Proteins synthesized on the rough ER are transported into THE LUMEN OF THE ENDOPLASMIC RETICULUM during the process of translation.
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What occurs during the lumen?
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-protein folds into its final three-dimensional structure
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With the assistance of what type of proteins?
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-chaperones
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Proteins are then often modified by the attachement of what?
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-carbohydrates
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How do folded, modified proteins leave the ER?
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-they bud off as transport vesicles
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Where are transport vesicles from the rough ER carried to?
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-the golgi complex
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What is the golgi complex?
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-a series of stacked membranes
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What occurs to proteins once they reach the golgi complex?
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-further processing –>in particular, a different set of carbohydrates is added
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What is formed when a vesicle filled with proteins destined for secretion buds off from the Golgi complex?
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-secretory granule/zymogen granule
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What is exocytosis?
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-the process process by which a cell directs the contents of secretory vesicles out of the cell membrane and into the extracellular space
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What is the opposite of exocytosis?
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-endocytosis
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What exactly is endocytosis?
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-an energy-using process by which cells absorb molecules (such as proteins) by engulfing them
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Material is taken into the cell when the plasma membrane ________ and buds off to form an ________.
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Material is taken into the cell when the plasma membrane INVAGINATES and buds off to form an ENDOSOME.
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Phagocytosis occurs when…?
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-large amounts of material are taken into the cell
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What do lysosomes contain?
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-a wide array of digestive enzymes
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How do lysosomes form?
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-in a manner analogous to the formation of secretory granules –>however, lysosomes fuse with endosomes instead of the cell membrane
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After fusion has taken place, what occurs?
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-the lysosomal enzymes digest the material
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What do they release?
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-small molecules that can be used as building blocks or fuel by the cell
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In addition to degrading extracellular materials, what other function do lysosomes perform?
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-the digest damaged intracellular organelles
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What is a second organelle that is unique to plant cells?
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-plant vacuoles
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Are these organelles double-membraned or single-membraned?
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-single membraned
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This organelle may occupy as much as _____% of a cell’s volume.
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-80%
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What do vacuoles store? Name three things.
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1. water 2. ions 3. nutrients
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What is familial hypercholestrolemia caused by?
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-the inefficient endocytosis of cholesterol from the blood
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What is tay-sachs disease caused by?
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-improper lysosome function

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