BIOL 2107K: QUIZ 2
133 Cards in this Set
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Amino Acid
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consists of central carbon atom connected by covalent bonds to four chemical groups
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Four Chemical Groups
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amino group, carboxyl group, a hydrogen atom, and a side chain or R group
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R group
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also known as side chain, makes the "letters" of the amino acid.
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Structure of Amino Acid
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tetrahedron (3 dimensional)
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Peptide Bond
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The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid
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Amino end
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contains a free amino group in the peptide bond.
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Carboxyl End
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contains a free carboxyl group in the peptide bond
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Polypeptide
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A polymer (chain) of many amino acids linked together by peptide bonds.
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shortest length of peptide bonds in human cell
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100 amino acids
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longest length of peptide bonds in human cell
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34,350 amino acids
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Amino Acid Residues
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amino acids that are incorporated into a protein.
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Primary Structure
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the sequence of amino acids in a protein
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Secondary Structures
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interactions between stretches of amino acids in a protein
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Tertiary structure
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longer-range interactions between these secondary structures that support the three-dimensional shape of the protein
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Quaternary structure
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proteins made up of several individual polypeptides that interact with each other
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How are Amino acids listed in a protein?
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in order from left to right, starting at the amino end and proceeding towards the carboxyl end
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How does the peptide chain fold?
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Hydrogen bonds forming between the carbonyl group and in one peptide bond and the amine group in another.
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Denatured
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a protein that has unfolded by chemical treatment or high temperature losing functional activity
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Chaperones
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protects slow folding, or denatured proteins until they can attain their proper three dimensional structure by binding with hydrophobic groups and non polar side chains to shield them from inappropriate aggregation.
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Transcription
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sequence of bases along part of a DNA strand is used as a template in the synthesis of a complementary sequence of bases in an RNA molecule.
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Translation
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sequence of bases in an RNA molecule is used to specify the order in which successive amino acids are added to a newly synthesized polypeptide chain
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Ribosomes
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complex structures of RNA and protein
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Where does translation take place?
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Ribosmes
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Transfer RNA (tRNA)
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A (aminoacyl), P (peptidyl), and E (exit site)
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Codon
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coding for a single amino acid in the polypeptide chain. It is constituted by a non overlapping of 3 adjacent nucleotides
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aminoacyl tRNA synthetases
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enzymes that connect specific amino acids to specific tRNA molecules. responsible for translating the codon sequence in a nucleic acid to a specific amino acid in a polypeptide chain
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Genetic code
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used by codons to specify an amino acid
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initiation
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first process of translation, initiator AUG codon is recognized and Met is established as the first amino acid in the new polypeptide chain.
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elongation
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second process of translation successive amino acid are added one by one to the growing chain.
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termination
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third process of translation, the addition of amino acids stop and the completed polypeptide chain is released from the ribosome.
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What does initiation of translation require?
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a number of protein initiation factors that bind to mRNA
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elongation factors
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breaking of high energy bonds of the molecule GTP bound with proteins
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protein release factor
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binds to the A site of the ribosome when a stop codon is encountered.
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polycistronic mRNA
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the ability to initiate translation allowing prokaryotic mRNAs to contain open reading frames for more than one protein.
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protein families
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up to 25,000 similar proteins that are structurally and functionally related.
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folding domain
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a region of a protein that folds in a similar way relatively independent from the rest of the protein. (globin fold, Rossman fold, TIM barrel, Beta barrel)
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Wherer is initiation in eukaryoutes?
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at the 5' cap in Monocistronic mRNA
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Where is initiation in prokaryotes?
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at any Shine-Dalgarno sequence (5'-AGGAGGU-3') in Polycistronic mRNA.
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Mutation
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a change in the sequence of a gene
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selection
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a process in a population of organisms where random mutations are retained or eliminated among the individualss' basis of their ability to survive and reproduce.
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amphipathic
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molecules with both a hydrophillic and hydrophobic region
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micelles
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lipids with bulky heads and a single hydrophobic fatty acid tail that are wedge shaped and packed into spherical structures
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lipid bilayer
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a two layered structure organized in such a way that the hydrophyllic portion faces out towards the aqueous environment and the hydrophobic portion faces the other hydrophobic portion away the aqueous environment through weak van der Waals structures. resulting in a closed structure with …
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liposomes
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nclosed bilayer structures that form when phospholipids are added to a test tube of water with a nuetral pH.
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fluidity
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how well membrane lipids can move in the plane of the membrane.
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cholesterol
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amphipathic, composed of a hydrophilic hydroxyl group, and a hydrophobic region of 4 interconnected carbon rings with an attached hydrocarbon chain. present in cell membranes
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What affects the fluidity of cholesterol?
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temperature. high at low temperatures, and low at high temperatures
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lipid rafts
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specific types of lipids assembled into defined patches
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transporters
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moves ions or other molecules across a membrane
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channels
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a transporter that allow movement of molecules through them
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carriers
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facilitate movement through the membrane
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receptors
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allows cells to receive signals from the environment
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enzymes
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catalyze chemical reactions
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anchors
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attach to other proteins that help to maintain cell structure and shape
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integral membrane proteins
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permanently associated with cell membranes and cannot be separated from the membrane experimentally without destroying the membrane itself.
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peripheral membrane proteins
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temporarily associated with the lipid bilayer with integral membrane proteins through weak noncovalent interactions
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transmembrane proteins
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span entire lipid bilayer, composed of two hyprophilic regions on each end of the membrane, and one hydrophobic region connected to the membrane
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fluid mosaic
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a model proposing the lipid bilayer is a fluid structure that allows molecules to move laterally within the membrane, and is a mixture of lipids and proteins
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plasma membrane
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encloses cells, also called the cell membrane. the boundary that defines the space of the cell
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cell wall
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in plant cells, maintaining the shape and internal composition of the cell
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homeostasis
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active maintenance of a constant environment
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selective barrier
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some molecules can move in and out freely in the plasma membrane.
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diffusion
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passive transport and random movement of molecules
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facilitated diffusion
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when a molecule moves by diffusion through a membrane protein and bypasses the lipid bilayer
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aquaporins
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allow water to flow through the plasma membrane more readily than facilitated diffusion
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osmosis
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diffusion of water
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Primary active transport
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uses the energy of ATP
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contractile vacuoles
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compartments that take up excess water from inside the cell and then expel it into the external environment in single celled organisms
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turgor pressure
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force exerted by water pressing against an object resulting in hydrostatic pressure in plant cells
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vacuole
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absorbs water and contributes to turgor pressure in plant cells
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nucleus
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houses genetic material in a membrane- bound space
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Prokaryotes
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include bacteria and archaea, and lacks a nucleus
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Eukaryotes
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plants, animals, fungi, and protists that have a nucleus
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nucleoid
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discrete region where DNA is concentrated
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plasmids
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carry a small number of genes
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organelles
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internal array of membranes in eukaryotes, that define the cell contents into smaller spaces
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endoplasmic reticulum (ER)
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involved in synthesis of proteins and lipids
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smooth ER
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lacks ribosomes, contains fatt acids and phospholipidssite of synthesis of lipids
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rough ER
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contains ribosomes, site of synthesis of proteins
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golgi apparatus
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modifies proteins and lipids produced in ER acts as sorting station
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lysosomes
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contain enzymes that break down macromolecules such as proteins, nucleic acids, lipids, and complex carbohydrates
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mitochondria
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harness energy for the cell
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cytoskeleton
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helps cells to maintain their shape and serves as a network of tracks for the movement of substances within cells
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chloroplasts
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that convert energy sunlight into chemical energy
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cytoplasm
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consists of all of the contents of the cell.
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cytosol
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includes the all of the organelles but the mitochondria.it compartmentalizes the cell.
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exocytosis
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vesicles fusing with the plasma membrane
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endocytosis
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vesicles fusing from organelle to organelle
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nucleus
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stores DNA, site of RNA synthesis
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nuclear envelope
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defines the boundary of the nucleus
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nuclear pores
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protein openings in the nucleus
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lumen
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interior of the endoplasmic reticulum
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cisternae
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series of flattened membrane sacs
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lysosomes
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specialized vesicles that degrade damaged or uneeded macromolecules
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protein sorting
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process by which proteins end up where they need to be to perform their function.
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signal sequences
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direct proteins to their proper cellular compartments
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nuclear localization signal
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enables proteins to move through pores in their nuclear envelope.
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signal-recognition particle (SRP)
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binds to both the signal sequence and the ribosome and brings about a pause in translation. binds with receptor on the RER. and dissociates and translation continues
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photosynthesis
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the capturing of energy of sunlight to synthesize simple sugars
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chloroplasts
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capture energy from sunlight
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thykaloid
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internal membrane-bound compartment in chloroplasts
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chlorophyll
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specialized light-collecting molecules called pigments
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adenosine triphosphate (ATP)
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the type of energy that cells use. currency of energy in cells
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phototrophs
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organisms that capture energy from sunlight
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chemotrophs
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organisms that get their energy directly from organic molecules
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autotrophs
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organisms that are able to convert carbon dioxide into glucose
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heterotrophs
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organisims that eat other organisms
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metabolism
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the entire set of chemical reactions that convert molecules and transfer energy in living organisms
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catabolism
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set of chemical reactions that break down molecules into smaller units, producing ATP
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anabolism
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set of chemical reactions that build molecules from smaller unitsand require an input of energy, ATP
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kinetic energy
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energy of motion
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potential energy
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stored energy. chemical energy is a form of this.
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first law of thermodynamics
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conservation of energy. energy is neither created nor destroyed
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second law of thermodynamics
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transformation is associated with an increase in entropy
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endergonic
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delta g that require an input in energy and are not spontaneous
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Gibbs free energy
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the amount of energy available to do work
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enthalpy
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total amount of energy
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exergonic
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reactions with a negative dela g that release energy and proceed spontaneously
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energetic coupling
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a spontaneous reaction drives a non-spontaneous one providing the thermodynamic driving force of a non spontaneous biochemical reaction.
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enzymes
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highly specific proteins that catalyze chemical reactions. reduce the activation energy of a chemical reaction.
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transition state
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intermediate stage between reactants and products
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activation energy
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the energy input necessary to reach the transition state
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substrate
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an uncatalyzed reaction. forms a complex with enzymes which is then converted into a product.
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active site
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portion of enzymes that binds substrate and converts to product. where enzymes and substrates form both transient covalent bonds or weak noncovalent interactions.
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inhibitors
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decrease the activity of enzymes
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activators
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increase activity of enzymes
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irreversible inhibitors
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form covalent bonds with enzymes and inactivate them
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reversible inhibitors
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form weak bonds with enzymes and easily dissociate from them
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competitive inhibitors
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bind to the active site of the enzyme and prevent the binding of the substrate.
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non-competitve inhibitors
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bind to the substrate and there is no competition between the binding of the substrate and the inhibitor.
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negative feedback
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where binding changes the shape of the enzyme, inhibiting its function
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allosteric enzyme
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bind to activators and inhibitors at sites that are different from the active site resulting in the change in shape and activity of the enzyme.
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cofactor
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a substance that associates with an enzyme and plays a key role in its function.
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BIOL 2107K: QUIZ 2