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355 Cards in this Set
- Front
- Back
- 3rd side (hint)
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The two basic cell types are:______ and______. What is the primary difference between the two?
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Procaryotes and Eucaryotes;
*Procaryotes have a single compartment (no organelles, nucleus) *Eucaryotes have compartmentalization which allows for the presence of various organelles (such as a nucleus) |
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Name 2 non-membranous organelles.
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*Ribosomes: protein synthesis
*Cytoskeleton: polarity and cell movement |
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What 3 things make up the cytoskeleton?
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*actin filaments
*microtubules *intermediate filaments |
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How does cell size compare b/t procaryotes and eucaryote?
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Procaryotes: 1-10 micrometers
Eucaryotes: 5-100 micrometers |
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Metabolic Function of Procaryotes and Eucaryotes...
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Procaryotes: anaerobic & aerobic respiration
Eucaryotes: aerobic respiration only |
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Three factors that effect the quality of an Optical Image?
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1. Magnification
2. Resolution 3. Contrast |
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Which elements make up 96.5% of an organisms weight?
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Carbon, Hydrogen, Nitrogen, Oxygen
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Two types of chemical bonds:
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Covalent and non-covalent bonds
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Def. Covalent bond
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Strong bonds that involve the sharing of electrons b/t atoms
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Def. Single vs. Double Covalent Bonds
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Single: sharing of 2 electrons (1 from each atom); allows for rotation around bond axis
Double: sharing of more than 2 electrons; shorter and stronger; no rotation allowed |
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What type of bond is the result of a positive charge being concentrated toward one end of the molecule (pos. pole) and a negative charge toward the other (neg. pole)---thereby attracting other poles of other molecules?
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Polar covalent bond
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Types of non-covalent bonds:
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*Ionic bond
*Hydrogen bond |
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What four families of small organic molecules make-up living organisms?
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*Sugars
*Fatty Acids *Amino Acids *Nucleotides |
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A reaction that is energetically unfavorable will occur if:
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it is enzymaticly linked to an energetically favorable reaction
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In metabolism, the hydride ion is a source of:
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reducing power
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The enzymes responsible for oxidative catabolism in eucaryotic cells are located in the:
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mitochondria
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What is meant by "polarity" of a polypeptide chain?
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the amino acids are arranged with their amino and carboxyl termini oriented in opposite directions, giving the chain two distinct ends
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What conds are necessary for non-covalent bonds to establish stable interactions b/t molecules?
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the two molecules must fit together, sufficiently well, so they can form large numbers of non-covalent bonds
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Living organisms require a continual supply of energy to exist because:
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they are creating order out of disorder inside their cells
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Which of the following is the most distinctive feature of eucaryotic cells?
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a nucleus
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Glucose, galactose and mannose are all examples of:
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isomers
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The most common type of reaction for attaining the subunits that make up a macromolecule is:
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dehydration
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The energy input required to initiate an energetically favorable chemical reaction is called the:
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activation energy
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Because of the second law of thermodynamics, what must always be produced during biosynthetic reactions?
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heat
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During oxidative catabolism, CO2 is produced as a by-product. Where does it come from?
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-from the oxidation of the carbon atoms from pyruvate coupled with the reduction of NAD+
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The _____________ in glycolysis produces a net gain of ____________.
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-Oxidation of Sugars
-ATP |
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How can the binding of a phosphate group or a nucleotide to a protein alter its activity?
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-by causing a change in three-dimensional shape of the protein
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What common property of the alpha-helix and the beta-helix makes them unviersal building blocks for the three-dimensional conformation of proteins?
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-because all of the peptide bonds are involved in hydrogen bonding, they are very stable and can be formed from many different amino acids
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What does an enzyme do?
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it accelerates chemical reactions by lowering the activation energy
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Proteins that help other proteins assume their proper three-dimensional conformation are called:
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molecular chaperones
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During each turn of the __________________, three molecules of NADH are generated.
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citric acid cycle
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During each turn of the citric acid cycle, three molecules of _______ are generated.
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NADH
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What happens to NADH in the reaction shown below?
NADH ---> NAD+ + H- |
It is oxidized
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Electrons passing along the electron transport chain move to _________ energy states.
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successively lower
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What type of interaction is primarily responsible for the folding of a polypeptide into a
beta-sheet? |
h-bonding between peptide bonds
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Proteins destined for destruction in the cytosol are usually tagged with ______.
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ubiquitin
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Motor proteins are usually what type of enzyme?
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ATPases
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What is the primary function of the citric acid cycle?
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to produce hydride ions
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When phospholipids form a bilayer in an aqueous solution, which part of the molecules occupy the interior of the bilayer?
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the fatty acids
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The phenomenon in which a protein changes shape as a result of binding to another molecule is referred to as:
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allostery
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Why do hydrophobic molecules such as lipids self-associate in aqueous solution?
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to minimize the disruption of hydrogen bonding between water molecules
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A negative ∆G for a reaction indicates that:
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the reaction is energetically favorable
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The quaternary structure of a protein refers to:
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the joining together of two or more polypeptide subunits
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The method most commonly used to determine the molecular weight of proteins is:
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SDS-polyacrylamide gel electrophoresis
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You might use antibodies to purify a particular protein from a mixture using the technique of:
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affinity chromatography
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The resolution of microscopes is improved by:
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decreasing the wavelength of the illuminating radiation and increasing the numerical aperture of the lenses
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Stable, three-dimensional structures that are evolutionarily conserved and appear in many different proteins are referred to as:
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Domains
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Which type of chromatography would be used to separate proteins on the basis of their charge?
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ion-exchange
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Is ATP produced during the citric acid cyle?
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no
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What is the main source of ATP in cells?
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electron transport
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A dye that fluoresces red when excited with green light is:
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rhodamine
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Coenzyme A is a carrier for:
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acetyl groups
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A phospholipid is composed of:
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one glycerol, two fatty acids, one phosphate group, and a polar head group
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Water molecules in liquid form are held together by ________bonds.
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hydrogen
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Fatty acids in a lipid micelle are held together by ________ interactions.
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hydrophobic
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The magnesium and chlorine atoms in magnesium chloride are held together by ______ bonds.
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ionic
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Covalent bonds are individually _________ than noncovalent bonds
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stronger
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Linked pair of chemical reactions in which free energy released by one serves to drive the other
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coupled reactions
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3-carbon sugar that is the terminal product of glycolysis.
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pyruvate
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General name of a molecule that binds to a binding site of a protein
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ligand
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Bond that attaches two adjacent nucleotides in a nucleic acid
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phosphodiester
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Polysaccharide composed exclusively of glucose units used to store energy in animal cells
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glycogen
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Bond that covalently links monosaccharides into chains
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glycosidic
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Compound composed of a purine or pyrimidine base linked to either a ribose or a deoxyribose sugar
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nucleoside
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proteins that bind and hydrolyze GTP
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G proteins
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5 steps in the preparation of tissues for microscopy:
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1. Fixation
2. Dehydration 3. Embedding 4. Sectioning 5. Staining |
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Tissue components that stain with acid are termed:
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Acidophilia (-ic)
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Tissue components that stain with BASIC dyes are termed:
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Basophilia (-ic)
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Double Staining includes:
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nuclear-stains and counter-stains
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Stains the DNA of the nucleus during double staining
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Nulear Stain
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Stains the components of the cytoplasm and/or ECM during double staining
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counter-stain
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Eosin is used as a:
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Counter-stain
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hematoxylin is used as a:
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Nuclear Stain
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Which contrast system is based on the princinple that light changes its speed when passing through cellular and extracellular structures with different refractive indices?
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Phase contrast light microscopy
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What material might be used during the embedding stage of tissue preparation for electron microscopy?
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plastic
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Formaldehyde is used for tissue fixation for which type of microscopy?
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light microscopy
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What chemical is used for tissue fixation when using an electron microscope?
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glutarladehyde andosmium tetroxide
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Designed to illuminate the sample with light of the excitation wavelength and collect the emitted light while excluding exciting light from the image
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Fluorescent microscopy
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Fluorescent microscopy. Which dye emits green light when excited by blue light?
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Fluorescein
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What do antibodies bind to?
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specific antigens
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What do enzymes bind with?
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substrates
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What does phallodin bind to?
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actin filaments
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What do ligands bind to?
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receptors
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This type of microscopy requires a high vacuum:
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electron microscopy
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2 Types of Electron Microscopes:
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1. Transmission Electron Microscopes (TEM)
2. Scanning Electron Microscopes (SEM) |
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List 4 characteristics of the TEM:
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1. analogous to brightfield electron microscope
2. uses a beam of electrons to penetrate sample 3. image formed on a phosphorescent screen from electrons that pass through the sample 4. used with ultra-thin sections and metal replicas |
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List 4 characteristics of the SEM:
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1. Analogous to television
2. uses narrow beam of electrons that scan over the surface of the sample 3. an image is formed on a video screen from electrons that are ejected from the surface of the sample an picked up by an electron detector that amplifies the signal 4. used with intact objects |
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How is contrast produced in a TEM--- to include the image?
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Contrast is produced by the scattering of electrons from the beam by atoms in the sample (electron scattering)--- it is more likely to repel and deflect the electrons from the beam. The image is formed by the electrons that are not deflected. Interaction between the electron beam and atoms in the sample produces X-rays and other types of radiation that provide information about the composition of the sample.
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Biosynthesis-
Reducing power supplied by electrons donated by _________. |
NADPH
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Biosynthesis-
Energy supplied by ______ of ATP |
hydrolysis
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biosynthetic reactions require:
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small biological molecules and energy
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Digestion
*occurs in digestive tract/_____ *provides _____ |
organelles.
small molecules |
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Glycolysis
*occurs in the ______ *does not require oxygen *basis of ____ metabolism |
cytosol
anaerobic |
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Oxidative Phosphorylation
*driven by electron transport across the __________ *generates _____ *requires _____ |
inner mitochondrial membrane.
ATP. oxygen. |
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Define: Digestion
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Enzymatic hydrolysis of macromolecules into their subunits.
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What enables Hydrolysis (reverse of the dehydration reaction used to attach the subunits together)?
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hydrolytic enzymes
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Digestion takes place _____ of the cell.
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"outside"
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Digestive tract (multicellular organisms), Digestivecompartments (_____)
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within cells
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Mechanism used to link ATP hydrolysis to the monomer addition in condensation reactions in polymer synthesis in cells is very complex and involves:
*________ *________ |
*Formation of high energy intermediates
*Different routs for ATP hydrolysis |
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Cells use various strategies to organize enzymes to increasetheir efficiency:
*Speed up reactions by _____ *Control reactions _____ |
spatially arranging enzymes:
-in multienzyme complexes -within membranes -on the surfaces of membranes -on the surface of cytoskeletal filaments * by separating enzymes from potential substrates -membrane-bound compartments -other controlled access compartments -in different cells |
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Metabolic reactions are ______ and catalyzed by enzymes
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highly controlled
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Enzyme-catalyzed reactions usually connected in series -______ of one reaction is a ______ for the next reaction
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product
substrate |
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What constitutes most of a cell's mass?
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Protein
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_________ execute nearly all of cell functions.
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Proteins
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Protein functions:
(9 total) |
1 Enzymes - catalyze covalent bond formation or breakage
2 Structural proteins - mechanical support in cells and tissues 3 Transport proteins - carry small molecules or ions 4 Motor proteins - generate movement in cells and tissues 5 Storage proteins - store small molecules or ions 6 Signal proteins - carry signals from cell to cell 7 Receptor proteins - detect signals and transmit them 8 Gene regulatory proteins - bind to DNA to switch geneson/off 9 Special-purpose proteins - highly variable functions |
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Proteins are the most _____complex and ____ sophisticated molecules known.
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structurally
functionally |
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Characteristics of Proteins:
(5 total) |
1 High molecular weight (10 - 1000 kD), 30-10,000 AA long
2 Polymers of subunits (monomers) held together by covalentbonds - polypeptides 3 Subunits attached via a dehydration reaction 4 Synthesis requires metabolic energy from ATP or GTP 5 Long polymers are flexible and can fold into 3D configurations determined primarily by noncovalent bonds |
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Define: Protein
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Macromolecules composed of one or more flexible chains of amino acids (polypeptides) held together by peptide bonds.
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Define: glycoprotein
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A protein covalently linked to one or more ologosaccharides.
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Three-dimensional conformation of proteins is determined by its amino acid sequence and interactions between atoms:
(3 total) |
-within the same molecule (intramolecular interactions)
-with other molecules (intermolecular interactions) like proteins and phospholipids -small molecules in the environment (water, inorganic ions, small ligands,etc.) |
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Most interactions within the same molecule are in the form of weak, non-covalent bonds: (3+1 total)
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*ionic bonds
*hydrogen bonds *van der Waals forces -Some interactions are in the form of covalent disulfidebonds (-S-S-) |
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Folding in cells assisted by molecular chaperones.
How? |
Bind to partly folded chains and help to fold, in crowded cell environment prevent association with other molecules until folding is complete, recognize products of mutated genes.
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Two families of molecular chaperones:
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hsp70 - acts early during initial folding of the polypeptide
hsp60 - forms a barrel-like cage into which misfolded proteins are placed and the folding corrected |
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Improper folding of proteins causes can form ____ and ___. This can cause disease, including some storage, and neurodegenerative diseases.
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aggregates and accumulate
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What are Prions?
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misfolded forms of proteins that can convert properly folded proteins into the abnormal configuration (PrP in scrapie, BSE, CJD)
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Protein structure is complex, come in variety of complicated shapes: (6 total)
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globular, fibrillar, can form filaments, sheets, rings, spheres
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Name the 4 different types of 3D protein models:
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backbone, ribbon, wire and space filling
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Common Folding Patterns:
-result from _____________ __________ __________ _____. Protein chain adopts a regular, repeating form (motif). -amino acid side chains are not involved -Can be illustrated showing all atoms in the polypeptide  backbone, backbone atoms only or cartoon symbols used to represent the a helix and the b sheet in ribbon drawings of proteins |
hydrogen bonds forming between N-H and C=Ogroups in the polypeptide backbone
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a helix
Short regions of alpha helix abundant in cell membrane proteins crossing lipid bilayer (non polar side chains face ___ and hydrophilic backbone face ____ of the helix) |
lipid
the interior |
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2 a helixes can form a Coiled-coil
Very stable structure (e.g. _____, or ___) Forms when 2 alpha helices have most of their hydrophobic side chains on one side Þ they twist around eachother (hydrophobic sites face each other avoiding interaction with the____ environment. |
alpha-keratin, myosin
aqueous |
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Proteins - Levels of Structural Organization:
Primary _______ determines the pattern of folding of a polypeptide. Secondary folding of the polypeptide into stable configurations some stable folding patterns occur repeatedly in polypeptides: ___,___,___. Tertiary full three-dimensional conformation formed by entire polypeptide chain (__,__,__,__,__) Quaternary association of two or more polypeptides into a ____ ______. |
-amino acid sequence
-ahelix, bsheet, coiled coil -a helices, b sheets, coiled coils and other loops and folds -functional protein |
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Proteins - Domains
Domains = regions of 100 - 250 amino acids that fold independently of the rest of a polypeptide to form stable, compact structures Define: Domain *often associated with different functions binding sites for _____ binding sites for specific ______. *single protein may contain one or more domains *domains are evolutionarily ____ and found in numerous proteins -Allows functions to be incorporated into to new proteins by ____ and _____. |
-the modular unit for construction of larger proteins
-specific ligands -DNA sequences structural features -conserved -genetic duplication and rearrangement |
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Evolution of Proteins
New proteins evolve primarily by ______ of existing proteins Define: Mutation What is elimination of cells with deleterious mutations and selection of cells with advantageous mutations? Conservation of domains Þ once developed,functionally useful domains tend to be conserved. Mutation of amino acid sequences outside of the domains Þmay confer new __,__, or ___ on old domains What combines old domains in new ways to form new proteins? |
-alterations
-random changes in amino acid sequence -Natural Selection -specificity, control, or function -Genetic recombination |
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Protein Families
Evolution has produced families of proteins that have amino acid sequences and functional domains in common Examples: *Serine proteases structurallysimilar proteins that differ in their specificity of ___ ____(trypsin, chymotrtypsin,elastase) *___-___ ___ contain a domain that binds calcium ions *ATPases contain a domain that ___ and ____ ATP |
-enzyme activity
-Calcium-binding proteins -binds and hydrolyzes |
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Types of Contrast in the Light Microscope:
(7) |
*Amplitude contrast (brightfield), colored dyes
* Phase contrast * Interference contrast * Differential interference contrast (Nomarski) * Hoffman modulation contrast * Darkfield * Fluorescence |
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Light Microscopy-
Histochemical Staining: |
detects and reveals the location ofspecific substances
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Sources of Contrast in TEM-
Positive staining of sections with ______________ reveals structures that bind the metal's structures appear dark compared to the background |
salts of heavymetals in solution (U, Pb, Os)
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Sources of Contrast in TEM-
_______ staining of structures with salts of heavymetals in solution (_,______) reveals structures that exclude the metal salts, producing a"negative" image structures appear light compared to the background |
-Negative
-U, phosphotungstic acid |
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Sources of Contrast in TEM-
Shadowing with __________(__) reveals structures that accumulate a coating of atoms ----structures appear dark against the background |
- evaporated metal atoms (Pt,W)
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Used to visualize surface details of small samples, including macromolecules, supramolecular structures, andviruses in TEM.
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Negative staining
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Traditional method to visualize the internal structures of cells in the TEM
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Ultrathin Sections
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Used to visualize surface details of small samples, including macromolecules, supramolecular structures, and viruses in TEM
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Negative Staining
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Creates a shadow-cast replica of the surface of a sample that can be viewed in the TEM
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Metal-carbon Replicas
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Freeze Fracture Replicas
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Reveals the interior of biological membranes by splitting the lipid bilayer in half
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What do they do?
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Contrast in the SEM is caused by the _______ of _______ electrons from the surface of the sample by high energy electrons in the beam.
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-ejection
-secondary |
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What is an isomer?
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A set of compunds with the same molecular formula but differrent structural formula
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This bond is the result of attraction between positively and negatively charged atoms in which one atom donates an electron from the other atom.
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ionic bond
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1. sugar + lipid
2. sugar + protein 3. Oligosaccharides 4. Polysacchardides |
1. glycolipids
2. glycoproteins 3. several sugar molecules 4. large number of sugar molecules |
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Why are the properties of water important in determining the chemistry of cells?
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Life evolved in an aqueous environment and cells are made up predominately of water
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two types of soluable molecules:
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-ionic substances
-polar substances |
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Insoluable molecules: (examples of)
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hydrocarbons and other non polar molecules.
-organic vs. aqueous |
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Describe a glycosidic bond:
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monosaccharides can be covalently linked to each other via a glycosidic bond to from chains
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Glycosidic bond formation:
1. describe 2. forming rxn 3. breaking rxn |
1. Can form between the oxygen associated w/ the 1- carbon and carbon carrying a hydroxyl (-OH) group.
2. condensation rxn (hydration rxn) 3. hydrolysis 3. |
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Alpha and Beta Links: Hydroxyl
1. describe 2. describe alpha 3. describe beta |
1. the hydroxyl group on the 1-carbon can change from one position to another
2. hydroxyl below the plane of the ring 3. hydroxyl above the plane of the ring |
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-COOH indicates a:
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carboxyl group
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--NH2 indicates a:
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amino group
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-C=O indicates a:
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carbonyl group
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-PO3^2- indicates a:
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Phosphoryl group
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-OH indicates a:
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Hydroxyl group
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_______ take up 26 percent of the total cell weight.
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proteins
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_____ takes up 70 percent of the total cell weight
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water
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Compunds with the general formula CH2-O are called
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sugars
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mirror image pairs of molecules are known as
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optical isomers
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The surfaces of most cells are decorated with sugar polymers that belong to _________ and _________. (which two groups?)
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-glycoproteins
-glycolipids |
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Chitin is a:
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polysaccharide
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Molecules such as fatty acids, which possess both hydrophobic and hydrophilic regions are termed:
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amphipathic
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A fatty acid consists of two main parts:
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-long chain hydrocarbon (hydrophobic)
-carboxyl group (acts as acid) |
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Phospholipid make-up:
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Head: polar group, phosphate, glycerol
Tail: Fatty acids |
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Fatty acids serve as:
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concentrated food reserve in cells
- can be broken down to produce 6 times the amount of energy of glucose |
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Fatty acids are stored in the cytoplasm of many cells in the form of:
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triacylglycerol molecules
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What is a triacylglycerol? (its make up)
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compunds made of 3 fatty acid chains joined to a glycerol molecule
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This class of biological molecules is a loosely defined collection with the common feature that they are insoluable in water and soluable in fat and oganic substances such as benzene
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lipids
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The most important function of lipids is:
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the construction of cell membranes
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Amino acids are the subunits of:
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proteins
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________ are a varied class of molecules with one defining property: they all possess a carboxylic acid group and an amino group, both linked to the same carbon atom called the ________.
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- Amino acids
- alpha-carbon |
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the covalent linkage b/t two adjacent amino acids in a protein chain is called a:
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peptide bond
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Peptide bonds are formed via ______ reactions
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condensation (hydration)
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Proteins have structural/ electrical polarity?
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Structural
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Only the _____ form of amino acids are found in proteins
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L-form
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L or D
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Nucleotides are the subunits of:
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DNA and RNA
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What is a nucleoside?
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a molecule made of a nitrogen-containing ring compound linked to a five-carbon sugar, which can either be ribose or deoxyribose
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A nucleoside sporting one or more phosphate groups attached to its sugar is called:
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a nucleotide
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Nuleotides containing ribose are known as ______ and nucleotides containing deoxyribose are known as ______.
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-ribonucleotides
-deoxyribonucleotides |
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Nuleotide Bases:
The three pyridmidines are: |
Cytosine (C), thymine (T), and Uracil (U)
|
|
|
|
Nucleotide Bases:
The two purines are: |
Adenine (A) and Guanine (G)
|
|
|
|
Above all others, the ribonucleotide ____________ participates in the transfer of energy in hundreds of cellular reactions.
|
adenosine triphosphate
|
|
|
|
The three phosphates in ATP are linked via:
|
phosphoanhydride bonds
|
|
|
|
The most fundamental role of nucleotides in the cell is:
|
the storage and retrieval of biological information
|
|
|
|
Nucleotides serve as building blocks for the construction of _____________.
|
nucleic acids
|
|
|
|
Define: Nucleic acids
|
Long polymers in which nucleotide subunits are covalently linked by the formation of a phosphodiester bond b/t the phosphate group attached to the sugar of one nucleotide and a hydroxyl group on the sugar of the next nucleotide.
|
|
|
|
Nucleic acids:
Long polymers in which nucleotide subunits are ________ linked by the formation of a _________ bond b/t the phosphate group attached to the sugar of one nucleotide and a _______ group on the sugar of the next nucleotide. |
-covalently
-phosphodiester -hydroxyl |
|
|
|
Long polymers in which nucleotide subunits are covalently linked by the formation of a phosphodiester bond b/t the phosphate group attached to the sugar of one nucleotide and a hydroxyl group on the sugar of the next nucleotide.
|
Nucleic Acids
|
|
|
|
Two main types of nucleic acids:
|
Ribonucleic acid (RNA) and Deoxyribonucleic Acid (DNA)
|
|
|
|
RNA contains the bases:
|
A,G,C, and U
|
|
|
|
DNA contains the bases:
|
A, G, C, and T (thymine)
|
|
|
|
________ bonds specify the precise shape of a macromolecule.
|
non-covalent bonds
|
|
|
|
The second law of thermodynamics states:
|
in the universe or any isolated system, the degree of disorder can only increase
|
|
|
|
The measure of a systems disorder is called:
|
entropy
|
|
|
|
The first law of thermodynamics states:
|
In a closed system, energy cannot be created or destroyed; it can only change form.
|
|
|
|
O2 is the byproduct of which stage of photosynthesis?
|
the first stage
|
|
|
|
Cells obtain energy by _______ of organic molecules.
|
oxidation
|
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|
|
ΔG is _________ and is defined as:
|
free-energy change; measures the amount of disorder created in the universe when a reaction takes place that involves these molecules
|
|
|
|
-ΔG denotes a energetically _________ reaction.
|
favorable; +ΔG = unfavorable
|
|
|
|
The rate the ezyme come into contact with its substrate is determined by the:
|
concentration of the substrate
|
|
|
|
The three most important activated carriers:
|
ATP, NADH, NADPH
|
|
|
|
The most widely used activated carrier molecule:
|
ATP
|
|
|
|
NADH and NADPH are important _________ _______.
|
electron carriers
|
|
|
|
The Role of NADH vs. NADPH
|
*NADPH operates chiefly with enzymes that catalyze anabolic reactions, supplying the high-energy electrons needed to synthesize energy-rich biological molecules.
*NADH has a special role as an intermediate in the catabolic system of reactions that generate ATP via oxidation of food molecules |
|
|
|
Hydrolysis reactions are energetically _________.
|
favorable
|
|
|
|
Define: Activated Carrier
|
a small molecule used to carry energy or chemical groups in many different metabolic reactions
|
|
|
|
What role does the single-strand binding protein play in DNA replication?
|
Monomers bind to single-strand DNA (on lagging strand) and stabilize it and prevent it from reforming base pairs
|
|
|
|
What forms of chromatin can be seen in a cell in interphase?
|
Heterochromatin and euchromatin.
|
|
|
|
What proteins are responsible for the coiling of DNA into nucleosomes?
|
Histones
|
|
|
|
Proteins have a variety of functions in the call and are grouped according to their common functions. Please list four examples of different functional groups of proteins.
|
four of the following: enzymes, structural, transport, motor, storage, signaling, receptors, gene regulation, or special purpose. (see list in notes)
|
|
|
|
Proteins (polypeptides)are made of ________ linked by covalent ________ bonds during _______ reactions. (fill in the blanks)
|
acids; peptide; dehydration/condensation
|
|
|
|
What are the four major families of small organic molecules in the cell?
|
Sugars, fatty acids, amino acids, and nucleotides
|
|
|
|
What type of bonds bind together the atoms that make small organic molecules (such as sugars, amino acids, and fatty acids)?
|
Covalent bonds
|
|
|
|
What forms of chromatin can be seen in a cell in interphase?
|
Heterochromatin and euchromatin
|
|
|
|
Proteins are also called:
|
polypeptides
|
|
|
|
The ___________ is formed from the repeating sequence of atoms along the polypeptide chain. Attached to this repetitive chain are any of the 20 amino acid _____________.
|
polypeptide backbone; side chains
|
|
|
|
Define: Amino Acid Side Chain
|
the parts of the amino acids that are not involved in forming the peptide bond.
* they give the amino acids their unique properties. |
|
|
|
Long polypeptide chains are very flexible: many of the _________ bonds that link carbon atoms in an extended chain of amino acids allow ____ ______ of the atoms they join.
|
covalent; free rotation
|
|
|
|
Each folded polypeptide chain is constrained by ____ ______ bonds that form within proteins.
|
weak noncovalent
|
|
|
|
The weak force that helps determine the folding of any protein is:
***deals with aqueous solution*** |
The distribution of the polar (hydrophilic) and nonpolar (hydrphobic) amino acids; important due to their interaction in aqueous solutiuon
|
|
|
|
Steroid function:
|
cell signaling
|
|
|
|
Triacylglycerol function:
|
energy storage and building blocks of other lipids
|
|
|
|
Fatty Acids (function):
|
energy storage and building blocks of other lipids
|
|
|
|
Phospholipids (function):
|
biological membranes
|
|
|
|
Polyisoprenoids (function):
|
Membrane synthesis
|
|
|
|
Glycolipids (function)
|
(lipid + oligosaccharide) cell signaling
|
|
|
|
Another Name For:
Unbranched hydrocarbon chains terminating in a carboxylic acid group... |
Fatty Acids
|
|
|
|
Two types of fatty acids:
|
saturated and unsaturated
*Sat: no double bonds; straight chain *Unsat: one or more C=C double bonds, kinked chain |
|
|
|
What is the purpose of Phospholipid Aggregates:
|
In aq. solution, phospholipids aggregate to form structures that remove the hydrophobic tails from contact with water
|
|
|
|
Three forms of aggregates:
|
1. Micelles
2. Lipid monolayers 3. Lipid bilayers |
|
|
|
Define: Micelle
|
Phospholipid aggregate; form in aqueous solution when the concentration of lipid is relatively low
|
|
|
|
Define: Lipid monolayer:
|
Phospholipid aggregate; form at the air-sfc of an aqueous solution film with hydrophobic tails in the air and hydrophilic heads in the solution
|
|
|
|
Define: Lipid bilayers
|
Phospholipid aggregate; form in solution at higher concentrations of lipids membrane composed of two-layers of lipid molecules with the hydrophobic tails in the center and the hydrophilic heads on the two surfaces
|
|
|
|
The same ___ amino acids make up the proteins of all life forms.
|
20
|
|
|
|
The structure and function of polypeptides is determined by the nature of the _____ ______ ______ ______.
|
amino acid side chains
|
|
|
|
Four families of amino acid side chains: (to include basic properties)
|
* Acidic-- can become negatively charged
* Basic-- can become positively charged * Uncharged polar-- neutral *Nonpolar-- some are insoluable in water |
|
|
|
Three components of a nucleotide:
|
1. Pentose Sugar
2. Nitrogen Base 3. Phosphate |
|
|
|
Base + Sugar = Nucleoside
Nucleoside + ______ = Necleotide |
Phosphate
|
|
|
|
Polymers of nucletides linked by __________ bonds.
|
phosphodiester bonds
*** very flexible unless stabilized by complimentary base pairing, do not branch *** |
|
|
|
How do the two primary types of nucleic acids differ in composition?
|
differ by a type of sugar in the sugar-phosphate backbone
* RNA = A G C U * DNA = A G C T |
|
|
|
How do the two primary types of nucleic acids differ in structure?
|
RNA = single-stranded chain
DNA= double stranded chain (double helix) |
|
|
|
Define: double helix--
|
two polynucleic chains running antiparallel, held together by hydrogen bonds between two bases
|
|
|
|
__________ is the sum of all of the chemical reactions that occur in living cells.
|
Metabolism
|
|
|
|
Def. Metabolism:
|
...is the sum of all of the chemical reactions that occur in living cells.
Anabolism + Catabolism = Metabolism |
|
|
|
Two types of metabolic reactions:
|
catabolism and anabolism
|
|
|
|
Def. Catabolism
|
reactions that break down complex molecules which releases energy that can be used by the cell; provides building blocks
|
|
|
|
Def. Anabolism
|
reactions that synthisize new molecules using energy and molecules released by catabolic reactions
|
|
|
|
What is the reverse rxn to photosynthesis?
|
Respiration
|
|
|
|
Review:
Oxidation |
The partial or complete loss of electrons
|
|
|
|
Review:
Reduction |
The partial or complete aquisition of electrons
|
|
|
|
A change in______________ measures the amount of energy released as heat (lost) when a reaction takes place.
|
Change in Gibbs Free Energy; is also a measure of the relative change in the amount of order
|
|
|
|
Negative (ΔG) equates to:
|
- a decrease in order
- an increase in disorder - indicates that the reaction is energetically favorable |
|
|
|
Positive (ΔG) equates to:
|
- an increase in order
- a decrease in disorder - indicates that the reaction is energetically unfavorable |
|
|
|
Define Activation Energy:
|
the energy required to initiate an energetically favorable chemical reaction
|
|
|
|
Why do we need activated carriers?
|
the energy derived from oxidation of food molecules must be stored temporarily before use in production of small organic molecules or macromolecules; they store energy in an easily exchangable form
|
|
|
|
What Groups are Transfered by the Following Carriers?
1. ATP 2. NAD, NADP 3. FADH 4. Coenzyme A 5. Biotin 6. S-Adenosylmethionnine 7. Uridine diphosphate |
1. phosphate
2. hydride ion (H-) 3. hydride ion (H-) 4. acetyl 5. carboxyl 6. methyl 7. glucose |
|
|
|
These serve as carriers for electrons (reducing power) and protons in oxidation-reduction reactions.
|
NADH and NADPH
|
|
|
|
Steps of Catabolism:
|
1. Digestion
2. Glycolysis 3. Citric Acid Cycle 4. Oxidative Phosphorylation |
|
|
|
Characteristics of:
1. Glycolysis 2. Citric Acid Cycle 3. Oxydative Phosphorylation |
1. occurs in cytosol; does not require oxygen; basis for anaerobic metabolism
2. occurs in the matrix of mitochondria; requires oxygen 3. drivin by electron transport across the inner mitochondrial membrane; generates ATP; requires oxygen |
|
|
|
Def. Digestion
|
Enzymatic hydrolysis of macromolecules into their subunits;
** Fats ---> Fatty acids ** |
|
|
|
Polypeptide = ________________________.
Protein = ________________________. |
a single chain of amino acids;
functional molecule composed of one or more polypeptides |
|
|
|
Two Families of Molecular Chaperones:
|
hsp 70 and hsp 60
|
|
|
|
Molecular Chaperones:
Acts early during the initial folding of the polypeptide |
hsp 70
|
|
|
|
Molecular Chaperones:
Forms a barrel-like cage into which misfolded proteins are placed and the folding corrected |
hsp 60
|
|
|
|
What are Prions?
|
misfolded forms of proteins that can convert properly folded proteins into the abnormal configuration (PrP in scrapsie, BSE, CJD, Mad Cow Disease)
|
|
|
|
Proteins:
Two Regular Folding Patterns: |
alpha-helix and beta sheet
|
|
|
|
Proteins:
alpha helix |
Hydrogen bonds formed b/t every 4th peptide bond (C=O of one peptide bond and N=H of another bond); helix with one complete turn every 3.6 amino acids
|
|
|
|
Proteins;
beta sheets |
Hydrogen bonding b/t adjacent peptide chains
|
|
|
|
Two types of beta sheets:
|
Parallel: adjacent chains have the same polarity
Antiparallel: adjacent chains have opposite polarity |
|
|
|
2 alpha helices can form a
|
coiled-coil--- very stable structure
|
|
|
|
When does a coiled-coil form?
|
Forms when 2 alpha-helices have most of their hydrophobic side chains on one side--- they twist around each other
|
|
|
|
What does it mean when a protein has a primary level of structural organization?
|
amino acid sequence--- determines the pattern of the folding of a polypeptide
|
|
|
|
What does it mean when a protein has a secondary level of structural organization?
|
folding of the polypeptide into stable configurations; some stable folding patterns occur repeatedly in polypeptides: alpha-helix, beta-sheet, coiled-coil
|
|
|
|
What does it mean when a protein has a tertiary level of structural organization?
|
Full three-dimensional conformation formed by the entire polypeptide chain (alpha-helix, beta-sheet, coiled-coil, and other loops and folds)
|
|
|
|
The modular unit for the construction of larger proteins:
|
Domains
|
|
|
|
Allows functions to be incorporated into new proteins by genetic duplication and rearrangement
|
Domains
|
|
|
|
Protein Families:
Calcium-binding proteins |
contain a domain that binds calcium ions
|
|
|
|
Protein Families:
Serine Proteases |
Structurally similar proteins that differ in their specificity of enzyme activity (trypsin)
|
|
|
|
Protein Families:
ATPases (do what?) |
contain a domain that binds and hydrolyzes ATP
|
|
|
|
Define Globular Protein
|
polypeptide(s) folded into a compact shape, e.g. enzymes
|
|
|
|
Define Fibrous Protein
|
polypeptide with a long, relatively simple 3-D structure, e.g. many extracellular matrix proteins (collagen, elastin) and cytoskeletal (actin, intermediate filaments)
|
|
|
|
What are Proteasomes?
|
large protein complexes in the cytosol in which individual proteins are degraded--- Act on proteins tagged with ubiquitin
|
|
|
|
Large protein complexes in the cytosol in which individual proteins are degraded--- Act on proteins tagged with ubiquitin
|
Proteasomes
|
|
|
|
What is ubiquitin?
|
Small "ubiquitous" cytosolic protein; covalently attached to proteins as multiubiquitin chain; marks cytosolic proteins for proteolytic degradation in a proteasome
|
|
|
|
Nature of proetin-ligand binding:
|
is always very specific; may alter the conformation of the protein; is mediated by non-covalent interactions b/t the ligand and the side chains of amino acids that surround the binding site
|
|
|
|
Example of protein-ligand binding:
|
enzymes, antibodies, etc.
|
|
|
|
Define Allosteric Protein
|
A protein that can adopt two or more stable conformations
* the change is shape usually alters the activity of the protein |
|
|
|
A protein that can adopt two or more stable conformations
|
Allosteric Protein
|
|
|
|
What causes the change in shape in an allosteric protein?
|
caused by the binding or release of one or more ligands
|
|
|
|
The conformation and activity of ____________ proteins can be changed as a result of cyclic gain loss of a phosphate group.
|
GTP-binding proteins
|
|
|
|
Five methods used to disrupt cells during study
|
1. Homogenization
2. Osmotic Shock 3. Ultrasonication 4. Mechanical Shear 5. Detergent extraction |
|
|
|
3 types of centrifugation:
|
1. Differential Centrifugation
2. Velocity Sedimentation 3. Bouyant Density Sedimentation |
|
|
|
What is purpose of centrifugation?
|
separates cellular components on the basis of size, denisty, or bouyancy using centrifugal force from a centrifuge
|
|
|
|
The material the collects on the bottom of the centrifuge tube:
|
The pellet
|
|
|
|
Fluid that is above the pellet in a centrifuge tube
|
supernatant
|
|
|
|
Centrifugation:
Differential centrifugation |
Used to separate cell component on the basis of their density and size
|
|
|
|
Centrifigation:
Velocity centrifugation |
Separates the components of cells into layers on the basis of their density, which is a function of their size and shape
|
|
|
|
Velocity Centrifugation:
Sedimentation Coefficient- S |
Characterizes the rate at which a component sediments during velocity centrifugation--- function of size and shape
|
|
|
|
Unit of measurement:
Sedimentation Coefficient |
(S)--- Svedberg Unit
|
|
|
|
Centrifugation:
Density Gradient Centrifugation |
Separates the components of cells into layers on the basis of their bouyant density, Independent of their size and shape
|
|
|
|
Column Chromatography: What is it used for?
|
Used to separate macromolecules, especially proteins
|
|
|
|
Types of chromatography:
|
1. Gel filtration
2. Ion-exchange 3. Affinity |
|
|
|
Chromatography:
Gel filtration |
separates on the basis of size
|
|
|
|
Chromatography:
Ion-exchange |
separates on the basis of electrical charge
|
|
|
|
Chromatography:
Affinity |
separates on the basis of specific binding = affinity
|
|
|
|
Electrophoresis:
|
separates macromolecules on the basis of their ability to move through a gel, either in a slab or in tubes, driven by an electrical current
|
|
|
|
Electrophoresis:
SDS-polyacrylamide gel electrophoresis |
Separates polypeptides on the basis of size
|
|
|
|
Electrophoresis:
Isoelectric focusing |
separates on the basis of isoelectric point
|
|
|
|
Isoelectric point:
|
pH at which the protein has no net charge
|
|
|
|
Electrophoresis:
2-dimensional gel electrophoresis (does what?) |
separates on the basis of both isoelectric point pI (first dimension) and size - molecular weight (second dimension)
|
|
|
|
A combo of SDS-PAGE and Isoelectric focusing
|
2-dimensional gel electrophoresis
|
|
|
|
Because of their high specificity of binding to antigens, _________ have become a principle tool for studying cells
|
antibodies
|
|
|
|
Uses of antibodies: (4)
|
1. as specific labels for light and electron microscopy
2. to purify molecules by immunoprecipitation 3. to purify molecules by immuno-affinity chromatography 4. to identify proteins on electrophoretic gels |
|
|
|
Structure of Antibodies:
|
Proteins with paired binding sites that recognize and bind with high affinity to specific molecular sequences on other molecules
|
|
|
|
Two types of antibodies:
|
polyclonal and monoclonal
|
|
|
|
Antibodies:
Polyclonal |
* made by injections of purified antigen into an animal
* Antibodies are obtained by drawing and purifying blood *Antibodies obtained from blood are always a mixture of antibodies directed against many different antigens *can be further purified by affinity chromatography, and attaching the antigen of interest to the column matrix |
|
|
|
Antibodies:
Monoclonal (how are they made?) |
* made by fusing Beta cells with a tumor cell in cell culture
* antibodies obtained from a single clone are specific for a single epitope (binding site) on a single antigen *large quantities of antibody can be obtained by injecting beta cells into the peritoneal cavity of a mouse and drawing out the ascites fluid which will be rich in a single antibody |
|
|
|
Provides an analysis of the amino acid sequence of polypeptides
|
Amino acid sequencing
|
|
|
|
X-ray crystallography
|
Reveals the three-dimensional structure of macromolecules
|
|
|
|
NMR spectrocopy
|
Reveals the structure of small molecules and parts
|
|
|
|
DNA:
Which purines connect to which pyramidines? |
A---->T
G---->C |
|
|
|
DNA strands are held together by ________ bonds.
|
hydrogen
|
|
|
|
Nucleotide subunits linked by _________ bonds.
|
phosphodiester
|
|
|
|
Def. Genome
|
complete set of genetic information in the cell
|
|
|
|
Site of rRNA synthesis and ribosome assembly
|
nucleolus
|
|
|
|
Def. Ploidy
|
number of sets of chromosomes per cell
*haploid-- one set of chromosomes per cell *diploid-- two sets of chromosomes per cell *tetraploid-- four sets of chromosomes per cell |
|
|
|
Def. Karyotype
|
display of the full set of mitotic chromosomes
|
|
|
|
Def. Genes
|
Segments of DNA containing instructions for making a specific protein or set of closely related proteins, or directing the RNA production
|
|
|
|
Segments of DNA containing instructions for making a specific protein or set of closely related proteins, or directing the RNA production
|
Genes
|
|
|
|
Describe interphase chromosomes:
|
tangled treats; cannot be easily distinguished in light microscope
|
|
|
|
Describe metaphase chromosomes:
|
highly condensed; easy to identify in light microscope
|
|
|
|
Solves end-replication problem in eukaryotes
|
telomere
|
|
|
|
Site where daughter chromosomes remain attached during division
|
centromere
|
|
|
|
DNA + Proteins = _________
|
chromatin
|
|
|
|
2 classes of chromosomal proteins:
|
Histone and Nonhistone chromosomal proteins
|
|
|
|
Responsible for first level chromatin packing:
|
Histones
|
|
|
|
Pack the DNA + nucleosomes into a coil:
|
H1 histones
|
|
|
|
The most highly conserved of all known eucaryotic proteins:
|
Histones
|
|
|
|
Def. Nucleosomes
|
fundamental packing units of DNA
made of: ---protein core: complex of 8 proteins ---double stranded DNA ---linker DNA: up to 80 nucleotides |
|
|
|
Formation of Nucleosomes:
|
1st level packing; converts a DNA molecule into a chromatin thread
|
|
|
|
Formation of 30nm fiber:
|
2nd level of packing; native form of DNA; nucleosomes bundled together by H1 histones
|
|
|
|
4 levels of DNA packing:
|
1. "Beads on a string"-- Nucleosomes linked by linker DNA
2. 30 nm fiber-- native form of DNA; nuleosomes bundled together by H1 histones 3. Looped Domain-- current model; loops of 30nm fiber attached to proteins that form the chromosomal axis 4. Metaphase chromosome: final level of packing |
|
|
|
Forms of chromatin in interphase cells:
|
-Heterochromatin (10% of chromatin)
-Active Euchromatin (10% of chromatin) -Inactive Euchromatin (80% of chromatin) |
|
|
|
Forms of chromatin in interphase cells:
Heterochromatin |
highly condensed; transcriptionally inactive; most of the heterochromatin does not contain genes; concentrated around centromeres and telomeres
|
|
|
|
Forms of chromatin in interphase cells:
Active Euchromatin |
least condensed; histone H1 less tightly bound; nucleosomal histones chemically modified
|
|
|
|
Forms of chromatin in interphase cells:
Inactive Euchromatin |
more condensed than active euchromatin; can become active euchromatin
|
|
|
|
The most condensed form of chromatin:
|
Sperm cells--- sperm head
|
|
|
|
DNA Packing:
Nucleosome replication and assembly: |
1. nucleosomes must be moved out of the way to permit DNA to replicate or be translated
2. new nucleosomes must be assembled as DNA is replicated 3. new histones are synthesized at the same time as DNA replication 4. new nucleosomes assemble on the daughter DNA helices shortly after the DNA is replicated |
|
|
|
Eucaryotic cells have mechanisms to adjust the local structure of chromatin:
|
Chromatin remodeling complexes and histone tails modifying enzymes may work in concert allowing rapid changes in chromatin structure according to cell needs
-chromatin remodeling complexes; reversible modification of histone tails; |
|
|
|
chromatin remodeling complexes:
Protein Machines |
use ATP to change nucleosome structure; make DNA more accessible to specialized proteins; inactivated during mitosis-- helps maintain tightly packed chromosome structure
|
|
|
|
Site on the DNA double helix where replication is initiated:
|
Replication Origin
|
|
|
|
Site where the double helix first opens:
|
Replication Bubble
|
|
|
|
Characteristics of the Replication Bubble:
|
Site where the double helix first opens;
-consists of specific nucleotide sequences recognized by initiator proteins -A-T rich (easier to separate) -100 base pairs in length |
|
|
|
Number of replication origins:
1. Procaryotes 2. Eucaryotes |
1. 1 replication origin per chromosome
2. multiple replication origins on each chromosome |
|
|
|
Y-shaped structure resulting from the separation of the DNA double helix into two strands during replication
|
Replication Fork
|
|
|
|
Replication of DNA occurs at:
|
Replication Forks
|
|
|
|
Initiator Proteins:
|
bind to the DNA and open the double helix
|
|
|
|
Enzyme responsible for DNA synthesis:
|
DNA Polymerase--- catalyzes the formation of phosphodiester bonds
|
|
|
|
Def. Protein Kinase
|
one of a very large number of enzymes that transfers the terminal phosphate group of ATP to a specific amino acid of a target protein (phosphorylation)
|
|
|
|
Def. Protein Phosphatase
|
Enzyme that removes, by hydrolysis, a phosphate group from a protein
|
|
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______________ allows for the base pairs to be packed in the most energetically favorable fashion in the interior of the double helix.
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complimentary base-pairing
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