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Cell Biology Review, Chemistry Review

The cell is the basic functional unit of the human body. Each cell: (list 4) 1. is surrounded by the plasma membrane 2. consists of fluid suspension, cytosol 3. contains nucleus, organelles and inclusions 4. contains cytoskeleton
What do you call all of the material within the plasma membrane that is NOT part of the nucleus? cytoplasm
What do you call the membrane bound unit that contains the vast bulk of genetic material (DNA) nucleus
Cytoplasm consists of cytosol AND... (list 3) organelles, inclusions and cytoskeleton
What part of the cell is unique to eukaryotes? plasma membrane
What is the critical factor in obtaining clear images for light microscopy? resolving power
What is the resolving power in light microscopy? the smallest distance between 2 particles at which they can be observed as separate particles.
What is the maximum resolving power of a light microscope? (of a human eye?) 0.22 um (100um)
What can you see smaller stuff with, an electron microscope or a light microscope? electron microscope
What is used to visualized cells and follow their movement? light microscope
How do you increase the resolution of a light microscope? decrease the wavelength of the illuminative radiation
What type of microscope requires thinn sections for penetration of the sample by illuminating radiation? electron microscope
Which type of microscopy is kinetic, dynamic? light microscope
What kind of microscopy do you use to capture cellular processes over time? light microscope
What kind of microscope can only capture static images? electron microscope
A longitudinal crossection is cut: along the long axis
a transverse crossection is cut: perpendicular to the long axis
an oblique crossection is: diagonal and neither longitudinal nor transverse
a tangential crossection is: a longitudinal crossection that is perpendicular to the radius
How can we isolate cell constituents? differential centrifugation
What are the steps in differential centrifugation? 1. dissociate tissue 2. separate by gravity 3. separate by repeated centrifugation, at progressively higher speeds
how can we study cell growth? cell culture
how can we study cell differentiation and function? cell culture
____ are the fundamental units of life which evolved ______ years ago. Cells; 3.8 billion
What is the approximate diameter of a human cell? 10 micrometers
What is the approximate length of a mitochondria? 1 micrometer
______ microscopy is much easier to use than _______ microscopy & allows for observation of live cells. light; electron
In light microscopy objects of about _____ can be seen. 1 micrometer
In light microscopy objects of about the size of a _______ can be seen. mitochondria
______ microscopy has a much higher resolution than light microscopy (10 nm). electron
Biochemical composition can be studied by isolation and characterization of different cellular components by: differential centrifugation
what do we use to study mechanics of cell growth, differentiation, cellular function, stem cell research and many other cell properties? cell culture
What are 6 structures that make up the intracellular membrane system? 1. RER 2. SER 3. Golgi 4. glycogen granules 5. Mitochondria 6. Lysosome
Where might diseases of improper protein folding/export originate? ER
What are 3 dx with dysfunctional ER origins? 1. hypothyroidism (protein folding prob) 2. CF (transmembrane regulator not exported due to mut.) 3. osteogenesis imperfecta (pro-collagen)
Why is the smoothe ER not rough? no ribosomes
Where does lipid metabolism take place? SER
Where does the detoxification of drugs take place? SER
What cellular structure might be referred to as a "mini liver"? SER
Which cellular structure uses enzymes in the cytochrome P450 family and why? SER for drug detoxification
what structure radiates off the nucleus? SER
What structure is covered by ribosomes on its outer surface? RER
What is the site for protein synthesis? RER
Protein secretory cells have what? more RER
What is continuous with the nuclear envelope? RER
proteins synthesized and packaged in the RER are transported where for modification and final packing? Golgi
Into what does the golgi package proteins for transport? secretory vescicles
what cell structure is a series of flattened, slightly curved membrane-bound cisternae Golgi
Which structure is almost continuous with the ER? golgi
Which structure has a secondary role of carbohydrate synthesis? RER
What type of microscope would you use to visualize vescicles going back and forth from the golgi? light microscope
What structure is the "sorting machine" that enable proteins to get to their place? golgi
Where are the three levels of cisternae in the golgi
which level of the cisternae is closest to the RER, entry phase and convex in shape? Cis-face
what is the middle of the cisternae called? medial face
Which part of the cisternae is convex? trans-face
what part of the cisternae is leading outside of the golgi to the exit phase? trans-face
What structure produces the storage form of energy? Mitochondria (ATP)
What structure has a smooth outer membrane and a folded inner membrane? mitochondria
What is the name for the inner folded membrane of the mitochondria? cristae
What is the variability in length of the mitochondria? 0.5 to 1 micrometers (and up to 7 micrometers)
What structure fuels cellular processes? mitochondria
What is the matrix of the mitochondria called and what's in there? called inter-cristae; mtDNA
Carioencephalomyopathy, deafness and Type II diabetes are all disorders of what cellular structure? mitochondria
what structure can divide by fission but also fuse? mitochondria
how big are peroxisomes? 0.2 to 1 micrometer
what structure utilizes oxygen, but does not produce ATP? peroxisomes
are peroxisomes membrane-bound? yes
what is the "work horse" of the peroxisomes? catalases
what structure is responsible for the catabolism of fatty acid chains? peroxisomes
what highly toxic material does a peroxisome contain? hydrogen peroxide
what happens inside a peroxisome? oxidation specific organic substrates remove hydrogen atoms transferred to molecular oxygen to form hydrogen peroxide
what changes the hydrogen peroxide into 2H20 and O2 in a peroxisome? catalase
what structure contains 40-50 oxidative enzymes, such as urate, oxidase, and catalase? peroxisomes
Zellewegers syndrome is an example of a _______(organelle) disorder. Disorders of this organelle are generally lethal. peroxisome
what is the approximate size of a lysosome? 0.3 to 0.8 micrometers
what organelle contains 40 different types of acid hydrolases (e.g. sulfatases, proteases, nucleases, etc.)? lysosome
what is the function of the acid hydrolases inside lysosomes? tear up proteins & microorganisms
what is the "trash can" of the cell? lysosomes
what organelle digests particulate matter that enters the cell? lysosomes
what organelle is a membrane-bound compartmentalization of degradative enzymes away from the rest of the cell? lysosome
what is the lumen pH of the lysosome? 5 (acidic)
why is the pH of the lumen lysome so low? degradative enzymes operate at optimal pH in these conditions
what cell structures have little or no metabolic activity, are not really considered organelles and consist mainly of accumulated metabolites? cytoplasmic inclusions
what is the storage form of glucose? glycogen
where is the storage form of glucose found? glycogen found mostly in liver and muscle cells
How large is glycogen? 10-40 nm
what is a storage form of fatty acids? triacyglycerols
what are lipids associated with in the cell? mitochondria??
what are cells enclosed by? a plasma membrane
what are the two regions that cells can be divided into? nucleus and cytoplasm
what is the part of the cell that excludes the nucleus and membrane-bound organelles? cytosol
_______ contains a concentrated mixture of small and large molecules which carry out many essential biochemical processes. cytosol
_____ are the site of protein synthesis ribosomes
_____ is a network of flattened sacs and tubules in the cytoplasm ER
this structure is the site of lipid synthesis and calcium accumulation and release SER
this structure is is the site of protein synthesis and packaging RER
______ modifies and stores proteins and pacakages them into secretory vescicles golgi
"powerhousees" of the cell mitochondria
this structure uses oxygen to remove hydrogen and form hydrogen peroxide peroxisomes
this structure digests particulate matter that enters into the cell lysosome
this structure contains it's own genetic information (chromosomes) mitochondria
what are 3 types of material transport in the cell? 1. gated transport 2. transmembrane transport 3. vesicular transport
this type of transport involves signal sequences for which protieins can recognize and bind to gated transport
in this type of transport, nuclear pores function as selective gates gated transport
this type of transport is used to move specific macromolecules & macromolecule assemblies gated transport
this type of transport allows for diffusion of smaller molecules gated transport
this type of transport is a receptor-driven event transmembrane transport
in this type of transport selected proteins from cytosol are moved to ER lumen, mitochondria or peroxisome transmembrane transport
in this type of transport, protein molecules usually must unfold to pass through the translocator transmembrane transport
this type of transport is usually by specific receptors that recognize signal peptides transmembrane transport
this type of transport allows for transfer of soluble proteins for ER to Golgi vesicular transport
this type of transport allows for their cargo to be discharged into target components vesicular transport
what is an example of vesicular transport? endocytosis
in this type of transport, vescicles are pinched off from the donor compartment and transported to the target component vesicular transport
this is a process by which a cell ingests substances from the extracellular space endocytosis
endocytosis of a LARGE vesicle is: phagocytosis
endocytosis of a small vesicle is: pinocyosis
what is it called when a cell catabalizes itself? autophagy
in this process a membrane forms around non-functional organelle or excess cytoplamsic structures, followed by fusion with lysosomes autophagy
what is the last step of endocytosis? vesicle fuses with lysosomes for digestion
what are different pathways to the lysosome? phagocytosis, endocytosis, autophagy
What is the process occuring following cell death resulting from injury ("Free for all") necrosis
what processes is necessary for separating digits? apoptosis
what process is messed up when there is a fusion between digits? apoptosis
What is programmed cell death called? apoptosis
of the two "cell death processes" necrosis and apoptosis, which involves inflammation? necrosis
in this process, cellular components are released as cells perish. Phagocytes do not consume the cells or their contents necrosis
in this process, an uncontrolled release of cell contents can trigger an immone response necrosis
what is notably lacking in apoptosis compared to necrosis? inflammation
in this porcess, there are characteristic patterns of changes in cell morphology resolting from degradation of organelles by activated caspases: apoptosis
what are some processes that occur during apoptosis (list 5) 1. blebbing of cell membrane 2. cell rounding/shrinkage 3. pyknosis (chromatin condensing) 4. fragmentation of nucleus/chromosomal DNA 5. break into vescicles called apoptotic bodies
Unlike ________, membranes around _________ bodies signal macrophages and surrounding cells to engulf. necrosis; apoptotic
in this process, nuclei are pyknotic apoptosis
in this process, large cytoplasmic blebs form and detach from cell, but remain within the plasma membrane (no cytoplasm is released) late apoptosis
cell death is characterized by: typical nuclear chages
what type of cell death is required for normal development of multicellular organisms? apoptosis
_________ is marked by chromatin condensation along the nuclear membrane apoptosis
What is the amino acid side chain whose pKa is closest to neutral? histidine
which of the following determines a protein's native structure? the protein's linear amino acid sequence
which of the following secondary structures is most likely to be found in a membrane-embedded portion of a protein? an alpha helix composed entirely of hydrophobic residues
which of the following best describes the arrangement of amino acid side chainsin an alpha helix? side chains point outward away from helical axis
which of the following best describes an alpha helical region of a polypeptide? Right-handed, 4.6 aa/turn
structural and biochemical aspects of polypeptide chain formation to create amino acid sequence is determined by primary structures
can two proteins have the same amino acid sequence? no; each protein has a unique amino acid sequence
peptide bond "backbone" is essentially ______ because of the rigid ________-like characteristics planar; double bond
what kind of bond involves the transfer of electrons where they're not truly shared ionic
two atoms with unpaired electrons in their outer shells can form _______ bons with eachother by sharing electron pairs covalent
what type of bond is a peptide bond? covalent
chemical reactions that require the most energy entail the breaking and forming of covalent bonds
ionic bonds can be described by __________ interactions and ______ law. electrostatic; coulomb
these bonds are weak electrostatic interactions: approx. 4-13kJ Hydrogen bonds
these bonds depend upon the distance between two atoms and the non-symmetrical charge distribution around each. van der waals interactions
what is the van der Waals contact distance? the point at which the two atoms exhibit the greatest attraction for each other
closer than van der Waalss contact distance results in: repulsive forces
what is considered the "universal solvent"? water
with the exception of van der waals forces, the non-covalent interaction is greatly affected by: water
Is non-covalent ionic bond strength greater in water or a vacuum? a vacuum. non-covalent interactions are very weak in water.
Water is a ________ molecule with an asymmetric distribution of charge. No net charge, but the ______________ ___________ creates a polar solvent that can interact with charged particles. polar; electric dipole
Water is highly __________ through hydrogen bond interactions. cohesive
water is an excellent solvent for ___________ molecules as it: polar; competes for electrostatic interactions between other polar molecules.
The ____________ of water diminishes the strength of electrostatic attractions between other polar molecules. high dielectric constant
what is the hydrophilic effect? water interacting with other polar molecules
what is the hydrophobic effect? describes water interacting with nonpolar molecules
Nonpolar molecules aggregate together in water which leads to: the release of free energy (higher entropy)
increase in entropy leads to a release of free energy
the hydrophobic effect and the release of free energy play a role in which biochemical rxn? correct protein folding
when water acts as an acid, it _______ a H+ donates
when water acts as a base it _______ a H+ accepts
when an acid is dissolved in H2O, it donates its H+ to a H2O molecule; in this case, H2O acts like a (acid/base)? base
when a base is dissolved, it accepts a H+ from an H2O molecule; in this case H2O acts like a (acid/base)? acid
a weak acid [HA] produces a _________ conjugate base= strong; =good pH buffering
a weak base [A-] produces a ________ conjugate acid= strong; =good pH buffering
a __________ produces a strong conjugate base weak acid [HA]
a ___________ produces a strong conjugate acid weak base [A-]
Strong acids (HCl) and bases (KOH) produce _________ which are _________ and thus unimportant to us weak conjugate bases/acids; poor pH buffers
What remains relatively constant when pH buffer is strong/good. [H+]
Henderson Hasselbach (H-H) equation predicts the pH of a buffer by: -log [weak acid]/[weak base]
when does the pH = pKa? when [A-]=[HA] or weak acid concentration equals weak base concentration
how do you make a strong pH buffer weak acid + strong conjugate base
what is the best pH for buffering the human body's acid-base balance? 7.4
when someone's breathing is shallow, there can be an increased H+ in blood due to hypoventilation and a build up of CO2. What is this called? respiratory acidosis
respiratory acidosis can be caused by pulmonary problems, head injury, drugs (sedatives, anesthetics) or brain tumor. How can these affect the blood's pH? Build up of CO2 leads to pH falling below 7.4 or becoming more acidic
when someone is hyperventilating, there is a decrease of H+ in the blood, expelling CO2 rapidly from circulation. What is this called? respiratory alkalosis
respiratory alkalosis can be caused by psychiatry anxiety, drugs such as asprin and caffeine, lung disease such as pneumonia, fever or stroke. How can these affect the blood's pH? decreased H+ in the blood leads to pH increasing above 7.4 or becoming more basic
what happens to pH and pCO2 during uncompensated respiratory acidosis? pH decreases, pCO2 increases
what happens to pH and pCO2 during uncompensated respiratory alkalosis? pH increases, pCO2 decreases
what are three ways the acid-base physiological equilibrium is achieved in the body? 1. renal elimination 2. chemical buffering within the body 3. pulmonary elimination (pCO2)
what type of ionic form do amino acids take on at physiological pH? zwitterion/hybrid ion/dipolar ion
in solution, the amino acid molecule appears to have a charge which changes with: pH
at low pH, what part of the amino acid is charged? amino terminus; positively charged
at high pH what part of the amino acid is charged? the carboxyl terminus; negatively charged
how do we define pI in terms of pH? the isoelectric point is the pH at which the total net charge=- and therefore will not move in an electric field
What type of amino acid isomers are most common in the human body? L isomers; D isomers are more rare (D found in bacterial cell walls and peptide antibodies)
which is the only achiral amino acid? Gylcine; it has a Hydrogen as an R-group
What are the non-polar, neutral R-groups? (name 6) Glycine (G), alanine (A), valine (V), leucine (L), Isoleucine (I) and Methionine (M).
What are the aromatic R groups? (name 3) Phenylalanine (F), Tyrosine (Y), Tryptophan (W)
Trp & Try or Y & W are equal to what percentage of amino acids in an average protein mixture? about 4.6%
what are the aliphatic hydroxyl R groups (polar)? (name 2) Serine (S) and Threonine (T)
the -OH groups on serine and threonine result in what? hydrophilic characteristics and stronger chemical reactivity
what are the aliphatic sulfhydryl (thiol) R groups (polar)? cysteine (C)
what are the basic R groups that are very polar and positively charged @ pH 7? (name 3) Lysine (K), Arginine (R) and Histidine (H)
what are the acidic R groups that are very polar and negatively charged @ pH 7? (name 4) Aspartate (D), Glutamate (E), Asparagine (N) and Glutamine (Q)
which is the aa "A"? alanine
which is the aa "K"? lysine
which is the aa "F"? phenylalanine
which is the aa "Q"? glutamine
which is the aa "E"? glutamic acid
which is the aa "R"? Arginine
which is the aa "W"? tryptophan
which is the aa "Y"? Tyrosine
what does it mean for something to be an essential aa? it means that it must be supplied in the diet as humans cannot synthesize these specific amino acids (total of 9 out of 20)
the alpha-carboxyl group of one amino acid is _____ linked to the alpha-amino group of another amino acid by a ________ bond. covalently; peptide (amide or covalent)
more than two amino acids linked together form a ___________. polypeptide chain
each _________ bond formed requires an input of free energy (+21 kJ/mol) and results in the loss of a water molecule covalent peptide
the peptide bond "backbone" is essentially a _______ structure because of rigid _______-like characteristics planar; double bond
for each pair of linked aa's there are X atoms within the same plane = amide plane X=6
amide bond has stability because of resonance characteristics
the aa backbone contains a carbonyl group (>C=O), a hydrogen bond _________ and an amine group (>N-H; except for _________) a hydrogen bond _______. acceptor; proline; donor
planar peptide bonds (amide plane) can have one of two configurations; one on each side of the peptide bond. What are they and which is more common? cis, trans; trans is more common
the angle of rotation between the nitrogen of the amino group and the alpha carbon is called: phi
the angle of rotation between the alpha carbon and carbon atom of the carbonyl is called: psi
what was YGGFL (Leu-enkephalin) used to demonstrate? the amino terminal is always at the beginning of the polypeptide chain and the amino acid sequence only goes in one direction
Disulfide bonds are formed by the ______ of the -SH side groups of a pair of cysteine residues to S-S, linking the two cysteines _________ to form one cysteine oxidation; covalently
the molecular mass of a protein is dependent on the number of _________ in the protein amino acids
what is the average molecular mass of one amino acid (in daltons)? 110 daltons
If most proteins contain between 50 - 2K amino acid residues (aa), what is the range of molecular masses for these proteins? (50 aa X 110 daltons= average molecular mass of one aa)= 5500 daltons; (2000 aa X 110 daltons) = 220,000; between 5.5kD and 220 kD
the alpha helix consists of a tightly coiled backbone with side chains extending _______ in a helical array outward
All alpha-helices in proteins are ___________ because there is ___________ right handed because there is less steric clash between R groups and the backbone
The alpha helix how many angstroms and residues per 360 degrees? 1.5 angstroms wide and 3.6 residues per 360 degree turn
stabilization of secondary structures occurs by _________ between N-H and C=O groups of the backbone that are ____ residues apart in a staggered array. ________ backbone N-H and C=O groups are ___________. hydrogen bonded; 4; ALL; hydrogen bonded
which type of alpha helix is predicted to be energetically favorable? right-handed helix
adjacent amino acids in the beta strand are ______ angstroms apart. 3.5 angstroms apart (greater than the alpha helix which is 1.5)
strands in a beta sheet can link as a mixture of both _______ and ___________. parallel and antiparallel
a beta sheet is formed by linking two or more beta strands by ____________. hydrogen bonds
this type of beta sheet has each amino acid on one strand H-bonded to two different amino acids on the opposite strand. parallel beta-sheet
this type of beta sheet has the N-H group and C=O group of each amino acid H-bonded to the C=O group and N-H group of one amino acid directly opposite anti-parallel beta-sheet
(T/F) proteins can have both alpha and beta structures True
what secondary structure is described as "Flat and twisted" beta sheets
Most proteins have compact globular shapes because of sharp bending of polypeptide chains, regardless of primary structure. The most common structural element to accomplish this is the: reverse turn (Beta-turn, hairpin loop)
what's an omega loop? another more elaborate structure responsible for chain reversals
are proteins ever symmetrical? no
how do we describe the spatial arrangement of proteins containing more than one protein chain (subunits) and the nature of their interactions? quaternary structure
Protein domains are compact globular protein regions of a __________ connected by flexible segment of polypeptide chain. Give example? single protein; CD4 (four similar protein domains extending from helper T-cell surface)
what is the "general rule" for amphipathic proteins? they're water soluble and amphipathic, folding into structures with nonpolar cores (hydrophobic cores) and hydrophilic R groups on the outside.
what is the example of exception to the general rule of water-soluble proteins? Porin: outer membrane of bacteria is hydrophobic and inner structures are hydrophilic.
What type of protein allows polar molecules through its channel? Porin: hydrophilic channel allows water and other polar molecules through
how do we describe the spatial arrangement of amino acid residues within the polypeptide chain that are far apart in sequence, including the patter of disulfide bonds? protein tertiary structure
What are the rules that govern folding of protein into tertiary structures? (name 2) 1. Thermodynamic stability: less energy to achieve 3-D is more desirable 2. contribution of each portion to overall polypeptide chain-folding mechanisms
one complete protein chain (eg. beta-chain of hemoglobin) represents what structure? tertiary
the four separate chains of hemoglobin assembled into an oligomeric protein represents what structure? quaternary
what is the name for the self-propagating form of chromosomally-encoded protein that is a proteinaceous infectious particle lacking nuclei prion
what diseases do prions cause? TSEs (transmissible spongiform encephalopathies); fatal neurodegenerative diseases affecting humans/mamals. Eg. CJD (1/million); scrapie, Bovine spongiform encephalopaty, chronic wasting disease; Kuru
normal prion proteins are ___________ and soluble. Prion dx are due to aggregates of insoluble __________. alpha helical; prion beta-sheets
Created by: UT2011