IUPUI BIOL-K324 : Exam 1
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What is the Central Dogma?
DNA -> RNA -> Protein
What do light microscopes allow us to see?
some of a cell's components
led to the discovery of cells
What is the limit of light microscopy?
100 nm
What do electron microscopes allow us to see?
fine structures of the cell
What are the two domains of prokaryotes?
Bacteria and Archaea
What different shapes to prokaryotes come in?
spherical, rod-shaped, spiral
Where did eukaryotic cells come from?
evolved from prokaryotes
What is the major difference between prokaryotes and eukaryotes?
Eukaryotes have a nucleus.
Where is DNA found in a prokaryotic cell?
Free floating in the cytoplasm, and some may be in a plasmid (a ring of DNA)
What are the cristae in the mitochondria?
ATP is made in the cristae
How are mitochondria inherited?
maternally
What is the major function of chloroplasts in plant cells?
capture the energy of the sunlight
What are thylakoids?
saclike photosynthetic membranes
What is the stroma of a chloroplast?
the fluid inside the chloroplast but outside the thylakoids
How did chloroplasts evolve?
Chloroplast's evolve via encapsulation of a Cyanobacteria. This Eukaryote then was secondarily encapsulated in a larger Eukaryote in different lineages.
What is the function of the cytoskeleton?
-cell division
-protein localization
-determination of cell shape
What is the function of the plasma membrane?
Control transfer of substances in and out of the cell.
What is the function of the Rough Endoplasmic Reticulum?
protein transport
What is the function of the Smooth Endoplasmic Reticulum?
Synthesize lipids
What is the function of the Golgi Apparatus?
-modification
-packaging
-secretion of materials
What is the function of the mitochondria?
produce ATP
What is the function of the lysosome?
Digests cellular waste.
What is the function of the peroxisome?
helps clean materials out of cells, detoxifies achohol
What is cytosol?
Fluid portion of cytoplasm
What is the cytoplasm?
the portion of the cell outside the nucleus
What is the function of the nuclear envelope?
A double membrane with nuclear pores to allow exchange between cytoplasm and nucleus.
What are nuclear pores?
holes in the nuclear envelope where things can pass into and out of the nucleus.
What is the nucleolus?
where ribosomes are made
What is the function of a ribosome?
protein synthesis
What is the function of a vesicle?
To store and transport molecules
What is a centrosome?
microtubule organizing center
What are centrioles?
Centrioles help organize cell division and are formed from tubulin and located near the nucleus.
What are intermediate filaments?
fibers with diameters in a middle range
What is the extracellular matrix?
a collection of extracellular molecules secreted by cells that provides structural and biochemical support to the surrounding cells.
What is the cell wall?
Found on the outside of plant cells, it is made of cellulose and strengthens the cell.
What is a nucleoid?
A dense region of DNA in a prokaryotic cell.
What is endocytosis?
process by which the cell takes in materials that are too large to pass through
What is exocytosis?
a process by which the contents of a cell vacuole are released to the exterior through fusion of the vacuole membrane with the cell membrane.
What is the cytoskeleton made of?
microfilaments and microtubules
What is the function of microfilaments?
Cell movement and cell contraction
What is the function of microtubules?
Movement of organelles and cell shape; they also play a role in mitosis by pulling the chromosomes to opposite sides of the cell
Most ciliates are also....
pathogens
Similarities between prokaryotes and eukaryotes
plasma membrane, ATP as energy, ribosomes
Differences between prokaryotes and eukaryotes
Eukaryotes have a nucleus and membrane-bound organelles and are plant and animal cells
Prokaryotes are mostly bacteria and do not have a nucleus or membrane-bound organelles
Prokaryotes do NOT contain:
microtubules, microfilaments, intermediate filaments, nucleus, endomembrane system
Prokaryotes do NOT go through these processes:
mitosis and meiosis, exocytosis and endocytosis
List some good model organisms:
- yeast
- E.Coli
- arabidopsis
- flies, worms, fish, and mice
How large is the human genome?
3 billion base pairs
What is a catabolic pathway?
release energy by breaking down complex molecules into simpler compounds
What is an anabolic pathway?
consume energy to build complex molecules from simpler ones
What are the two stages of photosynthesis?
light reactions and calvin cycle
What is the reactant and what is the product of a light reaction?
reactant: light and water
product: oxygen gas
What are the reactants and products of the Calvin Cycle?
reactants: water and carbon dioxide
product: glucose
What is also created during photosynthesis?
ATP
Energy is used to carry out essential reactions that support:
cell metabolism, growth, movement, and reproduction
The rest of the energy is lost as
heat
Catalysts are used to
speed up a reaction
Enzymes reduce the energy needed to initiate spontaneous reactions by
utilizing a catalyst
catalysis
the acceleration of a chemical reaction by a catalyst
Reaction coupling
The tendency of unfavorable biological reactions to occur concurrently with favorable reactions, often catalyzed by a single enzyme
Favorable reactions have
negative free energy
Unfavorable reactions have
positive free energy
metabolic pathway
Begins with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product.
The rate at which an enzyme catalyzes a reaction depends on
how rapidly is finds its substrates and how quickly the product forms and then diffuses away.
equilibrium constants govern
associations and dissociations that occur between macromolecules and small molecules in the cell
the larger the cell, the ________________ the equilibrium constant
larger
Is the formation of an activated carrier is a favorable or unfavorable reaction?
favorable
What is the most widely used activated carrier?
ATP
What are two activated carriers of electrons?
NADH and NADPH
Is catabolism favorable or unfavorable?
favorable
Is anabolism favorable or unfavorable?
unfavorable
What is the structure of ATP?
What is ATP hydrolysis?
catabolic reaction process by which chemical energy that has been stored in the high-energy phosphoanhydride bonds in ATP is released by splitting these bonds.
How does NADPH accept or donate electrons?
via the nicotinamide ring
What is the oxidizing agent for catabolic reactions?
NAD+
What is the reducing agent for anabolic reactions?
NADPH
What are the major activated carriers?
ATP, NADH, NADPH, FADH2, Acetyl CoA, Carboxylated biotin, S-adenosylmethionine, Uridine diphosphate glucose
What group does ATP carry?
phosphate
What group does NADH and NADPH carry?
electrons and hydrogens
Where is FADH2 used and what does it carry?
It is used in the Kreb's Cycle and it carries electrons and hydrogens
What group does Acetyl CoA carry?
acetyl group
What group does Carboxylated Biotin carry?
carboxyl group
What group does S-adenosylmethionine carry?
methyl
What group does Uridine Diphosphate Glucose carry?
glucose
What is the structure of Acetyl CoA?
What are enzymes?
biological catalysts
Give some examples of enzymes
DNA polymerase, protein kinase, alcohol dehydrogenase
What are structural proteins?
provide mechanical support to cells and tissues
Give some examples of structural proteins
-collagen, elastin, keratin, actin, tubulin
What are transport proteins?
proteins that transport other substances in and out of cell
Give some examples of transport proteins
serum albumin, hemoglobin, transferrin
What are motor proteins?
proteins that turn energy into mechanical work
Give some examples of motor proteins
myosin, kinesin, dymein
What are storage proteins?
storage of amino acids
Give some examples of storage proteins
ferritin, ovalbumin, casein
What are signal proteins?
carry extracellular signals from cell to cell
Give some examples of signal proteins
insulin, netrin, epidermal growth factor
What are receptor proteins?
response of cell to chemical stimuli
Give some examples of receptor proteins
Rhodopsin, acetylcholine receptor, insulin receptor
What are transcription regulators?
bind to DNA to switch genes on or off
Give some examples of transcription regulators
Lac repressor, DNA binding proteins
What are special purpose proteins?
highly variable proteins
Give some examples of special purpose proteins
antifreeze proteins, green fluorescent proteins,
How are amino acids linked together?
peptide bonds
A protein is made of amino acids linked together into a
polypeptide chain
What are peptide bonds?
covalent bonds between amino acids
What are optical isomers?
mirror images
What are the basic side chains?
arginine, lysine, histidine
What are the acidic side chains?
aspartic acid, glutamic acid
What are the uncharged polar side chains?
asparagine, glutamine, serine, threonine, tyrosine
What are the nonpolar side chains?
alanine, valine, methionine, tryptophan, leucine, isoleucine, glycine, cysteine, proline, phenylalanine
What is a poly amino acid?
random sequence of one or only a few amino acids
What is a peptide?
chain of amino acids, usually 20-30 amino acids long
What is a polypeptide?
long chain of amino acids
What is a protein?
polypeptide having a 3-D structure
How is the mass of a protein or peptide expressed?
In terms of Daltons (Da)
1 Dalton is equal to...
1 hydrogen
A proteins shape is dictated by....
the amino acid sequence
What are the three types of noncovalent bonds that help proteins fold?
hydrogen bonds, van der Waals attraction, electrostatic attraction
What helps proteins fold into compact conformations?
hydrophobic forces
Can denatured proteins recover their natural shape?
YES
What is Urea?
A chemical that comes from the breakdown of proteins
What is an alpha helix?
a rodlike structure in which the peptide chain coils clockwise around a central axis
What is a beta sheet?
a secondary structure of a protein that is formed by a hydrogen bond of the atoms in a peptide bond that lie within linear regions of polypeptide, chain may run in same direction (parallel) or opposite direction (anti parallel), also can turn and fold back on itself
What is a coiled coil?
a structural motif in proteins in which 2-7 alpha-helices are coiled together like the strands of a rope
In what two varieties will you find beta sheets?
parallel and antiparallel
What are prion diseases?
Prion Diseases are diseases caused by native folded proteins becoming misfolded. This occurs when exogenous misfolded proteins infect an animal and convert native prion proteins into a misfolded form.
What is the primary structure of a protein?
sequence of amino acids
What is the secondary structure of a protein?
1) Twisting of the alpha helix
2) Beta sheets
3) Hydrogen bonding
What is the tertiary structure of a protein?
3D structure including bending
What is the quaternary structure of a protein?
interactions between different polypeptide chains in proteins composed of more than one polypeptide (subunit interaction) MULTIMERIC
T or F? Many proteins are composed of separate functional domains.
TRUE
Identical protein subunits can
assemble into complex structures
An actin filament is composed of
identical protein subunits
A single type of protein subunit can pack together to form:
a filament, a hollow tube, or a spherical shell
Viral capsules are often
spherical protein assemblies
Disulfide bonds help....
stabilize a favored protein conformation
Is the binding of a protein to another molecule selective?
yes, it is highly selective
What is a ligand?
any molecule that binds specifically to a receptor site of another molecule
What is specificity?
ability of a protein to bind to one molecule or ion in preference to others
What is affinity?
degree of attractionâbetween the enzyme and substrate.
What is the ligand-binding site?
location on the receptor to which the ligand binds
how is affinity expressed?
dissociation constant
The dissociation constant and affinity are ___________________ proportional.
inversly
What is an antibody?
A protein secreted by plasma cells, they are part of the immune response and bind to antigens and mark them for destruction.
An antibody takes on what shape?
An antibody is Y-shaped and has two identical antigen-binding sites, one on each arm of the Y
What provides stability for an antibody?
disulfide bonds
What are the two chains of an antibody?
light chain and heavy chain
Enzymes convert _______ to _________
substrate, product
What is a competitive inhibitor?
a molecule that competes with the substrate to bind in the active site of an enzyme.
What is a lysozyme?
enzyme that kills bacteria
What does a lysozyme cleave?
polysaccharide chain
The cleft in an enzyme holds how many sugar residues?
6
Lysozymes have how many domains?
2
How does a lysozyme break a bond?
by adding H2O to the bond between sugars to break it
What are enzyme inhibitors?
Substances that interfere directly or indirectly with enzyme action
What does aspirin inhibit?
cyclooxygenase
Methotrexate kills cancer cells by inhibiting
dihyrdrofolate reductase
Statins inhibit HMG-CoA reductase and lower
cholestrol
What are prosthetic groups?
similar to cofactors, but they are bound to the enzyme, rather than being separate molecules or atoms
What is a cofactor?
a non-protein substance. Binds to active site on enzyme, allowing substrate to fit into active site.
What does the biological function of a protein depend on?
chemical properties of its surface and how it binds to other molecules
When a protein catalyzes the formation or breakage of a specific covalent bond in a ligand, the protein is called an _______________ and the ligand is called a ______________
enzyme;substrate
At the active site of an enzyme,
the amino acid side chains of the folded protein are precisely positioned so that they favor the formation of the high-energy transition states that the substrates must pass through to be converted to product
What is feedback inhibition?
the end product of a metabolic pathway shuts down the pathway
What is an allosteric protein?
protein that undergoes a conformational change affecting its affinity for some ligand
**can exhibit cooperativity
What is an allosteric enzyme?
an enzyme whose activity is regulated by the binding of a small effector molecule
What is an allosteric site?
a different location that is not the active site of enzyme catalysis
Allosteric enzymes have
2 or more binding sites that influence one another
What is cooperativity?
a form of allosteric regulation that can amplify enzyme activity
Phosphorylation causes
a conformational change in a protein
GTP-binding proteins are switched on and off by
the gain or loss of a phosphate group
What causes a protein to walk along a cytoskeletal filament?
changes in their conformation
What are scaffold proteins?
help hold the coils together; concentrate interacting proteins in the cell
What are intracellular condensates?
form biochemical subcompartments in cells
Most enzymes are
allosteric proteins that can exist in two conformations
When GTP is bound to the alpha subunit, the G protein is _____.
active
When GDP is bound to the alpha subunit, the G protein is
inactive
Covalent modificiations added to a proteins amino acid side chains can control....
the location and function of the protein and can serve as docking sites for other proteins.
affinity chromatography
uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest
Mass Spectrometry
a technique that separates particles according to their mass
Most proteins belong to
families
What is a PDB file?
Protein Data Base File
What three analyses can be used to determine the function and structure of a protein?
NMR Spectroscopy, x-ray crystallography, and cryoelectron microscopy