Quiz 1: Reading Info Flashcards
Cytoplasm
aqueous internal solution and suspended particles
Cytosol
just aqueous solution
Metabolite
intermediated in biosynthetic and degradation pathways
What limits cellular dimensions?
lower limit of size set by minimum number of biomolecules required by the cell
upper limit of size is set by the rate of diffusion: need a high surface-to-volume ratio for diffusion to occur
Are eukaryotes more closely related to bacteria or archaea?
Archaea
Share closer common ancestor
Types of single cell organisms
Archaea- extreme environments
Bacteria- soils, surface waters, tissues of other organisms
What organelles do all cells have?
cytoplasm, plasma membrane, ribosomes
What types of cells have a nucleoid?
Bacterial cell
Do bacteria cells have membrane bound organelles?
No
Cell envelope
the plasma membrane and the layers outside of it
differ in bacteria cells (gram+, gram-, etc.)
Gram positive bacteria
have a thick layer of peptidoglycan outside their plasma membrane but lack an outer membrane
Gram negative bacteria
have an outer membrane composed of a lipid bilayer
the cell wall is wedged between 2 membranes
What is in the outer membrane of gram negative bacteria?
1) porins: provide transmembrane channels for low molecular weight compounds and ions to diffuse
2) lipopolysacchrides
Do archaea have cell walls?
yes, normally made of peptidoglycan or hard protein
plasmids
small circular segments of DNA in the cytoplasm of bacteria
outside of the main DNA in the nucleoid
What gave the first hints that bacteria and archaea constitute different domains?
ribosomal differences
Size difference between eukaryotic cells and bacteria/archaea cells
5-100µm for eukaryotic cells
2µm for prokaryotic cells (less stuff to contain)
Mitochondria
site of most of the energy extracting reactions of the cell
Golgi complex
postmaster of the cell
processes, packages, and targets proteins to other organelles for export
Rough endoplasmic reticulum
site of much protein synthesis
Smooth endoplasmic reticulum
site of lipid synthesis and drug metabolism
Peroxisomes
oxidize fatty acids (breakdown fatty acids)
Lysosomes
filled with digestive enzymes to degrade unneeded cellular debris
vacuoles
store large quantities of organic acids
*large central vacuole found in plant cells
chloroplasts
sunlight drives the synthesis of ATP in the process of photosynthesis
*found in plant cells
Do plant cells have mitochondria?
Yes
Are plant cells or animal cells larger?
Plant cells
Thylakoids
site of light-driven ATP synthesis
Plasmodesma
provides path between two plant cells
How can you determine the function of the different organelles?
gently rupture the plasma membrane by physical shear
then centifuge the organelles
Cytoskeleton
protein filaments that crisscross the eukaryotic cell, forming an interlocking 3D meshwork
provide structure, shape and organization to the cell
3 types of cytoplasmic filaments
1) actin filaments
2) microtubules
3) intermediate filaments
Are cytoplasmic filaments set in place?
No! They constantly change locations and break down into protein subunits
Controlled by regulatory proteins when to move
Endomembrane system
segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur
Exocytosis and endocytosis
mechanisms of transport that involve membrane fusion and fission, provide paths between the cytoplasm and surrounding medium
allowing for secretion of substances produced in the cell and uptake of extracellular materials
How big are ribosomes?
20 nm
How big are amino acids?
0.5 nm
How big is the mitochondria?
1000 nm
What makes carbon so crucial to life?
Its ability to make 4 stable single bonds and its bonding versatility
What are the central metabolites?
small organic molecules that are the building blocks of life
these molecules may be polar or charged and are soluble in water: this traps them in the cell
Can polar molecules diffuse across the cell membrane?
Most cannot, unless very small
Metabolomics
the systematic characterization of the metabolome under very specific conditions, such as following the administration of a drug
Macromolecules
polymers with molecular weights above ~5000 that are assembled from relatively simple precursors
Oligomers
shorter polymers
What may macromolecules be assembled into?
Supramolecules such as ribosomes
Proteins
long polymers of amino acids
serve as enzymes, structural elements, signal receptors, or transporters
make up the 2nd largest fraction of the cell after water
Nucleic acids
either DNA or RNA
polymers of nucleotides
store and transmit genetic information
Polysaccharides
polymers of simple sugars such as glucose
energy-rich fuel stores, structure for cell walls, extracellular recognition elements that bind to proteins
Lipids
water-insoluble hydrocarbon derivatives
serve as structural components of membranes, energy-rich fuel stores, and intracellular signals
Types of macromolecules
Proteins, nucleic acids, polysaccharides, lipids
Informational macromolecules
proteins and nucleic acids
Stereoisomers have different…
configuration!
What is another name for cis/trans isomers?
geometric isomers
Configuration is conferred by the presence of either
1) double bonds around which there is little or no freedom of rotation
2) chiral centers around which substituent groups are arranged in a specific orientation
Chiral molecule
rotated molecule cannot be superposed on its mirror image
Enantiomers
stereoisomers that are mirror images of eachother
different R/S configuration
Diastereomers
stereoisomers that are not mirror images of each other
same R/S configuration
Racemic mixture
equimolar solution of two enantiomers that does not show optical rotation
enantiomers rotate plane polarized light
two different enantiomers will rotate the light in opposite directions and cancel eachother out
Conformation
the spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of rotation around single bonds
Difference between empirical and molecular formulas?
Empirical formula simplifies number of atoms; molecular formula lists them all out
Is a dyanmic steady state at equilibrium?
not exactly
in biochemistry, something is reaching equilibrium when it is dead and decaying
instead, there is a dynamic steady state when alive. the rate of breakdown equals the rate of anabolism
system
all products and reactants, the solvent that contains them and the immediate atmosohere
universe
the system and its surroundings
Isolated, closed, and open systems
Isolated- system shares neither matter nor energy with its surroundings
Closed- system shares energy but not matter with its surroundings
Open- system shares energy and matter with its surroundings (living organisms are open systems)
1st law of thermodynamics
although the form of the energy may change, the total amount of energy in the universe remains constant
oxidation-reduction reactions
almost all reactions involved in electron flow
one reactant is oxidized (loses electrons) while the other is reduced (gains electrons)
2nd law of thermodynamics
the total entropy of the universe is continually increasing
this applies to biochemistry, because it requires an input of energy to order things (ex: informational macromolecules have subunits in specific order)
What type of bond breaks in ATP?
phosphoanhydride
Bioenergetics
the study of energy transformations in living systems
concerned with how energy is coupled
What does the magnitude of delta G depend on?
how far from equilibrium the system is originally
delta G measures the change from the initial state to equilibrium
Do thermodyanmic constants like delta G tell us anything about how fast a reaction will occur?
No! That’s kinematics
Thermodyanmics only tell us where the final equilibrium for a reaction lies
What is another reason why ATP breakdown is exergonic (besides neg. charged phosphate groups)?
cells maintain a concentration of ATP far above equilibrium concentration
products want to be made then and breakdown ATP
Using ATP to make reactions exergonic
TRANSFERRING a phosphoryl group to another molecule (not just breaking down ATP)
Why are biological macromolecules stable?
they are thermodynamically unstable, but kinetically stable since it takes so long to break them down
this is where enzymes come into play
transition state
a state of higher energy than either the reactants or products
activation energy
the change in free energy from the initial state to the transition state (delta G double-dagger)
How do enzymes catalyze reactions?
1) providing a more comfortable fit for the transition state, and consequently lowering the activation energy
2) binding two or more reactants in a sterospecific orientation that favors the reaction
What is crucial about enzymes?
need to be able to use them selectively
pathways
sequences of consecutive reactions
the product of one reaction becomes the reactant in the next
metabolism
the overall network of enzyme-catalyzed pathways both catabolic and anabolic
feedback inhibition
if an enzyme is producing too many of a molecule, this higher concentration of molecule may inhibit the enzyme from working
What type of shape does water molecule have and corresponding bond angles?
Tetrahedral (two lone pairs)
104º bond angles
BDE of H-bonds
23 kJ/mol compared to 348 kJ/mol for C-C bond
How many hydrogen bonds can water make with other molecules?
up to 4 due to the tetrahedral structure
on average, makes about 3.4
Why does ice melt at room temperature and water evaporate?
reaction is spontaneous due to the increase in entropy
enthalpy is actually positive, so entropy drives this reactions
When are hydrogen bonds the strongest?
when the hydrogen atom and the two atoms that share it are in a straight line
places a positive charge directly between two negative charges
Why does salt dissolve in water, besides charges?
increase in entropy when salt leaves the ionic crystal lattice
Why are nonpolar gases poorly soluble in water?
for one, they are nonpolar. for two, they go from a gas to a liquid which is a decrease in entropy
clathrates
cystalline compunds of nonpolar solutes and water
What type of molecules make micelles?
amphipathic
van der Waals radius
every atom has an individual distance of how close the atom will allow another to approach it
How do nonpolar interactions become strong?
their cumulative effects
for example, nonpolar interactions dictate protein folding
Why are tightly bound water molecules important?
they allow for proton hopping to occur across them
they also can form part of binding sites
colligative properties
vapor pressure, boiling point, melting point, and osmotic pressure
solutes effect all four properties
How does water diffuse across the cell membrane?
aquaporins
How do cells prevent lysis?
1) cell walls
2) pump water out
3) maintain extracellular environment that has same osmolarity as inside cell (blood plasma)
4) pump Na+ and other ions into extracellular environment
What does the osmolarity of a solution depend on?
the number of solutes, not the mass of solutes
ex: macromolecules would have much less of an effect on osmolarity than their monomeric components
Turgor pressure
pressure exerted against the cell wall of plants
Do H+ protons exist in solution?
No! Hydrogen ions are immediately converted into hydronium molecules
What gives the extent of ionization?
the equilibrium constant, Keq
acidosis
the pH of blood is below the normal 7.4
often occurs in people with diabetes
alkalosis
pH of blood is higher than normal
Acids are
proton donors
Bases are
proton acceptors
What do titration curves reveal?
the pKa of weak acids
What happens at the midpoint of titration curves?
one-half of the acid is neutralized, so [HA]=[A-]
the amount of acid is equal to the amount of conjugate base
this leaves only [H+], so pH=pKa
How is consistency of pH primarily achieved?
through the use of biological buffers
buffering zone
characteristic pH zone in which a weak acid is an effective buffer
Phosphate buffer system
acts in the cytoplasm of all cells
maximally effective at 6.86, and thus has a pretty neutral buffering zone
Bicarbonate system
buffers blood plasma
Carbonic acid (H2CO3) acts as proton donor
Bicarbonate (HCO3-) acts as proton acceptor
How does the bicarbonate system work?
very little H2CO3 is in the blood plasma compared to bicarbonate (HCO3-), so you would think buffer would not work
BUT the large reserve of CO2(g) in the lungs and CO@(d) in the blood can be drawed upon to react with H2O and generate more H2CO3
What happens to blood buffer system during exercise?
lactic ACID is made, so there are more H+ ions
these protons are picked up by HCO3-
and then converted to CO2 which you breath out
Rate of respiration and the blood buffer system
rate of inhaling and exhaling can quickly adjust to keep the blood pH nearly constant
this is controlled by the brain stem which can detect differences in pCO2 or decreased blood pH
What happens to individuals with diabetes?
lack of insulin decreases the uptake of glucose from the bloodstream
dependence on fatty acids raises the concentration of carboxylic acids in the blood
this lowers the pH of blood plasma (<7.35) and causes acidosis
this pH prevents enzymes from working at optimal pH and can have severe side effects
Condensation reaction
two molecules come together and water is eliminated
endergonic reaction
Hydrolysis reaction
water is added and molecule breaks apart
exergonic reaction
hydrolases
catalyze hydrolysis reactions
what does the high specific heat of water do for living organisms?
acts as a “heat buffer”
what does the high heat of vaporization of water do for living organisms?
allows excess body heat to evaporate as sweat
How does acidosis occur if there is too much CO2 gas in the lungs?
CO2 (gas) –> CO2(aqueous)
CO2 + H2O –> H2CO3
H2CO3 –> H+ + HCO3-
What is reduced and what is oxidized in cellular respiration?
Oxygen is reduced
Glucose is oxidized
(makes sense when think of e values)
