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bio midterm
intro to molecular and cell bio- exam 1
475
Biology
Undergraduate 1
10/09/2011

Additional Biology Flashcards

 


 

Cards

Term
cell theory (3 things)
Definition

1. all organisms made of cells

2. cells are smallest unit of life

3. new cells only come from old cells dividing

Term
3 components of microscopy
Definition

magnification

resolution

contrast

Term
magnification
Definition
ratio b/w size of an image produced by microscope and actual size
Term
resolution
Definition
ability to observe two adjacent objects as distinct from each other
Term
contrast
Definition
how different one structure looks from antoher
Term
2 groups of microscopes based on source of illumination
Definition

1. light

2. electron

Term
light microscope
Definition
resolution = .2 micrometer (200 nm)
Term
electron microscope
Definition
resolution = 2 nanometers
Term
biggest single cell of species
Definition
egg
Term
things you can see with unaided eye
Definition
fish egg, bird egg
Term
things you can see with light microscope
Definition

plant and animal cells (most)

nucleus

most bacteria

mitochondria

Term
things you can see with electron microscope
Definition

smallest bacteria

viruses 

ribosomes

proteins

lipids

Term
2 types of electron microscopy
Definition

transmission (TEM)

scanning (SEM)

Term
transmission electron microscopes
Definition

you slice your sample into thin slices, then stain it with heavy metal, then shoot beam of electrons at it. 

some electrons are scattered (when hit metal), others are transmitted thru sample. 

--> forms an image, shows you cell ultrastructure

 

Term
scanning electron microscopes
Definition

sample is coated with heavy metal

beam of electrons scans surface, creating 3d image

--> shows contour

Term
2 categories of life
Definition

1. prokaryotes

2. eukaryotes

Term
prokaryotes
Definition

lack membrane enclosed nucleus (genomic DNA of cell is in cytoplasm)

 

either bacteria (abundant, most not harmful) or archaea (in extreme environments) 

Term
inside the typical bacterial cell, you'll find... 
Definition

plasma membrane (barrier) 

cytoplasm inside plasma membrane (contains organelles and DNA which is circular in bacteria)

nucleoid (where genetic material is found)

ribosomes (found throughout) 

Term
bacterial chromosomes vs plasmids
Definition

bacterial chromosomes- generally tethered to inside of cell

 

plasmids- free within the cytoplasm

 

Term
bacterial cells- what is outside the plasma membrane?
Definition

cell wall (for support and protection)

 

glycocalcyx- (saccaride coat on outside) traps water preventing dehydration, provides protection, esp against immune system

 

appendages- pilli (attachment) and flagella (for locomotion) 

Term
what types of cells have cell walls? 
Definition
plant cells, bacterial cells 
Term
key to eukaryotic cells
Definition
compartmentalization
Term
where is the DNA housed in eukaryotic cells? 
Definition
nucleus
Term
how do lysomes exemplify importance of compartmentalization?
Definition
they contain acid hydrolases that perfom hydrolysis but need a low pH (acidic) to funtion
Term
cytosol and metabolic activities of eukaryotic cells...
Definition

cytosol is central coordinating region for many metabolic activities of eukaryotic cells

 

Term
where does translation take place and what is it? 
Definition

takes place in ribosome

polypeptide synthesis- mRNA come here, the tRNA bring the amino acids. the rRNA (two subunits) facilitate

Term
what is cytoskeleton made up of? 
Definition

3 different types of protein filaments

1. microtubules

2. intermediate filaments

3. actin filaments

Term
purpose of microtubules
Definition

long hollow cylindrical structures that have dynamic instability

 

help with cell division, mobility (compose flagella), transport (can interact w/ proteins that help move things intracellularly) 

Term
subunit of microtubules
Definition
tubulin
Term
microtubules
Definition
hollow tubule with a plus end and a minus end that may be anchored- helps with cell shape, organization of organelles, chromosome sorting in cell division, intracellular movement of cargo, cell motility (cilia and flagella) 
Term
intermediate filaments
Definition

twisted filament (ropelike) with staggered alignment of filament proteins (multiple component proteins)

helps with cell shape, mechanical shape, anchorage of cell and nuclear membranes

Term
2 types of gradients across cell membrane
Definition

ion electrochemical (both electrical and chemical gradient)

 

transmembrane (concentration of a solute on either side) 

Term

diffusion across the plasma membrane: what is v. permiable? 

less so? 

not at all?

Definition

v. permiable: gases, v. small uncharged polar molecules

 

medium: water, urea, glucose

 

not at all: ions, macromolecules, ATP

Term
crenation
Definition
shrinking of animal cells in a hypertonic soln
Term
why is osmosis in plant cells different than in animal cells?
Definition
cell wall prevents major changes in cell wall- you either have turgor pressure (pressing against cell wall) or plasmolysis (plants wilt bc water leaves; gaps bw cell wall and plasma membrane) 
Term
2 classes of transport proteins
Definition
channels (a hole) or transporters (protein bonds to what is passing thru, conformational change occurs)
Term
t/f: most channels are gated...
Definition
true- gate is controlled by ligand (which binds to channel causing it to open), voltage, or mechanical (like your ear) 
Term

properties of amino acids lining inside of channel

 

Definition

inside: hydrophylic (otherwise ions couldn't cross into it)

 

outside: non-polar (they are associating with phospholipid tails) 

Term
aquaporin
Definition

Aquaporins are proteins embedded in the cell membrane that regulate the flow of water.

Aquaporins are integral membrane proteins

Term
vesicle vs. vacuole 
Definition

Vacuoles are sacs within the cell made out of the same material as the cell membrane. That's because vacuoles are usually formed by budding off of the membrane. Vacuoles may contain large food particles, enzymes, water, or many other substances. Autotrophic cells, which require a great deal of water, often have one large vacuole filled with water. On the other hand, animal cells do not usually have very large vacuoles.

Vesicles is a term given for very small vacuoles. Often vesicles are formed at an organelle known as a Golgi body in order to carry protein molecules either to other organelles or to the cell membrane.

Term
what is the principle pathway for the uptake of organic molecules? 
Definition
transporters
Term
3 types of transporters
Definition

1. uniporter- single molecule or ion

2. symporter/co-transporter- 2 or more ions of molecules transported in same direction

3. antiporter- 2 or more ions or molecules transported in opposite directions

Term
2 types of active transport (moving from low to high concentration)
Definition

1. primary- using a pump and energy directly to transport solute

2. secondary- using pre-existing gradient to drive transport of solute

Term
what is the name and chemical formula for the monomer of sugar?
Definition
monosacaride - CnH2nOn
Term
monosaccarides with C6H12O6 formula
Definition
glucose, fructose, galactose
Term
how are sugar monomers linked together to form polymers?
Definition
glycosidic bonds (two H and one O lost in the process- is dehydration/condensation)
Term
what is a lipid?
Definition
is made of C, H, O (more than two hydrogens for each oxygen; mostly made up of C and H) and is water insoluble (because they are non-polar)
Term
what is a triglyceride?
Definition
made up of 3 fatty acids and a glycerol
Term
what are the monomers of proteins? what are they made up of?
Definition

amino acids

made up of an amino group (NH2), a carboxyl group (COOH), and a side chain R- all attached to a central carbon

Term
how does environment of an amino acid impact whether the side chain of amino acid bears a charge?
Definition
amino acids in acidic environments thend to gain/retain protons (H+) while amino acids in basic environments tend to lose their protons
Term
hydrogen bonding between what features of an amino acid determine secondary structure? what determinds tertiary structure?
Definition

2ndary: hydrogen bonding between amino and carboxyl groups

3rdary: attractions/repulsions between side groups of amino acids

Term
peptide bond
Definition

Amino acids are joined together by a peptide bond. It is formed as a result of a condensation reaction between the amino group of one amino acid and the carboxyl group of another.

 

Term
"residue"
Definition
primary structure of a protein (chain of amino acids)
Term
secondary structure of a polypeptide
Definition
folding into alpha helix or beta pleated sheets- the shape of the polypeptide backbone (DOES NOT include side chains)
Term
tertiary structure
Definition

interactions between the side chains of the distinct amino acids

includes hydrophobic and ionic interactions, hydrogen bonds, covalent cross links, disulfide bridges.

Term
what makes up the plasma membrane in eukaryotic cells?
Definition

phospholipid bilayer

peripheral, intergral, and transmembrane proteins

Term
peripheral proteins
Definition
located on the surface of either inner or outer phospholipid bilayer; can be easily released
Term
integral proteins
Definition
proteins embedded in the phospolipid membrane that cannot be easily released
Term
transmembrane proteins
Definition
proteins that span the phospholipid bilayer
Term
what is a phospholipid made up of?
Definition
glycerol, 2 fatty acids and a phosphate group
Term
components of phospholipids and their solubility
Definition

head is hydrophillic (so is water soluble)

 

head is hydrophobic (so is water insoluble)

Term
two categories of transport across the cell membrane
Definition

active (against an existing gradient; requires energy)

passive (moves according to gradient of its concentration or according to molecular charge; requires no energy)

Term
more specific- proteins bound to membranes
Definition

1. integral or intrinisic membrane proteins

2. peripheral or extrinsic proteins

Term
2 types of integral/intrinsic membrane proteins
Definition

1. transmembrane

2. lipid anchored

Term
transmembrane proteins (structure)
Definition

one or more regions are physically embedded in the hydrophobic region of the phospholipid bilayer

-the amino acids of the proteins in the middle are hydrophobic to be able to interact with the hydrophobic phospholipid tails they are stuck to

-the amino acids on the outer edges of this protein are hydrophillic (interact with the aqueous enviroment on either side of the membrane)

 

Term
lipid anchored protein
Definition
integral/intrinsic membrane protein that is covalently attached by its amino acid side chain to a lipid in the plasma membrane
Term
peripheral membrane or extrinsic proteins
Definition

non-covalently bound either:

-to regions of integral membrane proteins coming out of the membrane

-to the polar head groups of phospholipids

Term
why are the carbs, lipids, proteins in plasma memberane referred to as fluid?
Definition
lipids and proteins can move relative to each other within the membrane
Term
amphipathic
Definition
to contain both a hydrophobic and hydrophilic portion
Term
true or false: cholesterol is found in both plant and animal cell plasma membranes
Definition
false: cholesterol is only in animal cells
Term
transmembrane protein (function)
Definition
signaling, channels to transport things in and out of the cell
Term
what does "movement of lipids within a membrane is semi-fluid" mean?
Definition
most lipids can spin around long axis and move laterally, but to "flip-flop" does not occur spontaneously, but requires ATP and ATP flippase
Term
how does length of fatty acyl tails impact fluidity of plasma membrane?
Definition
shorter acyl tails are less likely to interact with other tails, making the membrane more fluid
Term
how does presence of double bonds in acyl tails impact fluidity of plasma membrane?
Definition
double bonds in the tails create a kink within an individual tail so its harder for neighboring tails to interact and thus the membrane is more fluid
Term
how does cholersterol impact fluidity of plasma membrane?
Definition

cholesterol tends to stabalize membranes but depends on temperature

-in colder environments, cholesterol keeps membrane from geling

-in hot temperatures, cholesterol prevent membrane from being too fluid

Term
plasma membrane in artic fish
Definition
In an artic environment, fish would need a more fluid membrane because cold decreases membrane fluidity. Therefore they would need more unsaturated fatty acids (more chains with double bonds), and more cholesterol.
Term
passive transport only occurs thru
Definition
semi-permiable membranes
Term
forms of passive transport
Definition
simple (passive) diffusion, osmosis, facilitated transport
Term
diffusion
Definition
a small, lipid-soluble molecule passes directly thru the lipid bilayer, according to its concentraion gradient
Term
osmosis
Definition
the diffusion of water down its concentration gradient- depends on tonicity
Term
osmotic pressure
Definition
the higher the concentration, the higher the osmotic pressure, and water moves by osmosis to the region where osmotic pressure is the highest
Term
facilitated diffusion
Definition
passive transport that involves either channel or carrier proteins embedded in cell membrane
Term
channels in facilitated transport
Definition
passageways thru the membrane that are highly specific for a particular molecule- when channel is open (is often gated), molecules move according to concentration gradient
Term
carriers in faciliated transport
Definition
proteins that, when protein moving binds to them, undergo a conformational change that allows the molecule to move to the other side of the membrane based on the concentration gradient
Term
why does active transport require ATP?
Definition
because you are moving things from low to high concentration (and thus storing potential energy so need to put in some energy)
Term
sodium/potassium pump
Definition
an example of transmembrane protein that uses ATP to move 3 Na+ out of the cell for every 2 K+ ions that it brings in (an example of antiport)
Term
endocytosis- what is it?
Definition
bringing large substance into the cell- the cell membrane surrounds the target material sitting on the surface of the membrane until it is invaginated
Term
two types of endocytosis
Definition

1. pinocytosis

2. phagocytosis

Term
pinocytosis
Definition
when liquids and small particles are brought into the cell via endocytosis
Term
phagocytosis
Definition
when larger materials, like bacteria, are brought into the cell via endocytosis
Term
exocytosis
Definition
the cell puts material in a vessicle and sends it to the plamsa membrane- the vessicle binds with plasma membrane and expells the contents.
Term
what surrounds the nucleous of the eukaryotic cell? what is inside of it?
Definition

surrounded by- nuclear envelope

inside- chromosomes and nucleolus

Term
chromosomes
Definition
made up of DNA and proteins
Term
nucleolus
Definition
plays a role in making rRNA which is integral in synthesizing protein in the ribosomes
Term
golgi apparatus (function)
Definition
processes the proteins that were produced in the rough ER and packages them into membrane vessicles for storage or secretion; these vessicles bud off of the trans face and fuse with the plasma membrane to be expelled into extracellular space
Term
matter (definition)
Definition
contains mass, occupies space
Term
atoms cannot be broken down...
Definition
via ordinary chemical or physical means
Term
mass of the proton and neutron relative to the electron
Definition
~1,830 times more mass
Term
conclusions that can be made from Rutherford's gold foil experiment
Definition

atom is mostly empty space

the nucleous is slightly positivly charged (deflects a positivly charged alpha particle)

Term
how to think about where electrons are located
Definition
is not like a solar system, but orbitals are rather like clouds where electrons could be located- doesn't represent where exactly in space the electron is, but rather the probability of it being found there.
Term
rutherford's gold experiment (setup and results)
Definition
shot alpha particle (2 protons, 2 neutrons) at gold foil via an emitter; 98% of particles were undeflected; less than 2% were slightly deflected; .01% bounced back
Term
orbitals vs. shells
Definition

orbitals are s,p,d,f,etc; orbitals only hold 2 electrons each

shells are made up of orbitals- shells can contain different numbers of orbitals

Term
# of electrons and electron shells
Definition
the more electrons an atom has, the farther its outermost shell is from the nucleus
Term

1st shell:

2nd shell:

what is in them and how many electrons can they hold?

Definition

1st shell: 1s orbital; holds 2 electrons total

2nd shell: 1s orbital, 3 p orbitals; holds 8 electrons total

Term
atomic number
Definition
# of protons in the atom (= # of electrons in non-ion)
Term
trends in periodic table
Definition
by column (elements in same column have same # of valence electrons and so similar properties)
Term
atomic mass
Definition

protons + neutrons

(may not be a whole number because of prevalence of isotopes)

Term
weight
Definition
gravitational pull on mass
Term
dalton
Definition
unit of measurement for atomic mass; synonymous with amu
Term
1 mol
Definition
6.022 * 10^23 atoms
Term
95% of atoms in living organisms
Definition

hydrogen and oxygen (in water)

nitrogen (in proteins)

carbon

Term
compound
Definition
molecule made up of 2 or more elements
Term
3 types of bonds
Definition

covalent (either polar or nonpolar)

hydrogen

ionic

Term
covalent bonds only occur
Definition
between atoms whose outer electron shells are not full
Term
polar covalent bonds due to...
Definition

differences in electronegativity of the atoms in the molecule resulting in uneven distribution of electrons

ex. water

Term
hydrogen bonds responsible for holding together
Definition
strands of DNA
Term
t/f: exergonic rxns require a source of energy
Definition
true (have to have input = to activitation energy, even tho eventually release energy)
Term

hydrophobic or hydrophylic?

molecules with ionic bonds

Definition
hydrophilic
Term

hydrophobic or hydrophylic?

molecules with polar covalent bonds

Definition
hydrophilic
Term

hydrophobic or hydrophylic?

nonpolar molecules

Definition
hydrophobic
Term

hydrophobic or hydrophylic?

amphipathic molecules

Definition
both! (have both polar/ionized regions and nonpolar regions)
Term
colligative properties of water
Definition

adding solute to water:

lowers freezing point

raises boiling point

Term
ionization of pure water
Definition
[H+][OH-] = 10^-14
Term
pH
Definition
-log10 [H+]
Term
alkaline is a synonymn for
Definition
basic
Term
pH can affect
Definition

shape & function of molecules

rates of chemical rxns

ability of two molecules to bind

ability of ions or molecules to dissolve in water

 

Term
buffer (function)
Definition
to maintain homeostasis by having a rxn in body that can shift to create or consume H+ to adjust for pH changes
Term
buffer (biological example)
Definition

carbonic acid (CO2 & H20) to bicarbonate (H+ & HCO3-):

too much H+ in blood and lungs remove CO2, which raises the pH (by shifting rxn to produce carbonic acid)

to make blood more acidic- kidneys can remove bicarbonate, which will lower pH (break down more carbonic acid into bicarbonate and H+)

Term

polar or nonpolar:

C-C

C-H

C-O

Definition

C-C: nonpolar

C-H: nonpolar (similar electronegativity)

C-O: polar (oxygen much more electronegative)

Term
functional groups
Definition
group of atoms with special chemical features that are functionally important, each functional group exhibits the same properties in all molecules in which it occurs
Term

selected biologically important functional groups that bind to carbon:

amino

Definition
functional group found in proteins
Term

selected biologically important functional groups that bind to carbon:

ketones and aldehyde (a carbonyl group and something else)

 

Definition

steriods, waxes, proteins

keytones tend to be more in middle of molecules

aldehydes tend to be towards the end of molecules

Term

selected biologically important functional groups that bind to carbon:

carboxyl

Definition
amino acids, fatty acids
Term

selected biologically important functional groups that bind to carbon:

hydroxyl

Definition
steroids, alcohol, carbs, some amino acids
Term
CH3 and promoters
Definition
if you add a methyl group to a region of DNA called a "promoter" it will negatively impact expression of that gene
Term
charge of phosphate functional group
Definition
-2
Term
charge of sulfate functional group
Definition
-1
Term
where is sulfhydryl found? (SH)
Definition
in proteins that contain the amino acid cysteine
Term
structural isomer
Definition
contain same atoms but in different bonding relationships
Term
stereoisomers (definitions, types)
Definition

identical bonding relationships but in different spatial orientations

can either be cis/trans or enantiomers

Term
condensation and hydrolysis reactions are both...
Definition
... catalyzed by enzymes
Term
4 major types of macromolecules
Definition

lipids

carbs

proteins

nucleic acids

Term
2 examples of 5 carbon sugars
Definition
ribose, deoxyribose
Term
what are most of the carbon atoms in a carbohydrate linked to?
Definition
a hydrogen atom and a hydroxyl group
Term
an example of structural isomers?
Definition
glucose and galactose
Term
an example of cis trans enantiomers
Definition
alpha and beta glucose
Term
an example of enantiomers
Definition
D & L glucose
Term
disaccharide examples
Definition
sucrose, maltose, lactose
Term
polysaccarides involved in energy storage
Definition
starch (energy storage in plants), glycogen (excess glucose is converted into this and stored in liver)
Term
polysaccarides with structural roles
Definition
cellulose (plants structural), chitin, glycosaminoglycans
Term
what is a fatty acid?
Definition

a carboxylic acid with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated.

 

Term
formation of a fat: first step?
Definition

the hydrogens from each hydroxyl group in glycerol are removed

[image]

Term
formation of a fat: second step?
Definition

hydroxyl (OH) groups from each carboxyl group of the 3 fatty acids is removed

Term
formation of a fat: what is the bond between where the hydrogen had been on the glycerol and the hydroxyl had been on the fatty acid?
Definition
ester
Term
saturated fatty acid
Definition
all carbons linked by single covalent bond (solid @ room T)
Term
unsaturated fatty acid
Definition
contain one or more double bond- tends to be liquid at room T
Term
unsaturated fatty acids and cis/trans
Definition

cis unsaturated forms naturally

trans unsaturated formed by synthetic process- disease link!

 

Term
3 benefits to fats
Definition

more efficient energy storage

cushion

insulation

Term
which end of the phospolipid is hydrophillic?
Definition
the head (the polar, charged, phosphate region)
Term
which end of the phospholipid is hydrophobic?
Definition
the tail (the nonpolar fatty acid chains)
Term
describe what the phospholipid looks like
Definition
[image]Phospholipid
Term
steroid (made up of & water solubility)
Definition
four interconnected rings of carbon atoms that are typically not very water soluble
Term
one of most important steroids is....
Definition
cholesterol
Term
when thinking about which R group swap would least disturb protein function, factors to consider include...
Definition

size

polarity (or nonpolarity)

charge

Term
how many amino acids are there?
Definition
20
Term
in the protein ____ & _____ are across from each other on the alpha carbon
Definition

R group and hydrogen

amine group and carboxyl group

Term
which type of amino acids can form hydrogen bonds with adjacent amino groups?
Definition
amino acids with polar R groups (because differences in electronegativity)
Term
how are amino acids linked together?
Definition
peptide bonds
Term
every polypeptide has free whats?
Definition
a free carboxyl group and a free amino group
Term
the only level of protein structure encoded directly for in DNA is...
Definition
primary
Term
typically amino acid chain is described as beginning with what and ending with what?
Definition

begins with amino terminus

ends with carboxyl terminus

Term
what level of protein folding is the key determinant of the protein's characteristics?
Definition
secondary
Term
3 ways in which amino acid chain can fold in secondary folding
Definition
into alpha helix (like staircase), into B pleated sheet, or into random coiled region
Term
what type of bonding is responsible for secondary folding of proteins?
Definition
hydrogen bonding (proteins)
Term
name of protein that assists with protein folding?
Definition
chaparone
Term
disulfide bridges are what classification of bond? between what molicules do they occur?
Definition

covalent (so harder to break)

Disulfide bonds in proteins are formed between the thiol groups of cysteine residues.

Term
4 of the more temporary sorts of bonds that occur during protein folding
Definition

hydrogen bonds

ionic bonds (and other polar interactions)

hydrophobic effects

Van der Waal forces

Term
what sorts of interactions occur between one protein interacting with another protein?
Definition

hydrogen bonds

ionic bonds and other polar interactions

hydrophobic effects

van der waals forces

Term
2 classes of nucleic acids
Definition
DNA and RNA
Term
linc RNA
Definition
(long noncoding RNA): noncoding RNA that plays a role in the expression of certain kinds of genes
Term
3 kinds of movements of motor proteins
Definition

motor proteins move cargo from one place to another

motor protein is in place, causes filament to move

motor protein attempting to walk, but both it and filament are restricted in movement, so filament bends

Term
types of RNA
Definition

mRNA, tRNA, rRNA, linc RNA

(mRNA is copied from the DNA, comes out of the nucleus, rRNA facilitates creation of proteins by tRNA which carry amino acids)

Term
monomer of nucleic acid
Definition
nucleotide- made up of phosphate group, 5 carbon sugar (either ribose or deoxyribose), and single or double ring of carbon and nitrogen atoms known as a base
Term
what is the backbone of the nucleic acid that nucleotide monomers are held to?
Definition
sugar phosphate backbone
Term
what type of bonds link phosphate groups with sugars?
Definition
phosphodiester bonds
Term
describe what DNA looks like
Definition
its a chain of 5 carbon sugars that are linked by phosphodiester bonds and then there is an organic base that protrudes from each sugar.
Term
hydrogen bonds in DNA hold together what?
Definition
nitrogenous bases from the 2 polymer chains
Term
purines
Definition
adenine, guanine
Term
pyrimidines
Definition
cytosine, thymine, uracil
Term
which two pyramidines are switched out from DNA to RNA
Definition
thymine and uracil
Term
how many hydrogen bonds hold together adenine and thymine?
Definition
two hydrogen bonds hold together which nitrogenic bases
Term
how many hydrogen bonds hold together guanine and cytosine?
Definition
3 hydrogen bonds hold together which nitrogenous bases in DNA?
Term
what is the 1st law of thermodynamics?
Definition
energy is neither created nor destroyed but changes forms
Term
what is the 2nd law of thermodynamics
Definition
transferring energy increases disorder (bc when energy is converted from one form to another some of that energy is lost- no transformation is 100% efficient)
Term
fancy way of saying that total energy equals usable energy plus unusable energy
Definition
enthalpy (H) = free energy (G) + entropy (S)
Term
Gibbs free energy- definition and how to calculate it
Definition
change in free energy in a reaction in joules or calories; difference bw free energy of the products and free energy of the reactants
Term
if delta G is negative
Definition
free energy is released and so reaction occurs spontaneously
Term
if delta G is positive
Definition
free energy is consumed and reaction does not occur (unless it is coupled with reaction with negative delta G)
Term
does delta G's magnitude give you a clue as to rate of reaction?
Definition
nope- delta G's sign clues you into sponteniety but not rate of rxn
Term
what does the magnitude of delta G depend on?
Definition

delta H: the total energy that is added or released

 

delta S: changes in entropy

Term
how do large changes in entropy effect the magnitude of delta G
Definition
make magnitude of delta G more negative
Term
exergonic reactions
Definition
release free energy (negative delta G), catabolism, more disordered system
Term
endergonic reactions
Definition
store free energy (positive delta G), anabolic, system becomes more ordered
Term
what does delta G prime represent?
Definition
the delta G of a reaction under certain conditions (standard state, presence of water, pH of 7)
Term
what factors influence the delta G of a reaction
Definition

the delta G prime

the temperature

the concentration of products and reactants

Term
what does delta G at chemical equilibrium equal?
Definition
delta G = 0
Term
what does the statement "delta G is a state function" mean?
Definition

values only depend on the current state of the system and not how it achieved that state

(because of this, you can add delta G values --> coupling)

Term
generally two cool things ATP can do
Definition

releases lots of energy when hydrolyzed

 

can phosphorolate (donate phosphorus) to other molecules

Term
how much energy does ATP release when it is hydrolyzed?
Definition
about -7.3 kcal/mol
Term
why do cells phosphorolyate glucose to create glucose-6-phosphate?
Definition
to prevent it from leaving the cell via the plasma membrane (phosporic group is negatively charged so can't pass thru hydrophobic portion of bilayer)
Term
t/f: a catalyst is not consumed during a reaction
Definition
true: it's neither a product nor a reactant; may be consumed but will be reformed
Term
what are protein catalysts called?
Definition
enzymes
Term
what are RNA molicules with catalytic properties called?
Definition
ribozymes
Term
why do you need activation energy?
Definition
to allow the molecules to get close enough to cause bond rearrangement
Term
how do enzymes help catalyze a reaction?
Definition
by lowering the activitation energy by bringing the reactants together
Term
what does activiation energy do to the reactants?
Definition
changes them into unstable forms with higher free energy (called transition state intermediates)
Term
expansion on lock and key model of enzyme substrate fitting...
Definition
induced fit model- that the substrate's binding changes the enzyme's shape to even better accomodate the reaction
Term
why are enzymes different than coupling?
Definition

coupling changes the overall delta G by pairing with a negative delta G

 

enzymes ONLY lower the activation energy, making the reaction occur more quickly

enzymes DO NOT change the delta G (so a nonspontaneous rxn with a positive delta G won't occur even in the presence of an enzyme)

Term
by what mechanisms do enzymes work to lower activation energy?
Definition

strain bonds in reactants to make it easier to achieve transition state

position reactants together to facilitate bonding

change local environment thru v. temporary binding, making rxn more favorable to occur

Term
what factor is most important in determining what substrate will fit in an enzyme?
Definition
the shape of the active site
Term
what all interactions effect binding of the substrate to the active site of the enzyme?
Definition
hydrogen bonding, attraction and repulsion of electrically charged groups, and hydrophobic interactions
Term
what is it called when enzymes change shape when they bind to the substrate?
Definition
induced fit
Term
what enzyme is responsible for phosphorolating glucose to create glucose 6-phosphate during the first step of glycolysis?
Definition
hexokinase
Term
3 categories of enzymes partners
Definition

1. prosthetic groups

2. cofactors

3. coenzymes

 

--> ALL OF THESE ARE NON-PROTEINS

Term
prosthetic groups- what are they?
Definition
enzyme partners that are non amino acid groups bound to enzymes
Term
prosthetic groups- examples
Definition
heme, flavin, retinol
Term
cofactors- what are they?
Definition
a category of enzyme partners that are inorganic ions
Term
cofactors- examples
Definition
iron, copper, zinc
Term
coenzymes- definition
Definition
small carbon containing molecules that are not bound permanantly to the enzyme
Term
coenzyme (aka co-substrates)- examples?
Definition
biotin, NAD, FAD, ATP
Term
t/f: enzymes change neither the equilibrium constant nor the free energy values
Definition
true: enzymes shorten time for rxn by lowering transition state
Term
saturation point (in context of enzymes)
Definition
point at which all enzyme is bound to substrate (and so adding more substrate would have no effect on the reaction)
Term
what does the graph of concentration of substrate to reaction rate of a reaction without the enzyme present look like?
Definition
a straight line with a positive slope less than one
Term
what does the graph of concentration of substrate to reaction rate of a reaction WITH the enzyme present look like?
Definition
an exponentially increasing graph
Term
what is "Km"
Definition

the concentration of substrate at which you reach 1/2 of Vmax

it is used as a measure of enzyme affinity for substrate

Term
@ Vmax, you are also at...
Definition
@ saturation point, you are also at..
Term
how is Km a measure of the affinity of the enzyme for its substrate?
Definition
a small Km achieves maximal catalytic efficiency at low concentration of substrate, so high affinity
Term
Kcat (catalytic constant)
Definition
the turnover number- the # of reaction processes that each active site catalyzes per unit time
Term
relationship between Km and affinity
Definition
inversely related
Term
how do competitive inhibitors impact the measures of speed of a reaction
Definition
doesn't change the Vmax, and Vmax can still be reached, but it does increase the Km (so you have to add more substrate to be able to reach Vmax and you know affinity of the enzyme for the substrate is lower in the presence of the inhibitor)
Term
how does the presence of a competitive inhibitor change the lineweaver-burk plot?
Definition

X intercept (-1/Km) moves

slope (Km/Vmax) increases

yintercept (1/Vmax) does not change

Term
effects of noncompetitive inhibitors on reaction
Definition
the Km value is unchanged, the Vmax is lowered
Term
impact of competitive inhibitor on reaction
Definition
x-intercept is constant (-1/Km); slope increases (Km/Vmax) (because Vmax decreases as Km is the same)
Term
what type of respiration can occur not in the presence of oxygen? (anerobic)
Definition
glycolysis
Term
what does glycolysis begin with? what does it end with?
Definition

glucose

pyruvic acid

Term
overview of glycolysis- what happens in every step? how is energy stored?
Definition

hydrogen is given up or water is formed at every step.

every time hydrogen is broken up, energy within molecule is more concentrated and this energy is eventually stored in the bond of ATP

Term
anerobic respiration uses how many ATP?
Definition
2 ATP?
Term
anerobic respiration produces how many ATP?
Definition
4 ATP total (2 net, as two were used)
Term
t/f: each step of metabolism is coordinated by a specific enzyme
Definition
true!
Term
2 ways to make ATP:
Definition

substrate level phosphorolation

chemiosmosis

Term
substrate level phosphoraltion
Definition
enzyme directly transfers phosphate from one molecule to another
Term
chemiosmosis
Definition
energy stored in an electrochemical gradient is used to make ATP from ADP and Pi
Term
what components of cellular metabolism are classified as substrate level phosphorylation?
Definition
glycolysis and the Krebs cycle
Term
fermentation vs. respiration
Definition

fermentation uses an endogenous electron accepter (usually an organic compound)

 

respiration is where electrons are donated to an exogenous electron acceptor via an electron transport chain

Term
where does the aerobic phase of cell respiration take place?
Definition
inside the mitochondria
Term
overview of Krebs cycle
Definition
begins with pyruvate formed from glycolysis, converts it quickly into acetyl CoA, then breaks it apart bit by bit, storing energy in ATP. hydrogen atoms formed go onto oxidative phosphoralation (ETC)
Term
where does glycolysis occur?
Definition
in the cytoplasm
Term
by what method do both glycolysis and the citric acid cycle create ATP?
Definition
substrate level phosphoralation
Term
what happens to the hydrogen atoms that have been broken off during glycolysis and the citric acid cycle?
Definition
they go on to oxidative phosphorylation
Term
what is the fancy name of the stage where pyruvate gets converted to acetyl CoA?
Definition
pyruvate oxidation
Term
pyruvate oxidation- what does it start with, what does it end with
Definition

starts with the 2 pyruvates

forms 2 acetyl CoA, releases  2 NADH and 2 carbon dioxide

Term
what are all the things that glycolysis produces from the one molecule of glucose that it begins with?
Definition

2 pyruvate

2 ATP

2NADH

Term
where does pyruvate oxidation take place in eukaryotes?
Definition
in the mitochondrial matrix
Term
where does pyruvate oxidation take place in prokaryotes?
Definition
in the cytoplasm and plasma membrane
Term
actin filaments aka microfilaments
Definition

long thin filaments

help with muscle contraction, intracellular movement of cargo, ameboid movement, cytokinesis in cells

Term
what happens to the 2 NADH made during gycolysis in eukaryotes? 
Definition
makes more ATP in the electron transport chain via oxidative phosphoralytion
Term
what happens to the 2 NADH made during pyruvic oxidation in eukaryotes?
Definition
makes more ATP in the electron transport chain via oxidative phosphoralytion
Term
what does the citric acid cylce begin with and end with?
Definition

begins with 2 acetyl coA

ends with 4 CO2

also ends with 2 ATP (via substrate level phosphorolation), 6 NADH, and 2 FADH

Term
what happens to the 6 NADH and 2 FADH produced during the citric acid cycle?
Definition
makes more ATP in the electron transport chain via oxidative phosphoralytion
Term
by what mechanism does oxidative phosphoralation make ATP?
Definition
chemiosmosis
Term
t/f: oxygen is consumed during oxidative phosphorylation?
Definition
true
Term
what is the maximum output of oxidative phosphorylation? of glucose metabolism?
Definition

34 ATP

38 ATP

Term
what are the three phases of glycolysis?
Definition

energy investment

cleavage

energy liberation

Term
energy investment: glycolysis
Definition

2 ATP hydrolyzed to make fructose 1,6 biphosphate

 

Term
cleavage: glycolysis
Definition

fructose 1,6 biphosphate is broken down into two 3-carbon molecules of glyceraldehyde 3-phosphate

 

Term
energy liberaton: glycolysis
Definition
Two glyceraldehyde-3-phosphate molecules broken down into two pyruvatemolecules producing 2 NADH and 4 ATP
Term
what phosphorylates fructose 6 phosphate using ATP to make fructose 1,6 biphosphate?
Definition
phosphofructokinase
Term
how is gylcolysis controlled by feedback inhibition?
Definition
overproduction of ATP binds to an allosteric site on fructokinase (step 3) to inhibit it- so would not be able to phosphorolate fructose 6 phosphate
Term
what breaks down pyruvate into an acetyl group?
Definition
pyruvate dehydrogenase
Term
what happens during pyruvate oxidation?
Definition
a molecule of CO2 is removed from each pyruvate and remaining acetyl group is attached to CoA to make acetyl CoA
Term
in pyruvate oxidation, how many NADH are made for each pyruvate?
Definition
1 NADH per pyruvate
Term
what happens during slow arsenic poisioning?
Definition
arsenic allosterically inhibits pyruvate dehydrogenase (so can't convert pyruvate into acetyl CoA during pyruvate oxidation)
Term
citric acid cycle- chemical overview
Definition
acetyl is removed from acetyl CoA and is attached to oxalacetate to form citrate or citric acid; then oxaloacetate is regenerated to start the cycle again
Term
acetyl group (from acetyl CoA) + oxaloacetate =
Definition
citrate
Term
how is the citric acid cycle controlled by feedback inhibiton?
Definition
oxaloacetate is a competitive inhibitor of succiniate dehydrogenase (so succinate is NOT oxidized to fumerate)
Term
t/f: oxidative phosphorylation requires oxygen always
Definition
false- typically requires oxygen, but can use another molecule like sulfur as an electron acceptor
Term
what is responsible for phosphorylation during oxidative phosphorylation?
Definition
ATP synthase
Term
NADH can generate how many molecules of ATP
Definition
3ATP
Term
FADH2 can generate how many molecules of ATP?
Definition
2 ATP
Term
what are the actual components of the electron transport chain?
Definition
group of protein complexs and small organic molecules embedded in the inner mitochondrial membrane
Term
how do the protein complexes and small organic molecule in the inner mitochondrial membrane aid in chemiosmosis?
Definition
can accept and donate electrons in a linear manner in a series of redox rns- this movement of electrons generates H+ chemical gradient
Term
H+ chemical gradient in mitochondria- where are the most H+ charges?
Definition
outside of the mitochondrial matrix
Term
where is cellulose found in plants?
Definition
the cell wall
Term
NAD, NADH, etc in electron transport chain
Definition
NADH is oxidized to NAD+ and electrons are transferred to NADH hydrogenase. energy pumps H+ into intermembrane space. the electrons are transferred to ubiquinone.
Term
FADH, FADH2, etc in electron transport chain
Definition
FADH2 is oxidized to FADH- electrons are transfered to succinate reductase and then to ubiquinone
Term
what does ubiquinone do with its electrons in the electron transport chain?
Definition
it transfers its electrons to cytochrome b-c1. energy is used to pump H+ into intermembrane space. electrons are transferred to cytochrome c.
Term
what does cytochrome c do with the electrons it is given in the electron transport chain?
Definition
it transfers them to cytochrome oxidase which transfers electrons to oxygen, producing water. energy is used to pump H+ into the intermembrane space.
Term
what does "proton-motive force" refer to?
Definition
as the H+s flow down their electrochemical gradient thru ATP synthase, the energy in the gradient is used to generate ATP
Term
why is there such a thing as the "proton-motive force"?
Definition
because the lipid bilayer of the inner mitochondrial membrane is impermiable to H+ and so they (H+) has to pass thru ATP synthase
Term
ATP synthesis rarely achieves its maximal amount- why is this the case?
Definition

NADH is used in anabolic pathways

H+ gradient is used for other purposes

Term
how much energy is released by an electron donated by NADH?
Definition
25 kcal/mol
Term
how does direction of electron flow in electron transport chain relate to free energy per electron
Definition
the farther down the direction of electron flow you go, the less free energy per electron (NADH dehydrogenase releases the most)
Term
what experiment proves that ATP synthase requires an H+ electrochemical gradient?
Definition

when bacteriorhodopsin (a light driven H+ pump) is deprived of light, no H+ gradient is established and no ATP is produced by the ATP synthase

when bacteriorhodopsin is exposed to light, an H+ gradient is established and ATP synthase makes ATPs

Term
in which subunits of ATP synthase is there conformational change with bonding?
Definition
the beta subunit of ATP synthase
Term
steps in creating ATP synthase
Definition
ADP and Pi bind with good affinity; ATP is made; ATP is held together weakly and released; a new ADP and Pi bind weakly
Term
what is the warburg effect?
Definition
cancer cells preferentially use gycolysis (and not oxidative phosphorylation)- glycolytic enzymes overexpressed in 80% of all types of cancer bc mutations and low oxygen
Term
where do proteins enter in the cycle of cellular metabolism?
Definition
can start as pyruvate, acetyl CoA, or in citric acid cycle
Term
where does glycerol enter into cellular metabolism?
Definition
as glyceraldehyde 3-phosphate
Term
where do fatty acids begin into cellular metabolism?
Definition
as acetyl CoA
Term
what are the two strategies for cellular metabolism with lack of oxygen?
Definition

1. use substance other than O2 as final electron acceptor in electron transport chain

2. produce ATP only via substrate level phosphorylation

Term
other acceptors: what cool adaptations does E. coli have?
Definition
uses nitrate under anaerobic conditions; makes ATP via chemiosmosis even under aerobic conditions
Term
when does fermentation occur? and with what? ATP production?
Definition

when there is too much NADH

pyruvate is converted into either lactate (in muscle cells) or ethanol (in yeast)

produces far less ATP

Term
primary metabolism
Definition
essential for cell structure and function
Term
secondary metabolism
Definition
synthesis of secondary metabolites that are not neccesary for structure and growth, that are unique to a species or group, and help with defense, attraction, protection, competition
Term
phenolics
Definition

secondary metabolite- an antioxidant with intense flavors and smells

examples- flavanoids in vanilla

anthocyanins in pelargonidin (responsible for colors in geraniums, strawberries, etc)

Term
alkaloids
Definition

type of secondary metabolyte

bitter tasting molecule for defense

like atropine in the deadly nightshade

Term
terpenoids
Definition

secondary metabolyte

intense smells and colors

like beta carotene

Term
polyketides
Definition

secondary metabolyte

chemical weapons

streptomycin

Term
3 domains of motor proteins
Definition

head, hinge, and tail

(ground is cytoskeletal filament, leg is the head of the motor protein, and the hip is the hinge) (the body is the tail I suppose)

Term
flagella and cillia
Definition

flagella- usually longer than cillia and there are only one or two of them

cilia- shorter than flagella, tend to cover all or part of a surface of a cell

share the same internal structure (9+2 microtubal array)

Term
what does "9+2" microtubal array mean
Definition
Each of the two central microtubules consists of a single microtubule with 13 protofilaments arranged to form the wall of a circular tube. Each of the outer nine consists of a pair of microtubules that share a common wall (see the cross sections of microtubules in the figure)
Term
how does movement in flagella and cilia occur?
Definition
involves the propogation of a bend that begins at the base of the structure and proceeds towards the tip
Term
axonemes in the basal body (at base) vs. axonemes in the outer dublet microtubule?
Definition

in basal body- triplet microtubal

in outer dublet microtubal: a central microtubal pair and then 9 pairs around it

Term
what organelles does the endomembrane system enclose?
Definition

the nucleus, the endoplasmic reticulum, the golgi apparatus, lysosomes, and vacuoles; also includes plasma membrane

maybe directly connected or pass materials via vessicles

Term
chip28, aquaporin study
Definition

osmosis occurs more quickly in cells with transport proteins that allow the facilitated diffusion of water

(chip 28 codes for aquaporin, the integral membrane protein; frog cell with gene encoding for chip 28 had way more aquaporins and burst more quickly in hypotonic soln than a control cell)

Term
what sorts of cells have lots of aquaporins
Definition
kindey cell, red blood cells
Term
what is clathrin
Definition
a protein that plays a major role in the formation of coated vessicles- is a triangle shape that forms lattice around vessicles
Term
experiments on lateral transport of proteins
Definition

mouse and human cell fused together to create a heterokaryon, and mouse cells have proteins which bond to flourescent antibody

-@ cold temperatures, antibody only bonds to 1/2 of the cell

-@ normal T, membrane is fluid, so mouse protein spreads out, antibodies that have bound are distributed over entire cell

Term
depending on cell type, what percent of membrane proteins are restricted in their movement?
Definition
10%-70%
Term
2 reasons why integral membrane proteins may not be able to move
Definition

1. could be bound to cytoskeletal (so no lateral movement)

2. could be attached to molecules outside of cell, such as extracellular matrix

Term
what is the name of the protein that binds an integral protein to the cytoskeletal filament
Definition
linker protein
Term
what does FRAP stand for
Definition
flouresence recovery after photobleaching
Term

how does FRAP allow for the measurement of the lateral movement of membrane proteins?

 

 

 

Definition

you color a cell by engineering a cell to produce GFP (green flourescent protein) and then photobleach it by shining a light on it, eliminating the flourescence there

-if the area recovers, then you know there is fluidity in the plasma membrane

 

Term
with FRAP, length of time for recovery is proportional to...
Definition
fluidity of the membrane
Term
glycolysation (definition)
Definition
process of covalently attaching a carb to a protein or lipid (thus creating a glycoprotein or glycolipid)
Term
glycolysation: why do it?
Definition

1. recognition signals for other cellular proteins

2. plays a role in cell surface recongition

3. protective effects- cell coat (glycocalyx): carb rich coat on cell surface that shileds the cell.

Term
two fates of proteins being made by ribosomes
Definition

1. if the protein is going to stay in the cytosol, then ribsomemakes the peptide, then it folds and dissociates

2. if a protein being made is destined to go to an organelle, then protein is made with a signal sequence or localization sequence that helps direct it to where it needs

Term
t/f: gibbs free energy (delta G) tells us the total amount of energy in a system
Definition
false! enthalpy (H) tells us the amount of total energy in a system
Term
t/f: increasing the amount of reactants does not influence the delta G prime of the reaction
Definition
true: increasing the amount of reactants influences the delta G, not the delta G prime
Term
what is the definition of an inhibitor
Definition
a substance that reduces an enzyme's activity, either by influencing binding of substrate or turnover number
Term
what are two ways that irreversible inhibitors can disrupt the enzyme?
Definition

1. bind to the enzyme so tightly as to permanantly block activity

2. be a reagent that chemically modifies residues

Term
how does penicillin work? what type of inhibition does it do?
Definition

is an irreversible inhibitor- binds to the sering residue of an enzyme that catalyzes the crosslinkage in the bacterial cell wall

-penecillin looks like the R groups that would fit in the active site, so it binds covalently with active site, and thus impairs bacterial ability to grow cell wall (and thus its ability to grow)

Term
which type of inhibition is more important for metabolism?
Definition
impermanant (irreversible) inhibition
Term
what is the big difference between competitive and non-competitve inhibition?
Definition

competitive- substance directly competes with normal substrate for binding (does not affect catalytic activity of enzyme)

 

non-competitive- affects both substrate binding and catalytic activity

Term
what might various things look like that are competitive inhibitors?
Definition

like the substrate

 

transition state analogs look like the transition state intermediate

 

like neither of these

Term
what is an example of competitive inhibition and multiple substrates competing for binding sites?
Definition

both alcohol and methanol compete for enzyme alcohol dehydrogenase

 

(injesting methanol is bad because alcohol dehydrogenase converts it to formaldahyde and then to formic acid (bad!) but if consume ethanol or alcohol instead, will compete for alcohol dehydrogenase and prevent formation of formic acid)

Term
example of competitive inhibition- transition state analog competing for binding site
Definition

anti-viral drugs can inhibit virus's enzyme HIV protease

 

HIV protease inhibitors have the ring structure of the transition state substrate, so can bind to the HIV protease

Term
because competitive inhibitors don't change catalytic activity, what would we expect the lineweaver burke graph to look like?
Definition
same Vmax, but a greater Km (takes longer amt of time to reach); if you add enough substrate though it will change shape back like no inhibitor
Term
since noncompetitive inhibitors affect both substrate binding and catalytic activity, what do we expect to change on lineweaver-burke plot?
Definition
changes both Km and Vmax (doesn't impair at active site and then let go, but rather binds at site other than catalytic site so enzyme CAN'T eventually bind with substrate)
Term
why is non-competitive inhibition also called mixed inhibiton?
Definition
non-competitive inhibiors modulate both Vmax and Km
Term
what is an allosteric interaction?
Definition
a ligand binding at one site affects the binding of ligands at other sites (Allosteric enzymes are enzymes that change their conformational ensemble upon binding of an effector, which results in an apparent change in binding affinity at a different ligand binding site.)
Term
what is an example of an allosteric protein?
Definition
hemoglobin: it has multiple subunits that if binded to O2, then the binding to the next subunit is more favored
Term
most allosteric enzymes are what?
Definition
proteins with quaternary structure
Term
what are the regions of an allosteric enzyme
Definition

catalytic subunit (where the active site is located)

 

regulatory subunit (where inhibitors and activators bind)

Term
what is the molecule called that binds to the regulatory subunit of an enzyme, thus allosterically regulating it?
Definition
an effector molecule (can inhibit or activate an enzyme); also referred to as a modulator
Term
t/f: allosteric enzymes are sensitive to small changes in concentration of substrate
Definition
true! within a certain, range, reaction rates change based on substrate concentration
Term
allosteric enzymes are slightly sensitive to concentration of substrate but even more sensitive to what?
Definition
low concentrations of inhibitors!
Term
if you see a sigmoidal shape on the graph of reaction rate vs. concentration of substrate, what should you be thinking...?
Definition
... allosteric enzyme!
Term
what is the commitment step refer to?
Definition
the most regulated step in a chemical pathway; typically if the enzyme catalyzing this portion of the reaction is succesful, then the reaction will proceed to completion. typically is one of the earlier steps in the pathway
Term
what is feedback inhibition also called? what does it refer to?
Definition

aka end product inhibition

 

the final product acts as a noncompetitive inhibitor of the commitment step, thus shutting down the pathway.

Term
what kind of molecule is ATP
Definition
nucleotide (is adenine attached ribose sugar molecule with some phosphate groups)
Term
an example of allosteric regulation
Definition

feedback inhibition of ATCase (that makes N-carbamoyl aspartate from carbamoyl phosphate and aspartate in process to make CTP);

CTP is the high energy molecule (kinda like ATP) that helps synthesize RNA

Term
how does pH regulate enzyme activity?
Definition
pH changes electrostatic interactions, thus changing the shape of the enzyme (to restate this- it influences the ionization of functional groups)
Term
proteases: how location and pH optimal conditions are related
Definition

proteases are most active at the enzyme of the organism in which they break down proteins

pepsin, in the stomach, is best around pH 2

arginase, which works in liver and kidney, is most operational in pH 9.5

Term
example of enzyme mechanism: what do serine proteases do?
Definition
are reactive serines in the active site; digestive enzymes, important for development, blood coagulation, inflamation
Term
example of enzyme mechanism: what are examples of serine proteases?
Definition

chymotrypsin, trypsin, elastase

 

--> these all have serine as an amino acid in their active site

Term
example of enzyme mechanism: where are these serine proteases activated?
Definition
they are synthesized in an inactive form (called a proenzyme (or zymogen when a proteolytic enzyme)) and then are activated when they reach the digestive tract
Term
how do serine proteases chymotrypsin, trypsin, and elastase differ from one another?
Definition
have different reisdues within active site giving them substrate specificity (residues can be bulki, small, neutral, charged positively or negatively, hydrophilic or hydrophobic)
Term
why does temperature regulate enzyme activity?
Definition
at high temperature, noncovalent bonds break, enzyme loses tertiary structure and becomes denatured.
Term
what is an isozyme?
Definition

enzyme that catalyzes the same reaction, but have different properties, such as the optimal temperature

isozymes can be used to adjust to temperature changes

Term
enzymes in humans vs. enzymes in bacteria
Definition
enzymes in humans have higher optimal temperature than most enzymes in bacteria, so a fever can denature bacterial enzymes
Term
recyling of large molecules in an organism
Definition

most most large molecules exist for a relatively short peroid of time

half-life: time it takes for 50% of molecules to be broken down and recycled

Term
how does expression of genome allow cells to respond to change in their environment?
Definition
RNA and proteins are only made when needed, are broken down when not needed.
Term
in what ways in degradation of mRNA important?
Definition

you remove faulty copies of mRNA

 

you conserve energy by degrading mRNA for proteins you don't need anymore

Term
what are the two types of molecules responsible for breaking down mRNA?
Definition

exonucleases

exosomes

Term
what is the first step in mRNA degradation in eukaryotic cells?
Definition
shortening of the poly A tail
Term
what is the exonuclease and what does it do after cutting off the poly A tail?
Definition

its an enzyme that cleaves off nucleotide from the end

 

the 5' cap is removed and RNA is degraded from 5' end to 3' end

Term
what is an exosome and how does it function to break down RNA after the poly A tail is shortened?
Definition
it doesn't need to cleave the 5' cap, but just starts at the 3' end and chomps up to the 5' cap
Term
what degrades proteins? and how does it happen?
Definition

proteosomes break down proteins

 

the target proteins, which are misfolded and need to be broken down rapidly, have something come along and stick ubiquitin to them; then the protein goes to the proteasome cap and is unfolded and threaded thry the cap

Term
when proteins are degraded by the proteosome where are the small peptides and amino acids released into?
Definition
the cytosol
Term
what does the structure of the proteosome look like?
Definition
4 core proteasome rings stacked up with a cap on either end
Term
what substances are lysomomes responsible for breaking down? and what molecule do they use to do it?
Definition

they use hydrolases to digest substances taken up by endocytosis

break down proteins, carbs, nucleic acids, and lipids

 

Term
what is the term for recyling worn out organelles?
Definition

autophagy

(done by autophagosomes)

Term
transmission electron microscopy and staining the cell...?
Definition
the heavy metal dye binds tightly to the polar headed of phospholipids but does not bind well to the fatty acyl chains (which are hydrophobic)
Term
what is FFEM stand for and what is it?
Definition

freeze fracture electron microscopy

 

specialized kind of transimission electron microscopy

 

can be used to analyze the interiors of phospolipid bilayers

Term
what is the procedure that occurs during FFEM?
Definition
sample is frozen in liquid nitrogen, fractured with a kinfe; due to the weakness of the central membrane region, the leaflets split in two and can give 3d detail about membrane protein forms and shape
Term
what do the terms P and E face in the context of FFEM mean?
Definition

the P face: protoplasmic face (had been next to cytosol)

 

the E face: the extracellular face

Term
ribosomes begin synthesizing proteins- what happens if the protein is destined... to stay in the cytosol?
Definition
then the ribosome continues to make the protein in the cytosol until completion, they dissociate and protein goes into cytosol
Term
ribosomes begin synthesizing proteins- what happens if the protein is destined...to go to an organelle?
Definition

within the protein, there is a signal sequence (aka localization sequence) that helps direct it to where its supposed to go

 

(so sorting occurs post-translation)

Term
ribosomes begin synthesizing proteins- what happens if the protein is destined...to go outside the cell, to the plasma membrane, or to the lysosome? 
Definition

there exists a signal in the first few amino acids that tells the ribosome that it need to go to the ER; ribosome goes to the ER where completion occurs and it is shuttled to the golgi to be packaged to be sent out into the plasma membrane

 

(called cotranslational sorting to the ER)

Term
what does SRP stand for and what is its purpose?
Definition

signal recognition protein

 

it recognizes the sequence in the 1st few amino acids of a protein that signals cotranslational protein needs to occur; then SRP binds to the ribosome and brings it from the cytosol over to a channel protein in the ER membrane. the ribosome finishes making protein and it is "pooped out" into the ER lumen

 

Term
what organelle is the nuclear membrane contiguous with?
Definition
the endoplasmic reticulum
Term
when proteins are packaged in vessicles and sent to the golgi membrane, how does the golgi membrane "know" to pick them up (rather than allowing them to just keep on going over to the plasma membrane)?
Definition

there are t-snares (target snare) on the surface of the golgi membrane that grab certain v-snares (vessicular snare) that form coat proteins on the vessicle budding off from the ER membrane

 

Term
what systems work together in eukaryotes to synthesize most lipids? where does synthesis occur?
Definition

cytosol and endomembrane systems

 

process occurs at cytosolic leaflet of smooth ER

Term
what are fatty acid building blocks made by?
Definition
enzymes in cytosol or cells from foods that have been injested
Term
what enzyme in the ER membrane gets the fatty acids to stick to the glycerol phosphate?
Definition
acyl transferase
Term
what enzyme in the ER membrane chops the phosphorus off of the precursor of phosphobilipid?
Definition
phosphatase
Term
where does synthesis of membrane phospholipids occur?
Definition
the ER membrane, fool!
Term
transfer of lipids to other membranes:  how do lipids in the ER membrane go to nuclear envelope?
Definition
they can diffuse laterally!
Term
transfer of lipids to other membranes: how do they get to golgi, lysosomes, vacuoles, or plasma membrane?
Definition
vessicles!
Term
what do lipid exchange proteins do?
Definition
extract lipid from one membrane for insertion into another membrane
Term
except for proteins that are destined for semiautonomous organelles, most transmembrane proteins...
Definition
are directed to the ER membrane, from where they can be transferred via vessicles to the rest of the cell
Term
how are membrane proteins inserted into the ER membrane?
Definition
the ribosome is in the cytosol, comes up to the ER membrane, binds to channel protein; signal peptidase is adjacent. ribsome "poops" the protein out; the signal peptidase chops off the chain at the cleaved ER signal sequence; then ribsome keeps making the protein until a 20 amino acid long sequence of hydrophobic amino acids (which is the transmembrane part) wants to stay in the tail middle portion of the phospholipid bilayer. then ribosome keeps making other part of protein on other side of ER membrane (in the cytosol) until its done
Term
what are the two types of protein glycolysation we learned about?
Definition
N linked and O linked
Term
N linked glycolysation
Definition

attaching a carb to nitrogen atom of asparagine side chain

the ribosome is making a transmembrane protein and oligosaccharide transferrase comes up and sticks the carb tree on the nitrogen of asparagine. then ribosome finishes its business and you have glycolysated protein transmembrane

Term
O-linked
Definition

a type of glycolysation

occurs in golgi only

addition of sugars to oxygen atom of serine or threonine side chains

Term
cell fluidity experiments with heterokaryons
Definition

merge a cell, so half of fused membrane is mouse cell that gives off GFP, half is human cell

 

at low T, GFP is only given off on half cell (where all the mice cells were) so poor cell fluidity

 

at high T, GFP distributed across entire area, so good cell fluidity

Term
passive diffusion
Definition
diffusion of a solute thru a membrane without transport protein
Term
facilitated diffusion
Definition
diffusion of a solute thru a membrane without the aid of a transport protein
Term
active diffusion
Definition
requires energy because transporting substances against a gradient
Term
where is the chloroplast contained in the plant cell?
Definition
actually it is just floating around in the cytosol
Term
how many membranes does the chloroplast have?
Definition
three: an outer and an inner, and then the thylakoid membranes
Term
what do you call the stack of thylakoids in the chloroplast
Definition
granum
Term
what is the fluid inside the inner membrane of the chloroplasts that surrounds the granum?
Definition
stroma
Term
t/f: chloroplasts are found in all species of plants and algae
Definition
false: chloroplasts are present in nearly all species of plants and algae
Term

fill in the blank:

both mitochondria and chloroplasts contain their own _______ and divide by ________

Definition
DNA; binary fission
Term
anatomy of a mitochondria
Definition

[image]

 

1. inner membrane

2. outer membrane

3. christae

4. matrix

Term
what does the mitochondrial matrix hold on to in the mitochondria?
Definition

In the mitochondrion, the matrix contains soluble enzymes that catalyze the oxidation of pyruvate and other small organic molecules.

The mitochondrial matrix also contains the mitochondria's DNA and ribosomes.

Term
why are mitochondria and chloroplasts referred to as being semi-autonomous?
Definition
they depend on other parts of the cell for their internal components, even tho they can grow and divide by themselves
Term
major functions of the plasma membrane?
Definition

cell adhesion

membrane transport

cell signaling

 

(movement, morphological change, gene expression)

Term
receptor mediated signaling transduction
Definition
Signal transduction is the process by which an extracellular signaling molecule activates a membrane receptor, that in turn alters intracellular molecules creating a response.[1] There are two stages in this process: 1) a signalling molecule activates a certain receptor on the cell membrane 2) causing a second messenger to continue the signal into the cell and elicit a physiological response.
Term
do peroxisomes have their own DNA?
Definition
no! they can split once they are in the cytosol but its just the vessicle splitting off, not them having their own DNA to replicate
Term
peroxisomes can split up in the cytosol but the original peroxisome was made in the...
Definition
ER (where peroxisomes bud off from when they are in an immature stage, then they mature in the cytosol)
Term
certain reactions that break down molecules by removing hydrogen or adding oxygen produce what? and what breaks that down
Definition

hydrogen peroxide

 

peroxisomes! thanks to catalase, which breaks down H2O2 into water and oxygen

Term
vacuoles
Definition

function differs

in plants, central vacuoles: storage and support

contractile vacuoles in protists expel excess water

phagocytic vacuoles in protists and white blood cells degrade things

 

Term
what process is utilized during autophagy to recycle worn out organelles
Definition
endocytosis
Term
what are the names of the enzymes in lysosomes that perform hydrolysis?
Definition
hydrolases!
Term
Palade's pulse chase experiments: what was the setup?
Definition
he coated the pancreas of a gunea pig with radioactive film; then injects radioactive leucine into animal, then non-radioactive leucine; he then was able to follow the path of the radioactive leucine ("chase") to find out how the cell used it.
Term
Palade's pulse chase experiment: what was the finding?
Definition

he was able to determine the path of the leucine (and the protein it was incorporated into) and found:

5 mins: most staining was in the ER

15 mins: most staining was in Golgi

30+ mins: no radioactivity or radioactivity in vessicles nearby the plasma membrane

Term
why was the pancreas a good organ to study for Palade? and what did he determine (overall)?
Definition

pancreatic cells' primary function is protein secretion

 

his experiments provided the first evidence that secreted proteins more sequentially (proteins are synthesized into rough ER, then moved thru a series of compartments before they are secreted)

Term
golgi apparatus: is it contiguous with the nuclear membrane & ER?
Definition
No! that's why vessicles have to transport stuff between the stacks
Term
golgi apparatus: what does it look like and what is its function?
Definition

flattened, membrane bound compartments (like pancakes)

 

secretion, processing, protein storage, glcolysation

Term
what do cis, medial, and trans mean in the context of the golgi apparatus?
Definition

cis: side closest to ER and nucleus

 

medial- middle portion of golgi

 

trans: side of golgi closest to plasma membrane

Term
ER membrane: how is it setup?
Definition

network of membranes that form flattened, fluid filled tubules or cisternae

 

the ER membrane encloses a single compartment called the ER lumen

Term
rough ER: why is it so rough? and what does it do?
Definition

rough because its studded with ribosomes

 

involved in protein synthesis & sorting, as well as glycolysation of proteins

Term
glycolysation is a ___________ modification
Definition
post-translational
Term
what is smooth ER and what does it help to do?
Definition

doesn't have ribosome

 

helps with detoxyfication, carb metabolism, calcium balance, and modifying lipids

Term
how might where chromosomes occupying different territories in the cell nucleus impact cell?
Definition
may be that there is higher degree of gene regulation depending on what chromosomes are next to each other and where they are within the nucleus
Term
where does ribosome assembly begin? and where does it complete?
Definition
begins in the nucleolus; ends in the cytoplasm
Term
nuclear matrix of the nucleus
Definition
filamentous network that organizes chromosomes
Term
what is the name of the protein component of chromosomes?
Definition
chromatin!
Term
what are chromosomes made up of?
Definition
DNA and chromatin (protein)
Term
what are the two parts of a ribosome? where do they assemble?
Definition

rRNA part and protein part

 

ribosomal genes (in the nucleosis) are transcribed and rRNA is made in the nucleolus. then that comes out to the cytoplasm where the protein component is then stuck on

Term
why is it called a nuclear envelope?
Definition
its a double membrane structure (the outer membrane being the one connected to the ER membrane)
Term
what is the point of the nuclear pores?
Definition
passage for proteins in and out (like histones, which help with folding by being spool that DNA wraps around; or transcription factors) and mRNA out (to go to cytoplasm for transcription)
Term

overall in photosynthesis:

what is reduced?

what is oxidized?

what drives this rxn?

ender or exergonic?

Definition

CO2 is reduced

H20 is oxidized

energy from light makes it happen

endergonic rxn

Term
where does the majority of photosynthesis (occurs in chloroplasts) occur?
Definition
mesophyll
Term
what is the stoma (or stomata?)
Definition
a microscopic pore on the surface of the plant that lets in COs, expels O2
Term
what is between the outer and inner membrane of the chloroplast?
Definition
the intermembrane space
Term
what is the "3rd" membrane of the choloroplast?
Definition
the thylakoid membrane! (encloses thylakoid lumen)
Term

overview: light reactions:

what do they use for energy?

where do they take place?

what do they produce?

Definition

sunlight

thylakoid membranes

ATP, NADPH, O2

Term

overview: Calvin cycle rxns

what do they use for energy?

where do they take place?

what do they produce?

Definition

ATP and NADPH (with CO2)

in stroma

organic molecules

 

Term
how are wavelength and energy related in EM light?
Definition
the longer the wavelength, the less energy of the photon
Term
what kind of light do plants use?
Definition
light in the visible portion of the spectrum
Term
what influences the wavelength of light that a pigment absorbs?
Definition
it absorbs based on the amount of energy needed to boost an electron to a higher orbital (photons are quantum)
Term
name 3 kinds of photosynthetic pigment molecules: what are they made up of?
Definition

chlorophyll a & b; carotenoids

 

porphyrin ring

phytol tail

Term
absorbtion spectrum
Definition
wavelengths that are absorbed by different pigments in the plant
Term
action spectrum
Definition
rate of photosynthesis by whole plant at specific wavelengths
Term
what happens to the excited electrons of photosystem 2?
Definition

they travel to PSI

water is oxidized, making O2 and H+

energy is released in ETC that is used to make H+ gradient

Term
what is the primary role of PSI
Definition
to make NADPH (because adding H+ to NADP contributes to electrochemical gradient)
Term
under what category does the ATP synthesis in the light reactions of plants fall?
Definition
Chemiosmotic (driven by flow of H+ from thylakoid lumen into stroma via ATP synthase)
Term
how is the H+ gradient in light reactions of photosynthesis generated?
Definition
– ↑H+ in thylakoid lumen by splitting of water
– ↑H+ by ETC pumping H+ into lumen
– ↓H +  from formation of NADPH in stroma
Term
summary of light reactions of photosynthesis: how are O2, NADPH, and ATP produced during light reactions
Definition
1.  O2 produced in thylakoid lumen by
oxidation of H2O by PSII
–  2 electrons transferred to P680+
2.  NADPH produced in the stroma from
high-energy electrons that start in PSII
and boosted in PSI
–  NADP+ + 2 electrons + H + → NADPH
3.  ATP produced in stroma by H+
electrochemical gradient
Term
Z scheme: where is the lowest energy level of an electron; where is the highest energy level?
Definition
Electron of nonexcited pigment molecule
has lowest energy in PSII
Highest energy level from being boosted
by PSI
Term
why might one refer to PS 2 as a "redox machine"?
Definition
removes high energy electrons from a
pigment molecule and transfers them to a
primary electron acceptor
Term
what are the two types of electron flow going on during the light reactions?
Definition

noncyclic (electrons begin at PS2, transfer to NADPH; linear process makes ATP and NADPH in equal amounts) = Z scheme = from PS2 to PS 1

 

cyclic phoshorylation- electron cycling releases energy to transport H+ into lumen, driving synthesis of ATP; PSI electrons are excited, release energy, and eventually return to PS1.

Term
what are the two main components of PS2 (680)?
Definition

light harvesting antenna complex (directly absorbs photons, transfers energy via resonance energy transfer)

reaction center- which is unstable when excited and removes electrons from water to replace oxidized P680 after it has passed on its excited electron (thus producing O2 gas)

Term
what is used during the calvin cycle to make carbs?
Definition
ATP, NADH, CO2
Term
T/F: the end product of the Calvin cycle is glyceradlehyde 3 phospohate?
Definition
true: glucose is not directly made
Term
during the calvin cycle, for every 6 CO2 that are incorporated...
Definition
18 ATP and 12 NADPH are used
Term
overview: 3 phases of calvin cycle
Definition

carbon fixation

reduction and carb production

regeneration of RuBP

Term
carbon fixation
Definition

CO2 incorporated in RuBP using Rubisco

6 carbon intermediate splits into 2 molecules of PG

Term
reduction and carb production
Definition
ATP is used to convert 3PG into 1,3-
bisphosphoglycerate
–  NADPH electrons reduce it to G3P
–  6 CO2 → 12 G3P
•  2 for carbohydrates
•  10 for regeneration of RuBP
Term
regeneration of RuBP
Definition
10 G3P converted into 6 RuBP using 6 ATP
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