1 - CELL AND MOLECULAR BIOLOGY Flashcards
define electronegativity
ability of an atom to attract electrons
what are the 3 main type of chemical bonds
ionic
covalent
hydrogen
what are ionic bonds?
transfer of electrons between atoms of differing electronegativity
the one with a higher electronegativity, takes the electrons
what are covalent bonds?
sharing of electrons
atoms can be single/double/triple -bonded
what are non-polar covalent bonds?
equal sharing of electrons between two atoms of similar electronegativity
what are polar covalent bonds?
unequal sharing of electrons between two atoms of differing electronegativity
FORMS A DIPOLE!!
what are van der waal interactions?
weaker and more transient than hydrogen bonding. more of an interaction which gets stronger, the larger the molecule is
what are hydrogen bonds?
weak interaction between a hydrogen (attached to a highly electronegative atom) and a negatively charged atom of another molecule (F, O, N)
what are the 5 most important properties of water?
it’s a good solvent
it has a high heat capacity
ice floats. water expands as it freezes and becomes less dense
it has strong cohesion/surface tension. its strong cohesion between H2O molecules produces high surface tension
it has adhesion. adheres to unlike objects - water sticks to skin/glass
why is water a good solvent?
the dipoles (the slight positive and negative charges) of H2O break up charged ionic molecules, by disrupting the attractive forces between the atoms of that molecule
this makes it easier for water to dissolve substances
why does water have a high heat capacity?
due to the hydrogen bonds between water molecules which require (the absorption) heat to break
what is heat capacity?
the amount of heat needed to change the temperature of a substance by 1 unit (e.g. 1 degree)
why does ice float?
water expands as it freezes and becomes less dense
the H-bonds become rigid and forms a crystal that keeps molecules separated. their attractions arrange them into fixed positions
why is there strong cohesion between water molecules?
due to H2O’s ability to form hydrogen bonds - and the extremely electronegative oxygen and the comparatively positive hydrogen
why does water possess the adhesive property?
due to H2O’s polar nature, it can also attract “unlike” structures. it’s attracted to substances with charges
what are minerals?
inorganic ions the body needs to function
can be found intracellularly and extracellularly
what are vitamins?
organic molecules the body needs to function
what are the (2) major categories of vitamins? when consumed in excess, where are they stored?
fat-soluble
- deposited in body fat; overconsumption can lead to toxic levels in the body
water-soluble
- excreted in the urine
what is vitamin B? describe it
a water-soluble vitamin
8 types of vitamin B
vitamin B usually functions as coenzymes or their precursors in metabolic processes – also important in blood synthesis
what is vitamin C? describe it
a water-soluble vitamin
vitamin C is necessary for synthesizing collagen, an important structural protein, thus a deficiency in vitamin C can lead to scurvy (if the collagen structure is less stable, we get weakened connective tissues)
what are the (2) important water-soluble vitamins?
B and C
what are the (4) important fat-soluble vitamins?
A, D, E, and K
what is vitamin A? describe it
a fat-soluble vitamin
important for:
- vision (visual pigmentation)
- epithelial (skin) maintenance
what is vitamin K? describe it
a fat-soluble vitamin
important for blood clotting. it produces proteins involved in the process
what is vitamin D? describe it
a fat-soluble vitamin
regulates calcium and phosphorous levels by promoting its absorption from the intestine
synthesized by the skin in the presence of sunlight
what is vitamin E? describe it
a fat-soluble vitamin
an antioxidant which prevent cell damage by neutralizing free radicals which (highly unstable unpaired electrons which can destroy cells)
what are the key properties of hydroxyl (OH) groups?
polar and hydrophilic
generally a strong base. but can be acidic depending on conditions
what are the key properties of carboxyl (COOH) groups?
polar, hydrophilic, weak acid
what are the key properties of amino (NH2) groups?
polar, hydrophilic, weak base
what are the key properties of phosphate (PO4 -3) groups?
polar, hydrophilic, acid
what are key properties of carbonyl (C=O) groups?
polar and hydrophilic
what are key properties of methyl (CH3) groups?
non-polar and hydrophobic
what are the 3 disaccharides you need to know for the exam? list what monosaccharides are combined
sucrose: glucose + fructose
lactose: glucose + galactose
maltose: glucose + glucose
in a disaccharide, what joins the two monosaccharides?
glycosidic linkage
briefly describe the reactions of dehydration synthesis and hydrolysis
monomers combine together to form polymers via dehydration synthesis. water is formed during this process.
polymers are broken down to form monomers via hydrolysis. water is consumed
in a polymer, how are bonds broken and formed?
formed: dehydration synthesis; water is formed as by-product
broken down: hydrolysis; water consumed
this applies to all polymers, regardless of it’s a glycosidic linkage, a phosphodiester bond, or a peptide bond.
what are the (2) types of glycosidic bonds?
alpha and beta
determined by the -OH groups of the sugars
describe the alpha-glycosidic bond
between 2 alpha-monosaccharide molecules
the -OH groups forming the bond are both pointing down
describe the beta-glycosidic bond
between an alpha and a beta-monosaccharide molecule
the bond is between an -OH pointing down and an -OH pointing up
what are considered to be under carbohydrates?
saccharides, starch, glycogen, cellulose, chitin
how are starch and glycogen similar and different?
both are polymers of alpha-glucose molecules (thus, have alpha-glycosidic bond)
they differ in their polymer branching and where they are found
glycogen has more branching
glycogen found in animal cells and starch found in plant cells
where is starch found? what’s its function?
in plant cells
stores energy
where is glycogen found? what’s its function?
found in animals
stores energy
how does one differentiate between alpha and beta monosaccharides?
if the OH on the anomeric carbon is pointing DOWN, it’s alpha
if the OH on the anomeric carbon is pointing UP, it’s beta
describe cellulose
a polymer of beta-glucose
a structural molecule for walls of plant cell and wood
describe chitin
a polymer of beta-glucose that’s attached to a nitrogen containing group: (n-acetylglucosamine)
a structural molecule found in fungal cells and insects’ exoskeleton
how are cellulose and chitin similar?
they are both comprised of beta-glucose molecules (but chitin also includes N-molecules)
thus, they both use beta-glycosidic bonds
can humans digest glycosidic linkages?
our digestive system can digest only alpha-glycosidic linkages
they can’t digest beta-glycosidic linkages
- cows have bacteria in their gut that produces the enzymes that can break down beta-glycosidic linkages
what are the macromolecules (polymers) and their monomer components?
carbohydrates (aka polysaccharides): monosaccharides
lipids: a bit complicated, but generally composed of hydrocarbons - lipids are not really considered polymers but are macromolecules
proteins (aka polypeptides): amino acids
nucleic acids (DNA/RNA): nucleotides
briefly describe lipids. what bonds are seen in lipids?
long hydrocarbon chains that are non-polar and hydrophobic
they are not considered polymers bc they are not made of repeated units
covalent bonds between the hydrocarbons
what are the general functions of lipids?
insulation: preserves heat
energy storage: energy reserves we can burn when needed
endocrine molecules (steroid hormones)
structural (phospholipids and cholesterol are key components of the cell membrane)
what are triglycerides (triacylglycerols)
consists of 3 fatty-acid chains attached to a glycerol backbone (3 carbons). the fatty acids can be saturated or unsaturated
body converts calories it doesn’t need right away to triglycerides which are then stored in fat cells. later, hormones release them for energy (in between meals)
differentiate between saturated and unsaturated fatty acid chains
saturated has no double bonds which lead to straight chains. these straight chains can stack densely and form plaques - bad for health
unsaturated has double bonds which lead to kinks in the chains. they stack less densely - good for health. can be cis/trans
what are phospholipids (diacylglycerols)?
2 fatty-acids and a phosphate group (w/ +R) attached to a glycerol backbone
major component of cell membranes
they are amphipathic: has both hydrophilic and hydrophobic properties
- hydrophobic tail: fatty acids
- hydrophilic head: glycerol and phosphate group
what are steroids? what are considered steroids?
contains 3 six-membered rings and 1 five-membered rings (4 rings in total)
e.g. hormones and cholesterol
what’s the most common precursor to steroid hormones?
cholesterol
what are waxes?
esters of fatty acids and monohydroxy alcohol
used as protective coating of skin and exoskeletons
what are carotenoids?
fatty acid carbon chain with conjugated double bonds and five/six-membered rings at each end
- includes pigments which produces colour in plants/animals
subgroups: carotenes and xanthophylls
what are porphyrins? give 2 examples
4 joined pyrrole rings
often complexes with a metal in the center
- Fe in hemoglobin (from transporting O2)
- Mg in chlorophyll (for absorbing light)
what are adipocytes?
specialized fat cells
major energy storage site in the body
what are glycolipids?
similar to phospholipids, but instead of a phosphate group, they have a carbohydrate group
what are lipoproteins?
bc lipids are insoluble, lipoproteins are used to transport lipids in the blood
lipoproteins are a lipid core surrounded by phospholipids (lipid bilayer) and apolipoproteins
how does the cell membrane maintain its fluidity in different temperatures?
by changing membrane fatty acid composition
the cell membrane becomes more rigid in cold weather. to avoid rigidity, the cell membrane has cholesterol (prevents tight packing of phospholipids) and mono/polyunsaturated fatty acids incorporated into the membrane which increases fluidity
the cell membrane becomes more fluid and flexible in warm weather. to prevent itself from collapsing, cholesterol is added to restrict movement. the fatty acids become more saturated, allowing it to densely stack itself, increasing rigidity.
describe the general structure of an amino acid
a amino group, carboxyl group, a hydrogen group, and a R-side chain linked to an alpha-carbon
what functions do proteins have?
structural (e.g. collagen)
mechanical/movement (e.g. actin/myosin)
enzymes
hormones (e.g. insulin)
antibodies
fluid balance
acid-base balance - pH (albumin)
channels/pumps
transport (e.g. hemoglobin which moves oxygen)
storage (e.g. casein which stores amino acids in mammalian milk)
what do enzymes do? what do they not do?
catalyze reactions in both forward and reverse directions – lower the activation energy required for a reaction, accelerating the rate of the overall reaction.
they do not change the spontaneity of a reaction or the equilibrium
they have varying function based on pH and temp
what determines the efficiency of an enzyme?
temperature (it can cause denaturation), the ideal temperature for enzymes can vary. but as you raise temperature, you generally see an increase in enzyme activity and reaction rate due to the increase in kinetic energy, having molecules bounce around more quickly. BUT, if temperature raised too high, the enzyme will denature and lose its function
pH (it can cause denaturation), the ideal pH for enzymes vary
- e.g. pepsin prefers low pH
- urease and trypsin prefer moderate pH
substrate and enzyme concentration
presence/absence of inhibitors
what does amylase do?
catalyzes reaction that breaks the alpha-glycosidic bonds in starch
all enzymes are considered proteins, except..?
RNA enzymes / ribozymes / riboenzymes
what type of proteins are there?
storage, transport, enzymes
what are cofactors?
non-protein molecules that assist enzymes, usually by donating or accepting some component of the reaction, such as electrons or functional groups
some bind reversibly or some permanently
what’s a holoenzyme?
cofactor + protein
what’s a apoprotein/apoenzyme?
when an enzyme is not combined with a cofactor but requires it for activity
what’s a coenzyme?
an organic coenzyme, like vitamins
enzymes can also be inorganic (like metals, Fe2+ or Mg2+)!
can be categorized into prosthetic group (bind covalently) and cosubstrates (bind reversibly)
in regards to enzymes, what’s a prosthetic group?
if a cofactor is covalently or tightly bound to an enzyme
what are simple proteins?
proteins formed entirely of amino acids
what are the (2) types of simple proteins?
albumins & globulins: functional proteins that act as carriers or enzymes
scleroproteins: fibrous proteins with a structural function (e.g. collagen)
what are conjugated proteins?
a simple protein linked to a non-protein
what are (5) types of conjugated proteins?
lipoprotein: bound to a lipid
mucoprotein: bound to a carbohydrate
chromoprotein: bound to a pigmented molecule
metalloprotein: protein complexed around a metal ion
nucleoprotein: contains histone or protamine, linked to a nucleic acid
what are the different levels of protein structures? describe them
primary: sequence of amino acid, connected by peptide bonds
secondary: the 3D shape from hydrogen bonding between the carboxyl and amino groups of amino acids, side-by-side (involves the peptide backbone)
tertiary: 3D structure mainly from non-covalent interactions between the R-groups of amino acids
quaternary: 3D shape of a protein that is a grouping of 2 or more, separate peptide chains
how is the primary structure of a protein determined?
sequence of nucleotides in the mRNA determine the sequence of amino acids
what are the types of secondary structures of proteins?
alpha-helix
beta-sheet
when talking about the non-covalent interactions that hold the tertiary structure of a protein together, what does it include? (5)
hydrogen bonds
ionic bonds
hydrophobic effect/interaction: R-groups push away from water
disulfide (covalent interaction, an exception): between cysteines
van der waals forces
what are the (3) main protein categories?
globular
structural/fibrous
membrane
describe globular proteins
water soluble
mainly tertiary structures
diverse range of functions
enzymes are globular !!
describe structural/fibrous proteins
not water soluble
mainly secondary structures
long polymers
function: to maintain/add strength to cellular/matrix structures
e.g. collagen or keratin
describe membrane proteins
not water soluble
includes proteins that function as membrane pumps, channels, or receptors
what is protein denaturation?
when a protein reverts back to its primary structure
give (4) examples of denaturing agents
temperature, pH, UV light/chemical, and salt concentrations
a protein’s function is determined by what?
its overall shape! aka 3D structure
when denatured, it won’t be able to function properly
can protein denaturation be reversed?
generally irreversible, but in some cases, can be reversed by removing the denaturing agent
what does protein denaturation imply about the protein’s information?
all information needed for a protein to assume its folded, functional (native) form is encoded in its primary structure
differentiate between protein denaturation and digestion
denaturation reverses a protein to its primary structure
digestion eliminates all protein structures, including primary
what are the functions of nucleic acids?
to encode, express, and store genetic information
how are the strands of DNA connected?
via base pair
hydrogen bonds that occur between nucleotides on opposite strands
how are nucleotides bonded?
phosphodiester bond between the phosphate group of one nucleotide and the five-carbon sugar of another
describe the structure of nucleotides
nitrogenous base, a five-carbon sugar, and a phosphate group
differentiate between nucleosides and nucleotides
a nucleoside does not have a phosphate group
nucleotide: nitrogenous base, sugar, phosphate group
nucleoside: nitrogenous base, sugar
- e.g. “adenosine” instead of “adenine”
what are the nitrogenous bases for DNA and RNA?
DNA: guanine, cytosine, adenine, thymine
RNA: guanine, cytosine, adenine, uracil
in DNA and RNA, which nitrogenous base pairs with what? and how many bonds? what does that implicate
GCAT -> GC AT
guanine and cytosine - 3 hydrogen bonds
adenine and thymine - 2 hydrogen bonds
since G and C have more hydrogen bonds, they require a higher (melting) temperature to break
the same goes for RNA, just replace thymine with uracil
which of the nitrogenous bases are purines? pyramidines?
purines: guanine, adenine
pyrimidines: cytosine, thymine, uracil
differentiate between the structures of DNA and RNA
DNA: GCAT
RNA: GCAU
DNA: has deoxyribose sugar (missing an O on C2). it’s double helix, with 2 strands that are anti-parallel (both run 5’ to 3’ but in opposite directions)
RNA: has ribose sugar. USUALLY single stranded
in regards to DNA, why is the direction called “ 5’ to 3’ “ ?
phosphate is attached to C5 of the deoxyribose sugar and the OH group is attached to C3
looking at DNA we see that the phosphate (at C5) begins the sequence and the OH (at C3) ends it
what is chargaff’s rule?
the number of purines = the number of pyrimidines because they are base paired
A + G = T + C
A = T
G = C
describe the discovery of the cell. who? how?
robert hooke was the first to discover cells when he looked at a piece of tree bark under a microscope and observed the cell walls of dead plant cells
a decade later, van leeuwenhoek enhance the magnification of microscope lenses and was the first to observe living cells
what does the Cell Theory state (3+4=7)?
all living organisms are composed of 1 or more cells
the cell is the basic unit of function, structure, and organization in all organisms
all cells come pre-existing, living cells
NEW TENANTS FROM THE MODERN INTEPRETATION OF THE CELL THEORY:
activity of an organism depends on the total activity of independent cells (each cell contributes to the overall activity of an organism)
energy flow occurs within cells (cells have a functional metabolism)
cells carry hereditary information
all cells have similar basic composition among similar species
what characteristics are shared by all cells?
bound by plasma membrane: a selective barrier that separate its contents from the outer environment
contains genetic material (DNA)
contains ribosomes: synthesizes functional proteins from genetic material (RNA)
describe the RNA World Hypothesis theory. what does it state/believe? why? backed by what?
suggests that RNA was the precursor of current life (based on DNA, RNA, and proteins)
states that RNA stores genetic information like how DNA does, catalyzes chemical reactions like how enzymes do - a reason behind the belief that RNA played a major role in the evolution of cellular life
also backed by the fact that RNA is more unstable than DNA, due to its extra hydroxyl group which makes it more likely to participate in chemical reactions
what does the Central Dogma of Genetics (a theory) state?
states that information must travel from DNA -> RNA -> protein
cannot travel backwards from protein! information however, can travel back and forth between DNA and RNA in special cases
describe the stereomicroscope. what are the pros and cons?
uses visible light to view the surface of a sample
pros: can view living samples
cons: has low light resolution compared to a compound microscope
describe the compound microscope. what are the pros and cons?
uses visible light to view a thin section of the sample
pros: can view some living samples (single cell layer)
cons: may require staining for good visibility which kills cells - samples that are thin enough don’t require staining
describe phase contrast microscope. what are the pros and cons?
uses light phases and contrast for a detailed observation of living organisms. including internal structures if thin
pro: good resolution and contrast
cons: not ideal for thick samples. produces a “halo” effect around the perimeter of the samples
describe the confocal laser scanning microscope and fluorescence. what are the pros and cons?
used to observe thin slices while keeping a sample intact
pros: can observe specific parts of a cell via fluorescent tagging
cons: can cause artifacts - not naturally present and caused by the process
note: can be used with light instead of fluorescence
what is a common microscopy method used to observe chromosomes during mitosis?
confocal laser scanning microscope and fluorescence
describe scanning electron microscope (SEM)? what are the pros and cons?
shoots electrons across the surface of a specimen, allowing high definition image
pros: view surface of 3D objects with high resolution
cons: can’t use on living samples as the preparation kills samples. preparation is extensive as samples need to be dried and coated. and is costly
describe cryo scanning electron microscope (Cryo SEM). what are the pros and cons?
similar to SEM
pros: sample is not dehydrated, so you can observe samples in their more “natural” form
cons: can’t be used on living samples. samples must be frozen, which might cause artifacts
describe transmission electron microscope (TEM). what are the pros and cons?
electron beams passed thru a thin section of the sample, producing very high resolution 2D images. can see internal structures - not just tissue and cells
pros: can observe very thin cross-sections in high detail, and can observe internal structures with very high-resolution
cons: cannot be used on living samples. requires extensive preparation (samples must be dehydrated, fixed into resin, and sliced into thin sections) and is costly
which microscope has the highest magnification?
transmission electron microscope (TEM)
describe electron tomography. what are the pros and cons?
not a type of microscope, but a technique used to build a 3D model of the sample via TEM (transmission electron microscope) data
pros: can look at objects in 3D and see objects relative to one another
cons: same as TEM cons: cannot be used on living samples. requires extensive preparation and is costly
what is centrifugation?
common technique used to prepare sample for observation or further experimentation
it spins and separated liquified cell homogenates into layers based on density
in centrifugation, what is the order in which cells separate?
most dense to least dense
most dense will pellet to the bottom and so on
in differential centrifugation that deals with organelles, which parts are expected to separate first, to the bottom?
nuclei layer -> mitochondria/
chloroplasts/lysosomes ->
microsomes/small vesicles ->
ribosomes/viruses/larger
macromolecule
differentiate between differential centrifugation and density centrifugation
differential: density, shape, and speed
- spin, separate dense pellet, repeat
density: density
what should be noted about solubility in differential centrifugation?
differential centrifugation forms continuous layers of sediment, where insoluble proteins are found in pellet and soluble proteins remain in the supernatant, liquid above the pellet
differentiate between anabolic and catabolic processes/reactions
anabolic: small molecules assembled into bigger ones – requires energy
catabolic: large molecules broken into smaller ones – releases energy (CATACLYSM LOL!!!!)
what is ATP?
a common source of activation energy
ATP stores its potential energy in the form of chemical energy.
ATP is an unstable molecule because the 3
phosphates in ATP are negatively charged and repel one another. when one phosphate group is removed via hydrolysis, a more stable ADP molecule results. the change from a less stable molecule to a more stable molecule always releases energy
it provides energy for all cells by transferring phosphate from ATP to another molecule
how is new ATP formed?
via phosphorylation
ADP and phosphate come together using energy from an energy-rich molecule, like glucose
define Km and Vmax in regards to enzymes
Km: “michaelis constant”, represents the substrate concentration at which the rate of reaction is half of the max velocity (rate) of the enzyme, or Vmax
Vmax: max velocity (rate) of the enzyme
what are allosteric enzymes?
they have both an active site for substrate binding AND an allosteric site for binding of an allosteric effector (can be an activator/inhibitor)
they can have multiple sites for regulatory enzymes to bind
what is competitive inhibition? describe Km and Vmax in this situation
substance is an inhibitor (by mimicking the substrate) that binds at the active site, preventing substrates from attaching. this binding is reversible and brief
the effect of competitive inhibition can be combated by increasing concentration of substrate
competitive inhibitors increase Km (bc it directly interferes with how substrates bind) but Vmax remains the same
what is non-competitive inhibition? describe Km and Vmax in this situation
substance inhibits enzyme by binding somewhere other than the active site, allowing the substrate to still bind, but the enzyme’s ability to catalyze a reaction has decreased and reaction doesn’t reach completion (bc the enzyme conformation has changed but the ability of a substrate to bind has not been)
Kmax remains the same but Vmax decreased
what is allosteric inhibition?
substance binds to enzyme (at the allosteric site, affecting the ability of the active site to function) and induces its inactive form
does not follow Km and Vmax trends
what is uncompetitive / anti-competitive inhibition?
when an enzyme inhibitor binds to the enzyme-substrate (ES) complex – preventing the formation of the product
describe the relationship between Km and binding affinity
recall, Km: the substrate concentration at which the rate of reaction is half of the max velocity of the enzyme, or Vmax
Km inversely represents binding affinity
a higher Km = worse substrate binding
lower Km = better substrate binding
Km and binding affinity are both intrinsic properties so increasing/decreasing substate/enzyme concentration doesn’t affect this property
what is cooperativity, in regards to enzymes?
positive cooperativity: phenomenon where an enzyme becomes more receptive to other substrates after binding to a substrate at its active site
negative cooperativity: enzyme becomes less receptive to other substrates after binding to a substrate at its active form
cooperativity isn’t limited to enzymes can also be done by non-enzymes e.g. oxygen in hemoglobin
what are the (3) classifications of membrane proteins?
peripheral: loosely attached to surface of one side of the membrane
integral: embedded in the cell membrane
transmembrane: type of integral; travels all the way through the membrane
what are the (8) types of membrane proteins?
channel proteins
recognition proteins
ion channels
porins
carrier proteins
transport proteins
adhesion proteins
receptor proteins
what are channel proteins?
proteins that provide a passageway through the membrane for hydrophilic (water soluble), polar, and charged substances
can also be done for substances that can normally diffuse, to allow the protein to regulate how much goes in, more quickly, etc (e.g. aquaporins for water)
what are recognition proteins?
type of glycoprotein (has an attached oligosaccharide/carbohydrate) used to distinguish between self and foreign – healthy vs diseased – by immune cells
cell-to-cell recognition
what are ion channels?
used to pass ions across the membrane
they can be open or gated (3 types) so there are 4 types overall
referred to as gated channels in nerve and muscle cells
what are glycoproteins?
play a role in cell-cell recognition; immune cells can check membrane glycoproteins to identify if a cell is foreign or not
cell signaling: glycoproteins can act as receptors by binding to signalling molecules
used in cell adhesion by binding to molecules outside the cell help stabilize them
what are the (3) different types of ion, gated channels?
voltage-gated: responds to difference in membrane potential to open/close
ligand-gated: chemical (signalling molecule) binds to open channel
mechanically-gated: responds to pressure or vibration
AND open channel
what are porins?
allows the passage of certain ions and small polar molecules
increases the rate of water passing in kidney and plant root cells
tends to be less specific: if you can fit through the large passage, you can go through
what are transport proteins?
proteins that transport materials across the membrane
they do this by active transport and facilitated diffusion (note that only active transport uses ATP)
what are the types of transport proteins? (2)
carrier and channel
what are carrier proteins?
allows for selective transport across the membrane via integral membrane protein
changes shape (undergoes conformational changes) after binding to specific molecule that enables it to be passed across - also changes shape to release it
what’s the major difference between active transport and passive transport
active transport uses ATP
what are adhesion proteins?
attach cells to neighbouring cells and provide anchors for stability via internal filaments and tubules
what are receptor proteins?
these membrane proteins are binding sites for signalling molecules which then transmit changes to the inside of the cell
what are the (3) major components/properties that contribute to the cell membrane? describe them
phospholipid membrane permeability: allows small, uncharged, non-polar, hydrophobic molecules to freely pass through the membrane. polar molecules may pass through if they’re small and uncharged (everything else requires a transporter)
cholesterol: adds rigidity to the membrane in normal conditions and maintains fluidity at lower temperatures
glycocalyx: carbohydrate coat; covers the outer side of the cell wall (in some bacteria) or plasma membrane (in some animal cells).
what are the functions of the glycocalyx?
glycocalyx: carbohydrate coating on the outer side of the cell wall or plasma membrane
possible functions:
- adhesive capabilities
- barrier to infection and chemical/physical damage OR
- markers for cell-cell recognition
can be found on the inside of blood vessels where it helps to provide a protective barrier and maintains the vascular walls beyond the plasma membrane
what does the glycocalyx consist of?
glycocalyx: carbohydrate coating on the outer side of the cell wall or plasma membrane
consists of glycolipids attached to the cell membrane AND glycoproteins that may serve as recognition proteins
what performs the same role cholesterol does in animal cells’ membranes but in plant cells and prokaryotes?
cholesterol: adds rigidity to the membrane in normal conditions and maintains fluidity at lower temperatures
plant equivalent = sterols
prokaryotes equivalent = hopanoids
what are the (4) main functions of the cell membrane?
acts as a barrier between the inside and outside of the cell
allows for communication with other cells
has selective permeability to regulate transport of substances in and out of a cell
provides structural support and protection
what’s the fluid mosaic model?
a biological term used to describe the cell membrane
fluid: cell membrane components are constantly shifting around - even the phospholipids which frequently rotate and move laterally within the same layer (can even flip vertically into another layer)
mosaic: composed of multiple different parts (phospholipids and proteins)
how are peripheral proteins held in place to a side of the cell membrane? how can this attachment be disrupted?
peripheral membrane proteins are generally hydrophilic and held together by hydrogen bonding and electrostatic interactions
this can be disrupted by changing salt concentration or pH
how can integral proteins be detached from the membrane?
integral proteins are hydrophobic and can be detached using detergent
differentiate between chromatin and chromosomes
chromosomes are tightly condensed chromatin when the cell is ready to divide
how many chromosomes do humans have?
46
23 from their mother, 23 from their father
what’s chromatin?
general packaging structure of DNA around proteins (histones) in eukaryotes
tightness in packaging depends on the cell stage
what’s a histone?
proteins that provides structural support for DNA
what’s a nucleosome?
a unit of DNA wrapped around 8 histones
what’s the nucleolus?
found in the nucleus; the site of ribosome synthesis
briefly describe the process of ribosome synthesis
rRNA synthesizes in the nucleus
ribosomal subunits are synthesized using rRNA and ribosomal proteins (imported from the cytoplasm).
once ribosomal subunits have formed, they’re exported to the cytoplasm for final assembly of a complete ribosome
what is the substitute of cytoplasm in the nucleus? (what’s there instead?)
instead of cytoplasm, the nucleus has nucleoplasm
describe the outer layer of the nucleus and what it uses for transport
the nucleus is bound by a double layer nuclear envelope with nuclear pores for transport (for mRNA, ribosome
subunits, dNTPs, proteins like RNA
polymerase and histones).
the double membrane means it has two phospholipid bilayers
what is the nuclear lamina?
found in the nucleus of eukaryotic cells
a dense fibrillar network (intermediate filaments and membrane associated proteins) that provide mechanical support AND help regulate DNA replication, cell division, and chromatic organization
differentiate between the nucleus and nucleoid
nucleus found in eukaryotic cells
nucleoids found in prokaryotes
what’s the nucleoid?
for prokaryotes
contains all or most of the cell’s genetic material
what’s the cytoplasm?
most of the cell’s metabolic activity and transport happens here
the area includes the cytosol and organelles
what is cytoplasmic streaming?
the streaming movement within the cytoplasm
differentiate between cytoplasm and cytosol
cytosol is just the gel-like substance but cytoplasm is the gel-like substance and everything, including organelles, suspended within
what are ribosomes?
site of protein synthesis
made of protein and rRNA
one of the only organelles that are not membrane bound
found in both prokaryotes and eukaryotes
what are the 2 subunits of ribosomes in eukaryotes? in prokaryotes? (in S units)
eukaryotes:
60S + 40S = 80S
prokaryotes:
50S + 30S = 70S
the 2 subunits are created in the nucleus and moved to the cytoplasm where they are assembled into a single larger ribosome
s larger S value (Svedberg unit)
indicates a heavier molecule
where can you find ribosomes? what can be said about this?
floating in the cytosol or bound to the rough endoplasmic reticulum
ribosomes floating in the cytosol make proteins that function within the cell
ribosomes bound to the ER make proteins that will be exported
what is the endoplasmic reticulum?
an extensive network of interconnect membranes with flattened areas called “cisternae”
the ER membrane separates the cytosol from its inner contents, the ER lumen
what are the (2) types of endoplasmic reticulum?
rough ER
smooth ER
note that the rough ER is closer to the nucleus
describe the rough endoplasmic reticulum. what does it make? what should you note about rough ER in eukaryotes?
the ER is covered in ribosomes
creates glycoproteins by attaching polysaccharides to polypeptides as they are assembled by ribosomes
— in eukaryotes, the rough ER is continuous with the outer nucleus membrane
what is the process that occurs with proteins in the ER lumen? describe it
post translational modification
when ribosomes on the rough ER synthesize proteins, they’re injected into the lumen where it can be modified and prepared for transportation
can add groups like carbohydrates/phosphates to proteins!!
describe the smooth endoplasmic reticulum. what does it make? what unique function does it have in liver cell?
not covered in ribosomes, hence “smooth”
synthesizes lipids and steroid hormones for export
in liver cells, it break down toxins, drugs, and toxic by-products from cellular reactions
what is the sarcoplasmic reticulum?
smooth ER found in smooth and striated muscle
it stores and releases ions like Ca2+
where do proteins go after being synthesized?
golgi apparatus
what is the golgi?
aids in the transport of various substances in vesicles
helps sort, modify, and transport proteins
a series of flattened membrane sacs called cisternae
also creates lysosomes and transports lipids
what are lysosomes?
vesicles produced from the golgi
they contain digestive enzymes with low pH, function in apoptosis (by releasing their contents), and break down nutrients, bacteria, pathogens, and cell debris.
they can also partake in autophagy which is where they fuse with damaged organelles to break them down and recycle
how do lysosomes break down nutrients?
when a cell ingests food materials, the cell forms a food vacuole which the lysosome fuses with to break down its contents into useful nutrients
differentiate between the faces of the golgi
cis face: for incoming vesicles
trans face: for secretory vesicles
the cis face is more “bent” than the trans face
the cis face is closer to the endoplasmic reticulum
what are the steps the golgi takes in transporting and processing substances?
proteins are made by the rough ER or steroid hormones are made by the smooth ER
they’re packaged into vesicles and then sent to the golgi apparatus on the cis face where they can be further packaged and modified
transported in vesicles from the trans face to various parts of the cell or outside the cell
what happens to enzymes that escapes from the lysosome?
they remain inactive in the neutral pH of the cytosol
what are peroxiosomes? where are they found? what do they do (and in plant cells and in germinating seeds)?
found in the liver and kidney
break down substances, fatty acids, and amino acids. can also inactivate toxic substances
they produce hydrogen peroxide, H2O2, which they use to oxidize substrates, and can also break down H2O2 if necessary (H2O2 → H2O + O2) using the enzyme catalase
in plant cells, peroxisomes modify
by-products of photorespiration.
in germinating seeds, peroxisomes are
called glyoxysomes that break down
stored fatty acids to help generate
energy for growth
what are microtubules? what are they made up of? what do they do? where can they be found?
hollow tubes formed from polymers of the protein, tubulin
provides support and movement for cellular activities
act as spindle apparatus, guiding chromosomes during cell division
bundles of microtubules make up other cellular structures like: flagella and cilia of all animal cells and lower plants like
mosses and ferns. and in centrioles
describe intracellular transport
microtubules help support motility within the cell. they provide tracks along which organelles and vesicles are transported using motor proteins (kinesin and dynein)
kinesin is a motor protein that binds to the cargo it’s transporting on one end and the other end moves along the microtubule. moves from the center to the periphery (outer area of the cell, where the cell membrane is)
dynein. also binds to cargo on one end and moves with the other end. moves from periphery to center
what are cilia?
hair-like projections from a cell
made of microtubules
allows the cell to move. for cells that are in a fixed position (e.g. in the respiratory tract, the cilia move the debris that’s trapped in the mucus out of the airway), cilia move substances in the environment across the cell surface
what are centrioles?
are MTOCs (microtubule organizing centers), a structure that microtubules emerge from
2 centrioles, perpendicular to another, make up a centrosome
allows for development of spindle fibers of the spindle apparatus during cell division
they do not have a membrane
which organelles are not bound by a membrane?
ribosomes
centrioles
centrosomes
cytoskeleton
(FROM GOOGLE, UNSURE ACCURACY AND IF THERE’S MORE)
what are microvilli?
projections from the cell membrane composed of actin filaments that support the microvilli and maintain its shape
function to increase the surface area of the cell which leads to enhance absorption and secretion
commonly seen in cells of the digestive system
what is the arrangement of microtubules in flagella and cilia of all animal cells and lower plants like mosses and ferns?
in a 9+2 array - 9 pairs of microtubules with 2 singlets in the center
what are intermediate filaments?
provide physical support and stability for maintaining cell shape (e.g. keratin)
what are microfilaments?
made of actin
involved in cell movement
found in skeletal muscle, amoeba pseudopod, and cleavage furrows
what are microtubule organizing centers (MTOCs)? give 3 examples!
a structure that microtubules emerge from
includes centrosomes (centrioles) and basal bodies
BASAL BODIES: are found at the base of each flagellum and cilium; organization of eukaryotic flagella and cilia and the
CENTROSOMES: organization of the mitotic and meiotic spindle apparatus, which separate the chromosomes during cell division.
plant cells lack centrioles and divide
via cell plates rather than cleavage
furrows — note that plants do have
MTOCs called spindle pole bodies
how are microtubule organization centers (MTOCs) arranged?
unlike microtubules, MTOCs are found in a 9x3 array
they are made of 9 triplets of microtubules held together
what are transport vacuoles?
moves materials between organelles or organelles and the plasma membrane
what are food vacuoles?
temporary containers of nutrients that merge with lysosomes to break down food
what are central vacuoles?
found only in plant cells
generally large - can occupy most of the cell wall’s interior
exerts turgor when fully filled (pressure - pushes plasma membrane against cell wall - maintains rigidity)
stores nutrients and water
carries out functions performed by lysosomes in animal cells (degrades material taken up from outside the cell and to digest obsolete components of the cell itself)
what’s a tonoplast?
specialized membrane of central vacuoles
what are storage vacuoles?
where plants store starch, pigments, and toxic substances such as nicotine
ONLY FOUND IN PLANT CELLS
what are contractile vacuoles?
usually found in single-celled Protista organisms like amoeba and paramecium living in hypotonic environments
collects and pumps excess water out of the cell via active transport to prevent bursting
what are cell walls?
provides support in plants, fungi, protists, and bacteria
sometimes a secondary cell wall develops beneath the primary cell wall
what are cell walls made up (for plants, fungi, bacteria, and archaea - 4)?
plants: cellulose
fungi: chitin
bacteria:
- gram-negative: thin peptidoglycan layer surrounded by lipopolysaccharides attached to an outer membrane above the peptidoglycan layer
- gram positive: thick peptidoglycan layer above one membrane layer (no outer membrane here!)
archaea: polysaccharides
what happens when gram-negative bacteria is destroyed?
the lipopolysaccharides are released from the outer membrane as endotoxins, a toxic compound which can trigger an immune response
gram-positive doesn’t have lipopolysaccharides, so no toxins released
what is the extracellular matrix?
found in animals between adjacent cells (beyond the plasma membrane and glycocalyx) - provides mechanical support and helps bind adjacent cells
occupied by fibrous structural proteins, adhesion proteins, and polysaccharides secreted by cells
provides structural support (with it’s support proteins); cell adhesion (EM serves as an area of anchorage for cells to attach to); and transmits mechanical and chemical signals between the inside
and outside of the cell
describe the network of proteins found in the extracellular matrix that helps bind adjacent cells
collagen and proteoglycans and glycoproteins connected to integrins in the cell membrane via fibronectin
proteoglycan and glycoproteins are proteins that have carbohydrate groups attached. the carbohydrates in glycoproteins are short and branched (used in cell signaling and adhesion), while the carbohydrates in proteoglycan are long and unbranched (used for structural support).
collagen, an incredibly strong protein fiber embedded throughout the EM.
fibronectin attaches proteoglycans, glycoproteins, and collagen to integrin
integrin are proteins located in the cell membrane
by using fibronectin and integrin, cells can anchor themselves to the collagen, proteoglycan, and glycoproteins of the EM, facilitating cell adhesion
how do cells adhere/connect to the extra cellular matrix (2)?
focal adhesions (connection of the ECM to actin filaments in the cell) AND
hemidesmosomes (involve the connection of ECM to intermediate filaments like keratin)
what are fibroblasts?
cells that produce collagen and other connective tissue elements found in the extracellular matrix
what is collagen?
the most abundant protein in mammals
found in bones, muscles, skin, and tendons
fibrous protein present in tissue as triple helix (its structure provides strength)
a repeating pattern of amino acids, every 3rd amino acid is glycine
what are plastids? what does it include (6)?
organelles found in plant cells
includes:
chloroplasts (the site of photosynthesis)
leucoplasts: specialized storage of…
- starch [as amyloplasts]
- lipids [as elaioplasts]
- proteins [as proteinoplasts]
chromoplasts (store carotenoids)
what are chloroplasts?
double membrane layered organelle
site of photosynthesis (light -> sugar)
has its own circular DNA
most likely descended from a bacteria capable of photosynthesis, cyanobacteria
why do chloroplasts appear to be green?
they absorb red and blue wavelengths of light but reflect green
describe the structure of mitochondria
double-layered organelle (2 separate phospholipid bilayers)… multiple “layers”: outer mitochondrial membrane, intermembrane space, inner mitochondrial membrane (folded numerous times to increase surface area and ATP production), mitochondrial matrix
how does the mitochondria make ATP?
makes ATP thru aerobic cellular respiration
what does the endosymbiotic theory state?
states that mitochondria and chloroplasts were once prokaryotic organisms that lived on their own
they were absorbed by a larger cell and formed a symbiotic relationship (larger cell provides protection and they provide energy) with it. eventually they became organelles in eukaryotes
what evidence backs the endosymbiotic theory?
mitochondria and chloroplasts have their own genome (circular DNA — eukaryotes have linear DNA and prokaryotes have circular DNA) – also have their own ribosomes
mitochondria and chloroplasts divide by binary fission (they divide independently of the eukaryotic cell they reside in)
contain other structures similar to prokaryotes
what is the cytoskeleton? what are the components? where’s it?
helps cells maintain their shape, mechanical support/motility (helps move components within the cell as well), helps anchor/stabilize membrane proteins, and internal organization
includes microtubules (e.g. flagella and cilia), microfilaments, and intermediate filaments
found in eukaryotic cells
aids in cell division, cell crawling, and the movement of cytoplasm and organelles
what are microfilaments?
2 intertwined polymer strands of actin
involved in cell motility and other functions
used in skeletal muscle contraction
helps to form the amoeba pseudopod, a projection from a cell that’s used in movement and ingestion
forms the cleavage furrow that’s involved in separating cells at the end of mitosis
what are intermediate filaments?
tubes of intertwined coil proteins
the proteins that make up an intermediate filament depends on the type of cell they appear in
e.g. keratin in skin cells
describe the behaviour a plant cell undergoes when placed in a hypotonic, isotonic, and hypertonic solution (plant cell and water balance)
hypotonic solution (where there’s less stuff dissolved in water than in the cell): plant cells swell as their central vacuole fill up, making them turgid/firm. fungal cells stay firm in hypotonic conditions due to their cell wall
isotonic solution (where the concentration of dissolved stuff is the same inside and outside the cell): plant cells are flaccid - not swollen and not pushing against the cell wall
hypertonic solution (where there’s more stuff dissolved in water than in the cell): the cell shrinks and pulls away from the cell wall, a process called plasmolysis.
describe the behaviour an animal cell undergoes when placed in a hypotonic, isotonic, and hypertonic solution (animal cell and water balance)
hypotonic solution (where there’s less stuff dissolved in water than in the cell): animal cells undergo lysis and burst
isotonic solution (where the concentration of dissolved stuff is the same inside and outside the cell): water moves in and out at equal rates
hypertonic solution (where there’s more stuff dissolved in water than in the cell): water rushes out of the cell, making it shrink - plasmolysis
what is the endomembrane system? what does it include?
the network of organelles and structures, either directly or indirectly connected, that help in the transport of proteins and other macromolecules into/out of the cell
includes: plasma membrane, endoplasmic reticulum, golgi apparatus, nuclear envelope, lysosomes, vacuoles, vesicles, and endosomes
does not include: mitochondria and chloroplasts
differentiate between the movement of flagella and cilia
flagella: undulates like a snake
cilia: beats in rapid back and forth motions
what are the (2) methods of circulation throughout the cell?
intracellular
extracellular
describe intracellular circulation
follows brownian movement, the random particle movement due to kinetic energy; spreads small particles throughout the cytoplasm - prevents particles from settling down
the cyclosis (flow/stream of cytoplasm) the circular motion of cytoplasm within the cell
what is cyclosis?
movement by the streaming of cytoplasm within a cell. cytoplasm flow is driven by the movement of the cytoskeleton (generated by the contraction and relaxation of actin and myosin filaments)
circulates the cytoplasm around the cell which allows cellular components to be moved around
what organelle plays a key role in intracellular circulation? describe the role
endoplasmic reticulum
provides channel through the cytoplasm
provides direct continuous passageway from plasma membrane to nuclear membrane
describe extracellular circulation
through diffusion
if cells are close enough to their external environment, diffusion can fulfill food and respiration needs
also used for transport of materials between cells and interstitial fluid around cells in more complex animals
what are cell junctions?
protein complexes that connect cells
what are the (4) major cell junctions?
anchoring/adhesion
gap
tight
plasmodesmata
what are anchoring junctions? list the types (3) and describe them
desmosomes: (keratin intermediate filaments attached to adhesion plaques which bind adjacent cells via adhesion proteins), providing mechanical stability by holding cellular structures together (stronger than adherens)
- present in animal cells with tissue experiencing mechanical stress - including skin epithelial cells and cells in the cervix/uterus
adherens: also attached to actin filaments on the inside of the cell to further stabilize
hemidesmosomes: attach the cell to the extracellular matrix (prevents it from being detached from the surface easily); also attached to intermediate filaments on the inside of the cell. can be found in the epidermis, the skin’s outer layer
what are tight junctions? where could they be found?
fully encircles each cell, producing a seal that prevents the passage of materials between cells. made of transmembrane proteins
common to cells lining the digestive tract where materials are required to pass through the cells into the blood – tight junctions prevent materials to escape between the cells. the materials must enter the cells (via diffusion or active transport) to pass through the tissues in animal cells
what are gap junctions? where could they be found?
similar to transport proteins; narrow tunnels between animal cells that prevent cytoplasm of each cell from mixing but allows passage of ions and small molecules for effective cell-cell communication
basically channel proteins of two adjacent cells that are closely aligned
tissues like the heart include these to
quickly pass electrical impulses, because ions like sodium can spread directly from one cardiac muscle cell to the next
connexins: gap junction proteins
- basically channel proteins of two adjacent cells that are closely aligned
what is the apical side of the cell?
side of the cell facing the external environment or internal cavity (points outwards or outer surface/top side of the cell)
there are no other cells/tissues touching that surface
what is the lateral surface of the cell?
sides of the cell in the tissue
touching the cells adjacent to it
what is the basal side of the cell?
bottom of the cell
surface of the cell anchored to the underlying connective tissue
what are plasmodesmata?
narrow tunnels between plant cells
desmotubule: narrow tube of endoplasmic reticulum: exchanges material through cytoplasm surrounding the desmotubule
gated plant cell wall channels that allow the movement of molecules between cells
what are some features we should note about prokaryotes?
no nucleus
no chromatin level organization of DNA. DNA exists as single, circular, naked, and double-stranded
ribosomes are produced like 50S + 30S = 70S
has cell walls made of peptidoglycan but in archaea made of polysaccharides
flagella constructed from flagellum, not microtubules
define a hypertonic solution
higher solute concentration
define a hypotonic solution
lower solute concentration
define a isotonic concentration
equal solute concentration
what is bulk flow?
collective movement of substances such as blood in response to a force or pressure
what is considered passive transport? (6)
simple diffusion
osmosis
dialysis (diffusion of different solutes across a selectively permeable membrane)
plasmolysis (movement of water out of a cell that results in its collapse)
facilitated diffusion
countercurrent exchange (diffusion by bulk flow in opposite directions such as blood and water in fish gills)
differentiate between simple diffusion and facilitated diffusion
simple diffusion: no proteins used
facilitated diffusion: substances move down the concentration gradient with the assistance of transmembrane transport proteins
what is a concentration gradient? what role does this play in passive and active transport?
when substance is more concentrated on one side of the permeable membrane
a biological imbalance that’s energetically unfavourable
normally (to seek balance), substances would go down the concentration gradient (from high conc -> to low conc). this is passive transport
active transport is when the substances move against the concentration gradient
what is active transport?
movement of molecules against their concentration gradient – requires energy!
usually involves solutes like small ions, amino acids, and monosaccharides
what are the (5) types of active transport?
primary active transport
secondary active transport
group translocation
endocytosis: substances bought into a cell by enfolding them with cell membrane
exocytosis: similar to endocytosis, but transportation out of the cell
what are the (2) types of secondary active transport?
antiport: exchange
symport: cotransport
define primary active transport
energy (ATP) used to directly move against concentration gradient
describe receptor-mediated cytosis
a form of pinocytosis in which in which molecules called ligands bind to receptors
first, molecules outside the cell bind to receptors on the cell membrane. once they bind, a protein called clathrin attaches itself to the areas of the membrane that have bound receptors on the inside. these clathrin proteins form a lattice that pulls the membrane inward and creates a vesicle. the clathrin detaches.
define secondary active transport
energy indirectly used to move against concentration gradient (usually with an ion moving down its concentration gradient)
using an established electrochemical gradient to move a substance against its concentration gradient
example: if there’s a high conc of sodium outside the cell and high conc of glucose inside the cell. can link the transport of two together so when sodium moves in (favourable), glucose moves in (unfavourable)
the requirement is that one of the two substances must be moving down it’s concentration gradient
define group translocation
seen in prokaryotes when the substance
being transported across the membrane is chemically altered in the process –> prevents it from diffusing back out
what are the (3) types of endocytosis?
phagocytosis
pinocytosis “cell-drinking”
receptor-mediated cytosis
describe phagocytosis
engulfing particles by extending structures like pseudopods. packaged into a vesicle and can be fused/broken down later. this process is common in the immune system where pathogens can be bought into the cell and then fused with organelles like lysosomes to be destroyed. deals with more larger substance than pinocytosis would
describe pinocytosis
plasma membrane forms a pocket and pinches off to form a sort of vesicle in the cytoplasm around the extracellular fluid and dissolved material (liquid). a non-selective process, cell doesn’t care what it’s pulling in
what is one way we can trigger exocytosis to occur?
increasing concentration of calcium on the inside of the cell
what are (2) processes that tend to use exocytosis?
neurons releasing neurotransmitters
endocrine cells releasing certain hormones into the bloodstream
differentiate between diffusion and osmosis
in diffusion, SOLUTES move from higher conc to lower conc
in osmosis, SOLVENT (usually water) moves from higher conc to lower conc
describe the relationship between basal metabolic rate (BMR) and body size and body weight
BMR overall, increases as size increases
but BMR also actually decreases per kg as size goes up
(an elephant has a higher BMR than a squirrel. but a squirrel would have a higher BMR per kg)
describe the relationship between metabolism, temperature, and age
increased temp = increased metabolism
increased age = decreased metabolism
what’s kinetic energy? what’s potential energy?
kinetic: associated with anything with motion e.g. a flagella whipping back and forth
potential: found in objects not moving - the object has potential (stored) energy for later use e.g. energy stored within chemical bonds of glucose and glycogen stored in muscles
what is the formula for gibbs free energy? describe coupling in regards to it
G = deltaH - temperature(deltaS)
= change in enthalpy - (temperature x change in entropy)
if G is negative, the reaction is spontaneous (exergonic). energy is released
if G is positive, then non-spontaneous (endergonic). energy is absorbed
chemical reactions can be “coupled” together if they share intermediates. in this case, the overall Gibbs Free Energy change is the sum of the △G values for each reaction.
E.G. an unfavorable reaction with a positive △G1 value can be driven by a second, highly favorable reaction (negative △G2 value where the magnitude of △G2 > magnitude of △G1).
this principle of coupling reactions to alter the change in Gibbs Free Energy is the basic principle behind all enzymatic action in biological organisms, and is how ATP drives chemical work.
what is one of the most favourable reactions we can use to drive non-spontaneous reactions?
the breakdown of ATP, an exergonic reaction releasing energy
the bonds between the close together, negative phosphate groups of ATP release significant amount of energy when they’re broken via hydrolysis
NOTE: the formation of ATP from the oxidative phosphorylation of ADP is endergonic, requiring energy
what is metabolism? what are the (2) different pathways?
sum of all chemical reactions taking place
categorized into catabolic (energy releasing) and anabolic (energy consuming) pathways
provides the reactions necessary to produce the energy every cell needs
metabolism = catabolism + anabolism + energy transfer
what are the laws of thermodynamics?
1: energy can’t be created or destroyed - only transferred and transformed
2: the transfer of energy leads to an increase of entropy over time (for closed systems! – doesn’t apply to organisms that are living systems. our entropy decreases over time at the expense of the environment)
3: as a system approaches absolute zero temperature (0K), entropy approaches a minimum
how do catalysts lower the activation energy?
stabilize the transition state
provide an alternate pathway with a lower activation energy for the reaction
how do substrates bind to enzymes?
bind via induced fit: the structure of the enzyme’s active site changes in response to the enzyme binding to it. the tighter fit brings the chemical groups of the substrate closer together, creating a more favourable environment for the reaction
a series of weak interactions NOT strong covalent bonds
how do enzymes work?
a substrate binds to the active site of an enzyme and is held in place by temporary (non-covalent) bonds
while the substrate is bound to the active site, the enzyme catalyzes its conversion into a product molecule
the product molecule is released from the active site and a new substrate will bind
what are zymogens?
aka proenzymes
inactive precursor to enzymes; once cleaved, they’re able to function
e.g. pepsinogen –(low pH)–> pepsin
how can enzyme regulation take place? (3)
at the genetic level: genes that produce enzymes can be activated or disabled depending on the needs of the cell
at the physical level: enzymes can be stored in vesicles (contents released when cell requires their activity)
at the enzyme level:
- proenzymes (zymogens) can be cleaved to activate them
- can be activated/disabled via chemical modification (e.g. phosphorylation)
- can be modified by having another molecule bind to them, altering their level of activity
what is feedback inhibition (negative feedback)?
when the product of a reaction binds to one of the earlier enzymes in its metabolic pathway, inhibiting its activity
the enzyme will no longer function and the product will stop being produced
most enzymes are regulated by this type of feedback (prevents too much product from being formed) and it’s how the body maintains homeostasis
what is positive feedback?
a product of the enzyme triggers more product formation – creating a loop that increases in magnitude over time
e.g. labor contractions during birth (oxytocin production)
briefly describe cellular respiration and state the formula
cellular respiration is the overall oxidative/combustion, exergonic process (spontaneous) that breaks down (catabolic) glucose in order to derive energy in the form of ATP
considered oxidative because glucose is ultimately losing electrons which are used to make ATP
C6H12O6 + 6(O2) ——> 6(CO2) + 6(H2O) + energy (heat and ATP)
during respiration, high energy H atoms are removed from organic molecules (dehydrogenation)
in what 2 forms does cellular respiration produce energy?
heat and ATP
how is mitochondrial DNA inherited?
exclusively from your mother, since her eggs provides all the mitochondria to the growing embryo
where can the mitochondria’s DNA and ribosomes be found?
in the mitochondrial matrix
define substrate level phosphorylation and oxidative phosphorylation
substrate level phosphorylation: production of ATP using enzyme catalyzed reactions. direct transfer of phosphate groups to ADP
oxidative phosphorylation: ATP produced using energy from redox reactions of the ETC
what is external and internal respiration?
external respiration: entry of air into the lungs and subsequent gas exchange between alveoli and blood
internal respiration: exchange of gas between blood and the cells.
what (4) major steps make up cellular respiration?
glycolysis
pyruvate decarboxylation (links glycolysis and krebs cycle) (once for each pyruvate)
krebs cycle
electron transport chain
what is glycolysis? where does it take place?
decomposition of glucose into pyruvate in the cytosol
the purpose is to produce pyruvate (which will be used in the citric acid cycle) and ATP
takes place in the cytosol
describe the formula of glycolysis
glucose + 2NAD + 2ADP -> 2 pyruvate + 2ATP + 2NADH + 2H2O
reactants: glucose, NAD, ADP
products: pyruvate, ATP, NADH, and water
it takes the 6-carbon glucose and produces 3 2-carbon pyruvate
which step of cellular respiration produces the most ATP?
electron transport chain (ETC)
describe the (2) important steps of glycolysis
using ATP, hexokinase phosphorylates glucose to glucose 6-phosphate, which is important as this step is irreversible because glucose can’t diffuse out of the cell due to the negative charge it now has. since it can’t leave, it can be immediately usable for energy
LATER IN THE PROCESS,
phosphofructokinase (PFK), using ATP, adds a 2nd phosphate, to convert fructose 6-phosphate to fructose 1,6-bisphosphate, which is irreversible and commits the glucose to glycolysis. this is the rate limiting step
is glycolysis aerobic or anaerobic?
glycolysis can occur under both conditions as it does not require oxygen, thus, ANEROBIC
how is ATP produced in glycolysis?
ATP is produced via substrate level phosphorylation, which involves the direct transfer of a phosphate group via enzyme, to ADP (no extraneous carriers needed)
the energy for ATP formation comes from the coupled reaction
what is the importance of phosphofructokinase adding a 2nd phosphate to fructose 6-phosphate, converting it to fructose 1,6-bisphosphate? how does phosphofructokinase regulate glycolysis?
commits the glucose to glycolysis
the PFK step of glycolysis is the major
regulatory point of glycolysis and is a point of allosteric regulation that controls the overall rate of glycolysis
an example of negative feedback. when ATP in the cell is high, phosphofructokinase is inhibited and prevents glycolysis from moving forward. when ATP is low, phosphofructokinase is used in abundance, and the cell is free to use glycolysis to make more ATP
it is also the rate limiting step of glycolysis
describe the steps of pyruvate decarboxylation
pyruvate becomes acetyl CoA, while
producing 1 NADH and 1 CO2
(net: 2 NADH and 2 CO2 since 2
pyruvate formed in glycolysis)
reaction is catalyzed by PDC enzyme
(pyruvate dehydrogenase complex)
where does pyruvate decarboxylation take place?
mitochondrial matrix
but in prokaryotes, it takes place in the cytoplasm
describe krebs cycle (fate of pyruvate that is produced in glycolysis) and its steps
in the krebs cycle, acetyl CoA merges with oxaloacetate to form citrate, and the cycle continues with 7 intermediates
3 NADH, 1 FADH2, 1 ATP (via substrate level phosphorylation) and 2 CO2 are produced per pyruvate molecule. Each
glucose molecule forms two pyruvate in
glycolysis, so the cycle turns two times,
creating a net of 6 NADH, 2 FADH2, 2
ATP (technically GTP), and 4 CO2. The CO2 produced here is the CO2 animals exhale during breathing
where does the krebs cycle take place?
mitochondrial matrix
but it takes place in the cytosol for prokaryotes
where does the electron transport chain (ETC) take place?
in the inner membrane/cristae of the mitochondria (the folds increase surface area for more ETC action)
ETC is embedded into the membrane and the membrane can host multiple so more space = more ETC = more ATP produced
in prokaryotes, this process takes place in the cellular membrane
what are the (2) other names for krebs cycle?
citric acid cycle
tricarboxylic acid cycle
what is aerobic respiration?
aerobic pathway of cellular respiration
organic compounds and oxygen react in a combustion reaction that produces energy
why are muscle cells abundant in mitochondria?
mitochondria are responsible for synthesizing very large amounts of ATP for cells to survive. the higher energy needs of a cell are, the more mitochondria it will have
since muscle cells (like cardiac and skeletal) require lots of energy to move, they will have many mitochondria.
what is the purpose of pyruvate decarboxylation?
to synthesize acetyl-CoA
how is ATP produced in the citric acid cycle?
ATP is produced via substrate level phosphorylation, which involves the direct transfer of a phosphate group via enzyme, to ADP (no extraneous carriers needed)
describe the important steps of the citric acid cycle?
first, acetyl-CoA merges with oxalacetate forming citrate
this citrate will go thru multiple steps, progressively being turned into different intermediates. during this process, electrons are stripped away and used to form different products
at the end, oxalacetate is reformed and the cycle can repeat
NOTE: this cycle happened twice per glucose!! 1 glucose -> 2 pyruvates -> 2 acetyl CoA
what is produced in the citric acid cycle?
NAD, ATP, FADH2, CO2
note that we technically get 2 acetyl-CoA from glucose so this cycle happens twice
where does the CO2 that animals exhale come from?
citric acid cycle
what is the purpose of NADH and FADH2?
coenzyme nucleotide molecules that function as high energy electron carriers
during glycolysis and the citric acid cycle, electrons are removed from glucose and transferred, converting NAD+ and FAD to NADH and FADH2. these electrons are eventually used to create ATP in the ETC
what is the electron transport chain?
a series of proteins embedded in the inner membrane of the mitochondria
IN ANAEROBIC CELLULAR RESPIRATION, the electron transport chain is found in the cellular membrane
in this process, the proteins pass high energy electrons through the chain, ultimately allowing the production of ATP
what are the steps of the electron transport chain (ETC)?
NOTE: this is oxidative phosphorylation
first, NADH and FADH2 ferry electrons to the ETC and drop them off (converting back to NAD+ and FAD – they are oxidized!! – and go back to glycolysis/CAC to repeat their process) to other electron carriers/proteins
as electrons pass through the proteins of ETC, protons (H+ ions) are pumped across the inner mitochondrial membrane and into the intermembrane space, establishing an electrochemical gradient. the intermembrane space has a high proton concentration (high pH - acidic) while the mitochondrial matrix has a low proton concentration
note that as the electrons move through, they slowly lose energy due to the pumping of protons. the movement of electrons throughout the ETC is a highly exergonic reaction which is coupled with the endergonic pumping of protons against the gradient
in the final step of the ETC, electrons are transferred from a protein to oxygen gas (O2). which then combines with hydrogen ions in the mitochondrial matrix to form water. oxygen is the final electron acceptor, NOT water. water is the final PRODUCT
ATP synthase forms ATP from ADP via oxidative phosphorylation (powered by the series of redox reactions from the acceptance and transfer of electrons). the build up of protons (H+ ions) in the intermembrane space goes against the desired balance. the protons wish to even out and move down the electrochemical gradient into the mitochondrial matrix (chemiosmosis). these protons move down through ATP synthase which uses the flow of protons (proton motive force) to create ATP from ADP – like using wind for energy!
between NADH and FADH2, which has more energy? when is this seen?
NADH has more energy than FADH2 and is able to “pump” more protons across the membrane. NADH pumps 3 protons for every 2 protons FADH2 pumps.
in the ETC, how are protons able to be continuously pumped against the concentration gradient?
the movement of electrons throughout the ETC is a highly exergonic reaction which is coupled with the endergonic pumping of protons against the gradient
note that as the electrons move through, they slowly lose energy due to the pumping of protons
what is the final electron acceptor in the ETC?
in the final step, electrons are transferred from a protein to oxygen gas (O2). which then combines with hydrogen ions in the mitochondrial matrix to form water. oxygen is the final electron acceptor, NOT water
water is the final PRODUCT
what is proton motive force?
promotes movement of protons across membranes downhill the electrochemical potential – providing energy that can be used to power other reactions OR
its energy can either be used right away to do work, like power flagella, or be stored for later in ATP
what is chemiosmosis?
movement of ions across a selectively permeable membrane, down their electrochemical gradient
what is the total yield for 1 glucose molecule going through aerobic cellular respiration? why is there a discrepancy in numbers of the total of all the individual processes of respiration and the actual total?
glycolysis: 2 ATP & 2 NADH
- 2ATP for NADH to be transported into the cytosol
pyruvate decarboxylation: 2 NADH
citric acid cycle: 2 ATP & 6 NADH & 2 FADH2
electron transport chain: 34 ATP
total: 36 ATP (38 - 2)
how is ATP produced in the electron transport chain? describe the steps
via oxidative phosphorylation, series of redox reactions where electrons are transferred and accepted etcc
ATP synthase forms ATP from ADP via oxidative phosphorylation (powered by the series of redox reactions from the acceptance and transfer of electrons). the build up of protons (H+ ions) in the intermembrane space goes against the desired balance. the protons wish to even out and move down the electrochemical gradient into the mitochondrial matrix (chemiosmosis). these protons move down through ATP synthase which uses the flow of protons (proton motive force) to create ATP from ADP – like using wind for energy!
what’s the key difference between aerobic and anaerobic cellular respiration?
in anaerobic respiration, the last electron acceptor is not oxygen!
some alternatives: SO4, NO3, S, etc. – as long as it’s not oxygen
what is fermentation? how’s it different from respiration?
anaerobic process that isn’t respiration. there’s no citric acid cycle or ETC
fermentation allows for the regeneration of NAD+ without needing CAC or ETC. this is done thru the partial breakdown of glucose. note that, respiration is the complete breakdown of glucose
what are the steps of alcohol fermentation?
this is after glycolysis turns glucose into 2 pyruvate molecules
pyruvate is converted to acetaldehyde and CO2
acetaldehyde and NADH (from glycolysis) is converted to ethanol and NAD+
acetaldehyde acts as the final electron acceptor, becoming ethanol. ethanol is the final product
the NAD+ is replenished, allowing more glycolysis to take place
note that these fermentation steps do not produce any ATP
which organisms generally partake in alcohol fermentation?
yeast and some bacteria
what are the steps of lactic fermentation?
this is after glycolysis turns glucose into 2 pyruvate molecules
pyruvate and NADH is converted to lactate and NAD+
the NAD+ is replenished, allowing more glycolysis to take place
note that these fermentation steps do not produce any ATP
which organisms generally partake in lactic fermentation?
human muscle cells, fungi, bacteria
what happens to lactate in humans following lactic fermentation?
the lactate is transported from the muscle cells to the liver where it’s converted back to glucose via the cori cycle. the glucose is sent back to the muscle cells to use as energy
out of all human cells, why does lactic fermentation occur in muscle cells?
muscles turn to this process when we we have low oxygen availability due to physical exertion - to continue generating ATP
what are the two types of fermentation?
alcohol and lactic
where does fermentation occur?
in the cytosol – where glycolysis takes place
why do prokaryotes ultimately gain more ATP from aerobic respiration than eukaryotes? what’s the ATP difference?
NADH does not need to be transported into the mitochondrial matrix for prokaryotes
the transportation of NADH requires the consumption of 2 ATP. note that pyruvate doesn’t require ATP to be transported as its symport with protons
so, prokaryotes gain 38 ATP and eukaryotes gain 36 ATP
what other macromolecules can be used as an energy source when glucose has been used up?
other carbohydrates
lipids
proteins (lowk a last resort)
what is glycogenesis? describe how it works
occurs when we have more than the necessary amt of glucose
glucose monomers are linked together to form the polymer, glycogen
–
first, an ATP is used to turn glucose to glucose-6-phosphate. then a bunch of other steps…
lastly, we have our branched polymer of glycogen
where can glycogen be found?
generally in the liver and in skeletal muscles as they can store large amounts. but technically all cells can store glycogen
stored for later use
how are other carbohydrates like fructose and galactose used in metabolism?
they are converted to glucose-6-phosphate which can then be used in glycolysis and other metabolic pathways such as glycogenesis
what is glycogenolysis?
occurs when we are lacking in glucose
glycogen is broken down into glucose-6-phosphate which can be used in glycolysis
what is gluconeogenesis?
when other biological macromolecules such as lipids and proteins are converted into glucose
AKA conversion of non-carbohydrate precursors into glucose
where does gluconeogenesis mainly occur?
liver and kidneys
remember that gluconeogenesis is the conversion of non-carbohydrate precursors into glucose
how is carbohydrate metabolism regulated?
via two hormones produced by the pancreas: insulin and glucagon
what role does insulin play in carbohydrate metabolism?
insulin is released when blood glucose levels are too high.
what insulin does:
- cells will uptake glucose and make use of the glucose, producing ATP (promotes glycolysis). insulin activates the phosphofructokinase enzyme to promote glycolysis
- excess glucose made into glycogen (promotes glycogenesis)
what role does glucagon play in carbohydrate metabolism?
glucagon is released when blood glucose levels are too low
what glucagon does:
- glycogen is broken down into glucose for energy (promotes glycogenolysis)
- inhibits glycogenesis (to produce energy) and glycolysis (to conserve energy). it inhibits the phosphofructokinase enzyme to inhibit glycolysis
note that glycolysis is only inhibited in certain organs so organs that actually need it more have energy (like the brain)
how are proteins able to be used for energy?
proteins are broken into amino acids which are then converted in various molecules that can enter the citric acid cycle at various points, such as acetyl-CoA, pyruvate, oxaloacetate (depends on the amino acid)
first, remove the amino group from the amino acid through a process called deamination. this amino group will now exists as ammonia which is then converted into urea (more harmless than ammonia which is toxic when accumulated)
what is the purpose of breaking down nucleic acids?
different components can be “salvaged” to form new nucleotides and certain parts can be excreted in urea
how does a lipid, such as triglyceride able to be used for energy?
note that triglyceride is a glycerol carbon backbone connected to 3 fatty acid chains
first, the triglyceride must be broken down into its components. the enzyme lipase splits apart the glycerol backbone and fatty acids
the glycerol is phosphorylated to G3P, an intermediate is glycolysis. it enters the glycolysis cycle like this
fatty acids in the blood combine with the protein, albumin which carries them throughout the bloodstream. in the mitochondrial matrix, fatty acids are broken down for energy in a process called beta-oxidation. every time we break down a fatty acid, we take two of its carbons and combine it with another molecule to form acetyl-CoA. with each acetyl-CoA we produce, we also get 1 NADH and 1 FADH2 (-1 FADH2 per double bond from the total). this process repeats! we can get lots of ATP this way but note that 1ATP is used for activation of the fatty acid chain
what is beta oxidation? where does it take place?
fatty acids are broken down for energy in a process called beta-oxidation. every time we break down a fatty acid, we take two of its carbons and combine it with another molecule to form acetyl-CoA. with each acetyl-CoA we produce, we also get 1 NADH and 1 FADH2 (-1 FADH2 per double bond from the total). this process repeats! we can get lots of ATP this way but note that 1ATP is used for activation of the fatty acid chain
takes place in the mitochondrial matrix of eukaryotes and cytosol of prokaryotes
what does the brain use for energy when there’s no glucose?
ketones, a byproduct from the breakdown of fatty acids in the liver
these ketones can enter the citric acid cycle where they will produce ATP
how many calories do fats and carbohydrates and proteins store? what does this mean?
fats are 9 calories/gram, whereas carbohydrates and proteins are 4 calories/gram
fats store more energy than carbohydrates
per carbon - their carbons are in a more
reduced state – this explains the amount of calories for the macromolecules
briefly describe photosynthesis and state the formula
captures energy from sunlight and converts it into chemical energy – organisms that partake in this process are called photoautotrophs
plants take in CO2 and water and convert it into glucose and O2
6(CO2) + 6(H2O) ——> C6H12O6 + 6(O2)
what are chloroplasts?
photosynthesis takes place in chloroplasts which is found in plants and photosynthetic protists/bacteria
it contains a molecule called chlorophyll (found in proteins called photosystems embedded in the thylakoid membrane) that captures energy from sunlight and uses it the energy to make glucose from water and CO2
describe the structure of chloroplasts
outer membrane
intermembrane space
inner membrane
stroma: similar to the cytoplasm of cells. where all of the internal structures of the chloroplast are suspended in
stroma lamellae: connects thylakoid
thylakoid: membrane bound structures that look like flattened discs. the inside is called thylakoid lumen (some parts of photosynthesis take place in here). stacked thylakoids are called granum
what’s chlorophyll? how does it capture energy from sunlight?
embedded in the photosystems of the thylakoid membrane in chloroplasts.
chlorophyll contains a porphyrin ring centered around Mg
it captures energy from sunlight and uses it the energy to make glucose from water and CO2
photons from the sunlight hit electrons in the chlorophyll molecule and excites the electrons to a higher state which begins the photosynthesis process
what are the (2) sets of reactions that make up photosynthesis?
light dependent reactions: cyclic and non-cyclic photophosphorylation
light independent (dark) reactions aka calvin cycle: doesn’t require photons
what are the (2) important photosystems of light dependent reactions? what are their other names? briefly describe the two different photosystems and what they produce
photosystem I - 680nm
photosystem II - 700nm
their second set of names comes from the approximate wavelengths they absorb
photosystem II captures energy and starts the process of high energy electron transfer. primarily used to generate ATP
photosystem I gets electrons after they’ve been passed through photosystem II. it boosts them with energy again to eventually produce NADPH
describe the steps in the process of non-cyclic photophosphorylation (a light dependent reaction)
the photons from the sunlight excite the electrons (gained through photolysis) found in photosystem II, boosting them to a higher energy level
excited electrons passed to primary electron acceptor
primary electron acceptor will pass electron through the electron transport chain (ETC)
as the electron is passed, the energy from this process is used to pumps protons (H+ ions) from the stroma into the thylakoid lumen, against the concentration gradient. this establishes an electrochemical gradient
ATP synthase catalyzes the reaction of ADP to ATP using the flow of protons going down the gradient (proton motive force/chemiosmosis). note that 3 H+ ions produce 1ATP
the electrons that passed through the ETC arrive at photosystem I in a low energy state as it’s energy was used up as it moved from acceptors and moving protons against the gradient. photons hit photosystem I, exciting the electrons. the electron is passed to an acceptor at the start of another ETC.
as the electrons travels down the ETC, it combines with a molecule called NADP+ and H+ (from photolysis), forming NADPH
in the non-cyclic photophosphorylation, how much ATP is produced per 2 electrons going down the ETC?
2 electrons phosphorylate 1.5 ATP
in the cyclic photophosphorylation, how much ATP is produced per 2 electrons going down the ETC?
1 ATP
what is the purpose of the light dependent reactions of photosynthesis?
non-cyclic photophosphorylation produces:
ATP to be used in the light independent (dark) reactions and NADPH that will help power the formation of glucose in the dark reactions.
cyclic photophosphorylation produces:
more ATP (dark reactions require more ATP than NADPH)
what is the overall formula of the light dependent reactions of photosynthesis?
H2O + ADP + Pi + (NADP+) + light →
ATP + NADPH + O2 + (H+)
what is the overall formula of the light independent reactions of photosynthesis?
6CO2 + 18ATP + 12NADPH →
18ADP + 18 Pi + 12(NADP+) + 1 glucose (or 2 G3P)
what’s photolysis? what’s the purpose of it?
the splitting of water by light during photosynthesis. water splits into hydrogen ions, electrons, and oxygen. the hydrogen ions are used in the concentration gradient, the electrons are stored in the photosystems to be used in the light dependent reaction, and the oxygen is given off by plants into the atmosphere (what we breathe in)
occurs in the thylakoid lumen
where does photolysis occur?
thylakoid lumen
where does non-cyclic photophosphorylation, a light dependent reaction occur?
thylakoid lumen, it passes electrons to the thylakoid membrane
where does cyclic photophosphorylation, a light dependent reaction occur?
stroma lamellae
describe the steps in the process of cyclic photophosphorylation (a light dependent reaction)
note that only photosystem I is used in this process
–
REMEMBER THAT photosystem I gets its electrons from the ETC that feeds into it (direction of photosystem II)…. photons from sunlight excite the electrons residing in photosystem I
the electrons then get passed back to the
(beginning of??) ETC that pumped H+ ions across the membrane until it’s back at photosystem I, while also pumping H+ ions across
repeats
where does the calvin cycle take place?
in the stroma
what is the purpose of the calvin cycle of photosynthesis?
to convert CO2 into glucose
what’s carbon fixation?
taking carbon from an inorganic source and converting it into an organic compound
e.g. taking CO2 from the atmosphere and converting it into glucose in the calvin cycle
what (3) phases make up the calvin cycle?
carbon fixation: in this situation, carbon from CO2 is used to produce an organic compound
reduction: using the ATP and NADPH generated from the light dependent reactions
regeneration: recycling intermediates to regenerate RuBisCo, an enzyme
what is the most abundant enzyme on earth?
RuBisCO – essential for carbon fixation
describe the steps in the calvin cycle
enzyme, RuBisCo combines CO2 and ribulose biphosphate (RuBP) forming an organic compound — this is carbon fixation!!
the 6-carbon compound we formed into 2 phosphoglycerate (PGA)
using ATP and NADPH, the PGA molecules are phosphorylated into G3P. the now ADP and NADP+ go into non-cyclic photophosphorylation
some G3P is converted back to the ribulose bi-phosphate (to allow the calvin cycle to continue again) and some G3P is converted to glucose
in order to make ONE molecule of glucose, we need to calvin cycle to occur 6 times. out of the 12 G3P produced, 10 is used to reform ribulose biphosphate and 2 used to form glucose
what are the products of the calvin cycle?
glucose and regeneration of ribulose biphosphate
in order to make ONE molecule of glucose, we need to calvin cycle to occur 6 times. out of the 12 G3P produced, 10 is used to reform ribulose biphosphate and 2 used to form glucose
what is photorespiration?
when O2 is used instead of CO2 in the calvin cycle, producing a useless byproduct, a 2-carbon molecule (photosynthesis produces 3-carbon molecules). this byproduct can be broken down by peroxisomes
O2 competitively inhibits RuBisCo
what can competitively inhibit RuBisCo?
oxygen!
both O2 and CO2 can bind to RuBisCo
CO2 is preferred, O2 is not!
CO2 leads to calvin cycle
O2 leads to photorespiration
what are the types of photosynthesis? what plants partake in each?
C2 = photorespiration - an “accidental” process; all plants
C3 = normal photosynthesis; all plants
———- different versions of photosynthesis that prevents/mitigates certain problems
C4: mitigates photorespiration by spatial separation; corn and sugarcane
CAM: mitigates water loss by temporal separation; cactus and pineapple (found in locations with higher temps)
what is C4 photosynthesis?
it prevents photorespiration by physical separation of the light and dark reactions of photosynthesis
NOTE THAT IN C3 RESPIRATION, THE CALVIN CYCLE OCCURS IN THE MESOPHYLL CELLS. in C4 respiration, RuBisCo is found in the bundle sheath cell, so the calvin cycle only occurs there
oxygen can’t reach the bundle sheath cells, thus, unable to competitively inhibit RuBisCo
only occurs in plants that follow Kranz anatomy. has the following layers from outside to inside: mesophyll cells, bundle sheath cells, vascular tissue (veins)
describe the steps of C4 photosynthesis
first, PEP carboxylase combines CO2 with PEP (instead of RuBP), forming oxalacetate (a 4-carbon compound) which is then converted to malate. this occurs in a mesophyll cell (one of the outer cells).
the malate is then moved to a bundle sheath cell (a layer deeper). the malate is converted into 2 products: CO2 and pyruvate
the pyruvate is shuttled back to the mesophyll cell and converted back to PEP
the CO2 in the bundle sheath cell undergoes the calvin cycle to produce glucose
glucose can be shuttled to the vascular tissue for transport for plant cells that need it
what’s the main drawback of C4 photosynthesis?
the use of extra ATP to pump 4C compounds (malate) to bundle sheath cells
what’s the hatch and slack pathway?
aka the C4 photosynthesis pathway
explains that little presence of oxygen reduces competition while RuBisCo is deciding to fix either carbon dioxide or oxygen
what is CAM (crassulacean acid
metabolism) photosynthesis? why does this process exist (explain the problem this tries to prevent)?
prevents water loss from plants by temporal separation (day and night)
plants have stomata, pores found on the bottom of leaves, that serve as the site of gas exchange. it’s how CO2 enters and O2 leaves. usually, the stomata are always open to allow the plant to continuously take in CO2 to produce glucose. BUT, if these are open, water can also leave the plant through the stomata.
in CAM photosynthesis, the stomata is open at night and closed during the day.
describe the steps in the process of CAM photosynthesis
in CAM photosynthesis, the stomata is open at night and closed during the day
so at night, CO2 enters. rather than going through the calvin cycle right away (we can’t bc no sunlight!!), PEP carboxylase combines CO2 with PEP, forming maleic acid.
the maleic acid is then stores in the plant cell’s vacuole for later. when it’s daytime, the plant closes the stomata to prevent water loss (especially during higher temperatures)
the plant moves maleic acid out of its storage and converts it back into malate and then CO2 and PEP with the use of 1ATP.
the CO2 then goes through the calvin cycle to produce glucose.
what’s the role of carotenoids in photosynthesis?
main function is to absorb light energy in the blue-green and green regions of the electromagnetic spectrum that chlorophyll cannot absorb effectively. allows carotenoids to broaden the range of light wavelengths that can be utilized for photosynthesis.
carotenoids also help protect the plant from damage caused by excessive light energy. acts as antioxidants, neutralizing harmful free radicals produced during photosynthesis. helps prevent damage to the plant’s cells and tissues.
what results in the orangeness seen in leaves as they age?
as leaves age, chlorophyll breaks down to
extract valuable components like Mg2+,
and carotenoids become visible
what (2) processes make up cell division?
nuclear division: dividing the genetic material and nucleus
cytokinesis: dividing the cytoplasm (happens near the end of anaphase)
where on sister chromatids linked together?
in a constricted region called the centromere
how many chromosomes are in a human diploid? haploid
diploid: 46
haploid: 23
what are homologous chromosomes?
a pair of chromosomes that are similar in length, gene position, and centromere position. carry genetic information for the same shape but are not identical
one inherited from the mother, and one from the father
humans have 23 pairs but in a male, the X and Y sex chromosomes are technically not considered to be homologous
what’s miotic spindle?
full set of spindle fibers during cell division
the spindles attach to the chromosomes and separates them
how do spindle fibers attach to the chromosomes?
they attach to the protein, kinetochore, which adheres to the centromere
the kinetochore serves as an anchor point for spindle fibers, allowing them to change the position of the chromosomes during cell division
what are the (5) different phases of mitosis? just list them
prophase
prometaphase
metaphase
anaphase
telophase
cytokinesis, a separate process also occurs around the end of anaphase
what are the (5) different phases of mitosis? describe what happens during each
prophase
- chromatin condenses into chromosomes
- nucleolus disappears (where ribosomes are made) – nucleus still intact
- miotic spindles begin to form as the centrosomes it emerges from are slowly pushed to opposite ends
prometaphase
- nuclear membrane breaks down and disappears
- chromosomes condense further
- kinetochore proteins are attached to each chromatid
- miotic spindle fiber continues to develop, some of it has even attached to the kinetochores
metaphase
- chromosomes are lined up across the middle of the cell – “metaphase plate”
- centrosomes have reached opposite ends of the cell
- miotic spindle is fully developed and fibers are attached to all chromosomes via kinetochores
anaphase - shortest step of mitosis
- begins when miotic spindle begin to shorten, pulling the sister chromatids apart. each chromosome pulled to opposite end of the cell (important to note, once the sister chromatids are separate, each chromatid is considered a chromosome)
telophase (cytokinesis, a separate process also occurs around the end of anaphase)
- nucleolus redevelops and 2 new nuclear membranes develop
- chromosomes decondense into chromatin
- spindle fibers disassemble
what happens during prophase and prometaphase of mitosis?
PROPHASE
chromatin condenses into chromosomes
nucleolus disappears (where ribosomes are made) – nucleus still intact
miotic spindles begin to form as the centrosomes it emerges from are slowly pushed to opposite ends
PROMETAPHASE
nuclear membrane breaks down and disappears
chromosomes condense further
kinetochore proteins are attached to each chromatid
miotic spindle fiber continues to develop, some of it has even attached to the kinetochores
what happens during metaphase of mitosis?
chromosomes are lined up across the middle of the cell – “metaphase plate”
centrosomes have reached opposite ends of the cell
miotic spindle is fully developed and fibers are attached to all chromosomes via kinetochores
what happens during anaphase of mitosis?
begins when miotic spindle begin to shorten, pulling the sister chromatids apart. each chromosome pulled to opposite end of the cell (important to note, once the sister chromatids are separate, each chromatid is considered a chromosome)
this is the shortest step of mitosis
what happens during telophase of mitosis?
nucleolus redevelops and 2 new nuclear membranes develop
chromosomes decondense into chromatin
spindle fibers disassemble
differentiate between cytokinesis in an animal and plant cell
animal cell
- a structure called a cleavage furrow forms. it’s a contractile ring made of actin and myosin filaments
- the ring gradually tightens and gets smaller, pinching the cell into two separate cells - the actin and myosin filaments are shortening
plant cell
- a structure called a cell plate (made of vesicles from golgi bodies) forms in the middle. it extends and fuses with the cell wall, separating the cell into two cells
when karyotyping be performed during mitosis?
during metaphase
considered to be the most convenient time as chromosomes are fully developed and lined up, making them easy to separate
what are the (8) different phases of meiosis? describe what happens during each
prophase I
- nucleolus and nucleus disassembles
- chromatin condenses into chromosomes
- meiotic spindle begins to form and centrosomes begin to move towards opposite ends
- homologous chromosomes pair up (synapsis). they sit on top of each other in a structure called tetrad. crossing over occurs at the chiasmata (where they swap segments)
- microtubules from the meiotic spindle begin to attach to the kinetochores of the homologous chromosomes
metaphase I
- paired homologous chromosomes are lined up across the metaphase plate (independent assortment)
- kinetochores of chromosome are attached to microtubules emerging from the meiotic spindle
anaphase I
- homologous chromosomes within the tetrads will uncouple and be pulled apart to opposite sides of the cell in a process called disjunction
- note that sister chromatids are still paired together in their chromosomes
telophase I
- nuclear envelope redevelops
- chromosomes decondense
- each nucleus will have half the number of chromosomes that we started out with so we now have 2 haploids (note that the chromosomes are still in their duplicated state and not separated!!)
depending on the species, interphase may occur here in between meiosis I and meiosis II
prophase II
- nucleus and nucleolus disassembles
- chromosomes condense
- meiotic spindle develops and starts to attach to the chromosomes
metaphase II
- chromosomes line up across the metaphase plate
- meiotic spindle has fully formed and is attached to every chromosome at the kinetochore
- note that we have half the number of chromosomes than we did in metaphase I and that the sister chromatids are no longer identical to one another due to crossing over
anaphase II
- microtubules of the meiotic spindle shortens and the sister chromatids of each chromosome are pulled apart to opposite ends of the cell. as soon as they are apart, each chromatid is now considered a chromosome
telophase II
- nucleolus and nucleus reforms
- chromosomes decondense back into chromatin
- spindle fibers disappear
what’s the synaptonemal complex?
protein structure that temporarily forms
between homologous chromosomes; gives rise to tetrad with chiasmata and crossing over
differentiate between quiescent and senescent
quiescent is reversible in the G0 phase of the cell cycle
senescent is permanently in the G0 phase of the cell cycle
what happens during prophase I of meiosis?
nucleolus and nucleus disassembles
chromatin condenses into chromosomes
meiotic spindle begins to form and centrosomes begin to move towards opposite ends
homologous chromosomes pair up. they sit on top of each other in a structure called tetras. crossing over occurs at the chiasmata (where they swap segments)
microtubules from the meiotic spindle begin to attach to the kinetochores of the homologous chromosomes
what happens during metaphase I of meiosis?
paired homologous chromosomes are lined up across the metaphase plate (independent assortment)
kinetochores of chromosome are attached to microtubules emerging from the meiotic spindle
what happens during anaphase I of meiosis?
homologous chromosomes within the tetrads will uncouple and be pulled apart to opposite sides of the cell in a process called disjunction
note that sister chromatids are still paired together in their chromosomes
what’s disjunction?
homologous chromosomes within the tetrads will uncouple and be pulled apart to opposite sides of the cell
during anaphase
what happens during telophase I of meiosis?
nuclear envelope redevelops
chromosomes decondense
each nucleus will have half the number of chromosomes that we started out with so we now have 2 haploids (note that the chromosomes are still in their duplicated state and not separated!!)
what happens during prophase II of meiosis?
nucleus and nucleolus disassembles
chromosomes condense
meiotic spindle develops and starts to attach to the chromosomes
what happens during metaphase II of meiosis?
chromosomes line up across the metaphase plate
meiotic spindle has fully formed and is attached to every chromosome at the kinetochore
note that we have half the number of chromosomes than we did in metaphase I and that the sister chromatids are no longer identical to one another due to crossing over
what happens during anaphase II of meiosis?
microtubules of the meiotic spindle shortens and the sister chromatids of each chromosome are pulled apart to opposite ends of the cell. as soon as they are apart, each chromatid is now considered a chromosome
what happens during telophase II of meiosis?
nucleolus and nucleus reforms
chromosomes decondense back into chromatin
spindle fibers disappear
how does meiosis give rise to genetic diversity? (3)
crossing over (during prophase I)
- creates unique chromosomes that aren’t identical to the parents they come from
independent assortment (during metaphase I)
- the mix of which chromosomes in a homologous pair gets separated to which end of the cell is random
random joining of gametes
- the combination of which sperm fertilizes which egg
- NOTE: joining of gametes is random, but some sperm cells contain genetic material that gives them a competitive advantage - so they all aren’t “equally” competitive
what’s the interphase?
sequence of events that occurs before the cell undergoes cell division
this is where cells spend the majority of their time
what are the (3) separate phases of the cell’s interphase? what happens during these phases?
G1: cell grows in size. increases protein synthesis to prepare for cell division (e.g. DNA polymerase used in S) - most cell growth is here
S (synthesis): duplicates genetic material, forming sister chromatids. also duplicates centrosomes. cell also grows here
G2: cell continues to grow in size and synthesizing proteins. the cell will also replicate its organelles during this phase. cell checks to see if mitosis can proceed
what’s G 0? (the phase outside of the cell cycle)
“resting phase”
cells are still active and functional. they aren’t dividing or preparing to divide
nerve cells and muscle cells are often found in this phase
differentiate between quiescent or senescent
quiescent is temporarily in the G0 phase and can reenter the cell cycle when they need to divide.
senescent is permanently in the G0 phase due to damage or degradation.
why do our cells divide instead of just growing bigger?
there are functional limitations to what a cell can do when it passes a certain size due to the
- surface to volume ratio
- genome to volume ratio
why is the surface to volume ratio important for a cell’s function?
a smaller surface to volume ration (when the cell becomes bigger in size) leads to difficulties in cellular exchange
a large cell has a large volume which means it needs tons of nutrients and oxygen, so it needs a larger surface area to be able to facilitate its needs
this also applies to getting rid of waste
why is the genome to volume ratio important for a cell’s function?
as a cell grows larger in volume, the genome amount doesn’t change.
our genome is used to express genes and produce proteins. the larger a cell is, the more processes that need to be regulated
what are some exceptions to the genome/surface to volume ratio rule of cells?
skeletal muscles remain in the G0 phase and don’t divide. they’re even capable of growing larger with exercise. the skeletal muscle cells don’t follow this limitation bc
- they have multiple nuclei (large genome to volume ratio)
- long and cylindrical (large surface area to volume ratio)
what are the (5) ways in which the cell cycle can be regulated?
cell cycle checkpoints: to make sure the cell is ready to divide
density dependent inhibition: stops cells from dividing when overcrowded
anchorage dependence: makes sure cells are firmly attached to a surface to be able to divide — so a cell that comes loose and is traveling thru your lymphatic vessel or thru your blood can’t divide
cyclin-dependent kinases (CDK’s): a CDK enzyme activates proteins that regulate the cell cycle via phosphorylation. CDK’s are activated by protein cyclins, which vary in type and concentration throughout each phase of the cell cycle
growth factors: a secreted biologically active molecule that can affect the growth of cells. definition has become expanded to include secreted molecules that promote or inhibit mitosis or affect cellular differentiation. the plasma membrane contains receptors for growth factors
note that cancer cells can “defy” the last 4 methods of regulation
when are the (3) regulation checkpoints in the cycle? what do they check for?
end of G1 phase (before the cell enters S) aka restriction checkpoint
makes sure the cell is ready to replicate it’s DNA by checking:
- if the cell has proper nutrients to go thru cell division
- if it has necessary cell products to replicate its DNA
- if the cell has grown sufficiently large and if its DNA is intact and error-free and undamaged
end of G2 phase (before the cell enters mitosis)
checks to see if the DNA replicated properly: DNA has been duplicated and that the DNA is error-free and undamaged
if there’s any issues, the cell can pause here and make any repairs necessary or finish the DNA duplication
metaphase (mitosis) aka M checkpoint aka spindle checkpoint
checks that each of the sister chromatids is attached to a spindle fiber, if so, anaphase is triggered. if not attached, mitosis halts until all are chromosomes are properly attached to spindle fibers
what happens if the cell fails one of the cell cycle checkpoints?
the cell can either permanently enter the G0 phase and stop dividing or go thru apoptosis (cell death)
what happens if there are regulations for cell division?
the cell goes thru uncontrolled cell division eventually leading to cancer
describe the development of a cancer cell
a normal cell divides only when it’s supposed to but it can develop mutations that disrupt our ability to regulate cell division, which allows the cell to divide uncontrollably — increasing the amount of mutated cells — leading to large dangerous masses of cells called tumors
differentiate between malignant and benign tumors
malignant is when the uncontrollably dividing mutated cells have broken loose and spread to other tissues – this process is called metastasis
benign is localized
define metastasis
when the uncontrollably dividing mutated cells have broken loose and spread to other tissues – this is called a malignant tumor
what’s p53?
a tumor supressing gene – like Rb
limits cell division –> prevents tumors from forming
if the one of the p53 gene gets mutated, it becomes easier for the cell to divide uncontrollably. if both copies get mutated, the ability to stop cell proliferation has been impaired and cancer is likely to develop
what do cancer drugs do?
the main goal is to limit the amount of cell division
many drugs work by inhibiting mitosis directly
e.g. disrupting the ability of miotic spindle to form and disassemble during the cell cycle –further division no longer possible
what are the (3) names used to categorize cells based on how they divide?
labile: constantly dividing and replenishing themselves
- e.g. skin cells
quiescent: cell do not divide; but can be stimulated when needed
- e.g. liver cells
fixed/permanent cells: little to no capacity to divide
- e.g. cardiac muscle cells
how does fluorescence microscopy, a type of optical microscopy work?
use of a fluorescent marker to tag certain structures. we then shine light to excite the fluorescent probe.
assist in visually locating protein expression within a cell
can be used on living organisms
