all content Flashcards
macromolecules that can’t form polymers
lipids
what is the most abundant molecule in organisms
proteins, then nucleic acids
what is one way organisms benefit from consuming other organisms
all organisms are composed of the same macromolecules composed of roughly the same proportions
process by which monomers are added to a growing polymer
dehydration synthesis or condensation. an OH is removed from the monomer and a hydrogen from the polymer, forming a bond and releasing water
hydrolysis is the process of
breaking down a polymer to a monomer and. polymer minus 1. the water attacks the bond and leaves h on polymer and oh on the monomer
direction of protein synthesis
n terminus to c terminus, numbered 1 to n from n to c
protein structure
primary - sequence, secondary - backbone, tertiary - r group, quaternary - other polypeptides
types of primary structure
alpha helices and beta pleated sheets, both arise from hydrogen bonds on the backbone
proline can form what kind of secondary structure
none, it has a ring in its structure and so the nitrogen is not bonded to any hydrogens
types of tertiary interactions
hydrophobic interactions, ionic, disulfide, hydrogen bonds between r groups or between r groups and backbone
what is coiled coils?
happen when there are hydrophobic aas at every 4th position (one rotation is 3.6 aa), gives rise to fibrous structural proteins like keratin in hair
is folding a reversible process
typically yes
what are protein chaperones?
proteins which allow for the folding of new proteins (isolating them when they are newly syntehsized as polypeptides)
what are the building blocks of nucleotides
phosphate linked (to the 5 carbon) of a 5 carbon sugar linked to a nitrogenousbase(to the 1 carbon)
differences between ribose and deoxyribose
ribose is only in RNA whereas DNA has exclusively deoxyribose. ribose has a hydroxyl group on the 2 carbon whereas deoxyribose does not (deoxy, de oxy)
what is atp
energy rich molecule fro the 2 phosphate bonds on an adenine base
what are they pyrimidines and what are the purines
pyrimidines CUT purines (AG)
pyrimidines are smaller, bigger name
purines are bigger, CUT into pyrimidines
direction and mechanism of nucleotide synthesis
5’ to 3’, phosphodiester linkage formed between hydroxyl on 3 carbon and oxygen on phosphate of next molecule
big names of people involved in DNA structure discovery
rosalund franklin, Francis crick, James Watson
number of hydrogen bonds between purines and pyrimidines
GC 3 AT 2(same as AU)
how is DNA structured
double stranded, antiparallel, and helical.
has major and minor grooves when looked at from a fixed orientation
describe tRNA’s hairpin structure
there is a single stranded loop portion as well as a double stranded portion
anabolic reactions
synthesize molecules and requires energy
catabolic reactions
breakdown molecules and release energy
energy coupling
endergonic and exergonic reactions (catabolic and anabolic) are paired to make endergonic proceed spontaneously
driving forces of spontanaeity
enthalpy and entropy yield a relationship with temperature which is described by Gibbs free energy equation. negative energy is good
conditions for standard free energy
37 deg and 1 m of all reactants, actual g usually differs
can rate be predicted if free energy is known
no it cannot
function of catalysts
enzymes who catalyst reactions, don’t impact rate or overall change in free energy
how do catalysts function
bringing molecules together, charge isolation, mechanical strain to induce reaction
what are cofactors
things necessary for catalysis that are not polypeptides or enzymes. often are metal ions
differences between allosteric and competitive inhibition
competitive requires equal or greater concentration of regulatory molecule whereas allosteric does not
aldehydes vs ketones
carbonyl groups that are terminal for aldehydes or central for ketones
optical isomers exhibit chirality
this leads to stereoisomerisation
differences between alpha and betaglucose
are in equilibrium with the linear molecule, alpha hydroxyl points down (same orientation as 4 hydroxyl) whereas beta does the opposite
amylose
a starch (hydrocarbon) is linear and only has alpha linkages (helical)
amylopectin
another starch (like amylose) but can be moderately branched, is glycogen in animals (helical)
glycogen
storage of glucose subunits, alpha linkages, branched, functionally and structurally similar to amylopectin (helical)
cellulose
is symmetrical and is completely linear, exhibits strong h bonding due to its linear shape. beta 1 4 linkages
uses of lipids
energy, cell membranes, carotenoids (energy capture)hormones and vitamins, thermal and electrical insulation, hydrophobicity
composition of fatty acids
carboxyl group and a hydrocarbon tail
fats and phospholipids
form between fatty acids and glycerol molecule
phospholipid structure
choline head atop a phosphate molecule, attached to a diglyceride glycerol
formations of a phospholipid bilayer
thermodynamically favoured
fluid mosaic model
paints a picture of the membrane model. phospholipids and most proteins can float around as much as they want but don’t flip to the other side very often at all.
describe saturation of different fats
highly saturated means no double bonds in the hydrocarbon chain, makes it very non polar in that region, leads to IMFS
saturation of the bilayer
leads to reduced fluidity and permeability in saturated bilayers, the opposite is true for unsaturated ones
what does it mean to be amphipathic
having a region which is polar and others that are not
how does the amphipathicity of some proteins play into the mosaic model
the polar ends will reside on the outsides and the polar component of the layer with non polar components transversing the hydrophilic portions of phospholipid layer
meaning of peripheral or transverse(integral) proteins
peripheral is on either side, whereas transverse cut all the way through
permeability of different molecules and elements in thebilayer
gases molecules pas easily through, uncharged polar get through because of their small size, large uncharge have trouble and ions basically don’t
factors controlling rates of diffusion
distance between molecules, temperature, size of molecule and the steepness of the concentration gradient
osmosis mechanism
osmosis is the transfer of water through a semipermeable membrane, where water flows from low to high solute concentration (high to low water concentration)
types of non diffusion passive transport (name 2)
facilitated diffusion occurs by
- channel proteins - which allow for the flow of ions, usually voltage gated
- carrier proteins -binds the substrate and assists it out of the cell ( or in)
types and definition of active transport
requiring energy directly or indirectly. ex na k pump which pumps both ions across their gradients, described as active transport
secondary active transport are symporters and anti porters for example.
symport - same direction
antiport - opposite directions. the driver molecule always follows its gradient, assisting the target to move against
what drives glucose transport in gut cells:
sodium concentration (symport)
describe diffusion limit in context of cell size
cells must be small in order to permit adequate permeation of nutrients by diffusion.pertains to the sa/v ratio
describe the organizational plan of prokaryotes
small, no organelles, no nucleus. typically 10x smaller in diameter, 1000x in volume
describe the organizational plan of eukaryotes
large, many organelles, nucleus
describe the endomembrane system
says that the nucleus is continuous with the cytosol. rough ER is continuous with the nuclear membrane, Golgi apparatus communicates by vesicles. the cell membrane is also a part
describe the nucleolus
the origins of ribosome synthesis, location of high density DNA. outside the nucleolus but in the nucleus is loosely packed DNa
. IT IS SURRounded by the nuclear envelope
describe the rough ER
highly folded, many ribosomes, all membrane proteins are produced here
where is translation always started
in the cytosol, however the signal hypothesis says that it deposits proteins into the lumen of the ER by SRP receptors
describe smooth ER
lipids are synthesized here, detoxification occurs here. less ribosomes
are the proportions of organelles dependent on cell types
yes
cis/trans faces of Golgi apparatus
cis faces nucleus, trans faces membrane. Golgi is the sorting station for anabolic pathways
result/description of the pulse chase experimetn
basically the protein secretion pathway was validated,. used fluorescent things to monitor motion
describe receptor mediated endocytosis
macromolecules bind to surface receptors, an endoscope forms, digestive enzymes get added to the endoscope, turns the endosome into a lysosome,
what is phagocytosis
consumption of other cells, lysosomes fuse with the foreign body to digest them
what is the purpose of autophagy
recycling old organelles for their materials
how do vesicles know where to go in the cell
cytoskeleton
what are plastids
chloroplasts and mitochondria, they have DNA and reproduce independent of the host
what are cristae and the matrix
cristae is the inner membranes, the others is the matrix. Krebs, dna, and protein synthesis all occur in the matrix
what are thylakoids and stroma
thylakoids are membranes in chloroplasts, storm is the intracellular space.
evidence for endosymbiotic theory
own genome, own ribosomes (similar to bacteria), genes similar to bacteria, unique lipid synthesis and protein import
describe microfilaments
made of actin monomers, pull, present in cell division, move stuff around
intermediate filaments
are made of karatin or others, thicker than microfilaments, thinner than microtubules, maintain cell Shae by also pulling, anchor things
microtubules
alpha beta tubulin dimers, pushes and resists compression, move chromosomes, tracks for intracellular support
how many directions can myosin move actin in
one
what is cytokinesis assisted by
actin myosin interactions
microtubules start ___ and go outwards
at the nucleus
kynesin and dyenin in microtubules are functionally similar to what with actin
myosin. dyenin and kinesin also go in opposite directions
cilia and flagella are made of
microtubules
what are axonemes
typical structures of flagella, 9 microtubule pairs sorted around 2 in the middle
explain the role of collagen
fixing cells inter cellularly, is a secreted protein, (run in parallel and perpendicular),
what is integrin
a dimeric protein that attaches fibronectin (extra cell) to microfilaments in the cell
what are focal adhesions
connections between in the cell and out of (ecm) ie integrin
cell-cell adhesion
stable binding of certain types of cells which can lead to like sperm egg fusion, DNA exchange, phagocytosis
what are tight junctions
water tight seals as a cell-cell junction. example forcing solutes to force through epithelial cells to be sorted.
gap junctions are important because
they provide cytosolic connections between cells
describe feedback/endproduct inhibition
inhibition of surplus production, by inhibiting an enzyme earlier in the pathway
cooperative allostery
control is much better, reduces enzyme activity at much lower concentrations
net energy trapped from respiration
29
NAD+ is a carrier which means
it is a cofactor which can carry electrons and release a proton upon reduction
two phases of glycolysis
investment of ATP to activate sugar to split c6 to c3, and the payoff
in glycolysis, hexokinase adds a phosphate to glucose to
trap it in the cell, decrease cellular glucose concentration,
phosphofructokinase phosphorylates
the 6 c molecule again
g3p (a 3 c molecule in glycolysis) is oxidized by NAD+
once for each molecule (2 per glucose)
discuss the investment and payoffs of glycolysis
invest 1 glucose, 2 atp, get back 4 atp, and 2NADH and also 2 pyruvate
glycolysis happens where
in the cytoplasm
what is pyruvate oxidation
removal of CO2, making a 2c molecule, adding acetyl and reducing one NAD+ per pyruvate
dehydrogenase does what
removes co2 and reduces nad+
what is the end of the ETC
oxygen gets reduced and turns into water, is the final electron receptor
why does the ETC not short circuit?
enzyme specificity! the electrons from NADH can’t just jump to o2, even though this is more favourable
how does cyanide act
it binds to active site of cytochrome c, this does not allow for pumping of hydronium
what is the greater contributor to the PROTON MOTIVE FORCE
diffusion is much weaker than the voltage difference
how many hydronium are consumed by atp synthase to produce 1 atp by oxidative phosphorylation
3 lol
is oxidative phosphorylation and ETC independent
yes lol
what is energy uncoupling
the uncoupling of etc and atp production, h+ move across the membrane . this allows for the production of heat
how is respiration regulated
glycolysis - atp with phosphophructokinase
krebs - high NADH and H+ inhibits the first dehydrogenase of the cycle
ETC- low proton gradient results in faster ETC, too high slows it
in the absence of oxygen in respiration ->
increases proton gradient in the inter membrane space, which inhibits ETC flow, resultantly increases NADH concentration and inhibits dehydrogenase in krebs
what is the premise of fermentation
in the lack of oxygen, benefit from the atp yield of glycolysis by oxidizing pyruvate with NADH to start the cycle over again. it frees up NAD+ to oxidize glucose
alcohol fermentation
is the same as lactate fermentation except you remove a carbon and are left with ethanol
what happens if inadequate food is available? what is used first!
glycogen stores from muscle and liver undergo glycogenesis. then fats are used, then lastly proteins
NADP is only used in
anabolic pathways
reactions driven by its excess
plant cells typically have how many chloroplasts
40 to 50, but depends on the cell location and function
what are the three things that can happen to an excited electron in chlorophyll molecules
- can just decay and give off light and heat
- can decay by resonance, shifting energy to an adjacent molecule
- decay by successive electron transfers
the antenna system in photosynthesis is embedded
in the thylakoid membrane
the reaction centre in the light harvesting complex is
the final electron acceptor, which promotes the electron to pheophytin
the reaction centre acts like an energy sink (antenna molecules resonate electrons to it because…)
it has the longest wavelength (lowest energy) of the complex
describe the scheme of phosphorylation in photosynthesis
electrons are excited and brought to reaction centre in PS2, where electrons are promoted to pheophytin, carrying electrons to plastoquinone
as plastoquinone moves to the cytochrome complex, it pumps protons into the thylakoid lumen
atp is then produced in the stroma
describe noncyclic electron transfer
the ideal working of the system, splitting of water in ps2 happens to donate electrons to the system, oxidative phosphorylation occurs because of the transfer of electrons moving protons, ,, the electrons then move to ps1 to get excited again and move into the ETC
what establishes the proton gradient in the thylakoid membrane
splitting of water increases thylakoid concentration, using of nadp and h in the stroma decreases stroll concentration, plastoquinone directly increases the concentration
describe cyclic electron flow
instead of ferreredoxin taking electrons from ps1 to etc, brings them back to pq to pump more protons. this makes atp but doesn’t reduce the nadp
what is rubisco
Ribulose-1,5-bisphosphate carboxylase/oxygenase,
the most abundant protein in the world
a 5 carbon molecule
describe the Calvin cycle of carbon fixation
3co2 are added to 3 rubisco, then split to yield 63pg. this is the fixation step
you reduce these molecules by phosphorylating and and reducing from nadph to g3p
for every 3co2 that enter, you release 1 g3p to synthesisze carbohydrates
phosphorylate the g3pps again and bring them together to make your 3 rubisco again
what is photorespiration
so rubisco has a higher affinity for oxygen than co2, too much o2 halts the Calvin cycle essentially by forcing the plant to release co2 and consume atp without fixing any carbon
cell theory states
all organisms consist of cells
cells divide to produce new cells
higher organisms fuse cells to produce offspring
what are mitotic chromosomes
sister chromatids in mitosis
cell cycle phases
S phase or interphase (stationary/replication) is broken into G1, S, G2 M phase (mitosis/meiosis)
cancer can be
unregulated g1 s checkpoint fail because of excess cyclin E
what does hydroxyurea do
blocks replication inS phase so can’t proceed to G2,
however caffeine disables this checkpoint, allowing this to proceed, but then mitosis can’t happen rip
cyclins and cdks are involved in
cell cycle regulation
describe the g2 checkpoint
checks if chromosomes have correctly replicated and if DNA is undamaged.
metaphase checkpoint:
checks that all chromosomes are attached to the spindle apparatus
the G1 checkpoint
checks to see if cells are big enough and have enough nutrients, also for integrity of DNA
DESCribe mitosis
IPMAT
prophase: condensing of chromosomes, spindle apparatus begins to form
pro metaphase: nuclear envelope breaks down, kinetochore microtubules begin to make contact
metaphase: chromosomes migrate to middle of cell at the division/metaphase plate
anaphase: pulled to opposite sides of cell upon centromere dissolution
telophase: assembly of membrane, spindle apparatus disintegrates
centrioles are
the units in centrosomes
cytokenesis is
the purse string closing of actin myosin to separate cells
syncytial means
multinucleated
in humans, somatic cells are _____ and gametes are _____
diploid, haploid
what is meiosis
imagine doing mitosis twice with double the material. 1 cell yields 4 haploid gametes
describe meiosis 1
tetrad ( pair of homologs x4)
cross over in prophase 1
between non sister chromatids
break and repair chiasmata
meiosis 2:
mitosis with half the dna
risk of Down syndrome depends on
age of mother, nondisjunction in meiosis
odd ploidy organisms tend to be sterile because:
problems in meiosis1 separation
the ratio of homologs is more important
the probability of two independent events is
the product of the probability of those events happening in isolation
umber of gamete genotypes
its 2^n gamete genotypes where n is the number of independently assorting genes
colorblindness has
only males of unaffected parents are colourblind, females who are colourblind must have affected fatehrs
why does the Y chromosome always have the colourblindness alleel
it doesn’t, but it doesn’t have a colourblindness gene so there is no possibility for it to be good vision dominant
difference between dominant alleles linked in cis and trans
cis means the dominant (when considering 2 genes) are on the same chromatid, trans is the opposite
what are the factors that contribute to the heredity of a trait
number of genes controlling the trait, alleles in the population per gene, environmental effects
miescher was the first to
purify dna
explain Griffiths transformation principle
a chemical component of one cell is capable of influencing another cell
Hershey and chase showed that
dna is the genetic material of cells
at /gc _____between organisms
varies
Watson and crick used Rosalind franklins X-ray crystallography measurements to
untangle the structure of dna
explain how we found out that DNA replication was semiconservative
meselson stahl experiment: make DNA with heavy nitrogen, let it replicate, you’ll end up with light dna and intermediate dna ice u centrifuge in a slowing medium
explain the role of helicase
unwinds the dna during replication
explain the role of topoisomerase
to cut and anneal a strand to relieve tension during replication
synthesis of dna occurs in the
5prime 3prime direction
describe the lagging strand
the strand which is opposite the 5’ 3’ strand and must have inttermittent placement of primers to allow for replication
describe DNApolymerase1 and dna ligase
the protein responsible for excising rna fragments and replacing the with dna, ligase fuses the backbones
how are errors corrected in replication
proofreading by dnap3, mismatch repair (single nucleotide) and excision repair (in somatic cells, ripping out chunks)
