finals review Flashcards
energy
capacity to cause change, especially to do work (move matter against an opposing force)
kinetic energy
energy associated witht eh relative motion of objects
thermal energy
kinetic energy due to the random motion of atoms and molecules (heat)
chemical energy
energy available in molecules for release in a chemical reaction
potential energy
energy that matter possesses as a result of its location or spatial arrangement
first law of thermodynamics
the total amount of energy in the universe must always be the same
what is the ultimate source of energy
the sun
what is photosynthesis
converts electromagnetic energy in sunlight to chemical-bond energy in organic molecules
ANABOLIC
what is cellular respiration
extracts energy from organic molecules (food) by gradual oxidation
CATABOLIC
second law of thermodynamics
the degree of entropy (disorder) in the universe can only increase
how do cells not defy the second law of thermodynamics
increased order inside cell = increased disorder in cell’s surroundings
free energy (energy that could do work) is dissipated as heat
what is free energy (G)
amt of energy available in a molecule to do work in a system when the temp and pressure are uniform
units: joules or kcal/mole
where is free energy stored
in the bonds between individual atoms of a molecule
what does free energy cause
vibration, rotation and movement of the molecule through space
how can chemical reactions produce disorder
- reactions can decrease order in the cell (ex. preventing an interaction that prevents bond rotations)
- changes of bond energy of reacting molecules can cause heat to be released –> disorders environment
equation for free energy
A + B –> C + D
(delta)G = free energy (C + D) - free energy (A + B)
when is G negative
if the disorder of the universe increases
a chemical reaction that occurs spontaneously
when is deltaG 0
at chemical equilibrium
standard free energy skin
gain or loss of free energy as one mole of reactant is converted to one mole of product under “standard conditions”
used to predict the outcome of a reaction
coupled reactions
coupling energetically unfavourable reactions with energetically favourable ones makes life possible
exergonic vs. endergonic reactions
exergonic: reaction with negative change in free energy
endergonic: reaction with positive change in free energy
exergonic reactions
releases energy into its surroundings, SPONTANEOUS
energetically favourable
lower free energy level (more stable)
release free energy in bonds
endergonic reactions
require energy, NON-SPONTANEOUS
energetically unfavourable reactions
higher free energy level than substrate
can store energy in molecules
activated carriers
store energy as a readily TRANSFERABLE CHEMICAL GROUP or as READILY TRANSFERABLE ELECTRONS
important activated carriers
ATP, NADH, NADPH
(t/f) a spontaneous reaction is not necessarily an instantaneous reaction
F
highly favourable reactions may not occur unless there are enzymes to speed up the process
what lowers activation energy
catalysts
2 metabolic pathways
CATABOLIC, ANABOLIC
3 stages food molecules are broken down in
- in the mouth and gut
- in the cytosol
- in the mitochondria
most common chemical fuel in cells
monosaccharide glucose
what does burning of sugar in nonliving systems generate
heat
what catabolic processes harvest the energy in the chemical bonds of glucose? (3)
- glycolysis
- cellular respiration
- fermentation
glycolysis
begins glucose catabolism
10 enzyme-catalyzed reactions
glucose –> 2 pyruvate +ADP + NADH
ANAEROBIC, without CO2
what does cellular respiration include
1 pyruvate –> 3 CO2
includes pyruvate oxidation, citric acid cycle, ETC
AEROBIC
fermentation
no O2
converts pyruvate lactic acid OR ethanol into energy (but much less than cellular respiration
NADH gives up electrons in the cytosol, converted back to NAD+ to maintain glycolysis
(t/f) more reduced molecule = more energy stored in covalent bonds
T
key electron carrier in redox reactions
NADH (Nicotinamide adenine dinucleotide)
NAD+ = oxidized
NADH = reduced
how do cells harvest energy from glucose AEROBICALLY?
- glycolysis
- pyruvate oxidation
- citric acid cycle (krebs, tricarboxylic acid cycle)
- ETC/ATP synthesis
how do cells harvest energy from glucose ANAEROBICALLY?
- glycolysis
- fermentation
where does glycolysis take place
cytoplasm
3 phases of glycolysis
- ENERGY CONSUMING PHASE –> requires ATP
- CLEAVAGE
- ENERGY RELEASING PHASE –> produces ATP and NADH
where does cellular respiration take place
mitochondria
where does pyruvate oxidation take place
mitochondrial matrix
pyruvate oxidation
pyruvate is oxidized to an acetate molecule and CO2
creates 1 NADH
acetate then binds to coenzyme A to form acetyl CoA
citric acid cycle
starts with Acetyl CoA
8 reactions
acetyl group is oxidized to 2 CO2
creates 2 CO2 + 3 NADH + 1 GTP + 1 FADH2
what does the oxidation of 1 glucose give us
6 CO2
10 NADH
2 FADH2
4 ATP (2 from GTP)
what kind of process is oxidative phosphorylation
membrane-based process
2 steps of oxidative phosphorylation
- electron transport: electrons from NADH and FADH2 pass through the respiratory chain and create a proton concentration gradient
- chemiosmosis: protons diffuse back to the mitochondrial matrix and ATP is synthesized
ETC
NADH and FADH2 donate their high-energy electrons to the ETC
where does the ETC take palce
inner mitochondrial membrane
what happens as electrons pass between carriers?
free energy is released
what do electron transfers cause
movement of protons from matrix –> intermembrane space
what does proton pumping generate
steep electrochemical proton gradient across inner mitochondrial membrane
chemiosmostic mechanism
respiratory chain and ATP synthase produce ATP
what kind of motor is ATP synthase
ROTARY motor
–> top part lets in H+, bottom part rotates to expose active sire for ATP so ADP–>ATP
what energy does ATP synthase use to produce ATP
energy stored in the electrochemical proton gradient
(t/f) ATP synthase is a reversible coupling device
T
what does the inner mitochondrial membrane do
converts energy in NADH/FADH2 into phosphate bond of ATP molecules
–> coupled transport across membrane driven by proton gradient
what are fatty acids converted into in the mitochondrial matrix
fatty acid oxidation –> fatty acids are broken down into acetyl coA molecules –> enter citric acid cycle
allosteric regulation of glycolysis and citric acid cycle
- changing AMT of active enzyme by regulating its expression
- changing ENZYME ACTIVITY by covalent modifications
- substrate availability
- feedback regulation by building regulatory molecules (METABOLITES)
controls them at early steps –> increases efficiency and prevents excessive build-up of intermediates
how do animals store glucose
in the form of glycogen –> provides energy in times of need
where do light reactions take place
thylakoid membrane
2 pathways in photosynthesis
LIGHT reactions, CARBON-FIXATION reactions (light-independent)
where do carbon-fixation reactions take place
stroma
light reactions
convert light energy –> chemical energy (AYP, NADPH)
carbon-fixation reactions
ATP, NADPH CO2 –> carbs
pigments
molecules that absorb light in the visible spectrum
–> certain wavelengths are absorbed –> remaining are scattered/transmitted and make the pigment appear coloured
chlorophyll a, chlorophyll b, beta-carotene
–> most common in plants
photons
particles of light/packets of energy
light
form of electromagnetic radiation
propagates in waves, but has particle-like behaviours
electromagnetic radiation proportion to wavelength
amt of energy in radiation in INVERSLY proportional to wavelength
shorter wavelength = greater energy
(t/f) receptive molecules in plants absorb any wavelength of light
F
can only absorb specific wavelengths of light
what happens when a molecule acquires the energy of a photon?
raised from ground state to an excited state with higher energy
what do chlorophylls absorb
blue and red wavelenghts
chlorophyll structure
consists of a complex ring structure and a hydrocarbon tail
–> tail anchors chlorophyll in hydrophobic region of a membrane in thylakoid
chlorophyll a vs b
a has CH3 group, b has CHO group
photosystems
complex of proteins and pigments
where is the photosystem
thylakoid membrane
2 parts of a photosystem
antenna system, reaction center
pigments in antenna system absorb light energy –> transfer to chlorophyll a in REACTION CENTER
–> electrons from chlorophyll in reaction center transferred to ELECTRON ACCEPTOR
where are electrons transported through (photosynthesis)
thylakoid membrane
how do a pair of photosystems generate ATP and NADPH
- water molecules split to provide electrons for chlorophyll in reaction center of photosystem II
- protons are transferred from stroma –> interior of thylakoids during electron transport
–> movement of electrons powers production of ATP and NADPH
how is NADPH made from NADP+
through photosynthesis in the thylakoid membrane
electrons energy is boosted in photosystem I and transferred to NADP+
carbon fixation
uses ATP and NADPH to convert CO2 –> sugar
attaches CO2 to ribulose 1,5 - diphosphate
forms GLYCERALDEHYDE-3-PHOSPHATE
what do you need to form 1 glyceraldehyde-3-phosphate (G3P)
3 CO2, 9ATP, 6NADPH
what happens to G3P after its formed
some enters glycolysis and is converted to pyruvate
some enters glucohenesis to form glucose
what stimulates the calvin cycle
light-induced pH changes in the stroma activate calvin cycle enzymes
–> light induced electron transport reduces disulfide bridges in 4 of the calvin cycle enzymes –> activates them
(t/f) chloroplast’s inner membrane is impermeable to ATP and NADPH
T
–> they are used inside chloroplasts for the carbon-fixation cycle
–> resulting sugars are stored in the chloroplasts or exported to the rest of the cell
(t/f) mitochondrial membranes are impermeable to ATP
F
–> they are permeable
lyase
dissociates molecules, breaks covalent bonds without using water, oxidation, or reduction
ligase
joins 2 molecules together, forming covalent bonds
isomerase
rearranges bonds of a molecule
–> forms reactant or an isomer
transferase
transfers functional group from one molecules to another
hydrolase
uses water to cleave molecule, breaks covalent bonds with water
oxidoreductase
transfers electrons from one molecules to another, alters oxidation state of reactants
signal transduction
the conversion of one type of signal to another
–> receptors convert extracellular signal to intracellular signaling molecules
3 phases of cell signaling
RECEPTION, TRANSDUCTION, RESPONSE
endocrine signals
LONG RANGE
called hormones
remote signals –> target distant cells, transported by blood
what secretes endocrine signals
endocrine GLANDS (pineal, pituitary, parthyroid, thyroid, adrenal, pancreas, ovary, testis)
adrenaline
ADRENAL GLAND
derivative of acid tyrosine
increases blood pressure, heart rate, metabolism
cortisol
ADRENAL GLAND
steroid, derivative of cholesterol
affects metabolism of proteins, carbs, lipids
estradiol
OVARY
steroid, derivative of cholesterol
induces, maintains secondary female characteristics
insulin
BETA CELLS OF PANCREAS
protein
stimulates glucose uptake, protein synthesis, lipid synthesis
testosterone
TESTIS
steroid, derivative of cholesterol
induces, maintains secondary male sexual characteristics
thyroid hormone (thyroxine)
THYROID GLAND
derivative of amino acid tyrosine
stimulates metabolism in many cell types
paracrine signals
SHORT RANGE
act locally
synaptic signals
SHORT RANGE
act locally
contact-dependent
SHORT RANGE
act locally
types of signals
endocrine, paracrine, synaptic, contact-dependent
(t/f) each cell responds to an unlimited set of extracellular signals
F
cells have different SETS of receptors and SIGNAL TRANSDUCTION pathways that vary
(t/f) the same signal molecules can induce different responses in different target cells
T
signal interpretation depends on receptor, intracellular effector proteins, and other signals received by cell
what can chemical signals intruct cells to do
intructs cells to survive, grow, divide, or differentiate
fast cell responses to signals
change in cell movement, change in cell shape, change in metabolism, secretion
slow cell responses to signals
cell differentiation, cell dividion, cell growth
are cell responses involving gene expression fast or slow?
SLOW
what do signal molecules bind to (2)
membrane or intracellular receptors
–> MOST molecules are large and hydrophilic –> bind to CELL-SURFACE receptors
–> SOME molecules are small and hydrophobic –> cross membrane and biind to INTRACELLULAR receptors
where are intracellular receptors
in the cytosol or nucleus
where do steroid hormones bind to
INTRACELLULAR receptors
how does NO regulate enzyme activity
NO diffuses across the membrane and directly regulates the activity of an intracellular enzyme (guanylyl cyclase)
what does NO trigger
smooth muscle relaxation in blood-vessel wall
cell-surface receptors
bind the signal and create new intracellular signals
–> each intracellular signaling molecule activates or generates the next signaling molecules (proteins or small messenger molecules)
effector proteins
directly affect the behaviour of target cell
extracellular signal is _____ inside the cell
AMPLIFIED
(t/f) different extracellular signals are integrated
T
–> incoming signal is distributed to effector proteins
–> cross talk occurs between different signaling molecules
general flow of information during cell signaling (4)
- receptor-ligand binding
- signal transduction via second messengeres
- cellular responses
- changes in gene expression
different ways in which signals can be integrated
- 1 receptor activates miltiple pathways
- different receptors activate the same pathway
- different receptors activate different pathways –> 1 pathway affects the other
feedback regulations with extracellular signals
feedback regulations inside the cell adjust cellular responses to an extracellular signal (positive or negative)
molecular switches
some intracellular signaling proteins act as molecular switches
–> fluctuate between inactive and active state
activated molecular switches
stimulate/suppress other proteins in the signaling pathway
what are molecular switches activated by
some are activated by phosphorylation
some by G3P binding
molecular switched activated by phosphorylation
activated through phosphorylation by protein KINASES (signal in, ATP –> ADP)
inactivated by dephosphorylation by protein PHOSPHATASES (signal out)
SERINE/THREONINE KINASES and TYROSINE KINASES are 2 main types of protein kinases in intracellular signaling pathways
molecular switches activated by GTP binding
GTP binding proteins
activated by GTP binding (signal in)
–> GDP out, GTP in
deactivated by GTP hydrolysis (signal out)
–> phosphate out, GTP–>GDP
3 main classes of cell-surface receptors
- ion-channel-coupled receptors
- G-protein-coupled receptors
- enzyme-coupled receptors
ion-channel-coupled-receptors
responsible for muscle contraction
involves acetylcholin and acetylcholinesterase
g-protein-coupled receptors (GPCRs)
MOLECULE SWITCH
largest family of receptors
signals: odorants, light, ions, neurotransmitters, peptides, lipids, amino acids
1/3 drugs work via GPCRs
–>signaling molecules binds to G protein couples receptor –> G protein alpha subunit exchanges GTP –> GDP
–> alpha subunit dissociates from beta and gamma subunits, triggered response
–> GTP hydrolyzed to GDP (switch off)
what does stimulation of GPCRs activate
G-protein subunits (20 different types)
–> each type is activated by a set of receptors and activate a set of target proteins
G proteins and ion channels
some G proteins directly regulate ion channels
–> acetylcholine signal is transduced to K+ channel opening in pacemaker cells and slows down heartbeat
G proteins and enzymes
many G proteins activate membrane-bound enzymes
2 most frequent target enzymes:
- ADENYLYL CYCLASE: produces a second messenger cyclic AMP (cAMP)
- PHOSPHOLIPASE C: prouces second messengers inositol triphosphate and diacylglycerol
–> inositol triphosphate promotes accumulation of another second messenger, cytosolic Ca2+
2 principal signal transduction pathways that GPCRs activate
cAMP signaling pathway, PHOSPHATIDYLINOSITOL signaling pathway
cAMP signaling pathway
adenylyl cyclase (enzyme) generates cAMP from ATP
degraded by cAMP phosphodiesterase
caffeine blocks cAMP phosphodiesterase
ATP –> cAMP –> AMP
cAMP signaling in skeletal muscle cell
cAMP can activate a metabolic enzyme like adrenaline in skeletal muscle cell
–> can activate gene transcription
–> effect varies with type of target cell
cAMP signaling in ofactory receptors
- olfactory cilia have receptors that bind specific odorant molecules
- action potentials generated by odorant binding are transmitted to glomeruli in olfactory bulb
- neurons in a glomerulus receive input only from receptor cells expressing the same receptor gene
phosphatidylinositol signaling pathway
triggers rise in intracellular Ca2+
leads to saliva secretion
calcium binding
changes shape of CA2+ responsive proteins (calmodulin protein)
taste perception
GPCRs and phosphatidylinositol signaling are involved in taste perception
5 tastes: sweet. salty, sour, bitter, umami
–> sweet, umami, bitter detected by GPCRs
GPCRs and light detection
GPCRs are responsible for light detection in rod cells in retina
- absence of light: Na+ channels kept open by cGMP and create depolarizing dark current
- phodopsin obsorbs light energy
- activates G protein (transucin) that activates PDE
- activated PDE hydrolyzes cGMP, causes Na+ channels to close
–> cell hyperpokarizes
–> cGMP –> GMP, GDP –> GTP
light-induced signaling cascade in rod photoreceptor cells greatly amplifies the light signal
receptor tyrosine kinases (RTKs)
signals binding RTKs are growth factors and hormones
include EGFR, PDGF, FGFR and i insulin receptors
activate multiple intracellular signaling pathways
2 signaling pathways activated by RTKs
Ras/MAPK signaling, PI3K/AKT signaling
interaction domain
docked intracellular signaling proteins recognize specific phosphorylated tyrosines on receptor tails by interaction domain
activated RTKs
unactivated RTK activated bt signal molecule in form of a dimer
recruit a complex of intracellular signaling proteins
–> activation of downstream intracellular signaling pathways
what do RTKs activate
most activate the monomeric GTPase Ras
Ras
G protein and molecular switch
Ras function in normal cell
receptor activation leads to activation of G protein Ras
–> GDP out, GTP in
after stimulation of cell division, returns to inactive
–> GTP hydrolilzes to GDP
abnormal Ras function in a cancer cell
receptor activation leads to activation of Ras
–> STAYS ACTIVE –> constant stimulation of cell division
RTK activate PI 3-Kinase
RTks activate PI 3-Kinase (phosphatidylinositol 3-kinase) to produce lipid docking sites in plasms membrane
activated AKT
promotes cell survival by inhibition of apoptosis
AKT
stimulated cells to grow in size by activating serine/threonine kinase Tor
insulin and RTK
insulin binds an RTK, activates both MAPK and PI3K signaling pathways
notch receptor
transcription regulator
involved in contact-dependent communication
cytoskeleton
network of protein filaments that extend through the cytoplasm
highly dynamic, continuously reorganized
important for cell shape, interior organization, movement
cytoskeleton roles
- supports cell
- maintains shape
- holds cell organelles in position
- moves organelles around in the cell
- involved with movements of the cytoplasm (cytoplasmic streaming)
- interacts with extracellular structures –> helps anchor cell in place
3 types of protein filaments that make up cytoskeleton
MICROFILAMENT (actin), INTERMEDIATE FILAMENT, MICROTUBULE
microfilaments
polymers of actin proteins
actin
globular protein
–> bind each other to form helical polymers
–> 2 helical polymers = microfilament
–> REVERSIBLE
has distinct + and - ends
–> permit monomers to interact with each other to form double helix chains
microfilaments
diameter around 7nm
long, thin and flexible threads
POLARIZED structures
microfilament polymerization and depolymerization
microfilaments can disappear from cells by breaking down into monomers of actin
–> special actin-binding proteins mediate process
actin-binding proteins
control organization of actin filaments
microfilaments exist as:
- single filaments
- linear bundles
- 2D networks
- 3D gels
where are microfilaments highly concentrated
cortex
microfilament roles (2)
- determine and stabilize shape
- help entire cell or parts of cell move
microfilaments in cell shape
non-muscle cells: actin filaments are associated with localized changes in cell shape
also involved in cell movement, cytoplasmic movement, cell division, muscle contraction (actin filaments slide against myosin proteins)
microfilaments in shape
cells that line intestine –> folded into tiny protections (microvilli)
–> SUPPORTED BY MICROFILAMENTS
–> interact with intermediate filaments at base of each microvillus
myosin motor proteins
actin-dependent movements usually require actin’s association with myosin motor proteins
itnermediate filaments
tough, ropelike, flexible, good tensile strength
diameter 10nm
made of FIBROUS INTERMEDIATE FILAMENT PROTEINS
permanent structures
4 classes of intermediate filaments
CYTOPLASMIC
–> keratin filaments (in epithelial cells)
–> vimentin and vimentin-related filaments (in connective-tissue cells, muscle cells, glial cells)
–> neurofilaments (in nerve cells)
NUCLEAR
–> nuclear lamins (in all animal cells)
intermediate filament roles
- create strong durable network in cytoplasm
- support the nuclear envelope (nuclear lamina)
- gives mechanical strength (filaments extend across cytoplasm from one cell-cell function to another –> distributes mechanical stress in epithelial tissue)
nuclear lamina
just beneath the inner nuclear membrane
intermediate filaments form a meshwork
supports, strengthens nuclear envelope
microtubules
made of tubulin dimers
–> each dimer consists of 2 subunits (alpha tubulin and beta tubulin)
–> each microtubule consists of 13 protofilaments of tubulin
long, hollow, straight cylinders
25nm in diameter
more rigid than the other 2
POLAR
–> + and - end grow at their + end
what happens when microtubules are stretched
they rupture
where do microtubules grow out of
centrosomes
–> each microtubule grows and shrinks independently of its neighbors
array of microtubules anchored in a centrosome is constantly changing
–> new tubules grow, old tubules shrink
dynamic instability in growing microtubules
dynamic instability: switching back and firth between polymerization and depolymerization
leads to rapid remodeling of microtubule organization
important for microtubule function
dynamic instability
driven by GTP hydrolysis
–> tubulin dimers hydrolyze their bound GTP
GTP-tubulin attaches to GTP cap(plus end) –> rapid growth –> loss of GTP cap –> GDP tubulin is released –> catastrophic shrinkage –> GTP cap restablished
microtubule binding proteins
stabilize microtubules
microtubule will persist only if both its ends are protected from depolymerization
–> - end protected by centrosome
–> + ends are initially free but stabilized by binding to specific proteins
microtubule roles (2)
- form rigid internal skeleton for some cells
- act as framework along which motor proteins can move structures within the cell
microtubule tracks
microtubules provide tracks for movement of cytoplasmic material
–> motor proteins use them to transport vesicles, macromolecules, and organelles
types of motor proteins that use microtubules
KINESINS (towards - end), DYNEINS (towards + end)
microtubules in a dividing cell
microtubules distribute chromosomes in a dividing cell
microtubules in positioning
help position organelles in a eukaryotic cell
–> kinesin motor protein pulls endoplasmic reticulum outward along microtubules
–> dynein motor proteins pull golgi apparatus inward along the microtubules to its position near centrosome
microtubules in cilia and flagella movement
microtubules allow cilia/flagella movements
cilia/flagella –> movable appendages on eukaryotic cells
–> cilia move fluid across cell surface
–> epithelial cells lining human respiratory tract has huge numbers of beating cilia
–>flagella: propel sperm cells, much longer than cilia
cilia and flagella (microtubules)
microtubules are arranged in different patterns
eukaryotic cilia and flagella –> 9 doublet microtubules are arranged in a ring around a pair of single microtubules (“9+2” array)
what causes the movement of a cilium/flagellum
produced by ciliary dynein movement between 2 microtubules
nucleotides
building blocks of nucleic acids
4 nucleotides = 1 nucleic acid
composed of a base, sugar, and a phosphate group
growth of nucleic acid
5’ –> 3’ direction
nucleotides link to each other to make nucleic acids
how are DNA strands held together
held together with hydrogen bonds
–> purine and pyrimidines bases form H bonds (complementary base pairing)
van der waals forces occur between adjacent bases on the same strand
(t/f) 2 strands of DNA are parallel
F
–> 2 strands run antiparallel, opposite directions
each sugar-phosphate backbone has a free 5’ phosphate and a free 3’ hydroxyl
–> each end has one of each
what does the coiling of DNA strands create
coiling of DNA strands creates 2 grooves
–> outer edges of nitrogenous bases are exposed in major and minor grooves
–> base pairs in DNA can interact with other molecules
3 models for DNA replication
- semiconservative
- conservative
- dispersive replication
what kind of replication is DNA replication
semiconservative
semiconservative replication
produce daughter molecules with both an original and newly synthesized DNA strand
conservative replication
produce daughter molecule with either 2 original/2 newly synthesized DNA strands
dispersive replication
produce daughter molecules with a mix of both original and newly synthesized DNA in each strand
how does DNA synthesis proceed
replication proceeds by complementary base-pairing (C-G, A-T)
synthesis occurs in 5’ - 3’ direction
4 nucleotides (deoxyribonucleoside triphosphates)
dATP, dTTP, dCTP, dGTP (dNTPs)
ori
regions where DNA replication starts
DNA replication with a single ori
- ori sequence binds the pre-replication complex
- replication bubble consists of 2 replication forks that move away from one another during elongation
multiple ori
replication forks move away from each other during elongation
replication forks
2 Y-shaped junctions that replication origin creates when DNA unwinds
RNA primers
DNA synthesis begins with the synthesis of short sequences of RNA –> RNA primers
synthesized by primase (RNA polymerase)
DNA polymerase
elongates RNA primer
DNA helicase
uses energy from ATP hydrolysis to unwind/seperate strands
single-stranded binding proteins
bind to the unwound strands to keep them from reassociating into a double helix
sliding DNA clamp
increases efficiency of DNA polymerization
keeps DNA polymerase stably bound to DNA to many nucleotides can be added for each binding event
leading strand vs. lagging strand
leading strand is synthesized continuously
lagging strand is synthesized as fragments (Okazaki fragments)
DNA ligase
joins Okazaki fragments together
telomerase
replicates the ends of eukaryotic chromosomes
–>uses an RNA template (made by primer) to extend telomere
–> binds to template strand –> adds additional telomere repeats to template strand –>completion of lagging strand by DNA polymerase
2 types of cell division
MITOSIS, MEIOSIS
Xeroderma pigmentosum
extremely sensitive to sunlight
develop skin cancers after exposure to UV in sunlight
1/250K
mutations
permanent changes in DNA squence
–> most are harmful
could be in somatic cells or in germline
chromosomal mutations
mutations can alter large sequences of DNA
–> 4 types: deletions, duplications, inversions, translocations
point mutations
mutations affecting a single, or few DNA base pairs
difference effects of mutations on protein activity
- normal allele
- no effect
- loss of function
- gain of function
- wild type
- silent mutation
- missense mutation
- nonsense mutation
- loss of stop mutation
- frame shift mutation
2 most frequent chemical reactions that create serious DNA damage
DEPURINATION: leads to base pair deletion
DEAMINATION: leads to transition mutations (GC –> AT)
chemical mutagens
mutations can be induced by chemical reagents
ex. alkylating agents, base analogs, acridines, deaminating agens, hydroxylating agents
alkylating agents
induce transitions, transversions, frameshifts, chromosome aberrations
acridine dyes
induce frameshift mutations
nitrous acid
induces transition
mutations and radiation
mutations can be induced by radiation
–> UV radiation induces thymine dimers
–> x-rays and gamma-rays cause single/double stranded breaks in DNA
DNA proofreading
DNA polymerase has a proofreading activity
–> removes mispaired base
mismatch repair mechanism
repairs mispaired bases
–> restores original sequence –> decreases error rate even further
base excision repair mechanism
removes modified bases
nucleotide excision repair mechanism
repair thymine dimers
nonhomologous end joining
double-strand DNA breaks can be repaired by nonhomologous end joining
–> nuclease processes DNA end –> DNA ligase joins ends
homologous recombination
double-strand DNA breaks can be repaired
special nuclease processes broken ends –> double-strand break accurately repaired using undamaged DNA as template
APC (anaphase promoting complex)
loss of normal tumor suppressor gene APC –> small growth forms on colon wall –> benign, precancerous tumor grows
–> activation of oncogene RAS –> class II adenome (benign) grows –> loss of tumor suppressor gene DCC –> class III adenoma grows
–> loss of tumor suppressor gene P53 –> carcinoma (malignant tumor) develops
sickle-cell anemia
disease caused by a single nucleotide change
transcription
RNA synthesis of an RNA strand complementary to one strand of DNA
translation
protein synthesis
messenger RNA (mRNA)
code for proteins
ribosomal RNAs(rRNAs)
form core of ribosome’s structure and catalyze protein synthesis
microRNAs(miRNAs)
regulate gene expression
transfer RNAs (tRNAs)
serve as adaptors between mRNA and amino acids during protein synthesis
other noncoding RNAs
used in RNA splicing, gene regulation, telomere maintenance, and many other processes
RNA polymerase enzyme
responsible for transcription
1 RNA polymerase in prokaryotes, 5 in eukaryotes
5 kinds of RNA polymerase and their products
RNA polymerase I(nucleolus): ribosomal RNAs, excluding 55rRNA
II (nucleus): nuclear pre-mRNAs
III (nucleus): tRNAs, 55 rRNA, and other small nuclear RNAs
IV (nucleus(plant)): small interfering RNAs(siRNAs)
V (nucleus(plant)): some siRNAs plus noncoding [antisense] transcripts of siRNA target genes
3 steps of transcription
- initiation: RNA polymerase binds to the promoter and starts to unqind the DNA strands
- elongation: RNA polymerase moves along the DNA template strant from 3’ - 5’ and produces the RNA transcript by adding nucleotides complementary to the DNA template
- termination: when RNA polymerase reaches termination site, RNA transcript and polymerase are released from template
promotor
signal to start transcription in a DNA sequence
–> guides RNA polymerase
DNA sequences that indicate 2 things:
- transcription initiation site
- template DNA strand
terminator
signal to stop transcription in a DNA sequence
general transcription factors
recruit RNA polymerase to the promoter in eukaryotes
what do specific transcription factors do
increase or decrease gene transcription efficiency
what is the transcription initiation site indicated by
+1
5’ –> 3’ = downstream (+2, +3, +4, +5)
3’ –> 5’ = upstream (-1, -2, -3, -4)
NO ZERO
pre mRNA processing
5’ capping
3’ polyadenylation
splicing
eukaryotic mRNA is processed before translation
5’ capping`
a “cap” of modified GTP is added
3’ polyadenylation
a poly “A” tail is added
introns
eukaryotic protein-coding genes are interrupted by noncoding sequences (INTRONS)
exons
coding regions
splicing
process of intron removal from pre-mRNA
–> various mRNAs and proteins can be produced by alternative premRNA splicing
- small nuclear ribonucleoprotein (snRNPs) bind to pre-mRNA near both 5’ donor and branch point
- binding of snRNPs recruits many proteins
- a cut is made between the upstream exon and the intron
- after first cut at 5’ end, intron forms a closed loop
- free 3’ OH group at end of the cut reacts with 5’ phosphate
- downstream exon is cleaved at the intron junction and spliced to the upsream exon
–> after all introns are removed, mature mRNA is exported to the cytosol for translation
(t/f) transcription and translation occur simultaneously in prokaryotes
T
where are mature eukarytotic mRNAs exported
exported from the nucleus to the cytoplasm for translation
codon
every 3 ribonucelotides (triplet code)
specifies amino acids
genetic code contains 64 codons
initiation codon and 3 stop codons
initiation: AUG
3 stop codons:
UAA, UAG, UGA
which aminoacids are encoded by single codons
tryptophan, methionine
–> almost all amino acids are specified by 2, 3, 4 different codons
exceptions to the universal genetic code
UGA (normal: termination): altered–>Trp, comes from human and yeast mitochondria
CUA (n: Leu): altered –> Thr, from yeast mitochondria
AUA(n:Ile): a –> Met, from human mitochondria
AGA (n:Arg): a –> termination, from human mitochondria
AGG (n:Arg): a –> termination, from human mitochondria
UAA(n: termination): a –> Gln, from paramecium, tetrahymena, stylonychia
UAG (n: termination): a –> Gln, from paramecium
transfer RNAs
serve as translators for protein synthesis in ribosomes
tRNAs bind amino acids, bind mRNA, and interact with ribosomes
–> at least one tRNA for each amino acid
where are unusual bases found
tRNA
(t/f) the number of tRNA molecules = codons
F
–> there are less tRNA molecules than codons
wobble pairing
enables one tRNA to recognize multiple codons
–> enables a more flexible H bonding
allows 30 different tRNA types to accommodate 61 codons
tRNA attachment
1 tRNA for 1 aminoacyl-tRNA (amino acid)
- enzyme activates amino acid –> catalyzes reaction with ATP to form phosphate ion and high energy AMP amino acid
- –> enzyme catalyzes reaction of the activated amino acid with correct tRNA
- specificity of enzyme ensures the correct amino acid and tRNA acid are together
- charged tRNA delivers appropriate amino acid to join elongating polypeptide production of translation
aminoacyl-tRNA synthases
charge tRNAs
aminoacylation/charging
addition of an amino acid to the corresponding tRNA
ribosome
workbench for translation
aminoacyl-tRNA
A site –> where the charged tRNA anticodon binds to the mRNA
peptidyl-tRNA
P site –> where the tRNA carrying the growing peptide chain resides
Exit (tRNA)
E site –> where the uncharged tRNA resides
translation initiation
prokaryotes: involves recognition of Shine Dalgarno sequence
eukaryotes:recognition of the 5’ cap
translation elongation
involves peptide bond formation
translation termination
involves encountering a stop codon
- release factor binds to complex when a stop codon enters A site
- release factor disconnects polypeptide from tRNA in P site
- remaining components seperate
stop codons
bing release factors
–> allows hydrolysis of the bond between polypeptide chain and tRNA in P side
polysome formation
increases rate of protein synthesis
polysome
(polyribosome)
assemblage of mRNA, ribosomes, and their growing polypeptides
what happens after translation
proteins are modified
–> post-translational modifications are required for a new protein to become fully functional
post-translational processing (3)
phosphorylation: added phosphate groups alter shape of protein
glycosylation: adding sugars is important for targeting and recognition
proteolysis: cleaving the polypeptide allows the fragments to fold into diff shapes
proteins reach final cellular destination
- signal peptide binds to a signal recognition particle –> halts translation –> complex binds to receptor protein in membrane of RER and translation resumes
- signal sequence is removed by an enzyme in lumen of RER
- polypeptide continues to elongate until translation terminates
- ribosome is released –> protein folds inside RER
what guides proteins to its final destination
signal sequences guide proteins to their destination
how do proteins enter the mitochondria
protein translocators
how do selected proteins enter the nucleus
some proteins enter the nucleus through nuclear pores
–> nuclear localization signal of prospective nuclear proteins are recognized by nuclear import receptors (transport receptor)
where do proteins go during their synthesis
ER (endoplasmic reticulum)
–> ER signal sequence guides a ribosome to the ER membrane
–> enter via protein translocator
–> ER signal recognition particle and its receptor direct a ribosome to the ER membrane
membrane proteins remain in the ER lipid bilayer
where do soluble proteins go
cross the ER membrane and enters the lumen
where is Na+ most abundant
OUTSIDE the cell
where is K+ most abundant
INSIDE the cell
voltage difference
small excesses of positive or negative charge on 2 sides of the plasma membrane
membrane potential
the vooltage difference across the membrane
transporters
transfer small organic molecules/inorganic ions
channels
form tiny hydrophilic pores, allow substances to pass by diffusion
passive vs active transport
passive: downhill movement, requries no energy
active: uphill movement, requires energy
3 types of proteins for active transport:
- uniporter: transports 1 substance in 1 direction
- symporter: transports 2 diff substances in the same direction
- antiporter: transports 2 diff substances in opposite directions
3 types of endocytosis
receptor-mediated endocytosis: specific uptake of large molecules
pinocytosis: nonspecific uptake of extracellular fluid
phagocytosis: nonspecific uptake of large undissolved particles
exocytosis
release of large/small molecules
–> vesicle fusion with cell membrane
–> secretory vesicles fuse with plasma membrane and release its content into extracellular space
ATP-driven Na+ transporters
use energy supplied by ATP to expel Na+ and bring in K+
–> high Na+ conc outside cell represents a huge nstore of energy
primary active transport: Na+–K+ pump moves Na+ to create a gradient of Na+
secondary AT: Na+, moving with concentration gradient drives transport of glucose against its concentration gradient
ATP-driven Ca2+ transports
keep cystolic Ca2+ concentration low
–> binds to a variety of proteins in the cell and alters their activities
–> influx of Ca2+ into cell = intracellular signal
–> triggers cell processes like muscle contraction, fertilization, nerve cell communication
K+ leak channels
responsible for resting membrane potential
–> plasms membrane mostly permeable to K+ moving out of cell
leak channels
always open
voltage-gates ion channels
controlled by changes in coltage across membrane
ligand-gates ion channels
controlled by binding of molecule
polar substance more concentrated on outside –> binding of stimulus molecule –> pore opens –> polar substance diffuses
mechanically gated ion channels
controlled by a physical stimuli
ex. light, sound waves, pressure
action potential
rapid change in membrane potential
–> travels along axon, jump along myelinated axons
depolarization
neuron stimulation shifts membrane potential from -70mV to a less negative value
–> causes voltage gated Na+ channels to open
synapses
neurons connect to their target cels
–> separated by pre and postsynaptic cells and synaptic cleft
what kind of channels are neurotransmitter receptors
ligand-gated ion channels
what happens at a synapse
chemical signal is converted into an electrical signal
what ion channel is responsible for muscle contraction
ligand-gated ion channels
–>acetylcholine is the ligand responsible for Na+ ion channel activity in neuromuscular junction
phospholipid
have hydrophilic head and 2 hydrophobic tails
what links the hydrophilic head and hydrophobic tail
glycerol
what is the most common phospholipid in biological membranes
phosphatidylcholine
saturated vs unsaturated fats
hydrocarbon tail WITH double bond = UNSATURATED
–> unsaturated is MORE FLUID, bilayers with shorter fatty acid chains are more fluid
amphipathic
molecules with both hydrophilic and hydrophobic parts
cholesterol
controls membrane fluidity
2 kinds of membrane proteins
integral: extend through bilayer
–> can be removed only by disrupting the bilayer with detergents
–> usually crosses the bilayer as an alpha helix
peripheral: interact with integral membrane proteins/phospholipids
transmembrane protein
integral protein that extends all the way through the bilayer
–> hydrophilic R groups in exposed parts of protein interact with aqueous environments
–> hydrophobic R groups interact with hydrophobic core of membrane
which proteins can move laterally in the lipid bilayer
plasma membranes can move laterally in the lipid bilayer
how can cells restrict the movement of its membrane proteins
- bind meshwork of proteins inside cell (cell cortex)
- bind extracellular matric molecules
- bind proteins on surface of another cell
- be restricted by diffusion barriers
membrane domains
functionally specialized regions that can confine proteins to localized areas on the membrane
cell cortex
framework of proteins that support the cell membrane
carbohydrates on the cell surface
all the carbs on the glycoproteins, proteoglycans, and glycolipids is located on the outside of the membrane
–> coating is called the carbohydrate later/glycocalyx
–> function in cell recognition and adhesion
desmosomal adhesion
cell structure specialized for cell-cell adhesion
localized spot-like adhesions
randomly arranged on the lateral sides of the cell
tissues faced with mechanical stress
tight junctions
protein complex between 2 cells that create a seal to prevent any leakage of content through cell membranes
gap junctions
allow intracellular flow of ions and molecules between cytoplasms
bright field microscopy
light passes directly through cells
–> little contrast and details not distinguished
phase-contrast microscopy
contrast is increased by emphasizing differences in refractive index
–> enhances light and dark regions in cell
differential interference-contrast microscopy
2 beams of polarized light are used
–> looks as if cell is casting a shadow on one side
stained bright gield microscopy
stain enhances contrast, reveals details not otherwise visible
fluorescence microscopy
natural substance in cell or fluorescent dye that binds to a specific cell material is stimulated by a beam of light
confocal microscopy
fluorescent materials are used
–> adds system of focusing both stimulating and emitted light so that a single place through cell is seen
–> sharper 2D image
transmission electron microscopt (TEM)
beam of electrons is focused on the objects by magnets
–> objects appear darker if they absorb electrons
–> objects detected on fluorescent screen if electrons pass through
scanning electron microscopy (SEM)
electrons are directed to the surface of the sample where they cause other electrons to be emitted
cytoplasm
everything inside the cell except for the nucleus
cytosol
fluid cytoplasm
prokaryotic vs eukaryotic cell
prokaryotic cell has no nucleus or membrane enclosed compartments
gram positive vs gram negative bacteria
+ = thick peptidoglycan layer, no lipid membrane
- = thin peptidoglycan layer, have outer lipid membrane
nuclear pores
protein-lined channel in nuclear envelope that regulate the transportation of molecules between the nucleus and cytoplasm
endoplasmic reticulum
RER: site of protein synthesis
SER: sire of glycogen degradation, lipid/steroid synthesis, calcium ion storage
golgi apparatus
site of protein modification and osrting
add carbs to proteins
sort proteins to destination
lysosomes
site of macromolecule digestion
primary lysosomes bud from golgi apparatus
contain digestive enzymes to digest proteins, polysaccharides, nucleic acids, and lipids
interior is acidic
mitochondria
site of energy transformation
most likely ancient aerobic prokaryote engulfed by a pre-eukaryotic cell (endosymbiosis)
chloroplasts
sites of photosynthesis
chromoplasts
make/store red, yellow, and organde pigments
–> esp in flowers and fruits
leucoplasts
store starch
peroxisomes/glyoxysomes
accumulate toxic peroxides like H2O2
–> safely broken down in peroxisomes
glyoxysomes: same but in plants
vacuols
storage compartment in platns
what are plant vacuols involved in
- supports plant body
- reproduction
- digestion
- storage
where does protein synthesis take place
ribosomes
eukaryotic cell evolution
- ancient prokaryotic cell w no internal membranes
- cell membrane folds inward
- further membrane infoldings form ER –> surrounds nucleoid and forms nuclear envelope
