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BIO 311C
Chemical bonding can be classified into three primary types: covalent, ionic, and metallic bonds. Covalent bonds occur when atoms share electrons, which can be either nonpolar (equal sharing)
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NATURALLY OCCURING DOUBLE BONDS
also called unsaturated fatty acids or trans fatty acids, are a type of unsaturated fat that occur in small amounts in nature, but became widely produced industrially from vegetable fats
RESULTS IN TRIACYGLYCEROL
ALPHA
BETA
IN THE MIDDLE
IN THE TAIL
MALTOSE
SUCROSE
UNBRANCHED
BRANCHED
A CELLULOSE MOLECULE IS AN UNBRANCHED B GLUCOSE POLYMER
ABOUT 80 CELLULOSE MOLECULES ASSOCIATE TO FROM A MICROFIBIL THE MAIN ARCHTURAL UNOT OF THE PLANT CELL WALL
1-4 LINKAGE OF BETA GLUCOSE MONOMERS
IS FOUND IN THE EXOSKELETON OF THE ARTROPODS
CAN USED AS SURGICAL THREAD
STR SIMILAR TO CELLULOSE
GLUCOSE 6 PHOSPHATE
FRUCTOSE1,6 BISPHATE
GCOSAMINE, AND GALACTOSAMINE, AMINO GROUP INSTEAD OF A OH
POLYMER OF N ACETYL GLUCOSAMINE
A NUCLEOTIDE IS COMPOSED OF THRREE PARTS
A FIVE-CARBON PENTOSE SUGAR
IN RNA IT IS RIBOSE
DNA THE SUGAR IS DEOXYRIBOSE
A NITROGEN CONTAINING BASE
PURINES
ARE LARGE WITH A SIX MEMBERED RING FUSED TO A FIVE MEMBERED RING, THEY ARE ADENIN A AND GUANINE G
PYRIMIDINE
HE HAS A ONE SIX-MEMBERED RING OF CARBON AND NITROGEN ATOMS, CYTOSINE C, THYMINE, T AND URACIL U
AND ONE THREE PHOSPHATE GROUP
THE GENETIC MATERIAL THAT ORGANISM INHERIT FROM THEIR PARENTS
IS AN ORGANIC MOLECULE WITH BOTH AN AMINO GROUP AND CARBOXYL GROUP
FOUR LEVELS OF PROTEIN STRUCTURE
QUATERNARY
ASSOCIATION OF TWO OR MORE POLYPEPTIDES (SOME PROTEINS ONLY)
IS THE OVERALL PROTEIN STRUCTURE THAT RESULTS FROM THE AGGREGATION OF THESE POLYPEPTIDE SUBUNITS
EXAMPLE IS THAT OF COLLAGEN
TERTIARY
THREE DIMENSIONAL SHAPE STABILIZED BY INTERACTIONS BETWEEN SIDE CHAINS
SubtopicVERALL SHAPE OF A POLYPEPTIDE RESULTING FROM INTERACTIONS BETWEEN THE SIDE CHAINS R GROUPS OF THE VARIOUS AMINO ACIDS
HYDROPHOBIC INTERACTION, AS A POLYPEPTIDE FOLDS INTOITS FUNCTIONAL SHAPE, AMINO ACIDS WITH HYDROPHOBIC NONPOLAR SIDE CHAINS USUALLY WND UP IN THE CLUSTERS AT THE CENTER/CORE OF THE PROTEIN
COVALENT BONDS CALLED DISULFIDE BRIDGES MAY FURTHER REINFORCE THE SHAPE OF A PROTEIN, FORM WHERE TWO CYSTEINE MONOMERS, WHICH HAVE SULFHYDRL GROUPS ON THEIR SIDE CHAINS
SECONDARY
REGIONS STABILIZED BY HYDROGEN BONDS BEWTWEEN ATOMS OF THE POLYPEPTIDE BACKBONE
COILDE OR FOLDED IN PATTERNS THAT CONTRIBUTE TO THE SHAPE
RESULT OF HYDROGEN BONDS BETWEEN THE REPEATING CONSTITUENTS OF THE POLYPEPTIDE BACKBONE, THE OXYGEN
PRIMARY
LINEAR CHAIN OF AMINO ACIDS
ITS SEQUENCE OF AMINO ACIDS
ITS FOUR DIFFERENT PARTNERS
AMINO GROUP
A CARBOXYL GROUP
A HYDROGEN ATOM
VARIABLE GROUP CALLED THE R GROUP
BOND BETWEEN THEM IS CALLED A PEPTIDE BOND SO A POLYMER OF AMINO ACID IS CALLED A POLYPEPTIDE
TRANS ISOMER
the two Xs are on opposite sides
CIS ISOMER
THETWO Xs are on the same side
cyclohexane
benzene
two Butene
1-Butene
2METHYLPROPANE
BUTANE
PROPANE
ETHANE
the shape change causes the g protein to move away from the GPCR and ATP binds to the separated subunit and activates it
the activated subunit signals for the target protein to come bind to it, in this case is Adenylyl cyclase
the AC turns ATP to cAMP which kicks off the phosphorylation cascade
kinases add phosphates to kinases, thereby activating and deactivating kinases
this phosphorylation cascade amplifies the Original signal that was sent
once the cascade reaches a certain point it will do what the signal sent for
in this case of the epinephrine transduction pathway, the kinase will reach a certain molecule that when activated will begin to cleave off glucose from glycogen
the glucose will either stay in the cell and serve as fuel for that cell or be exported to the cytoplasm to be taken
THE SUBSTANCE BEING DISSOLVED
DISSOLVING AGENT
HYDROGEN BONDS THAT HOLD THE SUBSTANCES TOGETHER, IT CONTRIBUTES TO THE TRANSPORT OF NUTRIENTS AND WATER AGAINST GRAVITY IN PLANTS
THE CLINGING OF ONE SUBSTANCE TO ANOTHER, ADHESION OF WATER BY HYDROGEN BONDS TOO THE MOLECULES OF CELL WALLS HELP COUNTER THE DOWNWARD PULL OF GRAVITY
ANION IS NEGATIVELY
CATION IS POSITIVELY
EXAMPLE
Na and Cl
Na+ and Cl-
EXAMPLES
WATER H20
AMMONIA NH3
cell has less concentrated inside than the surrounding solution
lysed
plants
cell and solution is at equilibrium
Turgid
flaccid
cell is more concentrated than surrounding solution
Plants
plasmolyzed
Animals
Flaccid
uncontrolled cell growth
the cell is mutated in some way which causes this growth
loss of density dependent and anchorage dependent growth inhibition
able to invade and disrupt nearby and distant tissue
protoncogenes (growth factors) that are mutated to oncogenes are cancer causing m
Only accounts for about 10% of reproductive cycle
Prophase- nucleoli disappear
Metaphase-chromosomes align along plate
Anaphase- telomeres attach to the chromosomes
Telophase- chromosomes move to opposite sides of cell and duplicated organelles do too
Cytokinesis- the chromosomes and organelles are enclosed in a new cell membrane and the cell divides.
2 diploid daughter cells are produced
both cycles go through this about 90% of cell cycle is spent here
G1
organelles begin to duplicate
S
synthesis- chromosomes condense from chromatids and form sister chromatids these are connected at the centromere
G2
organelles finish duplication
must pass CDK checkpoint
begins reproductive phase
first round of division crossing over occurs homologs are separated
homologous chromosomes are separated, sister chromatids are still parired up to this point
prophase II
Metaphase II
ANAphase II sister chromatids are separated
Telophase II
Cytokinesis II
these are the same steps as mitosis but there is crossing over and the 4 resulting daughter cells are haploids instead of diploids
only has one half enough DNA to make a person
aka proton pump
used in chemiosmosis
helps generate ATP by creating chemical gradient
used in photosynthesis and glycolysis
sucrose/ proton cotransporter
Na/ K pump
Salty banana
resting potential -70 mV
stimulus comes and stimulates the membrane and it reaches threshhold -55mV
Depolarization sodium gates open and sodium floods the cell
Action potential +40 mV ligand gated sodium channels close promptly upon reaching +40mV
Repolarization potassium channels open and K floods out of the cell, making the cell more negative
Undershoot/ refractory period the cell potential reaches a very negative point and the K pumps lag to close
sodium potassium pump activates it pumps 2 Na+ out and 3 K+ in
cell membrane returns to resting state to
Operons- controlled with multiple start/ stop codons
Examples
Lac
is active in the presence of lactose
Lac absent, repressor bound to active site
Lac present, repressor bound to lac and genes are expressed
CAP and cAMP must be present for operon to function
if glucose is present the lac I repressor will bind to CAP thereby inhibiting gene Y,Z,A production
Trp
is active in absence or tryptophan
repressor is made inactive
trp is synthesized when there is none available
trp present- binds to inactive repressor, making it active and inhibiting production of trp
Negative regulation
the repression binds to the operator to keep the enhancers from binding and activating the sequence
no repressor- translation occurs
Positive regulation
Activator binds to the operator and is turned on
no activator- no translation
Not all genes expressed in every cell, compacted
Euchromatin
Less compacted genes expressed
Chromatin
Gets modified to DNA (gene) is available for transcription
Transcription, gets spliced to mRNA
Cap and tail added, exported to cytoplasm
Gets translated turned into polypeptide
is processed and turned into a functioning protein
has cellular function
Heterochormatin
Genes tightly packed, do not get expressed (this silences genes)
Control elements
Proximal (general)
Basal level expression
Very close to promoter, always "on"
can never turn expression "off", just basal level (which is basically off)
Distal (specific)
High level expression
Far from promoter May be upstream or downstream may even be in intron ex: enhancer., amount of activator protein is important for functionality
Activators bind to enhancer sequence
This signals for DNA bending protein to come in
Group of mediator proteins and general TF comes in
RNA pol II comes in and from transcription complex, begins transcription
Histone core (H2A,H2B, H3, H4)
Nucleosome
Tight helical fiber
Looped domains
Metaphase chromosome
active site
feedback inhibition
when the product of the transduction pathway is in abundance and no longer needs to be produced
the product will bind to the active site
this inhibits further production of the end product
where the enzyme binds to on the substrate is a 3D cleft/ crevice formed by folding of protein and amino acids
induced fit
does a "dance" with the enzyme to induce a better fit
lock and key
enzyme has very specific fit to the active site
CDK cyclin Functions in cell cycle regulation
Beta Galactosidase breaks down lactose to glucose and galactose
Kinases adds a phosphate group
phosphodiesterase converts cAMP to AMP
phosphatase removes phosphate groups
Adenylyl cyclase converts ATP to cAMP
p53 functions in cell cycle regulation tumor supressor gene
Ras mutation in this gene leads to formation of oncogene
Cyclins structurally and functionally related proteins
aquaporin integral membrane protein channel for water to more rapidly diffuse across the membrane
Hexokinase glucose to G6P
Phosphofructokinase F6P to F1,6Bis
ATP synthase uses chemiosmosis to generate ATP
RuBisCo combines RuBP and CO2 to make intermediate 6 carbon molecule
BRCA1, BRCA2 tumor supressor gene, helps repair DNA and kills cells that cannot be repaired
Enzymes known to be allosterically regulated are constructed from two or more subunits, each composed of a polypeptide chain with its own active site. Oscillates between two different shapes, one active and inactive
Allosteric regulation: any case in which a protein's function at one site is affected by the binding of a regulatory molecule to a separate site.
Feedback Inhibition
A metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the pathway
Cooperativity
Considered allosteric regulation due to the substrates binding affecting the catalysis in another active site
Amplifies the response of enzyme to substrates: the substrate primes an enzyme to act on additional substrates more readily
Another type of allosteric activation, substrate binds to one active site in a multisubunit enzyme and triggers a shape change in all the subunits, increasing catalytic activity at other active sites
Inhibitor
Stabilizes the inactive form of the enzyme
ATP binds to several catabolic enzymes allosterically, lowering their affinity for substrate and inhibiting their activity. IF ATP exceeds demand, then catabolism slows down as ATP molecules accumulate and bind to the same enzymes to inhibit activity.
Acivator
Stabilizes the shape that has functional active sites
ADP functions as an activator. If ATP production lags behind its use, ADP accumulates and activates the enzymes that speed up catabolism, producing more ATP
Non-competitive inhibitors: do not directly compete with the substrate to bind to the enzyme at the active site. They impede enzymatic reactions by binding to another part of the enzyme, causing enzyme to change shape and the active site to become less effective at catalyzing the reaction
Competitive inhibitor: reduce productivity of enzymes by blocking substrates from entering active sites.
Can be overcome by oversaturation of substrates
Humans and bacteria have enzymes that each have a specific optimal temperature and pH.
Rate of reactions increase with temperature because substrates collide more with active sites.
However, after a certain point, a super high temp will drop the speed sharply of the reaction. It disrupts the bonding and other weak interactions tht stabilize the active shpe of the enzyme
The enzyme has a region called the active sit and will bind to its substrate here, forming the enzyme-substrate complex
The more substrate molecules, the more frequently they access the active sites of an enzyme molecule
Substrate is held in active site by weak interactions like hydrogen and ionic bonds
The active site lowers activation energy and R groups of a few of the amino acids that make up the active site catalyze the reaction
Amino acids in active sites directly participate in chemical reactions like brief covalent bonding between substrate and the side chain of said amino acids in the enzyme.
If there are two or more reactants, the active site provides a template on which substrates can come together in the proper orientation for a reaction to happen
Enzyme can provide a microenvironment. An enzyme with amino acids with acidic R groups will provide an environment of low. acidic pH. In this case, an amino acid may facilitate the amount of H+ transfer to substrate as key step in catalyzing reaction
enzyme can stretch substrates toward transitional state forms, doing this breaks critical chemical bonds and reduces the amount of free energy to be absorbed
Substrate is converted to the product or products of the reaction due to the catalytic action of the enzyme
Lock and Key
Induced Fit: tightening of the binding after initial contact. Brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction
Catalysts will lower the activation energy of a process and delta G will be unaffected by catalyst
Energy coupling is the way the cells manage their energy resources to do these kinds of work
How ATP drives chemical work: Energy coupling using ATP Hydrolysis
c) delta G for glutamic acid conversion to glutamine is +delta G plus - delta G for ATP hydrolysis gives a - free change for the overall reaction. An exergonic process coupled with an endergonic reaction made the overall process spontaneous and exergonic
b) ATP phosphorylates glutamic acid, makes it less stable, more free energy and ammonia later displaces the phosphate group from glutamine
a) Glutamine synthesis from glutamic acid by itself is endergonic, non spontaneous
Energy coupling using ATP hydrolysis
Coupled reactions: Overall delta G is negative together, reactions are spontaeous
Step 2: Exergonic Reaction delta G is negative, reaction is spontaneous
Step 1: Endergonic reaction delta G is positive, reaction is not spontaneous
Mechanical Work: the beating of the cilia, contraction of muscles, and movement of chromosomes during cellular reproduction
ATP binds non-covalently to motor proteins and then is hydrolyzed, causing a shape change that walks the motor protein forward
Transport Work: pumping of substances across membranes against direction of spontaneous movement
ATP phosphorylates transport proteins, causing a shape change that allows transport of solutes
Chemical: pushing of endergonic reactions that don't occur spontaneously
Synthesis of polymers from monomers
Endergonic reaction is one that absorbs free energy from its surroundings
This reaction stores free energy in molecules, G increases, so delta G is positive
Photosynthesis
Heterotrophs
feed off of other livings things for nutrition (animals and decomposers)
Autotrophs
sustainable without eating other livings, use sunlight and minerals in soil for nutrition, (plants)
Chloroplasts capture light energy and converts it to chemical energy, stored in sugar and other molecules
C4 plants
C4 plants have no photosystem 2
Calvin cycle of C4 plants
Step 3: CO2 is released into the bundle-sheath cell, and enters the Calvin cycle
ATP is used to convert pyruvate to PEP, which allows intake of additional CO2
Step 2: Four carbon compound moves to bundle-sheath cell via plasmodesmata
Step 1: in mesophyll cells, enzyme PEP carboxylase adds CO2 to PEP, generating 4 carbon compound
Mesophyll cells
more loosely packed than bundle-sheath cells
Bundle-sheath cells
tightly packed sheaths around veins of leaves
Photorespiration
peroxisomes and mitochondria within plant cell rearrange and split, releasing CO2
product splits and two carbon compound leaves chloroplast
Rubisco has ability to bind O2 in place of CO2 in the Calvin cycle
when stomata is closed, 3 carbon compound C3 plants produce produce less sugar, because of lack of CO2
Stage 2: Calvin cycle
carbon is reduced using NADPH and ATP from light reactions to make carbohydrates
Step 3: Regeneration of CO2 accepter
G3P that exited cell cycle becomes starting material for other metabolic pathways
9 ATP and 6 NADPH used to synthesize 1 G3P
5 G3P molecules rearranged into 3 molecules of RuBP using 3 ATP
Step 2: Reduction
One molecule of G3P exits cycle to be used by plant cell, other 5 are recycled to regenerate 3 molecules of RuBP
Note: 3 CO2=6G3P formed
a pair of electrons from NADPH and a phosphate group is lost, generating glyceraldehyde 3-phosphate. (G3P)
Each 3-phosphoglycerate receives an additional phosphate group
Step 1: Carbon fixation
Each carbon dioxide molecule is added to a 5 carbon sugar using rubisco
6 carbon product splits in half, forming 2 molecules of 3-phosphoglycerate
Stage 1: Light reactions
light absorbed by chlorophyll
ATP generated by chemiosmosis through addition of phosphate to ADP (phosphorylation)
ATP provides energy to cells used in Calvin cycle
electrons from water transferred to NADP+
light reaction makes NADP+ become NADPH with added electron along with hydrogen from water
NADPH acts as reducing power
water absorbed by roots
chloroplast splits hydrogen dioxide (water) into hydrogen and oxygen
Oxygen gas is released into the biosphere
hydrogen becomes a source of protons and electrons
Carbon dioxide enters stomata
Chloroplasts found in cells of mesophyll inside leaves
made up of double membrane called stroma and sacs called thylakoids, which may be stacked as grana
Photosystems
Photosystems are areas of the plant cell populated in the thykaloid membrane that cooperate in light reactions, consisting of light-harvesting complex, reaction center complex, primary electron accepter, and pigment molecules
Linear electron flow
ATP and NADPH and synthesized by energizing both photosystems
Step 8: enzyme NADP+ reductase catalyzes transfer of electrons from ferredoxin to NADP+, two electrons are required for reduction to NADPH, NADPH is released
Step 7: photo-excited electrons passed in redox reactions from primary electron acceptor of photosystem 1 to a second electron transport chain through protein ferredoxin (no ATP produced)
Step 6: Light energy excites electron of P700 pair of chlorophyll a molecules in photosystem 1, electron transfers to primary electron acceptor in photosystem 1, making P700+
Step 5: Potential energy in proton gradient is used to make ATP through chemiosmosis
Step 4: photo-excited electrons are passed from the primary electron acceptor of photosystem 2 to photosystem 1 via the electron transport chain with protein plastocyanin (cytochrome complex), each carrying out redox reactions, releasing ATP
ATP used to pump protons into thylakoid space, contributing to a proton gradient across thylakoid membrane
Step 3: enzyme catalyzes splitting of water, electrons are supplied to P680+, H+ is released to thylakoid space, oxygen atoms combine and generate oxygen gas
Step 2: Electron transferred from P680 to primary electron acceptor, resulting in P680+
Step 1: Photon of light strikes pigment molecule in light harvesting complex in photosystem 2
light is absorbed by light harvesting complex in photosystems, consisting of chlorophyll a, the main photosynthetic pigment in plants, and chlorophyll b in algae
primary electron acceptor can accept electrons and become reduced
Photosystem 1
has a reaction center chlorophyll a called P700 because light is best absorbed by a wavelength of 700 nm (far red zone)
Cyclic electron flow
usually occurs in plants containing a single photosystem
Unlike linear electron flow, electrons cycle back from ferredoxin to the cytochrome complex, then to a P700 chlorophyll in the photosystem complex via plastocyanin molecule
As cycle repeats, ATP is generated
no NADPH formed or oxygen released
Photosystem 2
comes before photosystem 1
has a reaction center chlorophyll a called P680 because light is best absorbed by a wavelength of 680 nm (red zone)
Polymerization
Biosynthetic pathways
Pathways that consume energy to build larger, complicated molecules from simpler ones
Exergonic reaction proceeds with the net release of free energy
Chemical mixture looses free energy, G decreases, so delta G is negative
Cellular respiration
REDOX reactions
Reduction: Gaining electrons
Reducing agent reduces the oxidizing agent which accepts the electron
Oxidation: Loose electrons
Oxidizing agent oxidizes the reducing agent by removing its electron
Anaerobic respiration
Anaerobes
Obligate: Carry out only fermentation. These organisms can't survive in the presence of oxygen
Faculative: can make enough ATP to survive using either fermentation or respiration
Fermentation
Partial degradation of sugars or other organic fuels that occurs without the use of oxygen
Alcohol
c) Acetylaldehyde is reduced by NADH to ethanol, regenerating the the supply of NAD+ needed to continue glycolysis
Lactic Acid
Human muscle cells make ATP by Lactic Acid fermentation when oxygen is scarce, occurs in strenuous excercise, when sugar catabolism for ATP production outpaces the muscles supply of oxygen from the blood
b) 2 pyruvate is reduced directly by 2 NADH to form 2 lactate as an end product, regenerating 2 NAD+
a) Glycolysis resulting in 2 Pyruvate
Aerobic respiration
Step 4: Electron Transport Chain and Chemiosmosis (Both make up oxidative phophorylation)
g) the protons that were pumped out flow back down their gradient via ATP synthase which harnesses the proton motive force to phosphorylate, ADP, forming ATP
the process of H+ through ATP synthase uses the exergonic flow of H+ to drive the phosphoryation of ADP. Thus energy stored in an H+ gradient across a membrane couples the redox reactions of the ETC to ATP synthesis
f) electrons are shuttles from mobile carrier C to complex 4, the electrons are given to O2 which reacts with hydrogen ions, from the aqueous solution, forming water
e) electrons are shuttles to complex 3, then shuttle 3 shuttles them to mobile carrier c, pumping protons out of the matrix
d) FADH2 deposits its electrons via complex 2, which is the only one not along the membrane, so fewer protons are pumped
c) as complex 1 is about to shuttle the electrons to a mobile carrier Q, it pumps out protons from the matrix to the inner membrane space.
b) NADH carries and drops the electrons off at protein complex 1.
a) the NADH and FADH2 formed in glycolysis, pyruvate oxidation, and the citric acid cycle are electron carriers and shuttle these high electrons into an electron transport chain built into the inner mitochondrial membrane
Step 3: Citric Acid Cycle (Krebs Cycle); (occurs once fore each of the two Acetyl CoA so everything that is yielded in one cycle is doubled
h) substrate is oxidized, reducing NAD+ to NADH and regenerating the molecule that began the process by interacting with Acetyl CoA
So in total we gained 6 NADH, 2 ATP, and 2 FADH2 after citric acid cycle
g)addition of water molecule rearranges bonds in the substrate
f) Two hydrogens are transferred to FAD, forming FADH2 and oxidizing succinate, molecule formed after previous step
Total of 2 FADH2 formed after each acetyl CoA undergoes cycle
e) CoA displaced by a phosphate group, which is transferred to GDP, forming GTP, which can be used to generate ATP
Total of 2 ATP formed after each acetyl CoA undergoes cycle
d) another CO2 lost and he resulting compound is oxidized reducing NAD+ to NADH. The remaining molecule is then attatched to CoA
Total of 2 NADH formed after each acetyl CoA underges cycle
c) Isocitrate oxidized reducing NAD+ to NADH. Then the resulting compound looses a CO2 molecule
Total of 2 NADH formed after each acetyl CoA undergoes cycle
b) citrate is converted to its isomer, isocitrate, by the removal of one water molecule and the addition of another
a) Acetyl COA adds its two-carbon acetyl group to oxaloacetase, producing citrate
Step 2: Pyruvate Oxidation (In between the cytoplasm and the outer mitochondrial membrane)
c) Coenzyme A (CoA) a sulfur containing compound, is attached via its sulfur atom to the two carbon intermediate, forming Acetyl CoA. Since we start with 2 two carbon intermediates, 2 CoA's attach and we yield 2 Acetyl CoA's
So in total, 2 NADH were formed after pyruvate oxidation
2 Acetyl CoA's formed
b) Each molecule has two carbon fragments remaining. Each are oxidized and the electrons are transferred to 2 NAD+, storing energy to form 2 NADH
2 NADH released
a) 2 Pyruvates carboxyl groups are already somewhat oxidized, carrying a little chemical energy, and now fully oxidized giving off 2 CO2 molecules
2 CO2 released
Step 1: Glycolysis (in the cytoplasm)
Energy Payoff Phase
h) after two more steps occur, The phosphate group is transferred from 2 PEP to 2 ADP, yielding 2 ATP and 2 PYRUVATE with the help of PYRUVATE KINASE
So in total we gained a net of 2 ATP, 2 NADH, and 2 Pyruvate
g) The phosphate group in 1,3 BISPHOSPHOGLYCERATE is transferred to ADP in an exergonic reaction. The products yielded are 2 ATP and 2 3-PHOSPHOGLYCERATE. The carbonyl group of G3P has been oxidized.
2 ATP formed
f) two things happen. Each of the 2 G3P's are oxidized by the transfer of electron to 1 NAD+ with the help of the enzyme TRIOSEPHOPHATEDEHYGROGENASE, forming 2 NADH's. The energy from this exergonic reaction allows a phosphate group to be attached to the oxidized substrate, making two high energy products called 1,3-BISPHOSPHOGLYCERATE
2 NADH's formed
Energy investment phase
e) G3P and DHAP convert into each other and now, 2 G3P are used in the next step as fast as it forms
d) ALDOASE cleaves the sugar FRUCTOSE 1,6- Bisphosphate into two different three carbon sugars G3P and DHAP
c) PHOSPHOFRUCTOKINASE transfers a phosphate group from another ATP to the opposite end of FRUCTOSE 6- PHOSPHATE yielding FRUCTOSE 1,6- Bisphosphate
b) GLUCOSE 6-PHOSPHATE is converted to FRUCTOSE 6-PHOSPHATE by the enzyme PHOSPHOGLUCOISOMERASE
a) Enzyme HEXOKINASE transfers a phosphate group from ATP to GLUCOSE making it more chemically reactive. We yield GLUCOSE 6-PHOSPHATE
1 ATP used
Oxidative Phosphorylation
Powered by the redox reactions of the electron transport chain
Subtopic
Some ATP is made by direct transfer of a phosphate group from an organic substrate to ADP by an enzyme
Most efficient catabolic pathway, where oxygen is consumed as a reactant along with organic fuel
Pathways release energy by breaking down complex molecules into simpler compounds
Each catalyzed by a specific enzyme
If products have have more free energy than the reactants, energy is required for the reaction, and the delta G is positive
Non spontaneous
If reactants have more free energy than product, energy is released, and delta G is negative
Spontaneous
a measure of a systems instability, tendency to change to a more stable state
Open: both heat and matter can flow through
Closed: only heat can flow through, not matter
Entropy: the degree of randomness or disorder in a system
Viral DNA- can program cells
Takes over the metabolic fuctioning of the cell
Bacteriophages: viruses that infect bacteria
Phage T2: infects E. coli
The phage DNA entered the cell but not the phage protein
Tested to see what was really causing the cells genetic make up to be altered
Theories of the model of DNA
Dispersive: Mixture of daughter strands and molecules of old and new DNA
Conservative: two parental strands act as template, the strands come back together and there is a daughter helix
Semiconservative: two parent strands serve as templates for new complementary strands
Chargaff's Rules
For each species the percentages of A and T bases are roughly equal and so are G and C bases
DNA base compositions varies between species
Properties
Semi-conservative
Makes a full turn every 3.4 nm or every 10 layers of base pairs
Structure
Double helix
Held together by hydrogen bonding between bases
Two strands are anti-parallel to one other to form double helix
Backbone of made of alternating phosphates and pentose sugar deoxyribose
Phosphodiester bonds connect 3'carbon of one of one sugar 5' of adjacent sugar
Nucleotide bases
Pyrimidines
Cytosine
Thymine
Puries
Adenine
Guanine
Codons
Codon chart
Stop: a sequence of nucleotides in mRNA (UAA, UAG ,UGA) which signals the termination of translation
Start Codon: a sequence of nucleotides in mRNA (AUG) that provides the code for the first amino acid (Methionine) during translation
Polyribosome: several ribosomes simultaneously translating the same mRNA
Release Factors: the stop codon is read and the subunits break apart and the peptide chain is released
Elongation Factors: peptide bonds are joined together in a long sequence
Initiation Factors: the ribosome attaches at the mRNA binding site. Attaches subunits
Peptidyl transferase: Formation of peptide bond
Aminoacyl t-RNA synthetase: enzymes that catalyze the addition of an amino acid to a corresponding tRNA molecule
Amino acids
Ribosomes
The mRNA binding site on small subunit
The binding sites for tRNA; large subunit
E site (exit site
A site (Aminoacyl-tRNA binding site)
P site (Peptidyl-tRNA binding)
Composed of protein and RNA
Eukaryotes
Subunits are 60s and 40s
Prokaryotes
Subunits are 50s and 30s
tRNA
Anticodon: three bases on tRNA that recognize the codon on the mRNA
Single Stranded, clover leaf shape
Carries amino acid to translation machinery
mRNA messenger RNA
What is the same in prokaryotes/eukaryotes
Promoter: is a region of DNA that initiates transcription of a particular gene; located upstream of DNA
Downstream: Direction of transcription; starts at 1...2...3, etc.
Upstream: Location of the promoter starts at -1..-2..-3,etc.
Eukaryotes: process occurs in the nucleus
After processing: formulation of mature mRNA
Polymerases involved
RNA pol III: tRNA, 5S rRNA
RNA pol II: pre mRNA, snRNA, microRNA
RNA pol I: ribosomal RNA
What else is needed
Transcription Factors
RNA processing: modification of pre-mRNA before it leaves the nucleous
RNA splicing: introns removed and exons joined together
Alternative splicing: variations in the splicin
Spiceosome: an RNA-protein that cuts out introns and joins together exons
Introns: non-coding nucleotide sequences in eukaryotic genes that are removed
Exons: nucleotide sequences that cod for amino acids
poly-A-tail: 100 to 300 adenines added to the 3' end
Info to where this is added is at the poly A site
Cutting after AAUAAA by ribnuclease
Uses ATP
5'cap: Guanosine triphosphate that is added to the 5' end of the pre-mRNA; provides protection from enzymes that break down RNA
Prokaryotes: process of transcription occurs immediately
Operons are transcribed into a single NRNA called a polycistronic mRNA containing multiple open reading frames than encodes amino acids
Transcriptional units: DNA segments transcribed into 1 RNA molecules bounded by initiation and termination sites
Initiation: Sigma Factor of RNA polymerase recognizes initiation sites on DNA called promoters
Differences between prokaryotes and eukaryotes
Eukaryotes: multiple origins of replication and multiple bubbles
Prokaryotes: have circular chromosomes with one ORI and one replications bubble
Structures
Replication bubble: gap in between the separated DNA
Replication fork: Separation of the two stands of DNA
Strands:
Lagging: complementary strand that is put together in fragments; synthesized away from the replication fork
Okazaki fragments: a small segment of DNA formed on the lagging strand using and RNA primer
Leading: synthesized continuously that is compliments DNA
Origin of Replication: the point in the DNA at which replication begins; characterized by a particular sequence of nucleotides (the ORI sequence) containing a large number of A-T bonds
Proteins/Function
DNA ligase: Joins 3' end of DNA that replaces primer to rest of leading strand and joins Okazakii fragments of lagging strand
DNA pol I: Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides
DNA pol III: Synthesizes new DNA by covalently adding nucleotides to the 3' end of a pre-existing DNA strand or RNA primer
Primase: Synthesizes an RNA primer at 5' end of the leading and each of the Okazaki fragments of lagging strand
Topoisomerase: Relieves "overwinding" strain ahead of the replication forks by breaking, swiveling, and rejoining DNA strands
Single-Stranded Binding Protein: Binds to and stabilizes single-stranded DNA until it can be used as a template
Helicase: Unwinds parental double helix at replication forks
3. Elongation: Taq polymerase extends copy
2. Annealing: primers anneal or attach to template DNA
1.Denature: Heat DNA to seperate strands
Lag Exponential Saturation
DNA primers
dNTP
DNA Polymerase
Reaction buffer
DNA
Endomembrane system
mRNA attaches to ER
protein made in the ER is transported by microubules through vescicles
Golgi bodies add chemical tabs
Glycoprotein
Vesicles take it to the...
Lysosmes
Plasma membrane
The rough ER
To the organelles
protein goes to...
Nucleus
Chloroplast
Peroxisomes
Mitochondria
Point: a change in just one nucleotide in the coding strand of DNA
Base pair substitutions the replacing of one base pair with another in DNA
Missense: a mutation in DNA that results in the replacement of one amino acid by anothe
Nonsense: a mutation in DNA that results in the early termination of translation
Silent: a mutation in DNA that does not alter the amino acid sequence of the polypeptide chain
Frameshift: a mutation that alters the reading frame of the mRNA molecule
1. Abiotic synthesis of small organic molecules ( AA and nitrogenous bases) 2. Small molecules into macromolecules (proteins and nucleic acids) 3. Protocells packaging 4.The origin of self-replicating molecule that eventually made inheritance possible
Protocells: These are droplets with membranes that maintained an internal chem different from that of their surroundings
Cell Structures
Extracellular matrix: functions in the support and protection of the cell, as well as communication and association
Components used for structure and motility
Flagellum: a long cellular extension that lashes and enables that cell to move (structure differently than prokaryotic flagella
Cilium: a hair-like structure found in some eukaryotes that uses a rowing motion to propel the organism or to move fluid over cells
Microfilaments: two actin polymers that function in cell shape, muscle action with myosin, cytoplasmic streaming, cell division and motility, and anchoring proteins in the plasma membrane
Microtubules:cylinders made of tubulin that function in motility (e.g.: flagella and cilia), support of cell shape, or transport of chromosomes and vesicles
Intermediate filaments:fibers that stabilize cell structure—for example, maintaining the position of the nucleus and other organelles—composed of helical subunits of fibrous proteins
Cell components
Cell components of plant cells
Cell wall: a fairly rigid polysaccharide; supportive and protective layer that lies outside of the plasma membrane of all plants
Plasmodesmata
Nucleus: organelle in that contains genetic information, stored as DNA, organized as chromatin and chromosome
Nucleolus: a region of the nucleus that specializes in rRNA genes, ribosomal proteins, and ribosomal subunit assembly
Cytoplasm: the contents of the cell enclosed by the membrane; excluding the nucleus
Organelles: a discrete, membrane-enclosed cytoplasmic structure with a specific function
Organelles of animal cells:
Mitochondrion (mitochondria): an organelle with a double membrane that is the site of cellular respiration in eukaryotes and is also involved in regulated cell death; capable of autonomous replication
Crista: folds in the inner membrane of the mitochondria
Organelles of plant cells:
Central Vacuole a large membranous sac in a mature plant cell that helps to maintain cell shape and can be used to store nutrients and anti-herbivory chemicals
Golgi Apparatus: an organelle that routes proteins and lipids to various parts of the eukaryotic cell from the ER and synthesizes certain cellular products, notably non-cellulose carbohydrates
Endoplasmic Reticulum
Smooth ER: a region of the endoplasmic reticulum specialized for lipid synthesis; “smooth” because it lacks attached ribosomes
Rough ER: a region of the endoplasmic reticulum that specializes in protein synthesis; “rough” because of the ribosomes attached to its surface
Ribosome: a cellular structure composed of proteins and RNA at which new proteins are synthesized; can be either attached to the endoplasmic reticulum (ER) or free in the cytoso
Peroxisome: contains enzymes that transfer hydrogen (H2) from various substrates to oxygen (O2) producing and then degrading hydrogen peroxide (H2O2)
Vacuole: a water filled sac that serves various functions, including transport, structural support, and isolation of waste and harmful material
Vesicle: a small, membrane-enclosed sac found in cytosol
Lysosomes: a specialized vesicle with an acidic acid lumen containing enzymes that breakdown macromolecules
Plasma Membrane: phospholipid bilayer that forms the outer boundary of any cell; regulator
Cell Structures: *not present in all*
Cell Surface Structures:
Pili: Typically longer and few found per cell than fimbriae
Conjugative pili facilitate genetic exchange between cells
Fimbriae: hair like appendages
1) Enables organisms to stick to surfaces or form pellicles (thin sheets of cells on a liquid surface) 2) Short: ~2-10nm wide
Capsules: sticky layer of polysaccarides or protein
Protects against dehydration, and protect against immune defense systems
Cell Wall: gives bacteria shape and protection from lysis in diluted solutions
Peptidoglycan Layer: a polymer layer composed of modified sugars cross-linked by short polypeptides
Gram Stain: Technique that helps categorize bacteria based on cell wall compositions
Gram positive: thick peptidoglycan layer
Gram negative: thin peptidoglycan layer, with a LPS outer layer
Made with N-Acetylmuramic acid and N-Acetylglucosamine
Cellular components:
Nucleoid: space containing the genetic information
Endospores: original cell copies its chromosome and surrounds its self with a copy
1) Vegetative cell converted to non-growing, heat resistant, light refracting structure 2) GRAM positive 3) Only occurs when growth ceases due to lack of essential nutrients such as carbon/nitrogen 4)When conditions are fine the endospore will re-hydrate and resume functioning
Periplasmic space: contains hydrolytic enzymes and binding proteins for nutrient processing and uptake
Ribosomes: a cellular structure composed of proteins and RNA at which new proteins are synthesized
Gas Vacuole: buoyancy, decreases cell density
Motility Structures
Flagella: structure that assists in swimming (also in archaea)
Parts: Motor, hook, and filaments
Increase/decrease rotational speed relative to strength of proton motive force
Structure: tiny rotating machine, long thin appendages; helical shape
Shapes:
a. Cocci b. Bacilli c. Spirillum d. Streptococcus e. Staphylococcus f. Sarcina g.Spirochetes
Has a cell wall and branched lipids in membranes
