energy (light) to usable
Photosynthesis-->glucose-->glycolysis-->pyruvate-->anaerobic or aerobic
photosynthesis
use light energy to make high energy fuel compounds (i.e. glucose: lots of chem, energy)
glucose
(6CO2 +^H2O)-->C6H12O6 DeltaG=+686kcal/mol
hella energy stored
glycolysis
breakdown glucose and harvest the chemical energy in it to drive ADP+Pi-->ATP
Pyruvate (what do we do with it)
aerobic respiration preferred but anaerobic also works
aerobic enviconment
CELLULAR RESPIRATION (O2 present)
complete oxidation
waste products=H2O, CO2
Net energy trapped=32 ATP
Anaerobic environment
FERMENTATION
incomplete oxidation
waste products=Organic compounds and CO2
Net energy trapped=2 ATP
glycolysis and cellular respiration
Glycolysis>glucose>pyruvate
O2 present: Pyruvate oxidation-->
citric acid cycle-->
electron transport/ATP synthesis-->CO2 and H2O
BURN GLUCOSE TO MAKE ATP
C6H12O6--> 6CO2+6H2O
G=-686kcal/mol
glycolysis and fermentation
Glycolysis>glucose>pyruvate
O2 absent: Fermentationi-->Lactate or alcohol
Lots of oxidation and reduction n metabolism
oxidation and reduction are coupled (Follow H because H follows e)
if we have a very reduced compound and a very oxidized compounds we can transfer energy from one to the other
(reduced forms are high in energy)
reducing agent lose electrons and becomes o
glycolysis converts glucose to pyruvate
What do we harvest and how much??
net result: from each glucose--> 2 pyruvate, 2ATP, 2NADH and 2H+
ADP + Pi-->
ATP
After glycolysis what happens to pyruvate ?
moves to the mitochondrial matrix where it gets oxidized into acetyl CoA
PYRUVATE Oxidation
CITRIC ACID CYCLE
pyruvate oxidation
pyruvate (coenzyme A catalyst)--> Nad+--->NADH
CO2 released
--->Acetyl CoA
citric acid cycle
for every starting glucose go through citric acid 2x!!
in mitochondria
for each cycle: 6 NADH+2FADH+2ATP
each glucose yields
3 CO2, 10NADH +H+, 2FADH2, 4ATP
electron transport and atp synthesis
in the mitrochondria matrix
produce ATP by a chemi-osmotic mechanism
1NADH-->
3ATP
1FADH-->
2ATP
per starting glucose: how much ATP
36
what happens if oxygen is limiting?
electron transport chain will stall (and back up)
SO anaerobic fermentation
anaerobic fermentation
start with glycolysis
pyruvate will build up and 2 lactate will be formed (this is why you get lactic acid buildups when you work out)
OR ethanol will be made by alcohol dehydrogenase
lactate dehydrogenase
takes NADH and converts them back into NAD+
regulation by negative and positive feedback
a compound X can provide positive feedback to the enzyme catalyze of step that transforms A-->B or
a compound X can inhibit the enzyme catalyzing the conversion of C to F, blocking that reaction and ultimately its own synthesis
What atoms are commonly used in biology?
H (9.5% of human)
O (65% of human)
N (3.3 % of human)
C (18.5% of human)
H+O+N+C=96.3%
whats so special about HONC?
Bonding strength, stability and flexibility
they are the smallest atoms on the periodic table that can achieve stable electronic configurations by sharing 1,2,3, or 4 electrons
ONC are the only elements that can readily form double bonds, providing biomol
What other molecules are in a cell?
phosphorous and sulfur
-good carriers of energy
-important in protein structure
-sulfur engages in oxidation-reduction reactions
Na+,K+,Ca++, Mg++ are important in subsequent quarters, such as
-osmotic balance
-membrane functions(nerve conduction)
Functional/reactive groups
How a molecule "reacts" with another molecule?
Amino group
-NH2
amines
phosphate gropus
-OPO3 (2-)
organic phosphates
sulfhydryl
-SH
thiols
bond strengths
covalent bonds: 50-110 kcal/mol
ionic bonds: 3-7 kcal/mol
hydrogen bonds: 3-7 kcal/mol
hydrophobic interaction: 1-2 kcal/mol
van der Walls interacting: 1 kcal/mol
what is a cell composed of?
70% water
30% ions and small molecules and mostly macromolecules
macromolecules
proteins(polypeptides)
nucleic acids
carbohydrates (polysaccharides)
lipids
how do we build our macromolecules?
condensation-dehydration reactions require energy input: ATP
2 monomers
water is removed in condensation
a covalent bond forms between monomers
how do we break apart our macromolecules?
hydrolysis reactions do not require energy input
water is added in hydrolysis
a covalent bond between monomers is broken
ATP consists of
3 phosphate groups-ribose(sugar)-adenine (purine)
lipids-small macromolecules
cell membranes
-plasma membrane on outside of cell
-membranes for intracellular organelles(nucleus, mitochondria, ER, Golgi, Lysosomes, etc)
important energy storage material
the basic components are fatty acids and glycerol
unsaturated v saturated fatty acids
all bonds between carbon atoms are single in a saturated fatty acid and the chain is straight
-this allows a molecule to pack tightly among other similar molecules
double bonds between two carbons make an unsaturated fatty acid (carbon chain has kinks)
-k
glycerol
C3H5(OH)5
how do we build lipids?
glycerol+3 fatty acids +3 ATP--> a "triglyceride" + 3ADP +3Pi
3 condensation dehydration reactions occur
each fatty acid binds to an oxygen on the glycerol through a ester linkage
triglycerides
very important form of stored energy-can be broken down to smaller and smaller pieces releasing energy (ATP) for cells to use
they have almost no charge asymmetry so they are very insoluble in the cytoplasm and coalesce into "oil droplets"
in adipocytes (
phospholipid bilayer
amphipathic
hydropilic heads next to water
hydrophobic fatty acid tails in the middle
hydrophilic head
separates 2 aqueous regions
fluid mosaic model
carbohydrates are attached to the outer surface of proteins (forming glycoproteins) or lipids (forming glycolipids)
in animal cells, some membrane proteins associate with filaments in the extracelullar matrix
peripheral membrane proteins do not penetrate
membrane proteins can transport molecules of interest through the lipid bilayer membrane
ex: a carrier protein has a glucose binding site on the outside of the cell
if there is a high glucose concentration outside of the cell, glucose will bind to the protein, which then changes the protein's shape...releasing the glucose
the carrier protein
are the membrane proteins able to diffuse around in the plane of the membrane?
experiment
hypothesis: proteins embedded in a membrane can diffuse freely within the membrane
method: the mouse cell has a membrane protein that can be labeled with a green dye and the human cell has a membrane protein that can be labeled with a red dye
-the cells a
lipid raft
a segment in the phospholipid bilayer stacked with glycosphingolipids and cholesterol
membrane proteins in these regions cannot feely diffuse as equally because of the decreased fluidity from cholesterol
where do we get vitamin a
B-Carotene
polysaccharides
polymers of sugars, sugars are small molecules that serve many functions
sugars
(CH2O)n where n=3-7
sugars vary from one another largely by:
-the number of carbon atoms and the orientation of OH/H at each carbon
this means that different sugars can have the same, or similar, chemical compositions, but different structures and propert
a-D-glucose
OH on carbon 1 points same direction as OH on carbon 2
B-D-glucose
OH on carbon 1 points opposite direction of OH on carbon 2
five carbon sugars
pentoses
ribose has hydroxyl group on carbon 2
deoxyribose has only hydrogens are carbon 2
how do sugars polymerize
condensation/dehydration rxns
alpha glycosidic linkage
between a-D-glucose and fructose (a1,2glycosidic linkage)
between a-D-glucose and B-D-glucose (a 1,4-glycosidic linkage)
beta glycosidic linkage
between b-D-glucoses
alpha and beta links
the hydroxyl group on the carbon that carries the aldehyde of ketone can rapidly change from one position to the other. these two positions are called a and B
as soon as one sugar is linked to another, the a or B form is frozen
cellulose v starch and glycogen
cellulose (BC1-->C4 linkages)
starch and glycogen (aC1-->C4 linkages or aC1-C6 linkages)BRANCHES
glycogen
key to maintaining blood glucose levels
-glucogen is like glucose "in the bank" can break off individual glucose molecules when we need energy
Von Gierke's Disease
human glycogen storage diseases
patients build up normal glycogen stores but can't access them
-defective enzyme (glucose-6-phosphatase)
cori's disease
human glycogen storage disease
similar clinical symptoms to von gierke's
-different reason: they make glycogen incorrectly and can't access it with regular mechanisms
proteins
most abundant class of macromolecules
50% of dry weight of cells
most versatile macromolecules in the cell in terms of number of functions performed
how can proteins do so many different things?
there are 20 different kinds of amino acids
proteins are chains of ~10 to thousands of amino acids in length
therefore, there are a vast number of possible sequences
amino acids
20
all have the same basic structure (amino group NH2 and carboxylic acid group COOH) but each have a unique feature called "R"
3 positively charged hydrophilic amino acid side chains
2 negatively charged hydrophilic amino acid side chains
5 polar uncharg
how do we synthesize new proteins
peptide bond formation between N and C(condensation/dehydration rxn)
creates polypeptides
how many levels of protein structure are there?
4
primary level of protein structure
polypeptide linkage
covalent bods
secondary level of protein structure
hydrogen bonds create either a helix or b pleated sheet
tertiary level of protein structure
large scale intra-molecular folding interactions
how the alpha helices of b pleated sheets fold up
weak forces, such as ionic bonds
disulfide bridge generally part of tertiary structure(but can also be quaternary)
quaternary structure
intermolecular folding interactions
association of multiple independent polypeptide chains
disulfide bonds
contribute to protein folding (tertiary)
can also contribute to quaternary structure in antibodies
oxidizing environments like outside of the cell promote disulfide bond formation
reducing environments inside of the cell have rare disulfide bond formation
denaturing a protein
disrupts the tertiary and secondary structure of a protein and destroys the proteins biological functions
renaturation
reassembly into a functional protein
is sometimes possible, but usually denaturation is irreversible
how do proteins assemble into their final complex configuration?
sometimes, they can spontaneously assemble into the proper final configuration by maximizing all of the weak forces and disulfide bonds, thereby arriving at the lowest energy configuration
sometimes, they need help from chaparonins
chaparonins
protect proteins from inappropriate binding
a denatured protein binds to HSP60 and enters it
a lid seals the cage
the protein folds into its appropriate shape and is released
how many different proteins do we have
~25000 completely different human proteins
nucleic acids are composed of nucleotides
nucleotides have three components:
base + ribose or deoxyribose=nucleoside
nucleoside +phosphate= nucleotide
pyrimidines
one cyclic thing
C,T,U
purines
one cyclic group attached to another
A, G
distinguishing RNA from DNA
RNA (sugar=ribose)
bases= A,C,G,U
single strands (can also form intramolecular double stranded REGIONS as well as intermolecular double helices
DNA (sugar=deoxyribose)
bases= A,C,G,T
double strands
nucleotides
the phosphate group attaches to the 5' carbon
the base attaches to the 1' carbon
the next nucleotides phosphate group attaches to the 3' carbon
Griffith experiment
S" bacteria=pathogenic (virulent)
"R"bacteria= nonpathogenic (avirulent)
hypothesis: material in dead cells can genetically transform living bacterial cells
inject living S strain into mouse and it dies, living S strain cells found in heart
inject living
Avery Experiment
hypothesis: The chemical nature of the transforming substance from pneumococcus is DNA
method: heat to kill virulent S strain bacteria, homogenize and filter
-treat samples with enzymes that destroy RNA, proteins, or DNA
-add the treated samples to cultur
more evidence in favor of DNA being the genetic material
DNA is found only in the nucleus, and the nucleus is intimately involved in heredity
amount of DNA in all cells of an organism is constant, except for sperm and egg, where it is half of other cells
under normal circumstances, DNA is never degraded; in con
Hershey Chase experiment
label DNA with radioactive phosphorus (32P) phosphorus in the DNA backbone which emits a high energy B particle
label protein with radioactive sulfur (35S) sulfur in 2 amino acids (met and cys) emits a low energy b particle
infect bacteria and examine the
Chargaff's data
A=T
G=C
purines=pyrimidines
Wilkins and Rosalind Franklin
used Xray crystallography to learn about DNA structure, revealing the basic helical structure or DNA
Insights:
DNA is helical, like a spiral staircase
DNA is composed of more than one chain, like 2 or 3
DNA has a "regular" structure..long and narrow, cons
Crick and Watson
First model... whats wrong?
backbones on outside, bases on inside, each base H bonds to the same type of base on the other chain (A=A, C=C, G=G, T=T)
whats wrong:
ignores chargaff's data
can't have constant diameter
linus pauling dna structure
triple helix
sugar phosphate backbones on the inside
made no sense based on the available chemical data
did not account for chargaff's base composition data
Watson and Crick
Correct DNA model
double stranded helix
2 sugar-phosphate backbones on outside
bases on inside
10 bp/complete turn
1 purine and 1 pyrimidine per base pair
backbones run anti-parallel (base pairing in DNA is complementary)
three models for DNA replication.. which ones right?
semi-conservative replication: produces molecules with both old and new DNA< but each molecule would contain one completely old and one new
conservative: preserves the original molecule and generates an entirely new molecule
dispersive: produces two molec
meselsen and stahl experiment
label cells with 15N media and 14 N media (can determine whether DNA is heavy or light using a procedure called Density gradient centrifugation
method:
grow bacteria in 15N medium and transfer some to 15N medium
before the bacteria reproduce for the first
Arthur Kornberg and colleages
purified the first DNA polymerase in 1956
DNA polymerase found could only synthesize DNA in the 5' to 3' direction...so people hypothesize that there must be a different DNA polymerase that synthesizes in the 3' to 5' direction...but they never found it..
primer
NO DNA FORMS WITHOUT A PRIMER
primase binds to the template strand and synthesizes an RNA primer. when the primer is complete, primase is released. DNA polymerase binds and synthesizes new DNA
DNA replication
each new strand grows from its 5' to 3' end.
nucleotides are added to the 3' end
C-G A-T
Primase synthesizes a primer
the enzyme DNA polymerase adds the next deoxyribonucleotide to the -OH group at the 3' end of the growing strand and releases pyrophospha
lagging strand
primase forms an RNA primer
DNA polymerase II adds nucleotides to the new okazaki fragment only at the 3' end, continuing it until it encounters the primer on the previous okazaki fragments
DNA polymerase I hydrolyzes the primer and replaces it with DNA
D
sliding DNA clamp
increases efficiency of DNA replication
binds to DNA
DNA polymerase binds to the clamp-DNA complex
the clamp keeps the polymerase stably bound to DNA so that many nucletides can be added for each binding event
prokaryotic DNA replication
circular DNA
the ori sequence binds to the pre-replication complex
two replication forks move away from one another
eukaryotic DNA replication
there are multiple origins of replication. at each ori, initiation of replication occurs.
replication forks move away from each other.
telomeres and telomerase
very important for development, stem cells, cancer...
in most cells, the terminal nonreplicated nucleotides are removed and the chromosome is shortened.
in stem cells the enzyme telomerase uses an RNA template to extend the telomere
telomerase moves to th
DNA repair mechanisms
DNA proofreading
Mismatch repair
excision repair
DNA proofreading
during DNA replication, an incorrect nucleotide may be added to the growing chain.
the proteins of the replication complex immediately excise the incorrect nucleotide.
DNA polymerase adds the correct nucleotide and replication proceeds
Mismatch repair
during DNA replication, a nucleotide was mispaired and missed in proofreading
the mismatch repair proteins excise the mismatched nucleotide and some adjacent nucleotides
DNA polymerase I adds the correct nubleotides
in the last step, DNA ligase repairs th
excision repair
a nucleotide in DNA is damaged
the excision repair proteins excise the damaged nucleotide and some adjacent nucleotides
DNA polymerase I adds the correct nucleotides by 5' to 3' replication of the short strand.
in the last step, DNA ligase repairs the rem
PCR
polymerase chain reaction:
a dna molecule with a target sequence to be copied is heated to 90 C to denature it
when the mixture cools, artificially synthesized primers bond to the single-stranded DNA
heat-resistant DNA polymerase uses dNTPs to synthesize
RNA is very similar to DNA, EXCEPT:
uracil replaces thymine
riboses replaces deoxyribose
RNA is generally single stranded
RA chains can be of varying lengths, ranging from ~10 bases long to many thousands of bases long
RNA can fold up on itself into precise 3D structures much like proteins
3 traditional kinds of RNA
ribosomal RNA rRNA~95%.. structural component of ribosomes
transfer RNA tRNA~2%
messenger RNA mRNA~1-2%total
Central Dogma
coined by francis crick
DNA-transcription-> RNA-translation-> polypeptide
translation
initiation
elongation
termination
RNA synthesis i 5' to 3' just like DNA; but only one strand gets synthesized unlike DNA replication
ribonucleotide triphosphates are monomer is precursors
-U in RNA replaces T in DNA
several RNA polymerases can be on a gi
Marshall Nirenberg experiment
hypothesis: an artificial mRNA containing only one repeating base will direct the synthesis of a protein containing only one repeating amino acid.
method: prepare a bacterial extract containing all the components needed to make proteins except mRNA
Add an
transfer RNA
cloverleaf" model with base pairing between complementary nucleotides.
amino acid attachment site is always CCA
hydrogen bonds between paired bases results in 3d structure
the anticodon, composed of three bases that interact with mRNA is far from the ami
charging" a tRNA molecule
an activating enzyme (aminoacyl-tRNA synthase) is for a specific amino acid
+ATP+specific amino acid..the enzyme activates the amino acid, catalyzing a reaction with ATP to form high energy AMP-amino acid and a pyrophosphate ion.
specific tRNA comes and t
ribosome structure
irreularly shaped and composed of two subunits. each subunit contains rRNA and numerous proteins
there are 3 sites for tRNA binding. codon-anticodon interactions between tRNA and mRNA occur only at the P and A sites
translation initiation
the small ribosomal subunit binds to its recognition sequence on mRNA
methionine charged tRNA binds to the AUG "start" codon, completing the initiation complex
the large ribosomal subunit joins the initiation complex, with methionine charged tRNA now occu
translation elongation
codon recognition: the anticodon of an incoming tRNA binds to the codon at the A site
peptide bond formation: pro is linked to met by peptidyl transferase activity of the large subunit
elongation: free tRNA is moved to the E site, and then released, as th
translation termination
a release factor binds to the complex when a stop codon enters the A site
the release factor disconnects the polypeptide from the tRNA in the P site
the remaining components (mRNA and ribosomal subunits) separate
AUG
methionine start codon
direction of translation
forward 5' to 3' in units of 3 nts; NEVER skip a nt
polysome
multiple ribosomes on a single strand of mRNA
polypeptides grow longer as each ribosome moves toward the 3' end of mRNA
how do proteins know where they are supposed to go after they get syntheized??
a signal sequence moves a polypeptide into the ER
protein synthesis begins on free ribosomes in the cytosol. the signal sequence is at the N-terminal end of the polypeptide chain
the polypeptide binds to a signal recognition particle and then both bind to
post translational modifications of proteins
proteolysis
glycosylation
phosphorylation
proteolysis
cleaving the polypeptide allows the fragments to fold into different shapes
glycosylation
adding sugars is important for targeting and recognition
phosphorylation
adding phosphate groups alter the shape of the protein
missense mutation
mutation that places on nucleotide in instead of another
after transcription and translation the peptide may have another peptide
nonsense mutation
mutation that places one nucleotide instead of another resulting in a stop codon--> no protein is made
frame-shift mutation
mutation by insertion of nucleotide between two bases in DNA
all amino acids are changed beyond the insertion
silent mutation
A nucleotide is placed instead of another but the codon still codes for the same peptide
chromosomal mutations
deletion
duplication or deletion
inversion
reciprocal translocation
deletion
the loss of a chromosome segment
duplication/deletion
result when homologous chromosomes break at different points and swap segments
inversion
results when a broken segment is inserted in reverse order
reciprocal translocation
results when nonhomologous chromosomes exchange segments
how did we find out about noncoding DNA
nucleic acid hybridization
introns v exons
in eukaryotic genes
the exons and introns of the coding region are transcribed
the introns are removed
the spliced exons are ready for translation after processing.
spliceosome
an RNA splicing machine
small nuclear ribonucleoprotein (snRNP) particles bind to consensus sequences near the 5' and 3' splice sites
interactions between the two snRNPS and other proteins form a spliceosome
a cut is made between the 5' exon and the intro
MicroRNA
inhibits mRNA
binds to messenger RNA
protein assembly is blocked
pre-miRNA is diced into mature miRNA (a precursor RNA folds back on itself, forming a double-stranded RNA. the dicer protein complex cuts the RNA into small fragments. another protein comple
mRNA inhibition by microRNAs
DNA is transcribed
proteosome
breaks down or degrades proteins
a protein is targeted for breakdown; an enzyme attaches ubiquitin to the protein; and is recognized by a proteasome; ubiquitin is released and recycled; the proteasome hydrolyzes the target protein
NAD
an energy carrier that works by "redox