Hydrogen

bond- positively charged region of one water molecule approaching a neg charged
region of another water molecule. Electropositive hydrogen atom sahred by two
electronegative atoms.
Covalent bonds- when two atoms come very close together and share one or more of their
electrons.
Non-covalent bonds: electrostatic attractions (ionic bonds), hydrogen bonds, van der Waals
attractions (non-covalent bond specified by the radius between two atoms, the atoms can be
attracted until the distance between their nuclei is approx. equal to the sum of Van der waals
radii), hydrophobic force (folding of protein).
Ester-rxn by acid and alcohol
Acids-release protons in water, strong acids loose protons quickly. COOH-weak acid.
Base-accepting a proton from a water molecule. NaOH strong base. Weak bases weak tendency
to accept protons from water-NH2.
Buffer-relation between acids and bases, in cell- weak acids and bases release or take up
protons near pH 7.
Small organic molecules-sugars, fatty acids, nucleotides, aa-from macromolecules (polymers
fored by covalently linking small organic molecules
Proteins: enzymes, molecular motors,
Condensation rxn-formation of polymers, combination of 2 molecules to forma a larger
molecule with the lost of a small molecule, in proteins is the rxn for formation of a peptide
bonds, with the lost of water molecule. Unfavorable rxn, coupled to ATP
Covalent bonds-allows macromolecule rotation, . Prefer conformation by noncovalent bonds.
Second law-degree of disorder always increasesentropy, or systems change spontaneously.
Forms of energy in cell-chemical bond, heat.
Aerobic respiration-production of CO2 and H2O
Oxidation- removal of electrons, reduction-addition of electrons
Polar covalent bond- carbon atom becomes covalently bonded to an atom with a strong affinity
for electrons, oxygen, chlorine, sulfur.
Reduction-number C-H bonds increases, oxidation-number of C-H bonds decreases.
Free energy-energy directed to work or drive chemical reactions.
Activation energy-energy require to undergo a chemical reaction. Enzymes catalyst, reduces
activation of energy, by binding to substrate.
Binding between substrate and enzyme: transaltional motion (one place to another), vibrations
(back and forth movement of covalently linked atoms), rotations.
Diffusion
G, free energy (degree to create bigger disorder)- energy available to do work, deltaG<0 occurs
spontaneously, >0 unfavorable, only happen to coupled to another rxn.
Standar free energy-free energy change under standard condition. deltaG=deltaGstandar + RTln
[y]/[x].
deltaG=0, rxn equilibrium, eq constant K= [y]/[x]

Coenzymes or activated carriers- store energy in an easily exchangeable form, as a readily
transferable chemical group or as electron held at a high energy level. ATP-transfer phosphate,
NADH (reduced form), NADPH (reduced form)-transfer e and hydrogen

ATP hydrolysis coupled to others unfavorable rxns.

Coenzyme A- carries an acetyl group in a thioester linkage-transfer two carbons.
TCA-complete oxidation of acetyl-CoA

Proteins-long polymes formed by aa thorugh a peptide bond between the amine and the
carboxyl group of each aa.

Aminoacids
3 basic; lysine, arginine (very basic, positive side stabilized by resonance), histidine
2 acidic;aspartic acid, glutamic acid
5 uncharged; asparagine, glutamine, serine, threonine, tyrosine
10 non polar; alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine,
tryptophan, glycine, cysteine

Folding of a protein-by weak noncovalent bonds (electrostatic attractions (ionic bonds),
hydrogen bonds, van der Waals attractions, hydrophobic force), atoms in polypeptide and aa in
side chains (R groups). The folding is also determined by the distribution of its polar and
nonpolar aa, due to hydrophic force in which hydrophic molecules are force together in an
aquous environment. Nonpolar side chains tend to cluster in the interir of molecule, polar
groups arrange outside of the molecule, to form hydrogen bonds. Polar aa into the molecule
have hydrogen bonds between other aa in the chain or the backbone.
Conformation gives catalytic or structural function in the cell.
AA- plar (nega, positive, uncharged), nonpolar
Peptide bond is planar, rotation occur in Calfa-C bond (psi), and N-Calfa (phi), Ramachandran
plot represent a pair of angles in a protein, diff clusters represent diff secondary structures.
Conformation of protein-the oe that has the lowest free energy. Molecular chaperones assists
in protein folding.
Protein doamins- structural units that fold more or less independently of each other.
Alfa helix and beta sheet- hydrogen bonding between N-H and C=O in backbone
Alfa helix-hydorgen bond N-H from 4 aa away of the chain to C=O, turn every 3.6 aa, protein
memebranes. Alfa helix coiled coil-two or more have nonpolar sides that twist around each
other.
Beta sheet-adjacent chains run in opposite directions antiparallel or parallel
Primary structure-aa sequence
Secondary-stretches of polypeptide chain-alfa helix and beta sheet.
Tertiary-full 3D structure
Quarterly-more than one polypeptide chain (each one called protein subunit), ex hemoglobin.
Assemble into dimers, closed rings, spherical shells or helical polymers.
Rotein domain-a substructure produced by any part of a polypeptide chain that can fold
independently of the rest of the protein in a stable structure. Can have diff secondary structure
Example of family of protein- serine proteases-large family of protein-cleaving enzymes
Domain shuffling-large proteins evolved thourhg the joining of preexisting domains, same aa
seq
Example domains-protein kinases.

Binding site-site for interaction with another molecue through non covalent bonds.
Globular proteins-chain folds up into a compact shape with irregular surface. Enzymes tend to
be globular, having a rodunded shape
Fibrous proteins-3D elongated structure. Main component of ECM, example collagen, 3 chains,
glycine every 3 aa non polar, regular structure allows to have a triple helix
Elastin-unstructured polypeptide chains, covalently cross-linked producing a rubberlike
Disordered protein sequences- originate functions such as binding (low affinity, require energy
to fold), signaling (covalently modified to change binding preferences), tethering (protein
domains close), diffusion barrier
Information for assembly can be provided by special enzymes called assembly factors.
amyloid fibrils-stable beta sheets aggregates which are formed by identical chains layered one
over the other to create stack of beta sheets, with beta strands oriented perpendicular to the
fibril axis called Cross-beta filament-, function in excretion of secretory granules (in peptides
and protein hormones), package in dense cores.

Enzyme kinetics
Enzymes: catalytic proteins that speed up a reaction rates by binding the high-energy transition
states for a specific reaction path.
Rate of enzyme increase by joining to sinlge multienzyme complex, or enzyme and substrates
attached to protein scaffolds.
Kcat- rate constant that has a value equal to the number of substrate molecules processed per
enzyme molecule each second.
Km-measure of substrate affinity for an enzyme
Kd- dissociation constant for substrate binding to the enzyme
Kcat/Km= rate constant for reaction between free enzyme and free substrate
Steady-state level-enzyme is saturated by its substrate, requires activation energy. Rate of ES
breakdown=rate of ES formation
Enzymes can have active (recognizes substrate) or regulatory sites (recognizes regulatory
molecule), these enzymes are called allosteric enzymes
Feedback inhibition: product bind to the enzyme and slows down its catalytic action. Binding to
and inhibitor, protein shift to a conformation that enables its active site.
Metabolic pathways controlled by feedback regultation: small molecules inhibit and other
molecules activate enzymes early in a pathway
Proteins have reversible post-translational modifications: phosphorylation, acetylation,
methylation. These addition regulates activity of protein, changing its conformation, its binding
to other proteins.

DNA replication
Separation of DNA into two template strands, recognition of template by a free complementary
nucleotide.
Origin of replication in DNA sequences bind to a origin recognition complex, these DNA seq
must be rich in A and T, one binding site for proteins. Active zone of DNA replication moves
progressively creating a Y-shaped known as replication fork. These is achieved by DNA helicases
and single-strand DNA-binding proteins. They prevent herpin helices by straightening out the
regions of single-strand DNA.
Addition of deoxyribonucleotide to the 3 end of a polynucleotide chain by DNA polymerase.
Thhe new chain is guided by the template strand. Each reaction releases a pyrophosphate.
DNA polymerase in 5 to 3 direction.
Leading strand synthesized continuously, lagging strand synthesized discontinuously, fragments
known as Okazaki fragments, the most recent synthesized DNA will be near the replication fork.
After covalent binding to the chain, the enzyme undergoes a conformational change , double
chcking the correct base pairing. If the incorrect addition of nucleotide was made,
exonucleolytic proofreading takes place, in 3to 5 direction. Low error in DNA polymerization.
Direction in 5 to 3 only because a 5 end would terminate DNA synthesis, and will have the
activating triphosphate. It is possible to correct an error if nucleotide is added to the 3 end of a
DNA chain.
Leading strand uses a primer on site of replication, on lagging strand requires several primers.
Theses is achieved by DNA primase that uses short RNA primers. The short fragments are
finished when DNA polymerase reaches a previous 5 end of RNA primer. The continuous DNA
is produced by DNA ligase, that replaces that RNA with DNA and binds the strand, joining each
3 end to 5end. RNA acts as suspect copy that need to be replaced.
RNA primer at end of chromosome, is incorporated into telomers, telomerase replenishes
these seq when a cell divides.
DNA repair enzymes scan DNA and replaced damage nucleotides. DNA repair pathways: base
excision repairbase removed by DNA glycosylase enzyme, followed by excision of resulting
sugar phosphate. Nucleotide excision repair; small section of DNA is removed.












Transcription
1- General transcription factors (TFIIA, TFIIB, TFIIC, TFIID) help to position RNA polymerase at the
promoter, which is special sequence of nucleotides indicating starting point for RNA synthesis.

TFIID binds to a short double-helical DNA sequence, primarily composed of T and A nucleotides,
known as the TATA box (which is 25 nucleotides upstream from the transcription start site).
2- The region of unpaired DNA is called the transcription bubble, one strand is used as a template
for complementary base-pairing (A-T, C-G, A-U) with incoming ribonucleotides, two are joined
together by RNA polymerase to begin an RNA chain. RNA polymerase catalyze the formation of
phosphodiester bonds that link the nucleotides together to form a linear chain. RNA polymerase
moves stepwise along the DNA, unwinding the DNA helix just ahead of the active site for
polymerization to expose a new region of the template strand for complementary base-pairing.
The substrates for RNA nucleotides are ribonucleosides triphosphates (ATP, CTP, UTP, GTP). RNA
polymerase synthesizes in 5-to-3 direction.
3- Chain elongation continues until the enzyme encounters a terminator signal. There are several
termination signals, the process known as Rho destabilization is the common one, in which
protein Rho recognizes and binds preferably to sites in the RNA riches in C, one binds to RNA, it
unwinds RNA-DNA hybrids and release RNA from the transcribing process.
4- Ends of eukaryotic mRNA are modified, the 5 end is modified by capping (5-methyl cap) and
the 3 end by polyadenylation (cleavage of pre-mRNA transcript near 3end and addition of polyA tail). This is a way to confirm the presence of both ends before exporting it from the nucleus
and translating it into a protein.

Translation
Codon-group of consecutive nucleotides in RNA, means one aa or stop codon
Transfer RNAs recognizes codon by seq of anticodon, and carry a particular aa (at 3end)
tRNA, anticodon, third position can be mismatched or wobble
tRNA synthesized by RNA polymerase III, are covalently modified, tRNA suffers trimming (larger
precursor tRNA is trimmed to produce mature tRNA), splicing, copy and paste mechanism
catalyzed by proteins. Chemical modification improve recognition of mRNA codon by tRNA
molecule, an example is deamination of adenosine to produce inosine that affect conformation
and base-pairing of anticodon.
aa is coupled to tRNA by aminoacyl-tRNA synthetases, requires ATP hydrolysis
similar aa must pass through two-steps mechanism.
aa are being added to the increasing polypeptide chain at the carboxyl group of its end by the
amino group of the free aa, the carboxyl end reaming activated by its covalent attachment to a
tRNA molecule. Each aa carries the energy needed for the next aa. (peptidyl-tRNA)
Process occurs in ribosomes (rRNAs)-bind to ribosomal proteins that go into nucleus and the
exportes to cytoplasm. Ribosomes has one binding site for mRNA and three binding site for
tRNA (A, P and E sites)
Small subunit where tRNAs matched to codons, and large subunit catalyzes the formation of
the pepdite bonds.Join together only in translation by 5 end of mRNA, mRNA pulled through
ribosomes 3 nucleotides at a time.
mRNA seq is translated into aa seq using tRNA (aminoacyl-tRNA), when stop codon is reached,
ribosome finished protein.
Four reactions involved in addition of aa to elongating chain:
1-tRNA binding, 2-pepdite bond formation, 3-large subunit translocation (large subunit moves
relative to mRNA), 4-small subunit translocation, mRNA is moved three nucleotides and the
process starts again.

1- mRNA exit the nucleus and goes to the cytoplasm, where it is bind to the ribosome
complex in the small subunit of the ribosome in the 3 direction.
2- The large subunit in the ribosome consists of three binding sites, the A where the tRNA
binds, the P site that carries the forming polypeptide chain and the E site that
corresponds to the ejected tRNA.
3- The seq of mRNA is read by every 3 nucleotides, named codon, the tRNA carries the
anticodon and the respective aa.
4- The polypeptide chain starts to form when the tRNA bind to the start codon that
corresponds to methionine (AUG) the chains is synthesized in the n-terminal to Cterminal direction.
5- A tRNA binds to an A site, then new peptide bond is formed by the Cterminal end of the
forming polypeptide chain and the free amino group of the next aa, the large subunit
suffers a translocation, following a translocation in the small subunit by three
nucleotides. The tRNA in the exit position is ejected, the last tRNA is now in the P site,
and a new tRNA will bind to the A site.
6- Each cycle, elongation factors are involved that help to make the process efficient, use
hydrolyzing GTP and conformational changes.
7- The cycle continues until one of the three stop codons (UAA, UAG, UGA) signal to any
ribosome to stop translation, then the binding of a release factor occur and the
polypeptide is released.
8- The new polypeptide chain is fold up into its 3D conformation, bind to cofactors if
required, be modified by protein kinases or other proteins.
9- Some proteins require chaperones for their appropriate folding.