Cell + Molec I Flashcards
Polar covalent bond
A covalent bond where one atom has the electron shared more often than the other, resulting in polarity
Hydrogen bond
the result of a polar covalent bond, hydrogen being attracted to a polar molecule
Hydrophobic or hydrophilic dissolves in water?
Hydrophilic
What two weak noncovalent bonds make up electrostatic attraction?
Hydrogen bonds and ionic bonds
4 types of weak noncovalent bonds
hydrogen bonding, ionic bonding, van der walls attractions (weak attractions b/w nonpolar moelcules), hydrophobic force: (nonpolar substances ushed together by water)
Hydronium vs hydroxyl
h3o+ and OH-
what are acids and bases
acids add Hydrogen ions to the water, bases accept
what are fatty acids
hydrophobic lipids avec un hydrobcarbon tail and a carboxyl group (COO-)
amino acid components
alpha carbon, amino group, carboxyl group, 1 of 20 residues
nucleotid components
5-C ribose sugar, phosphate group, 1 of 4 nitrogenous bases
how are polymers formed?
via condensation reactions of monomers
how do you break apart polymers?
VIA hydrolysis
polysaccharide bonds
glycosidic bonds
single monomers of a polypeptide?
amino acids!
nucleic acid monomer
nucleotides
Metabolism
sum of all chemical reactions happening in a living system
Catabolism
breakdown of molecules, releasing energy (cellular resp. is an example)
Anabolism
biosynthesis; assembles molecules using E (ex. photosynthesis)
1st and second law of thermodynamics
E cant be made or destroyed, closed systems tend toward entropy
-delta G and +delta G
favorable and unfavorable chemical reactions
Free energy vs Heat
useful and unuseful energy in a system
How does metabolism harvest energy?
metabolism: oxidizing organic molecules and building up large molecules through reduction
Oxidation vs reduction reactions
removal of electron, sometimes by adding oxygen, adding an electron, sometimes by removing oxygen
Reduction oxidation reaction (redox reaction)
reducing something and oxidizing something else (oxidizing releases energy that then can be used for reduction)
What do enzymes lower?
activation energy
Catalyst
speed up chemical reactions without reacting or being used up
what do enzymes act upon
substrates
Equilibrium constant K
The ratio of reactant to product at equilibrium; higher means reaction is more favorable
what makes reactions go faster? (3)`
higher substrate to product concentration, higher temperature, more substrate concentration
Where does the enrgy to power unfavorable reactions come from
coupling favorable reactions with them
ATP name
Adenosine triphosphate
What is an activated carrier?
a small organic molecule that delivers energy for coupling; delivers one or more high energy bonds to a location
unfavorable: phosphorylation
Condensation of ADP to make phosphate bonds
Favorable: Hydrolysis of ADP
breaking bonds
What does Glutamine Synthase do?
Combine glutamic acid and ammonia to make glutamine; changes one aa to another (Uses STP to make glutamic acid into a higher energy state)
two examples of activated carriers
NADH and NADPH
what is NADPH used for?
light rxns in photosynthesis , Calvin cycle fixes CO2 to make sugar (Done by reducing NADP+ with hydrogen w 2 electrons)
what is NADH used for?
Catabolic rxns to synthesize ATP through cellular respiration
What BINDS to a protein?
A ligand
4 (1/2) levels of protein organization
aa sequence
alpha helices and beta sheets
helices sheets, loops and all
(protein domains)
interaction of multiple polypeptides
components of an amino acid
Central carbon, carboxyl group, aa side chain (residue), hydrogen, and amino group
what parts of an a.a. bind together in a condensation reaction
a carboxyl and amino group
Polypeptide backbone
repeating chain of N-C-C- that holds aas together
2 termini of an a.a. polypeptide
amino (N) terminus and a Carboxyl terminus (C)
What do chaperone proteins do?
speed up folding of proteins
what noncovalent interactions fold proteins?
electrostatic, Van der Waals, hydrophobic force,
What does secondary protein structure arise from?
the polypeptide backbone H-bonds
rigid structures of secondary organization
Alpha Helices; b/w C-O and N-H amino acids (1full turn is 3.6a.a.)
Beta Sheets; backbone H-bonding b/w nearby segments
intrinsically disordered segments
flexible segments b/w rigid structures
Disulfide bond usage
sturdier bonds for extracellular use (uses cysteine side chains, which have sulfur in em)
what holds together each of the protein organizations?
1’ – covalent bonds
2’ – hydrogen bonds
3’ – weak noncovalent bonds
and sidechain interactions
4’ – (same as 3’)
antibodies;
proteins that bind to specific antigens, their binding sites are intrinsically disordered sequences, the ‘variable domain’
antigen
the spp molecule an antibody binds to
epitope
the spp part of an antigen recognized by the antibody
what does antibody binding to an antigen do?
neutralizes it and marks it for destruction
what makes antibodies?
B lymphocyte
antigen structure
Quaternary structure that is Y shaped, with two heavy and 2 light chains, stabilized by disulfide bonds
Michaelis constant
Km; substrate whose enzyme is functioning at 1/2 Vmax
Lysozyme
it cuts polysaccharides in bacterial cell walls; its in our saliva tears and egg whites. 129a.a. // it hydrolyzes b/w sugars and can hold up to 6 polysaccharides at a time
enzyme process (4 steps)
substrate + enzyme, Enzyme-substrate complex, enzyme-product complex, enzyme + product
how does lysozyme break polysaccharides?
(basic)
when the polysaccharide is in the right conformation, water Hydrolyzes it without energy use because it is energetically favorable.
Cofactor
additional molecules needed for functionm (hemoglobin subunits have a *heme group)
Coenzyme
organic cofactor, activated carrier that transports functional groups (ex. ATP has a phosphorous group)
how does lysozyme break polysaccharides?
(advanced)
1) 6 sugars bind in active site and hydrolyzing happens D & E
2) ENZYME-SUBSTRATE COMPLEX, gLU35 GIVES AN ELECTRON via hydrogen,
Asp52 can bind to C1 on D (malforms sugar)
3) sugar is now in a transition state where it can be broken
Asp52 is covalently bonded to D
4) enzyme-product complex formed
H2o splits H+ to Glu35
Asp52 bond displaces
5) product released
What are all vitamins?
coenzymes
Nucleic acids are what?
polypeptides of nucleotides, and it is one DNA molecule.
Allosteric enzymes…
have 2+ binding/active sites (active is for enzymes), Binding in one site normally causes a conformational change, which changes function
nucleosome parts
nucleosome core particle + linker DNA
nucleosome core particle parts
8 histones and about 146-147 bp of DNA & linker DNA (string b/w beads)
name of histones that bundle nucleosomes
H1 Linker histone
widths of all the chromatin levels of chromatin and names
nucleosomes; 11nm
Chromatin fiber; 30nm
Loop domains; 300nm
1 mitotic Chromosome; 700
2 different chromatin packing and unpacking techniques
ATP-dependent chromatin-remodeling complexes: Change the position of DNA wrapped around a nucleosome
Histone-modifying enzymes; covalently modified histone tails (acetylation of lysine 9 turns heterochromatin on/off )
nucleotide parts
phosphate group, Ribose Sugar, R group (one of the 4 nitrogenous bases)
dNTP
deoxynucleotide triphosphate
purines and pyrimidines
purines are double ringed (A and T)
pyrimidines are single rings (G and C)
how are nucleotides combined together?
covalent phosphodiester linkage
what holds together the two nucleic acids in a DNA helix
hydrogen bonding of complementary base pairing
which are stronger; A-T or G-C bonds?
G-C bonds
name all the proteins for DNA replications and which use ATP
s-s binding P
helicase (ATP)
topoisomerase
ligase (ATP)
Clamp loader (ATP)
Sliding clamp
DNA pol I and III
Primase
how many catalytic domains does DNA pol III have and what is the purpose?
one is for replication and one is for proofreading; this lowers the error rate
