BCH Exam 1

Myosin

- 2 polypeptide chains that has 2 heads with binding sites for ATP, two light chains on each neck,heads act independently - tails associatie for form thick filament, headband to actin thin filament, in contracted position heads pull actin closer to center

Edman sequencing

- derivation of N term -N term hydrolyzed by acid - N term reacts with PITC causing LG creating original polypeptide minus its N term -can be repeated many times - can be bad bc acidity can cause whole polypeptide to break apart

Tubulin

- dimer permanently glued together by GTP, alpha tubulin and beta tubulin -forms hollow cylinder -13 protofilaments bind side by side to form a microtubule -beta tubulin can bind and hydrolyze GTP -assembly and disassembly faster at (+) end - used to make flagella and cilia -used to separate chromosomes in mitosis

name the three main structural proteins and their relative sizes

-Microfilaments, actin, small -Intermediate filaments, collagen, keratin, medium -Microtubules, tubular, big af

SDS-Page

-SDS: ionic detergent that denatures proteins, makes linear -PAGE: Gel matrix, proteins move toward positive electrode -mobility inversely proportional to size aka smaller size moves faster down gel

what can misfolded protein aggregation result in and what is caused by?

-caused by more exposed hydrophobic residues exposed -> hydrophobic effect - can lead to diseases like alzheimer's, parkinson's, "mad cow"

which amino acids are basic?

Arg, Lys

which amino acids are acidic?

Asp, Glu

what are the most abundant biological elements and what is their tier?

C, N, O, H, 1st tier

which amino acids contain sulfur?

Cys, Met

H

Enthalpy, heat of system, += energy absorbed, -= heat released

T/F Histidine is always an uncharged polar amino acid.

FALSE, histidine can be charged in certain PHs->protonated

G

Gibbs free energy, energy able to be used on a system for work, -deltaG= spontaneous exergonic energy released ,+deltaG= non spontaneous endergonic energy absorbed

Amino functional group

NH3+

T/F most proteins fold spontaneously

TRUUUUUUU

what are the three domains of life?

bacteria, archaea and eukaryotes. prokaryotes are bacteria and archaea

ionization of water

before anything is added to water there is already H3O+ ions present. k=[H+][OH-]/[H2O], Kw=10^-14 in pure water

what bonds are involved in Hydrogen bonding interaction?

covalent and hydrogen bonds, H atom tugged between two electronegative molecules

van der waals

distance from nucleus to surface, orbitals as close as possible without overlapping, no bond, dipole-dipole interactions-> between two polar molecules, london dispersion forces-> between non polar molecules

Hydrogen bond

electronegative element covalently bonded to H atom and electrostatically attracted to second H atom.

ionic bond

electrons transferred from one atom to another, low electronegativity of one atom is complemented by high electronegativity of another atom, all ionic bonds have some degree of covalence none are PURELY ionic

properties of water:

highly cohesive, can bond to four other water molecules at one time by H bonding,

which amino acids are cyclic?

his, thr, pro, try, trp

quaternary structure

special arrangement of polypeptide chains in a protein with multiple subunits, not all proteins have this, ionic bonds, van der waals, disulfide can be homo (collagen) or hetero subunits(hemoglobin)

characteristics of peptide bonds

-are resonance stabilized -brings C closer to N than in normal amine bond causing shorter stronger bond -no free rotation of C-N bond -strong tendency to form H bonds - atoms in peptide bond are strongly polar causing chains to fold so that it makes as many H bonds as possible while decreasing steric strain

similarity and difference between structure of Hb and Mb

-hemoglobin and myoglobin both carry heme prosthetic group, both have alpha helical chain with 8 helices, same function to carry oxygen, are homologous proteins -Mb is a monomer, heme group more exposed to solvent -while Hb is a tetramer -different in primary structure, only 18% similar

Y vs. pO2 for Mb

-hyperbolic curve -binding increases rapidly until most molecules are saturated -k= P50 where Mb is half saturated 2.8 torr -at low pO2 binding increases - myoglobin has high affinity even in low pO2 -at low pO2 Mb has 10 times the affinity for O2 than Hb

Intermediate Filaments

-made of elongated fibrous proteins -8 prototfilaments -V strong-> exclusively structural, static -keratin: dimer of coiled coil alpha helices, 7 residue repeat, #1 and #4 residues are non polar(hydrophobic) and line up along one side of helix to form van der waals interactions, part of hair and nails, cross linked s-s bonds -collagen: trimeric molecule, part of bones and tendons, most abundant protein in most vertebrates, every third residue is Gly,forms narrow left-handed helix, polypeptides form to make right handed helix, Gly in center->no other residue small enough to fit, triple helix stabilized by H bonds, processed after secretion from cell

kinesin

-microtubule associated motor protein -shorter neck than myosin, light chains at opposite end of polypeptide to hold onto vesicle --move by stepping precessive, one head always bound -ATP hydrolysis driven -heads work together

X-ray crystallography

-purify protein to homogeneity -crystallize under ideal conditions -bombard with x-ray -generated diffraction pattern that can analyzed -get 3D map of electron density -good for determining tertiary structure of amino acids

binding of O2 to Hb

-sigmoidal curve (S shaped) -p50=26 torr - at low pO2, O2 is reluctant to bind Hb - as pO2 increases, affinity increases -binding is cooperative meaning the first O2 binds with less affinity than the 4th oxygen (4th O2 has 100 times more affinity)->allostery:binding of one site affects binding at another

what protein structure is lost in denaturation? what causes denaturation?

-tertiary, then secondary -denaturation is caused by PH change, temp change, solubility and ionic strength

Actin

-two forms of actin: G actin which is globular and monomeric with ATP binding site and F actin which is filemental double chain subunits -(-) end with ATP site -grows faster at (+) end -ATP hydrolyzed after addition -older actin bound to ADP -polymerization of actin is reversible making it a dynamic -2 prtofilaments make microfilament

Hb binds to O2 very well in the lungs(high pO2 ) to bring O2 to the muscles ounce in the tissues(low pO2) it releases oxygen bc of low affinity in low Po2. Myoglobin takes over in tissues(low pO2) to pick up O2 and delivers it to the mitochondria

...

what are the four types of unit molecules and what are the characteristics of each?

1) Amino Acids- contain an amino group and a carboxylic acid group, contains at least two ionizable groups (+ and -) 2) Carbohydrates- C(H2O)n, multiple -OH groups, convertible between closed (ring) and open forms 3) Nucleotides- 5 carbon sugar with N counting base ring, phosphate groups 4) Lipids- amphipathic (both polar and non polar), mostly hydrophobic

order the bond interactions from strongest to weakest

1) covalent bond 2) ionic bond 3) hydrogen bond 4) van der waals interaction

name the 4 types of ways proteins can be processed after translation:

1) part of the protein can be clipped off -signal sequence: direct to location -prosequence: for digestive enzymes prevent them form vitally being active once clipped off they become active 2)another chemical group can be added -convert to active or inactive -further stabilization 3)may associate with cofactor: needed for function 4) may have >1 stable confirmation: enzymes often change confirmation during catalysis

name the three types of polymers and the bonds that form them.

1) proteins- polymers of Amino Acids formed by peptide bonds/amino bonds 2) Nucleic acids- DNA or RNA, polymers of nucleotides formed by phophodiester bonds 3)polysaccharides- polymers of carbs joined by glycosidic bonds

myosin mechanism

1) reaction begins with myosin bound to an actin subunit of thin filament. ATP binding alters the configuration of myosin head so that it releases actin. 2) the rapid hydrolysis of ATP to ADP + Pi triggers a conformational change that rotates myosin lever and increases affinity of myosin for actin 3) myosin binds to an actin subunit further along the thin filament increasing affinity for actin 4) binding actin cause pi and ADP to be released. myosin lever returns to its original position causing thin filament to move relative to thick filament (POWER STROKE) ATP releases lost ADP to repeat reaction cycle. - myosin head does not stay bound to ATP/ADP and filament at same time -power stroke at end of sequence

what are the two chiralitites that amino acids can be?

1)Levoratory-rotates polarized light to the left, "L-" 2) dextrotoray- rotates polarized light to the right, "R-" all amino acids FOUND IN PROTEINS are L-enantionmers

how many categories are there for amino acids?

3 polar charged polar uncharged nonpolar

tertiary structure

3D structure of entire peptide, H bonds, ionic bonds, disulfide bonds, van der waals, driven mostly by hydrophobic effect, hydrophobic residues buried within the middle of protein

how many other molecules can one H2O bind to by H bonding ?

4

about what percent of the human body is water?

60%

which of the following processes are spontaneous? a) a reaction that occurs with any size decrease in enthalpy and any size increase in entropy b) a reaction that occurs with a small increase in enthalpy and a large increase in entropy c) a reaction that occurs with a large decrease in enthalpy and a small decrease in entropy d) a reaction that occurs with any size increase in enthalpy and any size decrease in entropy

A, B, and C

which amino acids are technically not hydrophobic, polar, or charged?

Gly

proton jumping

H+ relayed through a network of water molecules, proton crown surfs over water molecules

whats the strongest acid that can exist in biological systems?

H3O+ because other strong acids like HCL dissociate completely in solution

which amino acids are aromatic?

HIs, Phe, Tyr, Trp

which amino acids are sometimes charge ar physiological PH?

His, Cys, Ser, Thr, Tyr

Which amino acids are polar charged?

KRED

binding of oxygen to myoglobin

Mb+O2=MbO2 unbound-> bound Ka=[MbO2]/[Mb][O2] can be backwards for dissociation as binding affinity increases K decreases amount of O2 bound to myoglobin is a function both O2 concentration(pO2) and its affinity for O2(k) pO2/(K+pO2)

which amino acids are polar uncharged?

NQSTY CH nasty cooch LMAO H can sometimes be charged

protonation of molecules:

PH<Pka protonated PH>Pka deprotonated

what is the relationship of PKa Ka and acid strength?

PKa=-logKa larger Ka= smaller PKa pKa decrease = increase in acid strength when PH=Pka [HA]=[A-]

what is the principal of coupling reactions?

Spontaneous biochemical reactions can be coupled with unfavorable reactions to net negative change in free energy

the side chains of amino acids are in what confirmation?

Trans confirmation

when PI=PH what is the net charge of the molecule?

Zero bihh-> its a zwitterion

aggregation of non polar molecules in water causes what?

a decrease in entropy of the non polar molecule, an increase in the entropy of water( less ordered bc its lipids lined up next to each other allowing less water molecules to surround the liquid than if the lipid molecules were separated), aggregation of non polar molecules is spontaneous obvi

define zwitterion:

a molecule that's an overall charge of zero and contains at least two ionizable groups of + and - charge showing characteristics of both acid and base. Amino Acids are zwitterions

T

entropy, disorder of the system

DeltaG=0

equilibrium, living systems are never at equilibrium, they work towards homeostasis which is a stable condition of non equilibrium where deltaG is <0 (neg)

what mutation leads to sickle cell anemia?

hemoglobin mutaion

what makes a hydrogen bond strong or weak?

liner alignment makes a hydrogen bond stronger, confers geometric constraints

What biological molecule cannot form polymers and why?

lipids cannot form polymers because they lack a common functional group to be joined by.

secondary structure

localized confirmation of polypeptide backbone, H bonds, -alpha helix->right handed, r groups face out, linear H bonds between amino acids 1 and 4 -beta sheets-> antiparallel (more stable bc of linear H bond) or parallel, H bonds are inter- and intra- chain

The Pk of CH3CH2NH3+ is 10.7 would the Pk of FCH2CH2NH3+ be lower or higher?

lower(more acidic) because the highly electronegative F causes the Nitrogen to pull less on its electrons

dielectric constant

measure of solvents ability to decrease electrostatic attraction of ions, measure of effectiveness as an insulator of charge, high dielectric constant= high polarity

condensation is usually involved in what?

modular construction of macromolecules

Chromatography

most common form of protein isolation. uses porous matrix of beads to separate size of proteins. size exclusion-> separation based on size -small molecules can fit in bead and are slowed down, large molecules cannot fit in bead so fall faster through the matrix

what type of reaction are most metabolic reactions?

most metabolic reactions are oxidation-reduction reactions

what type of bond is most of the cell's architecture held together by?

mostly held together by weaker bonds/ interactions because they can easily be broken and reformed which is vital for molecular dynamics. van der waals

metabolic reactions can be catalyzed by what?

mostly proteins, some RNA

at which PH would an amino acid bear both a -cooh and an -nh2 group?

no pH, not possible

Heme group

porphyrin ring central Fe2+ ion coordinated to 4 N atoms of porphyrin ring, alternating single and double bonds causing resonance, iron carries oxygen

PH= -log[H+]

power of hydrogen, as [H+] increases PH decreases (becomes more acidic)

what does the GroEL-GroES complex do?

prevents aggregation of misfolded proteins, allows it to fold inside center of chaperone by bidding to ATP

all proteins contain what type of protein structure?

primary, secondary and tertiary

what amino acid is the only Imino acid?

proline bc its side chain loops back on its own backbone, causes kinks in polypeptide chain

bronzed-lowry base

proton acceptor

bronsted-lowry acid

proton donor

PI

relates to charge state of an entire molecule PI has same relationship as Pka to everything else PH< PI positive charge on molecule

formation of peptide bond does what?

releases water

monomers in polymers are called what?

residues

primary protein strcture

sequence of amino acids, peptide bonds, dictates 3D structure

Covalent bond

strongest bond, two atoms share valence electrons, atomic orbitals overlap, shortest bond length-> strongest bond

what is the function of a buffer?

to resist PH change when [HA] and [A-] doffer by no more than a factor of 10. effective PH range for buffers is =PKa + or - 1

why do disulfide bonds form with cysteine residues?

to stabilize a protein in an oxidizing environment to prevent protein denaturation

what type of bonds is in one water molecule? how many sets of unpaired electron are there?

two hydrogens covalently bonded to an oxygen atom. too pairs of unpaired electrons causes water to be polar,unequal sharing of electrons

hydrophobic effect

water molecules have to be orientated with polar ends away from non polar molecules, decreases entropy(S) of system bc less movement allowed, blocks in hydrophobic molecules, water and oil, water molecules form cages around hydrophobic chains -> forces water molecules to be highly ordered. aggregation of these molecules causes a decrease in entropy of the non polar molecule, an increase in the entropy of water( less ordered bc its lipids lined up next to each other allowing less water molecules to surround the liquid than if the lipid molecules were separated), aggregation of non polar molecules is spontaneous obvi

Atomic orbital

where we are most likely to find an electron. can combine to form hybrid orbitals needed for molecular bonding interactions