Cell Lectures 6-9: Exam #1

Ch 1-4 (only half of 4)

How do we know when reverse or forward rxn is favored?

Where are phosphate groups found in activated carriers? Where are they not?

NADP+ and NADPH = phosphate groups

NAD+ and NADH = none

Anabolic rxns vs Catabolic rxns

NAD+ NADPH

What does ATP transfer in a high energy linkage?

phosphates

primary structure

amino acid sequences

secondary structure; where does bonding occur

a helices and b sheets in proteins

held together by non covalent bonds such as hydrogen bonding (C=O and N-H)

local folding pattern of polymeric molecules

hydrogen bonding occurs between atoms of two peptide bonds

tertiary structure

3D structure of fully folded protein

disulfide bonds, hydrogen bonds, ionic bonds and non polar hydrophobic interactions

quaternary structure; what determines them

multiple polypeptide chains to form larger complexes

held and determined by noncovalent bonds

what are amino acids held together by?

peptide bonds

how are peptide bonds created? what atoms of amino acids join them?

condensation rxns; C and N terminus

what is a protein comprised of?

polypeptide chains linked together

what part is not involved in forming peptide bonds?

backbone/ side chain (R group)

how are dipeptide bonds formed?

when two amino acids join by 1 peptide bond

when charge is unevenly distributed, it is

polar

what holds amino acids together?

peptide bonds

what is a protein aggregate? Solubility?

abnormal proteins formed into larger aggregate structure

tends to be insoluble

what do chaperones do? what is required for function?

binds newly synthesized or partially folded chains to help them fold through most energetically favorable pathway

Chaperone function requires ATP binding and hydrolysis

what are isolation chambers? what is required for function?

Where a single polypeptide chain within barrels of chaperones can fold without risk of forming aggregates in the crowded cytoplasm

requires input of energy (ATP hydrolysis) mainly for association and subsequent dissociation of cap that closes off the chamber

What is ATP hydrolysis?

releases energy present in high energy terminal phosphate bonds

provides energy needed for processes

What cleaves DNA?

deoxyribonuclease

what are alpha helices ?

stabilized by hydrogen atoms in every 4th amino acid

what a b sheets?

side by side hydrogen bonds with flat, ridgid structures

what are a helix and b sheets common folding patterns? what structures do they form?

result from hydrogen bonds that form between N-H and C=O (NO SIDE CHAIN INVOLVEMENT OF HYDR BONDING)

secondary structure

where are side chains found in a helix vs b sheets?

a helices: on the sides

b sheets: above and below

Hydrogen bonds in a helixes are created every

4th amino acid, linking C=O of one peptide bond to the N-H of another

where are a helix abundant?

proteins embedded in cell membranes such as transport proteins and receptors

ex: portions of transmembrane protein that cross the lipid bulayer usually form an a helix

How are a helices embedded in transmembrane proteins that cross the lipid bilayer?

amino acids w nonpolar side chains

polypeptide backbone (hydrophilic) is hydrogen bonded to itself INSIDE the a helix where its shielded by the hydrophobic lipid environment of the membrane, and had protruding nonpolar side chains on the OUTSIDE

hydrophilic and hydrophobic in a helix vs b sheets:

a helix: interior (hydrophilic) exterior (hydrophobic)

b sheets: interior (hydrophobic) exterior (hydrophilic)

what is a coiled coil?

a helices wrapped around one another forming stable structures

formes when a helices have most nonpolar side chains along one side so they can twist around to have their hydrophobic chains facing inward

what 2 varieties of b sheets are there?

parallel and anti

what are unstructured sequences?

continually bend and flex due to thermal buffering ; unstructured lengths of polypeptide chains

what is a subunit?

each completely folded polypeptide chain in a quaternary structure

what is a globular protein? fibrous proteins?

when a polypeptide chain compacts into a ball shape (irregular shape)

elongated 3D structures

what helps bind cells together to form tissues?

extracellular matrix

what are disulfide bonds? when are they formed?

sulfhydryl groups (S-S bonds) of two cysteine side chains used to reinforce structures of secreted proteins

formed in tertiary structures, but also before a protein is secreted by an enzyme in the ER that links the 2 -SH groups together that are adjacent in the folded protein; does not change a proteins conformation

quaternary structures will always have 2 or more…

protein domains

what are domains ? what are motifs?

multiple polypeptide chains or subunits; 3D protein structures independent folding unit (can fold on their own)

commonly repeated sequence patterns of secondary structures

is protein folding energetically favorable or unfavorable?

favorable bc it does not require energy input

are chaperones always needed?

Although chaperone proteins assist in protein folding, they do not provide the energy needed for a protein to fold into the correct conformation.

what forms disulfide bonds/ sulfide bridges?

cysteines

what do proteins outside of the cells start their life?

in the ER

how do peptide bonds join amino aicds?

condensation rxns

Nitrogen and carboxyl groups form

peptide bonds

How can we tell if an AA will span the membrane?

alpha helix spans them

1 turn helix =

0.54 nm

how many amino acids are found in 1 turn?

3.6 amino acids

what are motids?

constructed of secondary structure folds

domains are repeated

MOTIFS ; you can have multiple domains in one polypeptide chain

what binds something specific or has some kind of conformation allowing for a certain function?

motifs and domains

many motifs create

polypeptide chains (domains)

combo of many domains makes final

tertiary structure

each subunit is a fully folded

tertiary polypeptide

How far apart would hydrophobic residues have to be if you wanted to assemble a coiled coil?

• Roughly 4 amino acids - every 4 has to be hydrophobic (creates a strip)

  • Hydrophobic side groups must congregate more towards one side

  • Allows to make hydrogen bonds above each

    • between 1st and 5th = 2 residues in the backbone that are creating the box

    • Nonpolar 3x (must be on outside) Polar 1x (every 4th = polar)

what are condensation reactions? what type of rxn and characteristics?

creates peptide bonds/ polymers and releases and H2O

anabolic rxn / nonspontaneous / unfavorable

hydrolysis

breaks polymers or peptide bonds and consumes H2O

catabolic rxn / spontaneous / favorable

what is glycolysis? what kind of pathway

where each glucose is broken down into 2 molecules of pyruvate; involves the generation of 3 carbon sugar (pyruvate) from breakdown of glucose (6 carbons)

catabolic pathway

results in formation of active carrier ATP to then be used by cell to drive anabolic rxns

anabolic vs catabolic rxns

large molecules are made by smaller ones

complex molecules degredated into simpler ones

As O2 atoms are (+) or H atoms are (-), central carbon..

becomes more oxidized

decrease in electron density due to electroneg atoms present in molecule

what is an example of oxidation of carbon? reduction of carbon

formic acid —> CO2 or methane —> methanol

formladehyde —> methanol or formic acid —> formaldehye

the more reduced the molecule, the energy amount

increases from released oxidation process

what are enzymes?

lowers activation energy for one specific rxn leading to one product

specific for one desired pathway and end product

How do you overcome activation barriers?

molecules energy increase OR barrier decrease before reaction proceeds

What is free energy?

harnessed to do work

delta G = 0 @ equilibirum and no work can be done

free energy of rxn at its lowest point at equilibrium

what do high energy bonds allow for?

can be broken to yield energy (drives lifes metabolic processes)

contains phosphates

what maintains a balanced OH and H+ concentration?

buffers

what forms acids and bases

polar molecules

*Bases = charged molecules

what is pKa?

= topH at which half molecules are dissociated and half are neutral or undissociated

pH =

pKa + log[A-]/[HA] - products over reactants

what does pKa tell us?

allows us to understand how biological systems control acidity of aq fluids

pH above pKa =

deprotonated

pH below pKa =

protonated

what happens as pH increases

carbonic acid gives away its protons as it increases

what is an example of a buffer used in cells?

carbonic acid

carboxylate group

COO-

amino group

NH3+

guamodonium group

+H2N=C-NH2

what is the isoelectric point? how is it calculated?

pH at which molecule carries no net electric charge

pl = (pKa1 + pKa2) / 2

what is the chemical character of each amino acid side chain NH2

polar h

what does the pKa tell you about a molecule? how do you determine the pl?

protonation; pl = (pKa1 + pKa2) / 2

which amino acids would naturally be found on the inside of a protein? why?

nonpolar side chains of a protein tend to join on the inside to withstand the aqueous environment and hydrophilic forces

what do cells use to catalyze oxidation of organic molecules?

sequences of rxns that allow energy to be harvested from

what makes up a cells metabolism?

anabolic and catabolic pathways

do favorable rxns increase or decrease disorder?

increase disorder; unfavorable decreases disorder (more ordered)

how do cells obtain energy?

through oxidation of organic molecules

why do enzymes bind substrates to catalyze chemical rxns?

1. lowers activation barrier

2. specific to one rxn

3. remainds unchanged

what is free energy?

determines if a rxn will occur

decreased free energy = - delta G = favorable

increased free energy = + delta G = unfavorable

decreased free energy =

- delta G = favorable = less order (more disordered)

equilibrium constants

indicates the strength of noncovalent binding interactions

activated carriers

contains energy rich covalent bonds that store energy

store energy in an easily exchangeable form, either as a readily transferable chemical group or as high-energy electrons

biosynthesis

requires energy and can utilize stored energy from activated carriers

What does delta G help us determine?

whether or not a rxn is favorable and allows us to compare reactions

thicker arrow favors that direction

what do equilibrium constants tell us?

the direction of a given reaction AND indicates the strength of noncovalent binding interactions

what are coupling rxns?

to make unfavorable rxns possible

changes in bond energy cause…

heat to be released

enzyme substrate complexes, how are they stabilized?

by formation of many weak bond interactions

who locates who in enzyme and substrate?

substrate locates enzyme

when will 2 molecules bind? depending on what?

when free energy of resulting complex is less than sum of the free energies of the 2 when unbound

how do enzymes encounter their substrates?

diffusion and noncovalent bonding interactions (enzymes bind to specific molecules based on their chemical character)

Why would delta G change?

due to amount of energy stored in a molecule and concentration

changes as it proceeds to equilibrium

What yields more product for each molecule of substrate?

negative delta G