BMSC 200 - Midterm 1

what is all illness ultimately caused by

a malfunction at the molecular level

define biochemistry

the study of life at the molecular level using chemistry to explain biology

how different are pro and eukaryotes at the molecular level

identical; ecoli = elephant

what 4 elements make up 98% of living organisms

C,N,O,H

if all known life wasn't carbon based, what would be the next best option? why?

silicone- it is highly abundant in the earths crust, and also likes to form 4 bonds

why is carbon preferable over silicon

it can be recycled within the biosphere, and a carbon carbon bond has more energy than a silicon silicon

explain where we get each of the 4 major elements of life

Carbon - from plants that photosynthesize

N - haber process

O - air and water

H - water

what is sciences motto

on the word of no one

define a molecules conformation

molecules 3D shape. can be changed WITHOUT breaking covalent bonds

ex) 2 chair forms of cyclohexane

define a molecules configuration

the fixed spatial arrangement of a molecule

what gives us a molecules configuration in biochemistry

double bonds and chiral carbons

describe the isomers arising from double bonds and why they determine configuration

cis and trans isomers-can have very different properties

the double bond (pi bond) restricts rotation of atoms around it

describe chiral carbons.

carbons with 4 different substituents attached. 2 stereoisomers (L & D) arise from these.

when are l and d isomers "identical" and when are they different

chemically identical- but they differ when reacting with chiral molecules (left and right hands)

what is an important caveat for chirality substituents

the ENTIRE GROUP is considered as the substituent, not the atom its directly bonded to

why is it useful to construct biomolecules from simple building blocks

simplicity- use the same machinery

recycling - cow protein to human protein

diversity - infinite combo of molecules

how are lipids different from the other 3 biomolecules

they are aggregates, not polymers

does the human body have more prokaryotes or eukaryotes (by number)

prokaryotes - 100 trillion vs 30 trillion

why does context matter when studying biomolecules

biomolecules tend to behave differently in vitro, vs. in vivo

State the 1st Law of Thermodynamics

the amount of energy in the universe is constant

state the second law of thermodynamics

the total entropy of the universe always increases (the entropy of a system can decrease, but never the universe)

what does Gibbs free energy do

relates the enthalpy change and entropy change of a rxn, to tell us if it will be spontaneous (if it will proceed)

state the formula for gibbs free energy

△G = △H - T△S

what do the signs of delta G values tell us

greater than 0 = non spontaneous/ endergonic

negative = spontaneous/ exergonic

0= equilibrium

describe reaction coupling and what it is used for

coupling an endergonic rxn with an exergonic one (usually ATP hydrolysis)

differentiate between anabolic and catabolic

Anabolic = Build

catabolic = degrade

AB CD

why does protein folding SEEM to fly in the face of the second law of thermodynamics

because the enthalpy change is 0, and the structure gets MORE ordered

is a drug that kills 99% of e-coli an effective one?

no- they multiply so rapidly they would soon be back, and would start to select for drug resistant strains

what are the 3 requirements for life to continue that DNA fulfills

genetic info 1) stored in stable form

2) accurately expressed

3) easily reproduced

describe waters passive and active roles in biochemistry

passive= influence how proteins fold

active = dehydration synthesis

how do weak interactions allow for cells' amazing structures and functions

many weak interactions = very strong (phone book)

changing interaction means molecules can ADAPT to different functions

what percentage strength is a hydrogen bond relative to a covalent bond

5%

which atom is a hydrogen bond donor, and which is an acceptor in a h-bond

donor= supplies the hydrogen

why does the geometry of Hbonds have big implications

because shorter bonds are stronger (more stable)- so geometry matters when forming structures such as beta sheets

what makes the specific heat capacity and heat of vaporization of water so high

the fact molecules of water will Hbond with an average of 3.4 other waters. "flickering clusters"

why does hot water freeze faster than cold water

no one knows; the opposite is not true- cold water will NOT boil faster

what should you be thinking as soon as you see an O or N in a molecule

Hydrogen bonds! O and N are the primary acceptors and donors

what do all peptides start with

NH³⁺

which secondary structures can be amphipathic

alpha helices AND beta sheets

how is waters high specific heat capacity beneficial to humans

as isotherms, we burn our body weight in ATP each day- water helps keep us cool

why was "polywater" - lower freezing point, higher b.p, etc. such a scare

because life depends so much on water, it would go derp without it

define amphipathicity

having both polar and non polar regions

what is brownian motion

the inherent kinetic energy of molecules, due to temperature

what are the 2 things that determine a substances solubility in water

if its charged

if it can form hydrogen bonds (polar)

which would have greater solubility in water- a polar substance with hydrogen, or one without

with hydrogen- can act as donor AND acceptor

what does a single nonpolar molecule do when placed in water, w.r.t entropy

it DECREASES entropy of the WATER; makes the molecules around it more ordered

what allows proteins to fold in water, obeying the second law of thermodynamics

the fact that the proteins decreasing entropy will cause the water to increase entropy (less surface area of protein means more water can be disordered)

name the 4 types of noncovalent interactions

hydrophobic interactions, Hbonds, electrostatics, van der waals

state the function of phosphatases

remove a phosphoryl group

what are the 3 things a functional group in a biomolecule could Hbond to

intermolecular groups

intramolecular groups

water

does Hbonding CAUSE a protein to fold?

NO; it just determines HOW it folds

what Hbonding geometry is stronger

antiparallel

what is important to remember when discussing biochemical reactions

all occur in the context of water

what type of force can electrostatic interactions be

attractive or repulsive

why is the strength of electrostatic interaction greatly diminished in biomolecules

because water will come and shield it with Hbonds

what amino acids contain a carboxyl?

all of them!

(don’t answer questions too fast)

state the function of van der walls interactions/london dispersion

how important, non charged biomolecules interact.

the preferred distance atoms like to be (not too close, not too far)

where would you expect to find lots of van der waals interactions

in the core of folded proteins

describe hydrophobic interactions

the drive to have polar groups facing water and nonpolar groups hidden from water

explain the cheerio effect

2 cheerios placed in a bowl will eventually find each other, and stay that way

this is because the second law of thermodynamics states entropy always increases; and the entropy of WATER is higher when the cheerios are together (less surface area ordering water molecules)

what would happen if the pH of blood changed by 0.5 in either direction?

why is this?

coma, or death; pH is an important parameter of biological systems

one reason is H bonds may not form at other pH’s

what is physiological pH

7.4

what is Kw and what does it tell us

waters ionization constant- 1.0x10^-14

tells us how much water dissociates (ionizes)

what kind of pH changes do we deal with in biochemistry

very subtle ones

is a small pH change (ex. 0.1) insignificant?

NO; dont forget the pH scale is logarithmic

ie) every unit is tenfold change in [H]

what is Ka equal to?

what does a large Ka value mean

[products]/ [reactants]

large Ka = strong acid

what does a SMALL pKa value mean

a STRONG acid

how does our body maintain physiological pH

buffers (duh)

define a buffer

a solution that resists pH changes when acid or base added

what occurs when pH = pKa on a titration curve

[HA] = [A⁻]

ie) the acid is half dissociated

what is the ideal buffering zone/buffering capacity of a buffer

a zone that extends 1 pH unit on either side of pH = pKa

why would a molecule have 2 different buffering regions on its titration curve

it has 2 functional groups that can act as weak acids

What is the Henderson-Hasselbalch equation?

pH = pKa + log ([A-] / [HA])

define quaternary structure

as soon as there is more than 1 polypeptide chain interacting

are the subunits of quaternary structure the same or different

can be either

what does it mean if pH is above pKa

more of the UNprotenated form present

what does it mean if pH is below pKa

more of the protenated form present

how can we tell if a substance is buffer just by looking at its titration curve

if it has a flat portion = the buffering region

how many buffering regions is the minimum of every amino acid

2: every amino acid is at least diprotic

what determines a proteins 3D structure

the linear chain of amino acids

distinguish between peptide, polypeptide, and protein

peptide = 1-8 amino acids

polypeptide = 8-50 amino acids

protein = 51 amino acids (the length of insulin, the smallest protein)

what is the ideal protein source for a human

another human (same amino acid profile)

what amino acid is achiral

glycine. thats it

which amino acid isomers are used to make proteins

only the L isomers (Living)

what amino acid(s) allow for disulfide bonds

cysteins

in what kind of protein would you expect a lot of covalent linkages

proteins facing harsh conditions (extremophiles)

proteins that need tough structure (rhino horn)

Dechipher the phrase "Life Always Has A Goal"

Lysine, arginine, histidine, aspartate, glutamate

first 3 are the +, last 2 are the -

name 2 post translational modifications that we study

phosphorylation

and adding an -OH

state the function of kinases

add a phosphoryl (PO₃²⁻) group

list all the triprotic amino acids (may help to draw them)

Tyr, Cys, Asp, Glu, Lys, Arg, His

what determines a compounds solubility in water

polarity/ charge

hydrogen bonding capability

consider the peptide QYLH

which is the N terminus and which is the C terminus?

Q = n terminus

H = c terminus

(always presented N to C)

why does folding a polypeptide increase the entropy of water

because in an unfolded polypeptide, water molecules near non-polar portions have LESS freedom of movement/restricted movement

describe what a peptide bond forms between and how it occurs

forms between a carboxyl of one AA and the amino of another. forming it releases a water molecule

why should you not eat meat on a desert island

breaking down protein's peptide bonds is a hydrolysis reaction

what is the charge of a peptide bond

it is neutral

what does the resonance structure of a peptide bond result in

it locks the atoms around the bond in place

leads to cis/ trans isomers

what stereoisomer about the peptide bond is favoured?

why?

trans, because less steric strain between the side chains

what is secondary structure, and what are the 2 factors that an allowable form of it must meet

localized folding within a polypeptide

it must:

I) be an allowable/ realistic way of folding the chain

i) optimize MAIN CHAIN hydrogen bonds

what are the 2 angles that determine an allowable secondary structure

the phi angle between α C and nitrogen

the psi angle between a C and carbonyl carbon