Biochem Exam I Flashcards
List all of the IMFs
- van der waals
- dipole-dipole
- hydrogen bond
- ion-ion (salt bridges aka ionic)
- ion-dipole
- hydrophobic interactions
What are IMFs? and what language do we use when discussing molecules with IMFs? inTER vs inTRA?
1) language: “_____ is capable of participating in IMFs”
2) Intermolecular Forces are HOW molecules interact with each other and how that affects their environment; its the attraction that could exist; they “rule the world”; it is all based on charges and how opposites attract; this is HOW a cell knows what to do; proximity is important
3) inTER is what we’re talking about… between molecules; inTRA is within a single molecule
side note: all IMFs are non covalent interactions bc you never have an actual bond form where there is the sharing of electrons
ion-ion
salt bridges are formed; this is also known as an ionic bond; classic example is salt
what is a dipole?
unequal sharing of electrons leading to partial charges
ion-dipole interaction
this is an interaction between a charged molecule and a molecule with dipole interaction happening
write down some examples; draw them
dipole-dipole
2 partial charges from differences in electronegativities; arrow towards partially negative atom
van der waals
this interaction is dependent on proximity; basically there are changes in electron densities within a molecule (bc molecules don’t just sit still in one perfect distribution of densities) and you get TEMPORARY dipoles with any molecule in close proximity with an opposite partial charge
hydrophobic effect/interactions
with this interaction you have something that is not mixing with water
hydrophobic: water hating; nonpolar (can’t hydrogen bond); when they do dissolve they form a cage-like structure to get away from water
hydrophilic: water loving; polar
prime example: phospholipid bilayer in the cell membrane with a hydrophilic head and a hydrophobic tail… they arrange themselves so that hydrophilic is with hydrophilic and hydrophobic is with hydrophobic
hydrogen bonding
- you must have H bonded to either Nitrogen, Oxygen, or Fluorine
HOWEVER - there is no Fluorine in biochemistry so we ignore her - this is basically just a special dipole dipole interaction because H gets a partial positive charge and the N and O have partial negative charges
- very polar bond (strong)
- stable bond increases overall stability (higher melting and boiling point bc harder to break those bonds)
What is the trend for Ka values and how do you calculate it?
BIGGER Ka = STRONGER acid
[H+] [A-] Ka = ---------------
[HA]
What is the trend for pKa? How do you calculate it?
SMALLER pKa = STRONGER acid (an acid is stronger bc more of it dissociates; there is more product than reactant)
pKa = -log(Ka)
What is the henderson-hasselbalch equation and what do we use it for?
pH = pKa + log(A-/HA)
We can find the pH given concentration of conjugate base and concentration of acid
What are the important parts of a titration curve?
- half equivalence point
- equivalence point
- buffer region
What does a flat part of a titration curve signify?
The pH isn’t changing … this is where the 1/2 equivalence point where the acid has only dissociated half of the way. This means there are equal amounts of acid and conjugate base in the solution.
A buffer region
what does a steep portion of a titration curve signify?
The pH is changing rapidly and a lot. This is the equivalence point where the acid has fully dissociated; moles of base = moles of acid; they neutralize eachother
what is a titration?
slow addition of a titrant to a solution using a burette bc it has a stopcock
What happens at the 1/2 equivalence point?
pH = pKa; this is where half of the acid has dissociated; equal amounts of acid and its conjugate base; this is where the titration curve is flat
what happens at the equivalence point?
this is where the acid has fully dissociated; there are equal amounts of acid and base; this is the steep part of the titration curve
What is a buffer?
It is a solution that resists pH; but it is not unlimited bc it has a CAPACITY
What affects buffer capacity?
concentration of the buffer (more buffer higher capacity)
buffer region
This is the region of a titration curve where the pH is +/- 1 of the pKa value; these are the flat regions of the curve
When a titration curve has multiple flat points, what does this mean about pKa?
This means there are multiple pKa values at play
Example: you want to make a buffer of pH 6, what molecule do you use
- well you want something where 6 = + or - 1 of the pKa value
- need pKa around 6
What are the main components of a nucleotide?
- carbon backbone (pentose sugar)
- nitrogenous base
- phosphate group
How long is a typical covalent bond?
1.5 to 2ish Angstroms
How long is a hydrogen bond?
3 angstroms
what holds together the sugar phosphate backbone of nucleotide?
covalent BOND (keep length in mind)
the nitrogenous bases are split between what 2 groups? which bases fall in which category?
purine = adenine and guanine
pyrimidine = cytosine and (thymine or uracil)
purine vs pyrimidine
purine = 2 rings
pyrimidine = 1 ring
What are the base pairs? Why do they pair the way they do?
A + T or U
C + G
purines pair with pyrimidines
RNA vs DNA structure wise… where is this difference
RNA has a hydroxy group on the sugar phosphate backbone while DNA only has a hydrogen
This happens on 2’ carbon
Why do we use primes on some carbons when discussing nucleotides?
primes are used to distinguish between carbons of the backbone (prime) and carbons in the nitrogenous base
What are the significant carbons on the backbone of nucleotide?
1’ = nitrogenous base
2’ = OH for RNA or H for DNA
5’ = phosphate group
Why are DNA backbones negative?
because the phosphate group has a negative charge bc it is deprotonated
What is the directionality of nucleotides?
5’ to 3’
the 5’ end has a free phosphate group
the 3’ end has a free hydroxyl group
What process makes DNA? and what does it do?
Condensation: forms a new covalent bond between 2 molecules by losing a water molecule
Dehydration versus Condensation
both require a loss of water
Dehydration: form an ALKENE from alcohol (form a pi bond within ONE molecule)
Condensation: forms a new covalent bond between TWO molecules
Hydration vs hydrolysis
both ADD water in
hydration: addition reaction where you break a pi bond within ONE molecule
hydrolysis: add water in to break a sigma covalent bond
Why do we use condensation and hydrolysis in biochem instead of dehydration and hydration?
Water is endless supply; we constantly build things up and break them down
What is the phosphodiester link?
- link between more than one nucleotide
- polynucleotide formed through condensation
- ester group and phospho group
x-ray diffraction
- uses electromagnetic wave (part of spectrum of light)
- light bounces and when it hits things we get diffraction; these can be detected
- the x-ray tells us where things are that caused the light to bounce back
Where is DNA in the cell?
It is wrapped around histones; super coiled up; this is NOT a covalent bond
How does the double helix work?
- A+T and G+C - the edges are all the same distance apart perfectly
- base pairs are all the same length
- they can form 1, 2, or 3 hydrogen bonds which all have the same proximity of about 3 angstroms
- H is pointed to the O - its the right orientation
Hydrogen bonding makes this perfect
Basic short answer: what is transcription
DNA (5’ to 3’) to complementary RNA (3’ to 5’)
Uracil v. Thymine… what is important here
T is only in DNA - an enzyme outside of the nucleus would want to attack and kill it if it sees it
U is functional outside of the nucleus
What is rRNA?
- ribosomal RNA
- makes up ribosomes
- helps with protein synthesis
What is a ribosome?
it is a complex with proteins and rRNA that lives in the cytoplasm or the rough ER of a cell
function: helps with protein synthesis
tRNA
- this brings amino acids to peptide chains
- has a specific series of nucleotides (anticodon) and it binds to the codon
- it identifies the appropriate codon on the mRNA and adds amino acid to the growing protein chain
What is a codon?
it is a block of 3 nucleotides that corresponds to a specific amino acid (the genetic code)
mRNA
- ribosomes travel along this so that the genetic message can be read and translated into a protein
- complementary strand of RNA from the DNA
- it doesn’t TAKE the message it IS the message
- it leaves the nucleus for protein synthesis
why do we read in 3 nucleotide sequence?
this is the smallest number that will give us enough variability to code for each amino acid
Why do we have mRNA? Like why not just use DNA? Why do we have something different that leaves the nucleus?
Constitution example: you can see copies of it but you can’t see the actual real thing
What is RNA polymerase and how does it know what to do? What is the correct wording when discussing an enzyme?
- It “catalyzes” synthesis of RNA
- moves right to left but builds 5’ to 3’
Steps:
1. initiation = binding to promotor so it knows where to start the process
2. elongation = actual chemical reaction being catalyzed; condensation to form new, longer strand; adds NTPs; it knows what to add bc its complimentary to DNA
3. termination
NTP = nucleotide triphosphates complimentary to DNA
What is one thing that goes into making a molecule soluble?
charges
possible exam question: given a peptide of 8 amino acid residues long; recognize and label
structure is directly related to:
function
What is translation? story from nucleus (so includes transcription)
- nucleus: nucleotide (base pairs) are inserted to create an RNA strand from the DNA
- mRNA leaves the nucleus
- tRNA has complimentary anti codons
- amino acids form with from condensation rxn which adds to peptide chain
Each tRNA has what
an amino acid
Speed of translation?
QUICK!
- mRNA has a short 1/2 life so process has to happen quick
- hard to study HOW bc its so quick
1/2 life
the time it takes for half of a thing to decay
What are the 5 classes of amino acids?
- acidic
- basic
- polar
- aromatic
- nonpolar
What are Fischer projections? what do the parts mean?
- they show 3D arrangements
- vertical lines: bonds that go BEHIND the plane
- horizontal lines: bonds that come out of the page
What is amino acid stereochemistry based off of? Is the L or D enantiomer common in biochem?
- its based on glyceraldehyde
- L is the most common
What order are amino acids linked?
N to C terminus AKA amino to carboxy
MAGTRS
methionine
alanin
glycine
threonine
arginine
serine
What bond joins amino acids? What process does this?
condensation (loss of water); peptide bond
How are amino acids in biochem?
With charges bc of physiological pH; its the Zwitterion ph around 7 bc of charges (remember charges make things more soluble)
What is protein structure affected by?
- it’s all affected by rotation around bonds (conformations)
- peptide bonds can’t be rotated around at all - we know this bc of resonance structure of the peptide bond… you get a double bond!! and you can’t rotate around double bonds
- steric hindrance also affects this
primary structure of a protein
chain of amino acids
secondary structure of a protein
local folding; alpha helix and beta strands
(beta sheets only happen with multiple strands)
tertiary structure of protein
“higher order”; how secondary structures fold into 3D shape
- example: coil-coil
- models usually show what looks like an open space but it isn’t like that in reality- the side chains are just usually left off
quaternary structure of a protein
multiple protein subunits coming together; more than ONE polypeptide chain
- they fold to make one functional protein
- protein-protein interaction but still separate
protein v polypeptide chain
functional vs not?
subunit
2 or more biological molecules working together for a FUNCTION
Can we predict how a polypeptide chain will fold
not always correctly; we pretty much know that a specific part of the chain will likely fold the same way always
alpha helix
- hydrogen bond
- repeating pattern (oxygen perfectly aligns with nitrogen to make the H bonds)
- lots of H bonds = stability = energy required to break them
- side chains can help with stability/connection sometimes bc of IMFs (example: glutamate and lyseine close together … ion-ion salt bridge)
Is the alpha helix as a whole polar or nonpolar?
polar!
- many small dipoles all in ONE direction (vectors)
- electron density all at the top with partial positive all at the bottom
- this can create a negative patch on a protein (which means it can react with a ligand)
How many beta strands do you need for a sheet?
2
What 2 types of beta sheets can we get
parallel and anti parallel
anti parallel beta sheets
C <—— N
N ——->C
- they are backwards/opposite
- hydrogen bonds between strands (linear between 2 pieces)
- O from 1 strand and NH from the other
- distance (3ish angstrom bc H bond)
parallel beta sheets
C <——- N
C <——- N
- H bonds are diagonal instead of straight (less stable)
parallel vs antiparallel beta sheets
antiparallel = more stable and more common bc the H bonds are linear
parallel bonds are diagonal and less stable
What can you do with an alpha helix
you can make 1 side different from the other side: hydrophobic versus hydrophilic for example
fibrous proteins; list an example
- repeating amino acids
- long repeating secondary structures
- coil coil
- take 2 twisted strands and twist them together
- example: collagen
Why are fibrous proteins useful?
good for structure!
like silk from spiders
What about fibrous protein structure makes them so strong
cross-linking (covalent bonds)
Globular proteins
- compact structure
- chemical work of cell (synthesize, transport, metabolize)
- tertiary structure
- ribbon diagrams
- complex protein structure
- shape and IMFs affect what it can interact with (affects function)
- big negative patch –> maybe interact with something positive
What is an example of a DOMAIN of tertiary structure?
beta barrel
- example: TIM
- not actually hollow inside bc of side chains
Do tertiary structures of proteins vary?
YES! many domains exist
neuroaminidase = antiparallel beta sheets
TIM = beta barrel
How do we study how proteins fold?
- we still don’t fully understand it
- funnel model = energy funnels
- folding is super fast, so we use denature studies to make the proteins unfold and see if it can refold
- denaturants (like Urea) can disrupt IMFs like H-bonds which makes the structure of protein fall apart
- temperature increase means MORE kinetic energy so bonds break (irreversible)
disulfide bridge
amino acid cysteine forms it (bc it has an S)
- can undergo oxidation (where O is removed)
- covalent bond formed (NOT SALT BRIDGE)
- you can use BME to reduce it
- keep proteins strong and able to withstand forces from biological functions
temperature and unfolding (denature) as a titration curve
- middle inflection = melting point
- cool it down and heat it up (fold and unfold)
What does a protein require to refold when it unfolds (like in our studies)
RNAse
protein folding “funnel” model
- depth of model = energy
- width of model = number of conformations possible
- widest part of funnel = unfolded denatured conformations
- deepest/narrowest = folded parts of protein
- explains how the trajectory of protein folding is downhill/ proceeds with a decrease in energy (bc unfolded = high temp = high energy while folded = low temp = low energy); thermodynamically favored to be folded
