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Fall 2022 Junior Year > Biochem Exam I > Flashcards

Biochem Exam I Flashcards

1
Q

List all of the IMFs

A
  1. van der waals
  2. dipole-dipole
  3. hydrogen bond
  4. ion-ion (salt bridges aka ionic)
  5. ion-dipole
  6. hydrophobic interactions
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2
Q

What are IMFs? and what language do we use when discussing molecules with IMFs? inTER vs inTRA?

A

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

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3
Q

ion-ion

A

salt bridges are formed; this is also known as an ionic bond; classic example is salt

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4
Q

what is a dipole?

A

unequal sharing of electrons leading to partial charges

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5
Q

ion-dipole interaction

A

this is an interaction between a charged molecule and a molecule with dipole interaction happening

write down some examples; draw them

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6
Q

dipole-dipole

A

2 partial charges from differences in electronegativities; arrow towards partially negative atom

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7
Q

van der waals

A

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

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8
Q

hydrophobic effect/interactions

A

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

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9
Q

hydrogen bonding

A
  • 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)
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10
Q

What is the trend for Ka values and how do you calculate it?

A

BIGGER Ka = STRONGER acid

      [H+] [A-] Ka = ---------------
         [HA]
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11
Q

What is the trend for pKa? How do you calculate it?

A

SMALLER pKa = STRONGER acid (an acid is stronger bc more of it dissociates; there is more product than reactant)

pKa = -log(Ka)

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12
Q

What is the henderson-hasselbalch equation and what do we use it for?

A

pH = pKa + log(A-/HA)

We can find the pH given concentration of conjugate base and concentration of acid

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13
Q

What are the important parts of a titration curve?

A
  • half equivalence point
  • equivalence point
  • buffer region
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14
Q

What does a flat part of a titration curve signify?

A

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

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15
Q

what does a steep portion of a titration curve signify?

A

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

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16
Q

what is a titration?

A

slow addition of a titrant to a solution using a burette bc it has a stopcock

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17
Q

What happens at the 1/2 equivalence point?

A

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

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18
Q

what happens at the equivalence point?

A

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

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19
Q

What is a buffer?

A

It is a solution that resists pH; but it is not unlimited bc it has a CAPACITY

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20
Q

What affects buffer capacity?

A

concentration of the buffer (more buffer higher capacity)

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21
Q

buffer region

A

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

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22
Q

When a titration curve has multiple flat points, what does this mean about pKa?

A

This means there are multiple pKa values at play

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23
Q

Example: you want to make a buffer of pH 6, what molecule do you use

A
  • well you want something where 6 = + or - 1 of the pKa value
  • need pKa around 6
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24
Q

What are the main components of a nucleotide?

A
  • carbon backbone (pentose sugar)
  • nitrogenous base
  • phosphate group
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25
Q

How long is a typical covalent bond?

A

1.5 to 2ish Angstroms

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26
Q

How long is a hydrogen bond?

A

3 angstroms

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27
Q

what holds together the sugar phosphate backbone of nucleotide?

A

covalent BOND (keep length in mind)

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28
Q

the nitrogenous bases are split between what 2 groups? which bases fall in which category?

A

purine = adenine and guanine
pyrimidine = cytosine and (thymine or uracil)

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29
Q

purine vs pyrimidine

A

purine = 2 rings
pyrimidine = 1 ring

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30
Q

What are the base pairs? Why do they pair the way they do?

A

A + T or U
C + G

purines pair with pyrimidines

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31
Q

RNA vs DNA structure wise… where is this difference

A

RNA has a hydroxy group on the sugar phosphate backbone while DNA only has a hydrogen

This happens on 2’ carbon

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32
Q

Why do we use primes on some carbons when discussing nucleotides?

A

primes are used to distinguish between carbons of the backbone (prime) and carbons in the nitrogenous base

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33
Q

What are the significant carbons on the backbone of nucleotide?

A

1’ = nitrogenous base
2’ = OH for RNA or H for DNA
5’ = phosphate group

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34
Q

Why are DNA backbones negative?

A

because the phosphate group has a negative charge bc it is deprotonated

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35
Q

What is the directionality of nucleotides?

A

5’ to 3’
the 5’ end has a free phosphate group
the 3’ end has a free hydroxyl group

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36
Q

What process makes DNA? and what does it do?

A

Condensation: forms a new covalent bond between 2 molecules by losing a water molecule

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37
Q

Dehydration versus Condensation

A

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

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38
Q

Hydration vs hydrolysis

A

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

39
Q

Why do we use condensation and hydrolysis in biochem instead of dehydration and hydration?

A

Water is endless supply; we constantly build things up and break them down

40
Q

What is the phosphodiester link?

A
  • link between more than one nucleotide
  • polynucleotide formed through condensation
  • ester group and phospho group
41
Q

x-ray diffraction

A
  • 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
42
Q

Where is DNA in the cell?

A

It is wrapped around histones; super coiled up; this is NOT a covalent bond

43
Q

How does the double helix work?

A
  • 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

44
Q

Basic short answer: what is transcription

A

DNA (5’ to 3’) to complementary RNA (3’ to 5’)

45
Q

Uracil v. Thymine… what is important here

A

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

46
Q

What is rRNA?

A
  • ribosomal RNA
  • makes up ribosomes
  • helps with protein synthesis
47
Q

What is a ribosome?

A

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

48
Q

tRNA

A
  • 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
49
Q

What is a codon?

A

it is a block of 3 nucleotides that corresponds to a specific amino acid (the genetic code)

50
Q

mRNA

A
  • 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
51
Q

why do we read in 3 nucleotide sequence?

A

this is the smallest number that will give us enough variability to code for each amino acid

52
Q

Why do we have mRNA? Like why not just use DNA? Why do we have something different that leaves the nucleus?

A

Constitution example: you can see copies of it but you can’t see the actual real thing

53
Q

What is RNA polymerase and how does it know what to do? What is the correct wording when discussing an enzyme?

A
  • 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

54
Q

What is one thing that goes into making a molecule soluble?

A

charges

55
Q

possible exam question: given a peptide of 8 amino acid residues long; recognize and label

A
56
Q

structure is directly related to:

A

function

57
Q

What is translation? story from nucleus (so includes transcription)

A
  • 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
58
Q

Each tRNA has what

A

an amino acid

59
Q

Speed of translation?

A

QUICK!
- mRNA has a short 1/2 life so process has to happen quick
- hard to study HOW bc its so quick

60
Q

1/2 life

A

the time it takes for half of a thing to decay

61
Q

What are the 5 classes of amino acids?

A
  1. acidic
  2. basic
  3. polar
  4. aromatic
  5. nonpolar
62
Q

What are Fischer projections? what do the parts mean?

A
  • they show 3D arrangements
  • vertical lines: bonds that go BEHIND the plane
  • horizontal lines: bonds that come out of the page
63
Q

What is amino acid stereochemistry based off of? Is the L or D enantiomer common in biochem?

A
  • its based on glyceraldehyde
  • L is the most common
64
Q

What order are amino acids linked?

A

N to C terminus AKA amino to carboxy

65
Q

MAGTRS

A

methionine
alanin
glycine
threonine
arginine
serine

66
Q

What bond joins amino acids? What process does this?

A

condensation (loss of water); peptide bond

67
Q

How are amino acids in biochem?

A

With charges bc of physiological pH; its the Zwitterion ph around 7 bc of charges (remember charges make things more soluble)

68
Q

What is protein structure affected by?

A
  • 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
69
Q

primary structure of a protein

A

chain of amino acids

70
Q

secondary structure of a protein

A

local folding; alpha helix and beta strands

(beta sheets only happen with multiple strands)

71
Q

tertiary structure of protein

A

“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

72
Q

quaternary structure of a protein

A

multiple protein subunits coming together; more than ONE polypeptide chain
- they fold to make one functional protein
- protein-protein interaction but still separate

73
Q

protein v polypeptide chain

A

functional vs not?

74
Q

subunit

A

2 or more biological molecules working together for a FUNCTION

75
Q

Can we predict how a polypeptide chain will fold

A

not always correctly; we pretty much know that a specific part of the chain will likely fold the same way always

76
Q

alpha helix

A
  • 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)
77
Q

Is the alpha helix as a whole polar or nonpolar?

A

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)

78
Q

How many beta strands do you need for a sheet?

A

2

79
Q

What 2 types of beta sheets can we get

A

parallel and anti parallel

80
Q

anti parallel beta sheets

A

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)
81
Q

parallel beta sheets

A

C <——- N
C <——- N
- H bonds are diagonal instead of straight (less stable)

82
Q

parallel vs antiparallel beta sheets

A

antiparallel = more stable and more common bc the H bonds are linear
parallel bonds are diagonal and less stable

83
Q

What can you do with an alpha helix

A

you can make 1 side different from the other side: hydrophobic versus hydrophilic for example

84
Q

fibrous proteins; list an example

A
  • repeating amino acids
  • long repeating secondary structures
  • coil coil
  • take 2 twisted strands and twist them together
  • example: collagen
85
Q

Why are fibrous proteins useful?

A

good for structure!
like silk from spiders

86
Q

What about fibrous protein structure makes them so strong

A

cross-linking (covalent bonds)

87
Q

Globular proteins

A
  • 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
88
Q

What is an example of a DOMAIN of tertiary structure?

A

beta barrel
- example: TIM
- not actually hollow inside bc of side chains

89
Q

Do tertiary structures of proteins vary?

A

YES! many domains exist
neuroaminidase = antiparallel beta sheets
TIM = beta barrel

90
Q

How do we study how proteins fold?

A
  • 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)
91
Q

disulfide bridge

A

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

92
Q

temperature and unfolding (denature) as a titration curve

A
  • middle inflection = melting point
  • cool it down and heat it up (fold and unfold)
93
Q

What does a protein require to refold when it unfolds (like in our studies)

A

RNAse

94
Q

protein folding “funnel” model

A
  • 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

Fall 2022 Junior Year (9 decks)

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