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IUPUI / Chemistry / CHEM 384 / What is the difference between a nucleotide and nucleoside?

What is the difference between a nucleotide and nucleoside?

What is the difference between a nucleotide and nucleoside?


School: Indiana University Purdue University - Indianapolis
Department: Chemistry
Course: Fundamentals of Biochemistry
Professor: Blacklock
Term: Spring 2016
Tags: biochemistry, Physics, and Chemistry
Cost: 50
Name: Biochemistry Exam 1 Study Material
Description: This includes the lecture expectations and answers. I also suggest you look over the professors' lecture 1-3 problems on canvas and the quizzes. Good Luck!
Uploaded: 02/04/2018
14 Pages 8 Views 12 Unlocks

Exam 1 Study Material

What is the difference between a nucleotide and nucleoside?

Lecture 1-3 Expections

1.) What is the difference between a nucleotide and nucleoside? a. Nucleotide: Has a base, sugar, and phosphate. Has  directionality

b. Nucleoside: Missing the phosphate(s)

2.) Draw and name the 16 possible nucleotides/nucleosides that can be formed  from the 5 major bases

a. 5 major bases: Adenine, Guanine, Cytosine, Uracil, and  Thymine

b. Ribonucleotides:

i. Nucleotides: Adenylate, Guanylate, Uridylate, Cytidylate ii. Symbols: A, AMP; G, GMP; U, UMP; C,CMP

iii. Nucleoside: Adenosine, Guanosine, Uridine, Cytidine c. Deoxyribonucleotides:

i. Nucleotides: Deoxyadenylate, Deoxyguanylate,  

Deoxythymidylate, Deoxycytidylate

ii. Symbols: A, dA, dAMP; G, dG, dGMP; T, dT, dTMP; C, dC,  dCMP

iii. Nucleoside: Deoxyadenosine, Deoxyguanosine,  

Deoxythymidine, Deoxycytidine

What are the major features of B form DNA?

3.) Describe how nucleotides are joined together to form nucleic acids: a. Through phosphodiester bonds.

b. Phosphodiester bonds link C3’-OH of one nucleotide with C5’- Phosphate of the next

c. 5’ to 3’

4.) How are features of purines/pyrimidines responsible for the chemical/physical properties?

a. Pyrimidine attaches to sugar at C1’ in the ring while Purine  attaches to C9’. And purine is a larger molecule

5.) What is the Complementary of 5’-ATGATTCCTCG-3’. Write it as 5’ to 3’ a. Complementary  3’-TACTAAGGAGC-5’.  

b. 5’ to 3’  Flip it. 5’-CGAGGAATCAT-3’

6.) How did Watson and Crick come to their double helical DNA model? a. Chagaff’s Rule (A:T and G:C)

b. Correct tautomers of bases (Jerry Donohue)

c. X-ray diffraction photograph of DNA (Rosaline Franklin)

7.) What are the major features of B form DNA?

What is a Palindrome?

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a. Watson and Crick model

b. Right-handed helix

c. Most stable

8.) How is A form DNA different from B?

a. A is found in absence of H2O, wider and more compact, and  may be an artifact of crystallization

9.) How is Z form DNA different from B?

a. Z is left-handed helix, more extended, formed by particular  base sequences, and has a potential regulatory role

10.) What is a Palindrome?

a. Same forward as backward (Ex. Racecar) We also discuss several other topics like usc cs103

b. In RNA, it would be a series of characters that are the same 5’  to 3’ as 3’ to 5’

11.) What is a hairpin?

a. Palindromic on outsides of structure, but different between the two. Common in RNA

12.) What is a Cruciform?

a. 2 hairpins. 1 on top strand and 1 on the bottom

13.) How can single-stranded RNA have a secondary structure or tertiary  structure?

a. Tertiary is more complex than secondary, but less stable b. I believe Blacklock just wants us to understand there are two  different types of structures RNA can have and that they  involve hairpins, loops, and bulges

14.) What is the relationship between Tm and DNA denaturation? a. Tm is when 50% of the sample has been denature

b. Dependent on G+C content because this is stronger than the  A+T content

15.) What are the different DNA alterations that can occur? a. Deamination of bases

b. Hydrolysis of N-beta-glycosidic bond

c. UV-induced crosslinking

d. Alkylation

e. Oxidative Damage

16.) What is replication?

a. When DNA ‘replicates’ its structure (creates the same  sequence 5’ to 3’)

17.) What is transcription?

a. DNA is copied into RNA

18.) What is translation? Don't forget about the age old question of animal diversity notes

a. mRNA to protein

19.) Know how to deduce a RNA/protein sequence based on any RNA/DNA  sequence given the genetic code Don't forget about the age old question of gwendolyn hustvedt

a. Just know that DNA starts 3’ to 5’. Complementary would give  DNA 5’ to 3’.

b. DNA to RNA is the SAME sequence EXCEPT for T changes to U i. Example: 5’-GATTCG-3’ in DNA would be 5’-GAUUCG-3’ in  RNA)

c. RNA to protein is when you look at what the genetic code is.  Arg, Cys, Etc.

20.) What are the fundamental differences between RNA and DNA? a. The organic bases and Ribose units

21.) Determine sequence of a stretch DNA using radiolabelled or automated fluorescent Sanger sequencing and understand how these differ. Unknown.

Lecture 4 Expectations:

1.) Describe the main features of an amino acid

a. Amino Group

b. Carboxyl Group

c. Alpha Carbon

d. Side Chain (R)

e. BUT PROLINE IS DIFFERENT: It has a secondary amine)

2.) Draw all 20 Amino Acids, know the names, know the 3 letters, 1 letter  abbreviations

-Some hard to see: And pink means Hydroxylic Don't forget about the age old question of niel bohrs model

Alanine = Ala, A; Glycine= Gly, G; Phenylalanine = Phe, F;  Tryptophan = Trp, W; Tyrosine = Tyr, Y; Lysine = Lys, K; Serine = Ser,  S; Threonine = Thr, T

Isoleucine= Ile, I; Leucine = Leu, L; Proline = Pro, P; Valine= Val,V;  Aspartic Acid = Asp, D; Glutamic Acid = Glu, E; Arginine= Arg, R;  Histidine = His, H; Cysteine = Cys, C; Methionine = Met, M;  Asparagine = Asn, N; Glutamine = Gln, Q

3.) Be able to draw any peptide, including correctly drawing the peptide bond: a. Slides 24-26 help explain this  We also discuss several other topics like william francis crooks

4.) Determine net charge of peptide:

a. Slide 22

5.) Define:  

a. Cofactor: Help many proteins/enzymes function

b. Coenzyme: A cofactor that is organic  

c. Conjugated Protein: A protein with a tightly associated  cofactor

d. Prosthetic Group: The tightly associated cofactor  

6.) Why is protein purification important and what is the basic goal of all  purifications?

a. Importance: To identify and more clearly analyze proteins b. Goal: To maximize specific activity while losing as little of your  protein as possible

7.) Describe principles behind the different kinds of chromatography:

a. Ion Exchange Chromatography: Proteins stick to it based on  their net charge (can change with pH)

i. Anion Exchange: Resin is positively charged. More net  negative the protein is, the tighter it will bind

ii. Cation Exchange: Resin is negatively charged. The more  net positive the protein is, the tighter it binds

b. Gel Sizing Chromatography: Size of pores determines what  proteins can enter resin. Proteins small enough to enter take  longer to travel through column. Proteins too big to enter  elute quickly.

c. Affinity Chromatography: Protein binds ligand and remains on  column as other proteins flow through.

i. Protein must be eluted off column by solution that  

disrupts the protein-ligand interaction

8.) Understand principles of electrophoresis and advantages of SDS a. Electrophoresis: Method used to separate proteins.  i. Polyacrylamide matrix acts as sieve

ii. PAGE (polyacrylamide gel electrophoresis)

iii. Migration depends on charge and frictional coefficient a. µ = Z/f

b. Advantages of SDS:

i. Binds protein rather uniformly (1 SDS every 2 amino  Acids)

ii. Negates differences in mass/charge rations between  different proteins

iii. Allows separation based on size/length

9.) Understand basic principles behind protein sequencing:

a. Sanger Method: Identify amino-terminal residue of polypeptide b. Edman degradation: Identify amino-terminal residue; purify  and recycle remaining peptide fragment through Edman  process

i. Good for ~50 amino acids (chemical process is not 100%  efficient

1. Break it up into smaller pieces

2. Sequence those

3. Assemble to get full length

a. Trick: Generate overlapping sequences

10.) Be able to apply these principles of chromatography, electrophoresis,  purification, and sequencing to problems

Lecture 5 Expectations

1.) Identify the 4 levels of protein structure:

a. Primary

b. Secondary

c. Tertiary

d. Quaternary

2.) Describe partial double bond character of peptide bonds and its implications  for structure:

a. Character: Makes the C-N bond rigid, not rotation possible  about C-N, planar, weak dipole, most peptide bonds are trans b. Implications: Rotation possible about the bonds connected to  the alpha carbons (phi and psi)

3.) Understand the two types of dihedral angles

a. Phi: Alpha carbon---amide nitrogen bond

b. Psi: alpha carbon---carbonyl carbon

c. In fully extended polypeptide, both angles are 180 degrees

4.) Describe important features of an alpha helix (pitch; aa per turn; bonding;  dipole)

a. Tightly wound, backbone on inside so R groups face out, right  handed

b. Pitch: 5.4 Angstroms

c. 3.6 AA/turn

d. Bonding: Very stable structure. H-bonding

e. Helix has dipole!!!  

f. Amide “N” point towards N-terminus and Carbonyl “O” point  towards C-terminus

5.) Identify which amino acids are (are not) found in helices

a. Ala and Leu are frequently found in helices

b. Others depend on context. See table 4-2 on slide 19  c. Gly and Pro are rarely found in helices

6.) Describe features of beta sheet

a. Made up of a series of strands that adopt beta conformation b. Beta strands are More extended than alpha helices c. Several strands come together to form sheet

d. H-bonds occur between strands

e. R groups always on the same side of sheet

7.) Differentiate two types of beta turn

a. Occur when strands in beta sheets change direction b. 180 degree turn is accomplished over 4 amino acids c. Stabilized by H-bond from carbonyl “O” of n-th residue to  amide “H” of the (N+3)-rd

d. Proline in position 2 or Glycine in position 3 are common in  beta turns  

e. Often found at protein surface

8.) Fibrous Protein vs. Globular Protein

a. Fibrous: Typically insoluble; made from single secondary  structure

b. Globular: Water-soluble; Lipid-soluble membraneous protein

9.) Describe Key features of collagen responsible for its strength a. G-X-Y repeats: left handed alpha chain

b. Triple Helix: Three chains twist around each other to form this.  Super strong!

10.) Compare Motif vs. Domain in Globular Protein

a. Motif: Recognizable folding pattern found in a number of  proteins

i. 2 or more secondary structure elements. Large or small ii. May/may not be independently stable

b. Domain: Self-contained part of a protein

i. Definitely independently stable

ii. Folds autonomously

iii. Small proteins have 1 domain (domain would be the  whole protein)

iv. Large protein can have several

v. Can have its own function

11.) Identify four classes of protein

a. All Alpha

b. All Beta

c. Alpha divided by Beta (Alpha/Beta)

d. Alpha + Beta

Lecture 6 Expectations

1.) What factors influence folding? Specifically be able to explain hydrophobic  effect

a. Most proteins don’t have disulfide bonds to help stabilize them b. They have weak interactions

c. These add up and help stabilize protein

d. Hydrophobic Effect: Non-polar R groups exposed to solvent in  U state cause ordering of water (which means entropy of water is decreased)

2.) Summarize key findings of Anfinsen’s work

a. Ribonuclease A; RNaseA discovery

i. Found it was a VERY STABLE protein

ii. 8 cysteines and 4 disulfide bonds

b. Set-up

i. Native to Unnative  

c. Wanted to know what role cysteines played in catalysis i. Correct disulfide bond formation occurs only after the  protein achieves native teriary structure

d. Gibbs free energy of the whole system is lowest when the  protein is in the native state

3.) Understand implication of Levinthal’s paradox: Thermodynamic vs. Kinetic  control of folding

a. Given protein can’t and does not sample every possible  conformation at random

b. “Folding Pathways”

c. Folding CANNOT be purely thermodynamic because that would  take too long

i. So folding must also be under kinetic control

4.) Understand the Visualization offered by folding funnels

a. Folding can’t be just a tunnel to native state

b. So it must be a funnel where there is no “single” U state  where all molecules are in an identical conformation. So no  “single” pathway

c. “Rugged” Energy Landscape: Must account for intermediates,  multiple pathways

5.) Molten Globule:

a. Compact structure that contains some (or all) secondary  structure, but little/no tertiary structure, with a hydrophobic  core not yet fully buried

6.) Explain Why chaperones might be needed

a. Some proteins require help reaching the native state b. Chaperones assist both types of process: Folding off ribosome  and Returning folded protein to native state if it unfolds c. Prevent unwanted (or improper) interactions= aggregation 7.) Differentiate two types of chaperone function (holding vs. folding). How are  hsp70 and GroEl are examples?

a. Hsp70: Recognizes stretches of hydrophobic residues in  unfolded proteins and grab onto them

i. Utilize ATP to cycle between high and low affinity states ii. Does not work alone

iii. Weak affinity for substrate

b. “Holdase” Activity: Chaperones help go through steps to fold  protein (see slide 43)

i. Cycles of binding and release

ii. During release, protein has opportunity to fold

iii. If not fully folded…rebound

c. “Foldase” Activity:  

i. Actively promoting folding

ii. GroEL + GroES

1. Provide “Folding Chamber”

a. Protein can fold in peace away from other  

unfolded proteins to prevent aggregation  

(infinite dilution)

b. ATP is used to cycle between protein bound  

and released states

8.) Describe what conditions lead to aggregation:

a. Being around other unfolded proteins

b. High protein concentrations inside cells

9.) Amyloid

a. Highly ordered aggregate containing very stable beta-sheet  structures

b. Amylin can form amyloid

c. Amyloid can kill cells and cause issues

10.) Intrinsically Disordered Proteins:

a. No defined structure

b. “Natively Disordered”

Lecture 7 Expectations

1.) Define:

a. Induced fit: Only the proper substrate is capable of inducing  the proper alignment of the active site that will enable the  enzyme to perform its catalytic function

b. Allostery: The process where proteins transmit the effect of  binding at one site to another, like distal, functional site,  allowing for regulation of activity

c. Cooperativity: The shape of one subunit of an enzyme  consisting of several subunits is altered by the substrate or  some other molecule. End up in a sigmoidal curve (change  between high or low affinity states)

d. Homotropic Allostery: Binding of another copy of the “same  molecule” influences the binding of that molecule (eg. Binding  the first oxygen makes the binding of subsequence oxygens  easier

e. Heterotropic Allostery: Binding of “other molecules” influences the binding of your molecule of interest. (eg. Binding of CO2,  BPG, protons, can all influence binding of oxygen)

2.) Write the mathematical expression for KD and theta ϴ

a. KD = [P][L]/[PL]

b. ϴ: [PL]/[P]Tot (fraction of P bound by L)

3.) Locate KD on a binding Curve

4.) Understand basic structure of heme and how oxygen can CO bind to it: a. Heme = Iron + protoporphyrin IX

b. Rigid and planar. 4 Nitrogens for binding sites.



c. CO has similar shape to O2 to fit in the same binding site. d. Better than O2 to bind to free heme, because it has a filled  lone electron pair to donate to Fe2+. Protein pocket decreases  affinity for CO.  

5.)Understand how anatomy of myoglobin/hemoglobin contributes to oxygen  binding (role of proximal histidine; distal histidine; helices F and E) a. Myoglobin: Storage of oxygen for metabolism.


i. [O2]: Not easy to measure so use partial pressures

ii. ϴ: pO2/[pO2+P50)

iii. Would Myoglobin be a good O2 carrier from lungs to  tissue? No because it would hold on too tightly and not  

let go of the O2

iv. Hemoglobin: Two alpha and two beta subunits. Dimber of alphaBeta protomers. Subunit binds heme  heme binds  O2

v. Myoglobin and Hemoglobin are structurally similar.  

6.) Understand the significance of the sigmoidal binding curve of Hb for oxygen a. If there is an uptake of O2, the curve shifts to the left towards  high-affinity state

b. If there is an O2 release, the curve shifts to the right towards  the low-affinity state.  

7.) Differentiate between the T and R states of Hb

a. Slides 19, 38 and 39

8.) Express binding of oxygen to Mb and Hb mathematically (in terms of partial  pressure)

a. Slide 14?

9.) Understand the derivation of the Hill equation and what it (and the Hill plot)  tell us

a. Log|ϴ/(1-ϴ) = nlog(pO2)-nlogP50 is really y= mx+b

b. If slope = 1, then the binding of ligand is NOT COOPERATIVE c. If Slope > 1, binding IS COOPERATIVE

d. If slope = actual number of subunits, binding is COMPLETELY  COOPERATIVE

e. Slope m never reaches theoretical mas of n

f. For Hb, slope is about 2.8

g. nH = 1, no cooperativity. nH > 1, positive cooperativity. nH < 1, negative cooperativity

10.) Describe the differences between the MWC and KNF cooperativity  models

a. MWC: Concerted, “All-or-None” transition, no intermediate  states, all states in equilibrium

b. KNF: Sequential, Mixed states allowed, all states in equilibrium 11.) Understand how oxygen transport is affected by CO2, pH, and BPG a. BPG: Binds and stabilized T state.  

b. CO2: Binds as carbamate to each of the four amino termini in  Hb




12.) Know the cause and effect of sickle cell anemia

a. Single amino acid mutation in Hb beta

b. Glu  Val

c. Increases inappropriate interactions between beta subunits in  different Hb molecules

d. ^Interaction leads to strand formation and long fibers deform  cell shape (sickle cell).

e. Effect: Clog capillaries, painful and life-threatening if  


13.) Define:

a. Antigen: Toxin that induces immune response in the body,  especially production of antibodies

b. Antibody: Blood protein produced in response to antigen.  Antibodies combine chemically with substances that the body  recognizes as alien

c. Epitope: the part of an antigen molecule to which an antibody  attaches itself

14.) Understand basic structure of an antibody


15.) Describe use of antibodies in biochemical assays:

a. Slide 44

b. ELISA: In plastic dishes

c. Immunoblot (Western): On membrane after SDS-PAGE d. Used to detect presence of molecule of interest in sample e. Can be conjugated to beads and beads packed into column for  chromatography (affinity chromatography)

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