BCH210 FINAL EXAM Questions with 100% Correct Verified Answers Latest Update 2024 RATED A+, Exams of Nursing

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BCH210 FINAL EXAM Questions with 100 %

Correct Verified Answers Latest Update

2024 RATED A+

Which AA likes to form alpha helix? - ANSWER - Glutamate Which AA likes to form beta sheet - ANSWER – Valine which amino acids have aromatic side chains? - ANSWER - phenylalanine, tyrosine, tryptophan which amino acids are sulfur containing? - ANSWER - cysteine and methionine acidic amino acids? - ANSWER - asparagine, glutamine, aspartate, glutamate 4 basic amino acids - ANSWER - lysine, arginine, histidine, Which amino acids have aliphatic side chains? - ANSWER - alanine, glycine, valine, leucine, isoleucine, which amino acids have aliphatic hydroxyl side chains? - ANSWER - serine and threonine hydrophobic amino acids - ANSWER - alanine, glycine, valine, isoleucine, leucine, phenylalanine, methionine, proline hydrophilic amino acids POLAR - ANSWER - asparagine, glutamine, serine, threonine, cysteine hydrophilic amino acids CHARGED - ANSWER - arginine, lysine, histidine (basic), aspartic acid, glutamic acid

Amphipathic aromatic amino acids - ANSWER - tryptophan, tyrosine pg. 1

Alpha Helix- N-H residue and C=O - ANSWER - N-H group of residue i donates a H-bond back to the C=O group of residue i- 4 Features of the alpha helix: a) residues p/turn b) degrees between adjacent residues c) rise p/residue d) how many Å across backbone? e) inter/intrastrand bonds? - ANSWER - a) 3. b) 100 c) 1. d) 5 e) intrastrand In other words, there's a....of secondary structures into a define protein ... .. - ANSWER - - condensed

• tertiary (3°)
• (one polypeptide chain)
• might be final structure
• folding
• motifs and domains If you have multiple chains coming together, you have a.....structure (assembly of......into .....structures) - ANSWER - - quaternary (4°)
• distinct chains
• multi-subunit AAs are joined....in a......rxn. That rxn is.....and we lose....., which is why it's called a. .... rxn. - ANSWER - - enzymatically, condensation
• COOH + NH3+ - > peptide bond (O=C - N-H)

• 1 H2O molecule - 1 OH + 1H+ (might be 2 Hs on N, depending on protonation state)
• condensation rxn There are certain....of rotation allowed (can generate the..... plot) , ranging from....to.... - ANSWER - - angles
• Ramanchandran
• • 180 to +180 (????) There are only certain angles allowed in polypeptide bond rotations (some are not. ... ) because it can create....The preferred configuration is..... to.......because a lot of our side chains are very ..... that's better to be.....from each other (gives you a more......) - ANSWER - - permitted
• steric clashes
• trans
• minimize steric clashes
• bulky (Y, W etc)
• kept away
• extended structure The...configuration can be allowed if the....want to interact - ANSWER - - cis
• two side chains Which of the following AAs have the biggest impact on the path of the polypeptide backbone? A. G B. H C. P D. W - ANSWER - Answer: C - proline pKa of Arginine side chain - ANSWER - 12. pKa of Lysine side chain - ANSWER - 10.

pKa of Cysteine side chain - ANSWER - 8. Histidine pkA side chain - ANSWER - 6 Glutamic acid pKa side chain - ANSWER - 4. Aspartic Acid side chain pKa - ANSWER - 3. The backbone of the primary structure consists of.....and...., while the variable part are the..... - ANSWER

• • peptide bonds
• alpha carbons
• distinct R side chains You can have a zwitterion for a.....or a...., as long as the..... - ANSWER - - long polypeptide
• single AA
• net charge is neutral A single AA is called a..... - ANSWER - residue [SLIDE 5, unannotated] The sequence of AA is... - ANSWER - Y-G-G-F-L A peptide bond has.....(can....), which allows for the......of.....bond due to the. .. .. - ANSWER - - EN atoms
• H-bond
• movement/resonance
• double
• dipole on C and O

Due to the....bond, there is no....around the peptide bond (.....fixed, always in exact..... ) - ANSWER - - partial double

• rotation
• functional groups
• same orientation (O in one direction and H of N in the other, fixed positions of alpha Cs in two opposite directions) The...on N gives peptide a.......bond character due to....., preventing....of the peptide bond - ANSWER - - lone pair of e
• partial double
• resonance
• rotation features of the beta sheet: a) how many residues/repeat? b) how many Å in length/residue? c) inter/intrastrand? - ANSWER - a) 2 b) 3 c) interstrand B-turn positions of H-bonds?
• how many residues? - ANSWER - H-bonds to i- 3 b) minimum of 4 residues Sequence determines. .. .. - ANSWER - structure Learning Objectives - ANSWER - 1) Explain how protein structure is influenced by the AA sequence (primary sequence + interactions - > properties)

2. Distinguish b/w ≠ lvls/structures - primary, secondary (MAJOR), tertiary, quaternary (not in all proteins)

3. Describe the properties of the major types of secondary structures
4. Recognize the contribution of disulfide bonds (solidify structure) and ligands (or extra chemicals included w/ polypeptide chain) to final protein structure 20 AAs have distinct.....that contribute to......and thus contributes to a protein's..... - ANSWER - - side chains

• binding
• structure [SLIDE 3, unannotated] Protein structure can be represented in a.....view, where the.....represent bonds in AAs and you can identify some....(...green.) - ANSWER - - licorice
• sticks
• side chains
• F, 2nd side chain in green [SLIDE 3, unannotated] Polypeptide chain has.....that runs down the...., and...that sticks out and... w/ other R groups. You can see this in the......., where there are interactions like....run down the..... - ANSWER - - peptide bonds
• backbone
• R groups
• interact
• space-filling model
• disulfide bonds
• interface When the properties of AAs are.....(could be.....or......), it allows them to..... - ANSWER - - complEmentary
• H-bonding, VdW
• come together

Proteins are not simply.....of AAs, they.... to form .... .. - ANSWER - - linear chains

• fold
• complex 3D structures Primary (1°) sequence is....., has all...throughout the.....,and start at..... and end at..... - ANSWER - - the linear sequence of AA
• all covalent linkages throughout the backbone
• start at the N terminus (Nt) and end at the C terminus (Ct) The primary sequence is encoded by.... - ANSWER - codons/DNA gene On slide 4 the primary sequence starts from.....(attached to....) and ends at......(attached to.... ) - ANSWER
• • Pro, Nt
• Val, Ct When the primary sequence is translated, the....interact to form ≠ types of..... - ANSWER - - functional groups in side chains
• structures Secondary (2°) structure are.....even if ....(examples) Some AAs prefer.....structures - ANSWER - - are periodic (repeating/frequent) regular (common) structures that form in many ≠ proteins
• they might have ≠ primary sequences
• ex: α helix, β strands, β turns
• distinct When secondary structures come together to form a > .... structure, it's called the. ... structure (....polypeptide chain), and it might be the. .. structure

Peptide bonds are....but...... The first feature contributes to the peptide bond by allowing ...... , through the....... - ANSWER - - polar

• uncharged
• resonance
• breaking of the C=O bond The plane of the peptide bond is always in the. ... .. - ANSWER - same organization/structure While the peptide (also known as.....) bonds are planar (. ...... ), rotation is allowed around the bonds linking the......(....) and ......(....) to the....... - ANSWER - - omega (w)
• all atoms on same plane
• amide (phi, 𝜙 )
• carbonyl (psi, Ѱ )
• alpha Carbon Rotations around the......allows the polypeptide chain to.... Therefore, these two bonds dictate path of....... - ANSWER - - phi + psI bonds
• twist up and form > compact structures (PROTEIN FOLDING)
• path of backbone ...... structure.......

• .....structure....... (not always) - >.....structure (. .... )

• ....structure...... - ANSWER - - Primary ( AA residues)

• Secondary (α helix)
• Tetiary (polypeptide chain)
• Quaternary (assembled subunits)

A primary structure has....., which means that the..... is the start (AA#. ....) of the polypeptide chain, and the primary sequence is written from the.....to the....... - ANSWER - - directionality

• amino terminal
• 1
• Amino terminal residue to Carboxyl terminal residue N involved in a ring - > phi bond is fixed, can NOT rotate and can only adopt one angle (psi bond can though)

• restrict kind of structures present

• help protein structure fold

SLIDE 6: 3 FIGURES SLIDE 7: 3 FIGURES SLIDE 8: 1 FIGURE SLIDE 10: 1 FIGURE SLIDE 11: 1 FIGURE SLIDE 16: 1 FIGURE - ANSWER - alpha helix have..pointing out to the....., and forms when...... - ANSWER - - side chains

• outside of helix (green bulbs on slide 10)
• peptide bonds have ability to H-bond w/ each other alpha helix forms...... b/w......(example) - ANSWER - - INTRASTRAND H-bond
• O in backbone C=O of one AA (i) and H in H-N groups of another AA (i+4)
• ex: C1 H-bonds w/ C Alpha helix is formed because there are a lot of.....down the....of the helix, creating..which forms a. .. - ANSWER - - H-bonds buried
• center

• turns
• alpha helix Figure C (slide 10): looking from the....all H-bonds......., protect your........ Figure D (slide 10):.....model, there's NO.....in the middle, there are....that are. ... at the center - ANSWER
• • top
• hidden in the middle
• backbone/peptide bonds
• space-filing
• hole
• atoms that are H-bonding
• burried Alpha helix is considered a ....handed helix, because if you were to wrap your.......hand around the helix, your thumb's pointing in the direction of the helix (.....group to the right at the....of the helix, ..... group to the left at the...of the helix) - ANSWER - - right, right
• NH3+, top
• COO-, bottom Takes about. ... to make a complete turn (360 degrees turn) - ANSWER - 3.6 AAs (around 4) Each residue is about.... The width of an alpha helix depends on .... - ANSWER - - 1.5 Armstrong (Å) high (distance b/w side chains)
• contrast w/ Beta strand
• depends on other bonds present

• pg.
• pg.
• pg.
• pg.
• pg.
• pg.
• pg.
• pg.
• pg.

H-bonding in an alpha helix creates..... - ANSWER - - a more compact structure

• condense/shorten/contract a long strand into a > compact helix [SLIDE 11, unannotated]: Identify all AAs. # H-bonds? If the chain kept going..... - ANSWER - - S, H, C, M, E, L, K 3 H-bonds: b/w S (C1) and E (C5), H (C2) and L (C6), C (C3) and K (C7) other H-bonds can form w groups that can come before the Ser AA Since there's....in a chain, the peptide bonds are always forming in an..... of the......to the. ..... as you travel your way down the chain, from the.....to the.... - ANSWER - - directionality
• order
• O on the carbonyl of the carboxyl
• H on the amino group
• N terminus, C-terminus Do the R groups contribute to the alpha helical formation? - ANSWER - NO. Just H-bonds in peptide bonds contribute to alpha helical formation, but R groups can form other interactions An AA further down the chain can be H-bonding w/ something...., and sth.....as well - ANSWER - - down the chain
• up above it An AA can form....., .....from......and.....from.... Example - ANSWER - - 2 H-bonds
• one from O in carbonyl of carboxyl group

pg. 11

• one from H in amino group a C5 AA can H-bond w/ C1 through its AMINO group and H-bond w/ C9 through its CARBOXYL group (directionality) You need at least.....to form 1 H-bond, since a H-bond is formed b/w an....and an.....AA, .....AAs. .. can form.....H-bonds and ...AAs can form... H bonds Ability to H-bond w/ other groups: more. .. - ANSWER - 5 AAs (i, i+4) 6, 2 7,3 complicated All in all, the primary backbone is formed from .... interactions, and secondary structures are formed from.....interactions - ANSWER - - covalent (peptide bonds)
• non-covalent (H-bonding) Properties of the alpha helix depend on.....allow helices to....w/ other .. .. - ANSWER - the side chains (polar, hydrophobic or amphipathic)
• interact
• proteins/structures that are forming As you are....your AAs around the helix, you can form ≠ types of helices based on the....of the. .. - ANSWER - - rotating
• properties
• side chains [SLIDE 12 unanottated]

pg. 12

If all the side chains are.....in nature, your alpha helix has. .. characteristics Vs if you have M, L, A,...they can form.....AA sequence that will coil up and form a. .. alpha helix You can also form an....helix (which means....., so.....(......) - ANSWER - - polar, polar

• hydrophobic, hydrophobic
• amphipathic (dual properties - hydrophobic and hydrophilic faces)

• hydrophobic: W, L, I, V
• hydrophilic/polar: S, S, D, T [SLIDE 12] helical...., going through sequence as it.....through alpha helix Start w/ AA....at the...., the 2nd AA would be.....the 3rd AA would be..., the 4th AA would be...

• show us that we need.... Then go down to...., over to.....and....and.... - ANSWER - - wheels

• rotates Alanine, N-terminus, D, R, I

• need abt 4 AAs (3.6) to form a 360 turn K, S, W, V,... [SLIDE 12, unanotated] Primary sequence of an amphipathic secondary structure has. .... , which tells you what. ... is forming - ANSWER - alternating hydrophobics and hydrophilics

• tell you what kind of helix is forming