Chap 7 Biochem Proteins: Structure-Function Relationship

Front 1

Why does a peptide considered planar?

Back 1

There is no rotational freedome around the peptide bond - this adds rigidity. Due to partial double bond character of peptide bond.

Front 2

How does Pro influence backbone structure of polypeptide?

Back 2

Causes kink due to steric clashes - regardless of cis or trans formation.

Front 3

Where does flexibility of polypepetide come from?

Back 3

Phi and psi bonds around the alpha carbon. they provide freedom of rotation but most angles are not allowed. Folds are stabilized by non-covalent forces

Front 4

primary structure

Back 4

amino acid sequence

Front 5

secondary

Back 5

local conformations, alpha helix (INTRA strand H bonds), beta sheets (INTER strand H bonds), Reverse Turns, hairpin loops (H bonds, CO H-bonds to i+3 NH group)

Front 6

parallel sheet

Back 6

b strands of adjacent sheet have carboxyl terminals at same end

Front 7

antiparallel sheet

Back 7

carboxyl terminal of one beta strand is next to amino terminal of adjacent beta strand

Front 8

which confirmation, parallel or antiparallel, requires a longer polypeptide chain?

Back 8

Parallel - it requires a longer loop

Front 9

Loop region

Back 9

non repetative but not random and after connect the alpha helixes and beta strands
-form enzyme active sites and can h-bond polar and charged residues

- beta sheet loop, H-bond CO to NH -> i + 3

Front 10

reverse turns

Back 10

loops connecting adjacent antiparallel beta strands, smalls - they allow beta sheets to be formed

Front 11

Tertiary structure

Back 11

arrangements of secondary structures in 3-D bonding ( domains adn motiffs). Hydrophobic interactions

Front 12

Quatinary structure

Back 12

associations of several polypeptides, hydrophobic interactiosn, occasional ioninc bond, disulfide bonds

Front 13

Myoglobin vs. hemoglobin structure

Back 13

Myoglobin has no 4th structure bc it is a single polypeptide.
Hemoglobin is tetrameric.

both have simular beta subunits and heme group

Front 14

alpha helix

Back 14

right handed helical structure of polypeptide with H-bonding between CO residue,i, and NH residue i+4
-side chains extend outward helically
-INTRA helical H-Bond

Front 15

beta sheet

Back 15

composed of beta strands
- they run parallel or antiparallel to eachother and INTER H-bond

Front 16

How does h-bonding pattern of the main chain backbone in a loop region differ from that in an alpha-helix, or in a beta-sheet?

Back 16

Loop region, H-bond between CO & NH every i+3

alpha helix: i + 4, INTRAbonding

beta sheet: NOT regular/mathematical, INTERboning

Front 17

Why is proline not a good helix former

Back 17

It causes a kink in the backbone since N is not available for H-bonding. Steric hindrance - fits in 1st turn of alpha-helix, but elsewhere form a kink. CANNOT H-bond with other residues.

Front 18

supersecondary structure/motifs
List secondary structures:

Back 18

Relatively small arrangements of secondary structure that are recognized in many different proteins. They have a particular function - but too small to function alone.

Helix-loop-helix
Helix-turn-Helix
Leucine Zipper
Zinc Finger Motif

Front 19

Helix-loop-helix

Back 19

allows Ca2+ binding

Front 20

Helix-turn-Helix

Back 20

Helps DNA transcription factor fit

Front 21

Leucine Zipper

Back 21

Mediates Protein-Protein interactions (acts as velcro)

Front 22

Zinc Finger Motiff

Back 22

DNA Binding

Front 23

Domain

Back 23

functionally stable tertiary structures.

Globin fold is made of alpha-helices and loops.
Function: Binds oxygen through heme groups
If protein malfunctions could be due to domain defect

Front 24

collagen posttranslational modification

Back 24

collagen helix is composed of: Gly, Pro, and hydroxylated Pro. The hydroxylated Pro occurs after translation. The three chains are held together by INTERhelical hydrogen bonds with Hydroxylated Proline.

Every 3rd residue to Gly - it is small and can fit within the interior of the chain. Any other amino acid would deform the helix.

Front 25

Globin Fold - ion coordination

Back 25

coordinates Fe2+ atom in the Heme (Alpha Domain Structure) protophynn and central iron atom. O2 binds to the heme and then Fe 2+ is pulled back into the plane of the ring - a confirmation change has taken place. This initial change causes all the other heme groups in hemoglobin to have a greater affinity to oxygen too.

Front 26

Zinc Finger Motif - ion coordination

Back 26

present in transcription factors. Zinc atom coordinates a stable finger structure interacting with cystein and histidine. The finer region interacts with DNA, without Zinc transcription factors cannot bind to DNA

Front 27

Amino Acid Residues that are good metal ligands

Back 27

Cystine - side chain thiol can be a nucleophile and has a high affinity for metals

Histidine - can easily be protonated to carry a positive charge on the imidazole ring.

Front 28

Leucine Zipper

Back 28

Two alpha helixes wound together, every. Haplad repeat is leucine every 7th residue. Every 7th residue the coil is faces the same surface and leucines interact hydrophobically and hold the coil together tightly.

It medicates protein-protein interaction.

It does NOT bind to DNA

Front 29

Primary structure and post-translational modification affect folding, ribonuclease A

Back 29

the Amino acid sequence is determined by primary structure which dictates where the hydrophobic regions, covalent bonds, H-bonds and induced dipoles, disulfide bonds.

Ribonuclease A is stabilized by 4 disulfide bonds.

When urea and mercatoethanol are added to Rib A tey break the disulfide bond and it becomes inactive. Removal of urea and mercatoethanol reactivates it.

Front 30

Protein denaturation:
1. extreme pH
2. chemical
3. temperature

ex: pH on globular protein

Back 30

protein looses its tertiary and secondary structure due to external stress
1. ionize chains buried in hydrophobic environments (his, tyr) - disrupts salt bridges
2. break covalent and ionic bonds, peptides too
3. affects weak interactions, h-bonds

ex: denature it by affecting histine heme group - O2 would not be able to be stabilized

Front 31

How many hydrophobic residues are needed to span lipid bilayer

Back 31

7

Front 32

protein denaturation vs protein conformational change

Back 32

PD affects tert and sec. structure - protein is left non-functional. PC changes shape due to environmental factors - protein may become more of less functional.

Front 33

What is structural differenc ebetween normal PrPc and disease PrPSc states of Prion proteins?

Back 33

Normal PrPc have alpha helices that DO NOT aggregate

Diseased, PrPsc, have Beta strands that H-bond and cause aggregations that form amyloid plaques.

Alpha cannot H-bond because H are inside helix.

No one knows what causes switch from alpha helices to beta strands.