Lecture 5 Flashcards by she ign

general formula of an amino acid

alpha carbon in center
amino group
carboxyl group
(20) side chain
hydrogen

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at pH 7 the amino acid is a

zwitterion

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all amino acids have a stereoisomer except

glycine

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only – amino acids are found in proteins

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stereoisomers have same – but different –

same physical characteristics but different biological characteristics

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Basic side chains (+)

lysine, arginine, histidine

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Acidic side chains (-)

aspartic acid, glutamic acid

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Nonpolar side chains

alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan glycine, proline, cysteine

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uncharged polar side chains

asparagine, glutamine, serine, threonine, tyrosine

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a polypeptide is a polymer of –

amino acids

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the primary structure of a protein is the –

specific linear sequence of AA

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the – of AA makes each protein different

arrangement

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AA are linked by –

covalent peptide bonds

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backbone of a peptide chain has directionality

N-terminus –> C-terminus

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What makes up the peptide backbone?

N of amino group, alpha carbon, C of carboxyl group

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– determine the properties of the protein

side chains

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a – in the primary sequence can cause devastating results in the structure and function of a protein

single change

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secondary structure is determined by the –

peptide backbone interactions

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the polypeptide backbone provides many sites for –

H-bond formation

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Where can hydrogen bonds of the peptide backbone be found?

O of carboxyl and H of amino group

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hydrogen bonds are between – residues in the backbone

nearly adjacent

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How many residues per turn?

3.6

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in an alpha helix, H bonds are – to the axis

almost perfectly parallel

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alpha helices are abundant in –

transmembrane proteins

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in B sheet the hydrogen bonds between backbone atoms in --

neighboring chains

the -- contain extensive regions of B sheet

core of proteins

B-sheet produce -- structures

rigid

H bonds are perpendicular to the backbone in -- B sheet

anti-parallel

fixed bond angles in the backbone produce

a pleated contour

change the direction of a polypeptide

B turns

Most common residues in a turn

- glycine (small) can squeeze in small places | - proline bends the backbone

final folding of a single polypeptide

tertiary structure

proteins fold into a conformation with the

lowest energy state

Oil drop model of protein folding in a water environment

hydrophobic core and hydrophilic surface

a protein's conformation (3D structure) is determined solely by

its linear sequence

protein domain

a substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable strucutre

a domain usually contains

40-350 residues

different domains of a polypeptides are usually associated with --

different functions

motifs is often a signature for a --

specific function

small structural domains

structural motifs

motifs are -- structures composed of a defined arrangement of alpha helices and/or beta sheets

tertiary

structural motif

same structure but different sequence

sequence motif

same sequence and same structure

helix-loop-helix contains

2 alpha helices connected by a short loop

the loop is made up of

glutamate and aspartate

What would happen to the helix-loop-helix motif if the [Ca2+] decreases in the cytoplasm?

it will straighten out

coiled-coil structural motif

2 alpha helices wound around each other to form a rod-shaped protein

coiled-coil motif is composed of

repeats of 7 AA

coiled-coil is stabilized by the interaction of

the hydrophobic side chains of the 1st and 4th amino acids

protein domains are -- from which larger proteins are built

modular units

at least 40% of human protein-coding gene can be assigned to -- by sequence comparison

500 protein families

many large proteins have evolved through the joining of preexisting domains

domain shuffling

domain shuffling during vertebrate evolution has given rise to many -- of protein domains

novel combinations

binding site

reacts with another molecule through non-covalent interaction

dimerization region

where two different polypeptides interact with one another

active site

region where catalysis takes place

regulatory site

binding site for molecule which may increase or decreases the activity of an enzyme through allosteric regulation

interactions between two or more protein subunits

quaternary structure

quaternary structure describes the -- in multi metric proteins

number and relative positions of the subunits

2 identical protein subunits

homodimer

2 different protein subunits

heterodimer

protein subunit

one polypeptide chain

the most common covalent cross-linkage in proteins

disulfide bond

interchain disulfide bond

quaternary structure

intrachain disulfide bond

tertiary structure

the cysteine n side chain contains a -- which can form a covalent disulfide bond to a second cysteine

reactive sulfhydryl group

disulfide bond usually exists

outside the cell (oxidizing environment)

protein molecules often serve as subunits for the assembly of large structures by --

non-covalent interactions

T/F: all structures held together by noncovalent bonds self-assemble

false

the special protein aggregate that cause prion diseases

amyloid fibril

normal functions fro -- amyloid fibril

reversible

primary structure stabilized by

peptide bonds

secondary structure stabilized by

H bonds between groups along the peptide-bonded backbone

interaction between R-groups or between R-groups and the backbone stabilizes

tertiary structure

interactions beween R-groups, and between backbones of different polypeptides stabilizes

quaternary structure

steric limitation of -- restrict the possible 3D conformations of atoms

planar peptide bonds

rotations around alpha carbon and N

phi

rotations around alpha carbon and C

psi

partially double bonded peptide created by --

resonance

folding of protein in vivo is promoted by

molecular chaperones

bind and stabilize newly synthesized or unfolded proteins thereby preventing these proteins to interact with other proteins and become degraded

molecular chaperone (Hsp 70)

form a small folding chamber into which an unfolded protein can be sequestered, giving it time and environment to fold properly

chpaeronin (hsp-60-like)

information directing a protein's folding is encoded in its

amino acid sequence