BIOL 3361 Exam 2 Flashcards

The probability that two proteins will \_______ have similar sequences is negligible. Therefore, sequence similarity implies \____________.

by chance, evolutionary relatedness

Proteins with similar sequences are described as \_________.

homologous

__________ proteins are from different species(ancestral gene)

__________ proteins are from the same species(gene duplication)

orthologous, paralogous

Computer programs optimally align sequences in databases e.g. _________.

BLAST or Basic Local Alignment Search Tool

_______ represent changes at one or more sites in the amino acid sequence of a protein.

Mutations

Score alignment based on ___________ amino acids

matching or similar

Also put in \______ which bring penalties

gaps

Alignment can be \________.

local or global

The amino acid difference between two \____________ sequences is proportional to the phylogenetic difference between the species from which they are derived.

cytochrome c

What does the number represent on a Cytochrome–c phylogenetic tree?

The amino acid changes

Some proteins share \___________ structural features but carry out \____________ functions.

similar, different

Proteins with _________ structure scan carry out _________ functions.

different, similar

Proteins have partial \______________ character

double bond

The peptide backbone only has \______ degrees of freedom

two

Angle about the ______ bond is denoted φ (Phi)

Cα–N

Angle about the _________ bond is denoted ψ (psi)

Cα–C

Which values are forbidden due to steric crowding?

φ = 0, ψ = 180

φ = 180, ψ = 0

φ = 0, ψ = 0

\___________ stabilize proteins.

Weak interaction

Most stable structure has the largest number of \_________.

interactions

Polarity of H–bonding groups __________ if they are in the hydrophobic core.

must be neutralized

What are the secondary structures?

• Helices (particularly alpha)

• Beta sheets

• Beta turns

• Random coil

What are super secondary structures?

• Coiled coils

• Beta hairpin

• Beta–alpha–beta

The α–Helix has \_________ residues per turn

3.6

The angles for the α–Helix are:

φ =

ψ =

–60, –45 to –50

The α–Helix has a diameter of \_______

6 Angstroms

Helix pitch or rise?

5.4 Ang (1.5 Ang per res)

Almost always ___________ due to the close approach of side chains of amino acids

right–handed

Left–handed helices are shorter and contain \_________.

glycine

The α–Helix gives a ______________ at the amino end

partial positive charge

The α–Helix gives a ______________ at the carboxyl end

partial negative charge

Which two are the important helix breakers?

Glycine, Proline

The ß–sheet has \__________ between C\=O and N–H residues on different strands.

H–bonds

Strands can be:

– _________ with bent H bonds

– ____________ with straight H–bonds

parallel, anti–parallel

Anti–parallel is more \_______

favorable

Qualities of a parallel beta sheet?

• φ = −120°, ψ = 105°(small range)

• > 5 strands

• Hydrophobic sidechains on both sides

Qualities of a Anti–parallel beta sheet?

• φ = −135°, ψ = 140°(large range)

• < 5 strands

• Hydrophobic sidechains on one sides (alternate insequence)

What is the rise for antiparallel strands with 5 residues?

3.47 Å

What is the rise for parallel strands with 5 residues?

3.25 Å

Each strand of a β–sheet is \__________ residues long

5–10

In the ß–Turn Carbonyl C of one residue is \__________ to the amide proton of a residue three residues away (1st and 4th)

H–bonded

\________ and \_________ are prevalent in β–turns

Proline, glycine

What makes the Beta turn important?

It promotes the formation of the antiparallel sheets

Random coils are not \____________,just no recurring bonding pattern

random or coiled

Random Coils are rich in ____________ residues.

charged and polar

Random Coils are \________ and participate in binding events.

flexible

What is a Beta–hairpin?

Two adjacent anti–parallel strands joined by a 2–5 residue loop

What is ß–α–ß Motif

Two adjacent parallel ß–strands connected by an α–helix that is commonly positioned above the ß–plane.

What is a Coiled Coil

Two helices wound around each other in a supercoil or super–helix

Secondary and super secondary structures combine to make ____________.

domains (

What is a domain?

a polypeptide chain or part of a polypeptide chain that can fold into a stable tertiary structure in aqueous solution

Domains can combine to make \________

multi-domain proteins

Often, large proteins don't contain larger domains, just \________

more domains.

Proteins consisting of multiple domains probably evolved by the \________

fusion.

\________% of domains re-occur in different proteins

90.

The __________________________ database recognizes five overarching classes (1995)

Structural Classification of Proteins (SCOP)

SCOP is based on levels that embody the ________________________ relationships among known proteins (manual curation)

evolutionary and structural

**__________________________________** is another system

**CATH** (standing for Class, Architecture, Topology, Homologous superfamily)

CATH differs from SCOP in combining ____________ analysis with _____________________ analysis

manual, quantitative algorithmic

Protein Classification : Class

is determined from overall composition of secondary structure elements in a domain

Protein Classification : Folds

describes the number, arrangement, and connections of these secondary structure elements

Protein Classification : Superfamily

includes domains of similar folds and usually similar functions

Protein Classification : Family

usually includes domains with closely related amino acid sequences

Four major classes of protein structure

All α, All ß, α/ß, α+ß

What was Anfinsen’s Classic Experiments result?

All of the information necessary for folding the peptide chain into its ‘native’ structure is contained in the primary amino acid structure of the peptide

proteins are ___________ and ________

marginally, dynamic

The ΔG for protein folding is typically -20 to -40 kJ/mol (__________)

small

Microcalorimetry of protein unfolding indicates a favorable ____________ change is the principal contributor to folding

enthalpy

A number of _______________ are linked to abnormalities of protein folding

human diseases

The _____________ is the temperature at which 50% of the protein is unfolded

melting temperature or Tm

Called _______________ as they are upregulated when cells are exposed to heat

heat-shock proteins (HSPs)

The principal chaperones are ________________ , and Hsp90

Hsp70, Hsp60 (the chaperonins)

What are the three protein folding pathways

Chaperone-independent folding. \n Hsp70-assisted protein folding. \n Folding assisted by Hsp70 and chaperonin complexes.

Proteins of the _________ class bind to nascent polypeptides while they are still on ribosomes

Hsp70

In bacteria, Hsp70 is called __________

DnaK

Hsp60/Chaperonins/GroES-GroEL sequester partially folded proteins in an enclosed space referred to as an ______________

“Anfinsen cage”

Substrate polypeptides in this complex undergo _________________ that bury hydrophobic residues to produce the native form

forced unfolding followed by folding processes

This complex process is _________

ATP-driven

_________ tells us how fast a favorable reaction will occur

Kinetics

Enzymes are mostly (but not always) _________ that bind substrate through ____________ at their active site

proteins, weak interactions

In the active site, the ___________ of key _____________ \n influences enzyme __________

protination, amino acids, mechanism

Enzymes catalyze thermodynamically favorable reactions causing them to proceed at ______________________.

extraordinarily rapid rates

Accelerate as much as _________ times ________________.

10^21, over uncatalyzed rates

Enzymes bind ____________ substrates and catalyze specific reactions with high (>95%) yields

specific

Enzymes are ______________ and are the agents of metabolism

regulated

Catalytic power (or the ratio of the catalyzed \n rate to the uncatalyzed rate) for Urease is ______________.

1x10^14

What are the 6 classes in enzyme classifications?

Oxidoreductases, Transferases, Hydrolases, Lyases, (“synthases”), Isomerases, Ligases (“synthetases”)

Rapid equilibrium assumption is that __________________.

k_1 and k_-1 >> k_2

Allosteric enzymes are an _____________ to the Michaelis-Menten model.

exception

k_cat , the turnover number, is the number of substratemolecules converted to product per enzyme molecule per unit of time, ______________________.

when E is saturated with substrate

If the model fits, ___________.

k2 = kcat

What is an inhibitor?

Any ligand, natural or synthetic, that decreases the velocity of an enzyme-catalyzed reaction

What is the effect of an inhibitor?

A change in KM and/or VMax

How do inhibitors work?

By reversible binding to one or more of the enzyme forms present during the reaction

____________________ synthesizes __________________ in bacteria (humans use dietary folate or vitamin B 9 ) using _________ as a substrate

Dihydropteroate synthase, tetrahydrofolate, PABA

Methanol is converted by liver … to formaldehyde, which is highly \n … (blindness, death)

alcohol dehydrogenase, toxic

… with methanol for binding to alcohol dehydrogenase, slowing production of formaldehyde

Ethanol competes

What happens in non-competitive inhibitors?

I does not bind the same site as the S

What is Pure non-competitive inhibition?

Binding of I does not influence binding of S; this is quite rare

What is Mixed non-competitive inhibition?

Binding of I influences binding of S; common

What is Uncompetitive inhibitors?

I combines with ES (not E)