2. Biomolecules and Enzymes Flashcards by huh? yunjin.

made of long
unbranched chain of
these amino acids

proteins

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repeating sequence of
atoms along the core of
the polypeptide chains

polypeptide backbone

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give amino acids its unique properties

side chains

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bonds of protein foldings

hydrogen bonds,
electrostatic attractions, and van der Waals

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assist in protein folding

molecular chaperones

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generated when a single
polypeptide chain twists around
on itself to form a rigid cylinder

a helix

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form from neighboring segments of the polypeptide backbone that run in the same orientation

parallel chains

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hydrogen bonding of the peptide
backbone; helices and β sheet

secondary structure

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from a polypeptide backbone that folds back and forth upon itself, with each section of the chain running in the direction opposite of that of its immediate neighbors

antiparallel chains

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formed from two or
more have most of their nonpolar
side chains on one side

coiled-coil

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amino acid sequence

primary structure

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full 3D organization of a polypeptide chain

tertiary structure

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readily recognized when the genome of any organism is sequence

protein families

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protein molecule formed as a complex of more than one polypeptide chain

quaternary structure

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human genome have how many coding genes

21,000 protein-coding genes

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tests to be undergone for protein sequence viewing

x-ray crystallography and nuclear
magnetic resonance (NMR)

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the basic units of proteins that can fold, function, and evolve
independently

protein domains

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process of creating new combination of gene functional domains

domain shuffling

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during vertebrate evolution has given rise to many novel
combinations of protein
domains

domain shuffling

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the subset of protein domains, mobile during evolution

protein modules

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recognition domain – only in
humans

Major Histocompatibility
Complex (MHC) antigen

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any region of a protein’s
surface that can interact with another molecule

binding site

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forming a symmetric complex of two protein subunits (dimer)

head to head arrangement

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ropelike structures;
important component of the cytoskeleton

intermediate filaments

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two identical α-globin subunits and two identical β-globin subunits, symmetrically arranged

hemoglobin

why is a helix a common structure in biology?

all subunits are identical, they can only fit together in one way – rarely straight line resulting in a helix

intrinsically disordered regions of proteins are frequent in nature, WHY?

to form specific binding sies for other protein molecules that are of high specificity

abundant outside the cell; main component of the gel-like extracellular matrix

fibrous proteins

main component in long lived structures

keratin filaments

a dimer of two identical subunits

a-keratin

elongated three-dimensional structure

fibrous protein

___ can spontaneously assemble into the final structure under the appropriate condition

purified subunits

another abundant protein in ecm; highly disordered polypeptide

elastin

4 process of disoerdered polypeptide chain

binding signaling tethering diffusion barrier

consists of three long polypeptide chains, each containing that nonpolar amino acid glycine at every 3rd position

collagen

2 examples of prion diseases

scrapie in sheep, Creutzfeldt-Jakob disease (CJD) in humans Kuru in humans bovine spongiform encephalopathy (BSE) in cattle

guide construction but take no part in the final assembled structure

assembly factors

Can Form from Many Proteins; self propagating, stable β-sheet aggregates

amyloid fibrils

example of capable of self assembly from its component parts

tobacco mosaic virus (TMV)

consist of amyloid fibrils – acts like a vesicle containing peptide and hormones

secretory granules

the substance that is bound by the protein

ligand

each protein molecule can usually bind just one or a few molecules out of many thousands

specificity

secretes proteins that form long amyloid fibrils projecting from the cell exterior that help to bind bacterial neighbors to biofilms

in bacteria, secretory granules

Proteins aggregates may be released from dead cells and accumulate as

amyloid

Which disease can produce amyloid

Prion diseases

The ability of a protein to bind selectively and with high affinity to a ligand depends on the formation of a set of _____

weak noncovalent bonds

4 weak noncovalent bonds

hydrogen bonds electrostatic attractions van der Waals attractions favorable hydrophobic interactions

the region of protein that associates with a ligand

Binding site

the interaction of neighboring parts of the polypeptide chain may _____

restrict the access of water molecules to that protein’s ligand binding sites

the clustering of neighboring polar amino acid chains can _______

alter their reactivity

3 types of interface

* surface-string interaction * helix-helix * surface-surface

binds tightly to a particular target molecule (antigen), inactivating directly or making it for destruction

Antibody or immunoglobulins

complementary to a small portion of the surface of the antigen molecule

Y-shaped molecules with two identical binding sites

cause the chemical transformations that make and break covalent bonds in cells

Enzymes

Enzymes + substrates 

Products

Speeds up reactions, act as catalysts

Enzymes

Enzymes that hydrolytic cleavage reaction

Hydrolases

Break down nucleic acids by hydrolyzing bonds

Nucleases

Breaks down protein

Proteases

Synthesize molecules

Synthases

Joins together two molecules

Ligases

Catalyze the rearrangement of bonds

Isomerases

Catalyze polymerization reactions

Polymerases

Adds phosphate group

Kinases

Catalyze the hydrolytic removal of phosphate group

Phosphatases

Oxidized and redox

Oxido-reductases

Hydrolyze ATP

ATPases

Hydrolyze GTP

GTPases

Formula of enzyme substrate complex

E + S → ES → EP → E + P

the maximum rate of reaction divided by the enzyme concentration

Turnover number

enzymes achieve ______ of chemical reactions

extremely high rates

enzymes greatly increase the local concentration of both these ____ at the _____

substrate molecule at the catalytic site

unstable intermediate state

Transition state

the free energy required to attain the transition state

Activation energy

adds a molecule of water to a single bod bet. two adjacent sugar groups in the polysaccharide chain, thereby causing the bond to break

Hydrolysis

catalyzes the cutting of polysaccharide chains in the cell walls of bacteria.

Lysozyme

assisting the hydrolysis reaction. In other enzymes, a small organic molecule serves a similar purpose. Such organic molecules are often referred to as

Coenzyme

a large protein assembly; allows the product of enzyme A to be passed directly to enzyme B, and so on

Multienzyme complex

controls how many molecules of each enzyme it makes by ____

regulating the expression of the gene that encodes that enzyme

controls enzymatic activities by confining sets of?

enzymes to particular compartments

a product produced late in a reaction pathways inhibits an enzyme that acts earlier in the pathway

Feedback inhibition

prevent an enzyme from acting

Negative regulation

regulatory molecule stimulates the enzyme’s activity rather than shutting the enzyme down

Positive regulation

Greek words ___ meaning “other” and _____ meaning “solid or 3d”

Allos, stereo

Enzyme having two binding sites – active and regulatory site

Allosteric enzymes

Recognizes the substrates

Active site

Recognizes a regulatory molecule

Regulatory site

Interaction between separated sites on a protein

Conformational change

positive regulation caused by ____ between two separate binding sites

conformational coupling

if the shift of a protein to a conformation that binds glucose best also causes the binding site for X to fit X better, then the protein will bind glucose more tightly when X is present than when X is absent

Positive regulation caused by conformational coupling between two separate binding sites

if a shape change caused by glucose binding decreases the affinity of a protein for molecule X, the binding of X must also decrease the protein’s affinity for glucose

Negative regulation caused by conformational coupling between two separate binding sites

can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site

Cooperative allosteric transition

transfer of the terminal phosphate group of an ATP molecule to the hydroxyl group

Protein phosphorylation

Phosphorylates

Protein kinase

phosphate removal, dephosphorylate

Protein phosphatase

phosphate is part of guanine nucleotide GTP; addition and removal of phosphate

GTP-binding proteins (GTPases)

What happens when a tightly bound GTP is hydrolyzed by the GTP-binding protein to GDP,

Conformational change then inactivated

They generate forces responsible for muscle contraction and the crawling and swimming of cells; a series of conformational changes

Motor proteins

they help to move chromosomes to opposite ends of the cell during mitosis

Motor proteins

coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein

unidirectional conformation changes

Membrane bound transporters with function to export hydrophobic molecules from the cytoplasm

ABC Transporters (ATP-binding cassette)

proteins binding sites for multiple other proteins

Scaffold proteins

they serve both to link together specific sets of interacting proteins and to position them at specific locations inside a cell

Scaffold proteins