Chapter 4 Cell Bio

Active site

a region on an enzyme that binds to a protein or other substance during a reaction.

Allosteric

Describes a

Alpha helix

A coiled region constituting one form of the secondary structure of proteins, arising from a specific pattern of hydrogen bonding between atoms of the polypeptide backbone (not the side chains).

amino acid sequence

The order of the amino acid subunits in a protein chain. Sometimes called the primary structure of a protein.

Antibody

protein produced by B lymphocytes that specifically reacts with a foreign antigen

Antigen

Molecule or fragment of a molecule that is recognized by an antibody

Beta sheet

Folding pattern found in many proteins in which neighboring regions of the polypeptide chain associate side by side with each other through hydrogen bonds to give a rigid, flattened structure.

Binding site

Region on the surface of a protein, typically a cavity or groove, that interacts with another molecule (a ligand) through the formation of multiple noncovalent bonds.

C-terminus

the end of a polypeptide or protein that has a free carboxyl group

Chromatography

A technique that is used to separate the components of a mixture based on the tendency of each component to travel or be drawn across the surface of another material.

Coenzyme

a small molecule that binds tightly to an enzyme and helps it to catalyze a reaction

coiled coil

stable, rodlike protein structure formed when two or more alpha helices twist around each other

Conformation

Precise, three-dimensional shape of a protein or other macromolecule, based on the spatial location of its atoms in relation to one another.

cryoelectron microscopy

Technique for observing the detailed structure of a macromolecule at very low temperatures after freezing native structures in ice

Disulfide bond

Covalent cross-link formed between the sulfhydryl groups on two cysteine side chains; often used to reinforce a secreted protein's structure or to join two different proteins together.

Electrophoresis

Technique for separating a mixture of proteins or DNA fragments by placing them on a polymer gel and subjecting them to an electric field. The molecules migrate through the gel at different speeds depending on their size and net charge.

Enzyme

protein that catalyzes chemical reactions for organisms

feedback inhibition

A form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway.

Fibrous proteins

A protein with an elongated, rodlike shape, such as collagen or a keratin filament.

Globular protein

Any protein in which the polypeptide chain folds into a compact, rounded shape. Includes most enzymes.

GTP-binding protein

Intracellular signaling protein whose activity is determined by its association with either GTP or GDP. Includes both trimeric G proteins and monomeric GTPases, such as Ras.

Helix

An elongated structure whose subunits twist in a regular fashion around a central axis, like a spiral staircase.

Intracellular condensate

A large aggregate of phase separated macromolecules that creates a region with a special biochemistry without the use of an an encapsulating membrane

intrinsically disordered sequences

Region in a polypeptide chain that lacks a definite structure.

Ligand

General term for a molecule that binds to a specific site on a protein.

Lysosomes

A membrane-enclosed organelle that breaks down worn out proteins and organelles and other waste materials as well as molecules taken up by endocytosis; contains digestive enzymes that are typically most active at the acid pH found inside these organelles

mass spectrometry

Sensitive technique that enables the determination of the exact mass of all of the molecules in a complex mixture

Michaelis constant

A constant, Km, that is a measure of the kinetics of an enzyme reaction and that is equivalent to the concentration of substrate at which the reaction takes place at one half its maximum rate.

Motor protein

Proteins such as myosin or kinesin that uses energy derived from ATP hydrolysis to propel itself along a protein filament or polymeric molecule.

N-terminus

the end of a polypeptide or protein that has a free amino group

Nuclear magnetic resonance

Technique used for determining the three-dimensional structure of a protein in solution.

Peptide bond

Covalent chemical bond between the carbonyl groups of one amino acid and the amino group of a second amino acid

polypeptide chain

A chain of amino acids linked together by peptide bonds.

polypeptide backbone

Repeating sequence of atoms (-N-C-C-) that forms the core of a protein molecule and to which the amino acid side chains are attached.

primary structure

the amino acid sequence of a protein

Protein

Macromolecule built from amino acids that provide the cells with their shape and structure

Protein domain

Segment of a polypeptide chain that can fold into a compact stable structure and that usually carries out a specific function.

Protein family

A group of polypeptides that shares a similar amino acid sequence or three-dimensional structure, reflecting a common evolutionary origin. Individual members often have related but distinct functions, such as kinases that phosphorylate different target pr

Protein kinase

enzyme that catalyzes the transfer of a phosphate group from ATP to a target protein

Protein machine

Large assembly of protein molecules that operates as a unit to perform a complex series of biological activities, such as replicating DNA.

Protein phosphate

Enzyme that catalyzes the removal of a phosphate group from a protein, often with high specificity for the phosphorylated site.

protein phosphorylation

The covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; serves as a form of regulation that usually alters the activity or properties of the target protein.

quaternary structure

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.

Scaffold protein

Protein with multiple binding sites for other macromolecules holding them in a way that speeds up their functional interactions

Secondary structure

regular structure formed by proteins by intramolecular hydrogen bonding between the oxygen atom of one amino acid residue and the hydrogen attached to the nitrogen atom of another amino acid residue

Side chain

Side chain is another name for an R group, and is a group of atoms attached to the main part of a molecule and having a ring or chain structure.

Substrate

- the molecule upon which an enzyme acts

Subunit

A monomer that forms part of a larger molecule, such as an amino acid residue in a protein or a nucleotide residue in a nucleic acid. Can also refer to a complete molecule that forms part of a larger molecule. Many proteins, for example, are composed of m

tertiary structure

The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.

Transition state

Transient structure that forms during the course of a chemical reaction

Turnover number

maximum number of substrate molecules an enzyme molecule converts to product each second

Vmax

maximum initial velocity or rate of an enzyme-catalysed reaction.

X-ray crystallography

A technique that depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule to study the three-dimensional structure of the molecule.

Aspartic Acid

Asp
D
Negatively charged

Glutamic Acid

Glu
E
Negatively charged

Arginine

Arg
R
positively charged

Lysine

Lys
K
Positive charged

Asparagine

Asn
N
Uncharged polar

Glutamine

Gln
Q
uncharged polar

Serine

Ser
S
uncharged polar

Threonine

Thr
T
uncharged polar

Tyrosine

Tyr
Y
uncharged polar

Alanine

Ala
A
nonpolar

Glycine

Gly
G
nonpolar

Valine

Val
V
nonpolar

Leucine

Leu
L
nonpolar

Isoleucine

Ile
I
nonpolar

Proline

Pro
P
nonpolar

phenolalanine

Phe
F
nonpolar

Methionine

Met
M
nonpolar

Tryptophan

Trp
W
nonpolar

Cysteine

Cys
C
nonpolar

What are the 3 types of non covalent bonds that help proteins fold?

1. Hydrogen bonds
2 electrostatic attraction
3. Van der Waals attraction

What do hydrophobic forces help proteins do?

Fold into compact conformations

What do hydrogen bonds do for proteins?

Stabilize its folded shape

Can denatured proteins be renatured?

Yes

How can a protein be denatured?

temperature, pH AND salt

What assists protein folding in living cells? (Hint: it's a special protein)

Chaperone protein

What are the 2 types of pattern sheets polypeptide chains can fold into?

Alpha and beta

When will a helix form?

When a series of similar subunits bind to each other in a regular way

2 types of Beta sheets?

antiparallel and parallel

Many proteins are formed of separate ________ domains.

Functional

Favored protein confirmations are stabilized by _______ bonds.

Disulfide

Protein binding to a molecules is _______ _________

Highly selective

What happens when molecules have poorly matching surfaces? What occurs?

Few covalent bonds occur and the two molecules disassociate as a rapidly as they form

How do binding sites allow proteins to interact with specific ligands?

The folding of polypeptide chain creates a crevice or cavity on the folded protein's surface where specific amino acid side chains are brought together allowing the formation of of a set of non covalent bonds only with CERTAIN ligands

Describe the shape of an antibody.

Y shaped with 2 identical antigen binding sites one on each arm

How are enzyme-substrate complexes formed?

Each enzyme has a site to which substrate molecules bind forming the complex

Name the enzyme functional classes? (Hint: there are 10)

1. Hydrolase
2. Nuclease
3. Protease
4. Ligase
5. Isomerase
6. Polymerase
7. Kinase
8. Phosphatase
9. Oxido-reductase
10. ATPase

What does an enzymes performance rely on?

How rapidly it can process a substrate

Enzymes do what to substrate molecules?

Chemically alter and bind to

What are the 3 ways an enzyme can encourage a reaction?

1. Holding reacting substrates together in a precise alignment
2. Rearranging the distribution of a charge in a reaction intermediate
3. Altering bond angles in the substrate

function of feedback inhibition

Regulates the flow through biosynthetic pathways

Function of feedback inhibition at multiple points

Regulates connected metabolic pathways and triggers a confrontational change in an enzyme

What happens with the binding of a regulatory ligand?

It can change the equilibrium between the two protein conformations

Due to changes in conformation proteins can "______" along a cytoskeleton filament

Walk

What do scaffold proteins do?

Ensure that signalling molecules are in the right location to speed up signalling.