Chap by hcj

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									Protein Structure and Function
The most abundant organic macromolecules by mass (weight) in cells are ________________.

Write the names of all 20 amino acids, their 3-letter abbreviations, and the condition of their side
chains.
Amino acid                         Abbreviation                  Side chain

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________

________________________            ___________                  ___________________


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Each type of protein differs in its _________________ and _______________ of amino acids.

The C – N bond that holds amino acids together is called a __________________ bond. The peptide

bond actually involves ______ atoms. Draw a peptide bond.


The atoms involved in the peptide bond are held _________________, but free _______________ is
possible around other bonds in the polypeptide. Polypeptides can, therefore, fold up into a wide
variety of shapes.

The repeating sequence of atoms along the amino acid chain = _______________________________.

Write the sequence along the polypeptide backbone for 4 amino acids.

__________________________________________________________________________________

The __________________ is the part of each amino acid that is different = the part that gives each
amino acid its unique properties.

It is, therefore, the sequence of ___________ ____________ that makes each protein unique.

The final folded structure adopted by a polypeptide chain = __________________________.

What determines the final conformation (shape) and therefore function of a protein?

1. The distribution of _________________, ______________ and ______________________ side
chains in the amino acid sequence.

2. Sets of weak noncovalent bonds - ________________________, ________________________, and

_________________________________________.

Where would you expect to find polar and nonpolar amino acids on functional proteins in solution?

The nonpolar side chains are ____________________ and tend to cluster in the ________________

of the molecule to avoid contact with ______________ inside the cell. Polar side chains tend to

arrange themselves near the __________________ of the molecule where they can form

____________________ bonds with water and other polar molecules.

3. Though many shapes are possible for any polypeptide chain, the conformation generally adopted is

the most stable one, the one of ______________ ______________.

Unfolding of a protein = ______________________            Refolding = ____________________


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Levels of organization of proteins:

__________________ structure = the _____________ ___________ sequence

__________________ structure = structures held together only by ________________ ___________.

Two common patterns in the secondary folded structure

1. _________________________

2. _________________________

These 2 patterns are particularly common because they result from _______________________

between the ______ of the ___________ or _________ group and the _________ of the ___________

or __________ group every fourth peptide bond. No hydrogen bonding between ______________

___________ is involved.

The alpha helix is especially abundant in ________________________ proteins such as transport or

___________________ proteins and ____________________ proteins.

Beta (β) sheets are formed from neighboring polypeptide chains running ________________ to each

other or parts of the same chain folded back and running ________________________. This produces

a rigid structure held together by ____________________ bonds connecting the __________________

bonds of _______________________ chains.

__________________ structure = folded, complex, _____________________________

conformation of a ______________ polypeptide chain.

_____________________ stucture = complete protein conformation with ______________________

_____________________ chain.

Each polypeptide chain in a protein made of more than 1 polypeptide chain is called a protein

_______________.     A functional protein complex made of 2 polypeptide subunits = ____________.

A functional protein complex made of 4 polypeptide subunits = ______________________________.

The first protein to have its amino acid sequence determined was the hormone __________________.

Insulin is a ___________________. Insulin consists of _________ polypeptide chains with
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__________ total amino acids.

____________________ is a tetramer made of 2 copies of _________________ and 2 copies of

_____________________.

The complete structure of a protein may be displayed as a __________________________________,

________________________, _______________________, ________________________________.

Protein domain = any part of a polypeptide chain that can ____________ _____________________

into a compact, _________________ conformation.

Binding site = also enzyme _______________ __________ - the region of a protein surface to which
another molecule (substrate) binds – often the protruding loop regions in the ribbon model.


Protein Assemblies:

1) __________________ proteins fold up into compact shapes with irregular surfaces. Examples are

(A) ___________________, which is the oxygen-carrying pigment in red blood cells,

(B) ___________________, a peptide hormone, which regulates the uptake of glucose by the liver, and

(C) ___________________, the enzyme in tears that dissolves bacterial cell walls.

2) ___________________ proteins are __________________ proteins having functions that require
   them to span longer distances.

________________ proteins each with 2 different _____________ _________ will often form long

_______________ _____________. These helical filaments assemble into sheets or long fibrils.

(A) They are common in _______________, the most abundant protein inside eukaryotic cells. Actin

and _________________ are the proteins found in _____________________________, and actin

also forms the microfilaments of the cell’s_______________________ , which underlies and supports
the plasma membrane.

Actin & myosin filaments also form the ____________________ ring during cytokinesis.

(B) The α helix was first discovered in the protein _______________________, which is abundant in

_______________ and its derivatives - ________________, ______________, & _______________.


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Keratin forms __________________ _________________ in ___________________ cells and gives

epithelial cells remarkable ability to ___________________ and remain intact. Keratin is extremely
stable.

(C) Microtubules are long, hollow cylinders made of the protein __________________, which is an

αβ _______________. Microtubules form part of the _____________________, the ______________

during cell division, and enable _______________ and _________________ to beat.

(D) Fibrous proteins are especially abundant outside of cells where they form the gel-like

_________________________ _______________.

_____________________ secrete the fibrous proteins _____________________ & _______________

to form the extracellular matrix.

(a) _____________________ is a triple helix, formed by 3 polypeptide chains, that gives enormous

____________________ to tissues. Collagen is the most ____________________ protein in higher
vertebrates.

(b) ____________________ forms a rubber-like meshwork in the extracellular matrix. Elastin

polypeptide chains are _____________________________ together to form _____________-like,
elastic fibers.

__________________ is a major component of the extracellular matrix of the _________________ of

the skin, the _________________, and __________________. Elastin gives tissues the ability to

_______________, uncoil, and recoil without tearing.


Disulfide Bonds = stabilize _________________________ proteins

   -   rare ______________ bond between two ____________ atoms = __________________

   -   stabilize polypeptide chains in proteins attached to the __________________ of the cell’s

       plasma membrane or _______________ as part of the ______________________ __________

   -   only in proteins that function in the ______________________ environment

   -   form between 2 _______ groups of ______________ side chains that are adjacent in the folded
       protein.


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   -   Disulfide bonds help to stabilize a ___________________ protein ______________________
       for extracellular proteins.

   -   Examples

       1. ___________________ fibers in __________ and nails are covalently cross-linked.

       2. ___________________ in tears retains its antibacterial activity longer because it is stabilized
          by S-S bonds.

       3. __________________ in the extracellular matrix.

       4. __________________ has disulfide bonds between the 2 polypeptide chains and within the
          A chain.

How proteins work
Proteins function by __________________ to other molecules.

   -   the binding is always _________________

   -   The molecule to which the protein binds is called a ____________________.

   -   The region of a protein that associates with the ligand is known as its _____________ _______.

   -   Many __________ _____________ bonds must be formed ______________________.

   -   A binding site consists of a particular arrangement of ______________ __________ ________.

   -   May the long-lasting or temporary

   -   Remainder of protein structure is important as a “________________”. A change in the amino
       acids (mutation) in the interior can change the 3-D shape of the protein and destroy its ability to
       function.

   -   __________________ defines __________________.

Binding strength between protein and ligand depends upon
1. the _______________ ____________ of the _________________ _____________ to the ligand

2. the ___________________ of ______________________ bonds formed between the protein and its
        ligand.
3. the ___________________________

4. the ___________________________

Binding strength does NOT depend upon the _______________________ of the protein or its ligand.


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Antibodies have a highly developed binding capacity.
Antibodies, or _______________________, are proteins produced by the _______________ system

in response to foreign molecules such as those on the surface of invading __________________ &

___________________.

The ligand with which a particular antibody binds is called an ___________________. Each antibody
has a specific antigen with which it binds.

Antibodies form _________________ with the target antigens to facilitate destruction of the invading
pathogens.

Each antibody is a __________ -shaped molecule with _____ _____________ ___________
________ for its antigen, one on the end of each arm of the Y.

Each antibody molecule is composed of _____ polypeptide chains - ____ identical _____________

chains and _____ identical and smaller ______________ chains.

Antibodies are made by a class of ___________ ________ ________ called ___________________.

or ____________. Each resting B cell carries a different ______________ molecule on its surface that

recognizes and _____________ with a specific ______________. When the specific antigen binds

with its receptor, the B-cell is stimulated to divide and make more of the same ________________ and

_____________ it in a soluble form.


Enzymes as Catalysts
The ligand to which an enzyme binds is called the __________________. Enzymes work in teams so

that the _________________ of one chemical reaction is the __________________ for the next.

Enzymes catalyze (speed up) chemical reactions by __________________ or ____________________

____________________ bonds without being changed themselves.

Outline of enzyme action:

1. Binds to __________________ in precise alignment to encourage a reaction.

2. Enzyme changes the ______________ of the substrate to make it ___________________. This


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  unstable state is called the ______________________ state.

3. Enzymes _____________ the ____________________ energy necessary for the reaction to occur.

Regulation of Catalytic Activities of Enzymes:

1. A cell controls the production of each enzyme by regulating the _______________________ of the

  ________________that encodes the enzyme.

2. Some sets of enzymes are confined within _____________________ _____________________

  called ____________________, which contain the enzyme ______________________.

3. ____________________ _______________________ is negative regulation. An _______________

  acting early in a reaction pathway is _________________ by a _____________ ________________
  of that pathway.

4. ___________________ regulation = A ____________________ in _______ __________________

 of a metabolic maze _____________________ the activity of an ____________________ in another

 pathway of the maze. Example: A high concentration of ______________ stimulates enzymes in

 glycolysis and the citric acid cycle to increase the production of _____________.

Question 4-7 page 151




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Most enzymes have two different ______________ ___________ on their surfaces.

The _________________ __________ that recognizes the __________________, and a second site

recognizes a ___________________ molecule. Binding of the ligand at the regulatory site causes

the folded _____________ or ___________________of the enzyme or other protein to ____________
slightly.

The _____________________ ________________ either _______________ or _______________

binding at the _________________site.

Enzymes and other protein molecules that can adopt two or more different conformations are said to be

_______________________ from the Greek allo = ____________ and stere = _______________.

If enzyme binding with the regulatory molecule inhibits substrate binding = ___________________
regulation.

If enzyme binding with the regulatory molecule stimulates substrate binding = _________________
regulation.

Protein Function Regulation by Phosphorylation:

   -   Enzyme is modified by _______________ bonding a ________________ group to one of it’s
       a.a. side chains

   -   Phosphate group carries two ________________ charges

   -   Addition of phosphate group to amino acid side chain causes major ______________________
       change

   -   Addition of phosphate group requires another enzyme = _______________________________

   -   Addition of phosphate group is called ______________________________________________

   -   Removal of phosphate group requires another enzyme = _______________________________

   -   Removal of phosphate group is called ______________________________________________

   -   Energy is derived from the hydrolysis of ___________________.

   -   Phosphorylation can either ______________ or _______________ a protein’s activity.




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GTP (_______________ ___________________)- Binding Proteins
GTP-binding proteins function as ________________ ________________ in cells.

When GTP is bound, the protein is _________________.

When GTP is hydrolyzed to GDP, protein becomes __________________ until GDP is slowly

released and replaced by _____________ again.

GTP – binding proteins bind to other proteins to control ________________ activities.

Motor Proteins
Motor proteins generate _________________ within cells and tissues to move other molecules.

Motor proteins are responsible for

   - movement of _____________________ during cell division

   -   movement of _______________ along a ___________________ during replication &
       transcription

   -   movement of _________________ along microtubules within the cell

   -   enables eukaryotic ________________ and _________________ to beat.

   -   The motor protein __________________ is responsible for ________________ contraction –
       movement of the skeleton.

The _____________________ of ____________ (or GTP) to ___________ releases ______________,

which causes _______________________ changes in motor proteins producing ________________ in

a ____________direction.

_______________________ causes a motor protein to change from conformation 1 to conformation 2.

_______________ released in ATP hydrolysis causes the motor protein to change from conformation 2
to conformation 3.

_________________ of _________________________ causes the shape of the protein to change back
to conformation 1.

Why is the motion of a motor protein unidirectional and not reversible?

The conformational changes are accomplished by the ___________________ of __________ to


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___________ and Pi. To undergo a reverse shape change as would be required to move backward

would require __________________ of ___________ from ADP + Pi, a highly energetically

___________________________ reaction, requiring the input of ~ 12 kcal/molecule.

Functional Classes of Enzymes:

1. ___________________ = Enzymes that hydrolyze ATP. ______________ proteins and

 __________________ _______________ proteins are ________________.

2. ___________________ = catalyze the __________________ of __________________ groups to
   molecules

3. ___________________ = catalyze the hydrolytic __________________ of a phosphate group from
   a molecule

Kinds of Proteins:

   1) __________________ (e.g. _____________________)

   2) ___________________ Proteins (e.g. ________________)

   3) ___________________ (immunoglobulins)

   4) _________-binding proteins (__________________ protein)

   5) Functional __________________ (e.g. _____________________, _____________________,

       and _________________________.)

   6) Peptide _________________ (e.g. __________________)

   7) ____________________ proteins (e.g. ________________ in ___________ and

       ________________ in ______________)

   8). Fibrous proteins

   •   Muscle fiber protein = _______________

   •   Extracellular matrix proteins = ____________________ and ________________

   •   ___________________ in hair and nails

   •   Mitotic Spindle = __________________

   •   _______________________ = tubulin, keratin, and actin
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