proteins part 2 Flashcards by BABAS CHRISTINE MAY

____________ are biological catalyst –ex:
Pepsin, Trypsin

Enzymes

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_______________ include antibodies
(Immunoglobulins) which are specific
protein molecules produced by
specialized cells of the immune system
in response to foreign antigens.

Defense Proteins include antibodies
(Immunoglobulins) which are specific
protein molecules produced by
specialized cells of the immune system
in response to foreign antigens.

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Membrane-bound immunoglobulin on the surface of immature and mature B cells
First antibody produced in a primary response to an antigen
First antibody produced by the fetus
Efficient in binding antigens with many repeating epitopes, such as viruses
Classical complement activation

IgM (serum level-5%)

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Membrane-bound immunoglobulin on the surface of mature B cells
No biological effector function known

igD (serum level-0.3%)

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Predominant antibody class in secretions (saliva, tears, breast milk) and mucosa
First line of defense against infection by microorganisms

igA (serum level 7-15%)

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Most abundant class with four isotypes - IgGI, IgG2, IgG3, IgG4

Crosses the placenta

-Opsonization

igG (serum level-85%)

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Defense against parasite infections
Associated with hypersensitivity reactions (allergies)
Found mainly in tissues

igE (serum level- 0.02%)

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_______________ carry material from place to another in the body. Ex: transferrin,
Hemoglobin and Myoglobin.

Transport Protein

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____________ controls many aspects of cell
function, including metabolism and
reproduction. Ex: Insulin and Glucagon

Regulatory Protein controls many aspects of cell function, including metabolism and reproduction. Ex: Insulin and Glucagon

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_______________ provide mechanical support to large animals and provide them with their outer coverings. Ex:
Keratin

Structural proteins provide mechanical support to large animals and provide them with their outer coverings. Ex:
Keratin

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______________ are necessary for all forms of
movement. Ex. Actin and Myosin, Flagella of sperm cell.

Movement Proteins

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______________ serves as source of Amino acids for embroyos or infants. Ex: Albumin and Casein

Nutrient Protein

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• It is the amino acid sequence of the protein chain.
• This structure will determine its biological active form.
• It results from the covalent bonding between the amino acids in the chain

Primary Structure of Proteins

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This level of structure describes the local folding pattern of the polypeptide backbone and is stabilized by hydrogen bonds between N-H and C=O groups. The most common are the orderly repeating forms known as the a helix and the b sheet.

Secondary Structure proteins

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The most common type of Secondary structure may it be in coiled of helical conformation.

Special Feature:
-Every amide hydrogen and carbonyl oxygen associated with the peptide backbone is involved in a hydrogen bond when the chain coils into it.
- Every carbonyl oxygen is hydrogen bonded to an amide hydrogen four amino acids away in the chain.

a-Helix

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– are structural proteins arranged in fibers or sheets that have only one type of secondary structure.

Fibrous Proteins

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– are fibrous proteins that form
the covering (hair, nails and fur) of most land animals.

α-Keratins

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The second common secondary structure in proteins resembles the pleated folds of drapery.

All the carbonyl oxygen and amide hydrogens in this are involved in hydrogen bonds, and the polypeptide chain is nearly completely
extended.

β-Pleated Sheet

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What are the 2 Orientation of B-Pleated
form?

Parallel
Anti-parallel

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• Beta sheets are ______ if the polypeptide strands run in the same direction,
N-terminus to C-terminus. The N-terminus of one beta strand will be opposite the N-terminus of the other beta strand.

the arrangement is less stable because the geometry of the individual amino acid molecules forces the hydrogen bonds
to occur at an angle, making them longer and thus weaker.

parallel

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• Beta sheets are ___________ if the polypeptide strands run in opposite directions. The N- terminus of one beta strand will be opposite the C-terminus
of the other beta strand.

in this the arrangement hydrogen bonds are aligned directly opposite each other, making for stronger and more stable bonds.

anti-parallel

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________________________ forms when a polypeptide chain sharply reverses direction. This can occur in the presence of two consecutive proline residues, which create an angled kink in the polypeptide chain and bend it back upon itself.

Anti-parallel beta-pleated sheet forms when a polypeptide chain sharply reverses direction. This can occur in the presence of two consecutive proline residues, which create an angled kink in the polypeptide chain and bend it back upon itself.

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A protein whose structure is an antiparallel B-pleated sheet.
The polypeptide chains of a B-pleated sheet are almost completely extended, and silk does not stretch easily.

Silk Fibroin

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___________ accounts for nearly half of the amino acids of silk fibroin. Alanine and serine account for most of the others,

Glycine

•it is the complete **three-dimensional (3-D) structure of a polypeptide.** It is formed spontaneously and stabilized both by side chain interactions and, in extracellular proteins, by **disulfide bonds.** This folding brings distant sequences in a linear polypeptide together into a stable structure

Tertiary Structure of Proteins

Tertiary structure is maintained by the following molecular interactions: - ______________ between the R groups of non polar amino acids that are hydrophobic. - _______________ between the polar R group of the polar amino acids - _______________ (salt bridges) between the R groups of oppositely charged amino acids - _______________ between the thiol containing amino-acids.

Tertiary structure is maintained by the following molecular interactions: - **Van der Waals Forces** between the R groups of non polar amino acids that are hydrophobic. - **Hydrogen bonds** between the polar R group of the polar amino acids - **Ionic bonds** (salt bridges) between the R groups of oppositely charged amino acids - **Covalent bonds** between the thiol-containing amino acids.

______________ generally have a more compact and rounded shape and have functional roles (they do something)

Globular proteins

• some proteins are made up of multiple polypeptide chains, also known as **subunits**. When these subunits come together, they give the protein its _________________. • The forces that hold the structure of a protein are the same as those that hold the tertiary structure.

Quaternary Structure

_______________ – when a non-protein group is added to the functional protein. Ex: Glycoprotein

Prosthetic group

Protein digestion is the degradation of protein by cellular enzymes in a process called _________

Protein digestion is the degradation of protein by cellular enzymes in a process called **hydrolysis**

The macromolecules are the _________ or polypeptides themselves, and the subunits are the ______________.

The macromolecules are the **proteins** or polypeptides themselves, and the subunits are the **amino acids.**

Protein Digestion • It takes place in two different phases: - In the stomach - In the small intestine. Both of these phases of digestion are based on several types of enzymes that are called ___________ and __________.

__________ –endo & exo peptidases: - Enzymes that degrade proteins by hydrolysis of peptide bonds

Proteases

__________ - endo peptidases; proteases that show specificity for intact proteins

Proteinases

_____________ – Stimulates Parietal cells to secrete HCl; Chief cells of the gastric glands to secrete pepsinogen.

Gastrin

_______________ - Denatures protein stucture. Activates pepsinogen (**Zymogen**) to pepsin.

HCI / Hydrochloric Acid

_________ - Hydrolyzes proteins to smaller polypeptides and some free amino acids.

Pepsin

The remainder of protein digestion occur in the ____________ as the result of the action of enzymes such as **trypsin** (secreted by the pancrease) and **petidases** (located in the cells that line the small intestine).

small intestine

____________ - Stimulates the pancreas to secrete bicarbonate into the small intestine to neutralize the gastric HCl

Secretin

_______________- Stimulates secretion of several pancreatic enzyme with activity optima pH 7 to 8.

Cholecystokinin

- Activates chymotrpsinogen → chymotrypsin - **Further hydrolyze the peptides that were produced by pepsin** in the stomach specifically the peptide bonds next to **Lys and Arg.**

Trypsin

____________ - Cleaves peptide bonds next to Phe, Tyr, Trp, Met, Asp and His

Chymotrypsin

Occur when the organized structures of a globular protein, the a-helix, the B-pleated sheet and tertiary folds become completely disorganized. However, it does not alter the primary structure.

Denaturation of protein

Factors that cause Denaturation

- Temperature - Coagulation - pH - Organic solvents - Heavy metals -Mechanical Stress - Detergents

As the ___________ increase, molecular movement also increase and the bonds within the cells vibrate more violently which results to disruption of protein structure.

As the **temperature** increase, molecular movement also increase and the bonds within the cells vibrate more violently which results to disruption of protein structure.

occur as the protein molecules unfold and become untangled. At this point they are no longer in solution; they have aggregated to become solid

Coagulation

A high concentration of hydrogen ions (low pH) will result in more groups being protonated. Carboxyl groups (aspartic acid, glutamic acid, the carboxy terminus) and phenolic groups are uncharged when protonated. The nitrogen groups (amines on lysine, guanidino of arginine, and imidazole in histidine, etc.) are charged when protonated

_____________ such as rubbing alcohol (2-propanol), denatured proteins by disrupting hydrogen bonds within the protein, in addition to forming hydrogen bonds with the solvent, water Nonpolar regions of these solvents interfere with hydrophobic interactions in the interior of the protein molecules, thereby disrupting the conformation.

Polar organic solvent

- Mercury (Hg2+) or Lead (Pb2+) may form negatively charged side chain groups. - may also bind to sulfhydryl groups of a protein that can accompanied by loss of function.

Heavy metals

__________ have hydrophobic region and hydrophilic. When it interacts with proteins, they disrupt hydrophobic interactions, causing the protein chain to unfold.

Detergent

- Stirring, whipping, or shaking can disrupt the weak interactions that maintain protein conformation. This is the reason that whipping egg whites produces a stiff meringue.

Mechanical Stress

amino acid sequence of a protein is encoded in ______ .

amino acid sequence of a protein is encoded in **DNA**

amino acid sequence of a protein is encoded in ______ .

amino acid sequence of a protein is encoded in **DNA**

Proteins are synthesized by a series of steps called __________ (the use of a DNA strand to make a complimentary messenger RNA strand -mRNA) and translation (the mRNA sequence is used as a template to guide the synthesis of the chain of amino acids which make up the protein)

Proteins are synthesized by a series of steps called **transcription** (the use of a DNA strand to make a complimentary messenger RNA strand -mRNA) and **translation** (the mRNA sequence is used as a template to guide the synthesis of the chain of amino acids which make up the protein)

________ can change by the process of mutation during the course of evolution. A mutation of this can result in a change in the primary acid sequence of a protein.

Genes

The ______________ is the result of hydrogen bonding between the amide Hydrogen and carbonyl oxygens of the peptide bonds.

The **secondary structure** is the result of hydrogen bonding between the amide Hydrogen and carbonyl oxygens of the peptide bonds.

Types of Secondary Structure

1. α-Helix 2. β-Pleated Sheet

Types of Secondary Structure

1. α-Helix 2. β-Pleated Sheet