Chapter 3_Protein Structure and Function Flashcards by Fai Zah

Derived from the Greek word

proteios meaning “first” to indicate the central
roles that proteins play in living organisms

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are the indispensable agents of biological function

Protein

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are the building blocks of proteins.

Amino Acid

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The stunning diversity of the thousands of proteins found in nature arises from the intrinsic properties of

only 20 commonly occurring amino acids.

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These features include:

(1) the capacity to polymerize
(2) novel acid–base properties
(3) varied structure and chemical functionality in the amino acid side chains, and
(4) Chirality (or handedness, means that an object or molecule cannot be superimposed on its mirror image by any translations or rotations)

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Functions of proteins:

1)Enzymes
2) Defense Proteins
3) Transport Protein
4)Regulatory Proteins
5) Structural Proteins
6)Movement Proteins
7)Nutrients

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Functions of proteins:
Enzymes

are biological catalysts. Reactions that would take days or weeks or require
extremely high temperatures without enzymes are completed in an instant.

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Functions of proteins:
(2) Defense proteins

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

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Functions of proteins:
(3) Transport proteins

carry materials from one place to
another in the body.

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Transferrin

transports iron from the liver to the bone marrow, where it is used to synthesize the
heme group for hemoglobin.

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Transferrin is synthesized and
secreted

into serum mostly by the liver. Synthesis of
transferrin is regulated by iron.

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The proteins hemoglobin and
myoglobin

are responsible for transport and storage of oxygen in higher organisms, respectively.

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Functions of proteins:
(4) Regulatory proteins

control many aspects of cell function, including metabolism and reproduction. We can function only within a limited set of conditions.

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Functions of proteins:
(5) Structural proteins

providemechanical support to large animals
and provide them with their outer coverings.

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Functions of proteins:
(6) Movement proteins

are necessary for all forms of movement

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Functions of proteins:
(7) Nutrient proteins

serve as sources of amino acids for embryos or infants. Egg albumen and casein in milk are examples of nutrient storage proteins.

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these compounds contain both an amine and an acid

Amino Acids

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Amino Acids

Hundreds are formed both naturally and synthetically; Only 20 are common in nature; All 20 are α-amino acids; 19 out of the 20 are stereoisomers (Glycine does not have a chiral carbon)

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is the only common amino acid that is
not chiral

Glycine

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Nonpolar Class

class has hydrophobic R groups

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Polar, neutral

have a high affinity for water, but are not ionic at pH

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Polar acidic (Negatively charged) have ionized carboxyl groups in their side chains

(Negatively charged) have ionized carboxyl groups in their side chains

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Polar basic

(Positively charged) are basic as the side chain reacts with water to release a hydroxide anion

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The terrm __________ is reserved for those amino acids that must be supplied in the diet for proper growth and development.

Essential Amino Acid

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“PVT. TIM HALL”

Phe, Val, Thr, Trp, Ile, Met, His, Arg, Leu, Lys

______ and ______ are semi-essential; they not synthesized in sufficient quantities during infancy stage

His and Arg

α-carbon is attached to a:

* Carboxyl group (̶ COOH) * Amino group ( ̶ NH2)

* Carboxyl group

(̶ COOH)

* Amino group

( ̶ NH2)

At physiologic pH the amino acid has:

* Carboxyl group in –COO- * Amino group in –NH3+ * Neutral molecule with equal number of + and – charges is called a zwitterion

At physiologic pH the amino acid has: Carboxyl group in

–COO-

At physiologic pH the amino acid has: Amino group in

–NH3+

Neutral molecule with equal number of + and – charges is called

a zwitterion

(from the German word “zwitter” which means “hybrid” or “hermaphrodite”)

zwitterion

Amino acids are ________ with _______ and ________.

white crystalline solids high melting points high water solubilities

The pH point at which there is no net charge on the zwitterions is called the

isoelectric point (pI)

The isoelectric point (pI)

is the pH at which it bears no net charge.

At pH values below and above the isoelectric point, the molecule will bear a ____ or _______ , respectively

net positive or net negative charge

A molecule with a net charge of zero will not migrate in an electric field, whereas one bearing a positive (+) or negative (-) charge will migrate towards the ________ or _______, respectively.

cathode (-) or anode (+)

is an analytical method for identifying amino acids by observing their migration as a function of pH under an applied electric field gradient.

Electrophoresis

The amino acid carries a POSITIVE CHARGE at pH

NEGATIVE ELECTRODE (cathode)

The amino acid carries a NEGATIVE CHARGE at pH>pI and migrates to the

POSITIVE ELECTRODE (anode)

Linkage is an _____ or _______.

amide bond or peptide linkage

Carboxyl group of one amino acid is linked to the amino group of __________.

another amino acid

Condensing or dehydrating two amino acids produces

a dipeptide

Amino acid with a free a-NH3+ group is the

amino terminal amino acid, N-terminal for short

Amino acid with a free –COO ̶group is the

carboxyl terminal amino acid, C-terminal for short

Amino acid structures are written with the N-terminal ____ ___ _____.

on the left

amino acids are polymerized into ____ and ____.

Proteins and peptides

In general, protein is used for molecules composed of over 50 amino acids

over 50 amino acids

_________ is used for molecules of less than 50 amino acids

Peptide

Sold under the trade names Nutrasweet and Equal

Aspartame (Asp-Phe)

is the artificial sweetener used in almost every diet food on the market today.

Aspartame (Asp-Phe)

It functions as an antioxidant, protecting cellular contents from oxidizing agents such as peroxides and superoxides

Glutathione (Glu-Cys-Gly)

natural painkillers produced in the body; bind to receptors in the brain to give relief from pain.

Enkephalins

This effect appears to be responsible for the runner’s high, for the temporary loss of pain when severe injury occurs, and for the analgesic effects of acupuncture.

Enkephalins and endorphins -

stimulates uterine contractions in labor

Oxytocin

is an antidiuretic hormone that regulates blood pressure by adjusting the amount of water reabsorbed by the kidneys.

vasopressin

Primary structure is the ____________ of the polypeptide chain

amino acid sequence

A result of covalent bonding between the amino acids

the peptide bonds

R groups on adjacent amino acids are____________ because of the rigid peptide bond.

on opposite sides of the chain

When the primary sequence of the polypeptide folds into regularly repeating structures,

Secondary Structure forms

Secondary structure results from ________between the ______ and ______ of the peptide bonds

hydrogen bonding; amide hydrogens (N—H) ;carbonyl oxygens (C=O)

Most common type of secondary structure

Coiled and Helical

The Secondary Structure of Proteins: α-Helix: Important features:

- Each amide H and carbonyl O is involved in H bonds locking the helix in place - Carbonyl O links to amide H 4 amino acids away - H bonds are parallel to the long axis of the helix - Helix is right-handed - Repeat distance or pitch is 5.4 angstroms - 3.6 amino acids per turn

The three-dimensional structure, which is distinct from secondary structure

Tertiary Structure

forms spontaneously and is maintained by interactions among the side chains or R groups

Globular tertiary structure

defines the biological function of proteins

Tertiary Structures

Types of Interactions Maintaining Tertiary Structure

Disulfide bridges Salt bridges Hydrogen bonds Hydrophobic interactions

bridges between two cysteine residues

Disulfide bridges

between ionic side chains –COO– and –NH3+

Salt Bridges

between polar residue side chains

Hydrogen Bond

two nonpolar groups are attracted by a mutual repulsion of water

Hydrophobic interactions

The functional form of many proteins is not that of a single polypeptide chain but an aggregate of several globular peptides

The Quaternary Structure of Proteins

the arrangement of subunits or peptides that form a larger protein

Quaternary structure

a polypeptide chain having primary, secondary, and tertiary structural features that is a part of a larger protein

Subunit

Quaternary structure is

maintained by the same forces which are active in maintaining tertiary structure

Protein Functions Follow Shape: Fibrous proteins:

* Mechanical strength * Structural components * Movement

Protein Functions Follow Shape: Globular proteins:

* Transport * Regulatory * Enzymes

a protein to which another chemical group (e.g., carbohydrate) is attached by either covalent bonding or other interactions

Conjugated Proteins

is the oxygentransport protein of higher animals

Hemoglobin

is the oxygen storage protein of skeletal muscle

Myoglobin

Oxygen is transferred from hemoglobin to myoglobin as

myoglobin has a stronger attraction for oxygen than hemoglobin does

is an essential component of the proteins hemoglobin and myoglobin

Heme Group

ion in the heme group is the oxygen binding site

* Fe2+

is the loss of organized structure of a globular protein

Denaturation

Does not alter primary structure; the disruption of bonds in the secondary, tertiary, and quaternary protein structures

Trypsin Cleaves at

Carboxyl end Lysine and Arginine

Chymotrypsin cleaves at

Carboxyl Ends of Phenylalananine; Tyrosine; tryptophan; and Leucine

Elastase Cleaves at

Glycine and Alanine

Pepsin cleaves at

cleaves peptide bonds at the amino end of the three aromatic amino acids: phenylalanine, tyrosine, tryptophan; acidic amino acids, Asp and Glu; and Ile

Thermolysin cleaves at

cleaves peptide bonds at the amino end of the three aromatic amino acids,Phe, Tyr, Trp; and amino acids with bulky nonpolar R groups, Leu, Ile, and Val

The key reagent in Sanger's method for identifying the N-terminus

1-fluoro-2,4-dinitrobenzene

1-Fluoro-2,4-dinitrobenzene reacts with the _______

amino nitrogen of the N-terminal amino acid.

cleaves all the peptide bonds leaving a mixture of amino acids, only one of which (the N-terminus) bears a 2,4-DNP group.

Acid Hydrolysis

Can be done sequentially one residue at a time on the same sample. Usually, one can determine the first 20 or so amino acids from the N-terminus by this method

Edman Degradation

The key reagent in the Edman degradation is

phenyl isothiocyanate.

Phenyl isothiocyanate reacts with the

amino nitrogen of the N-terminal amino acid.

hydrazine reacts with all amino acids whose carboxyl group is bound in peptide linkage, creating amino acyl hydrazides.

Hydrazine Method

hydrazine reacts with__________, creating ______.

all amino acids whose carboxyl group is bound in peptide linkage;amino acyl hydrazides.