Chapter 3: Protein Structure and Function Flashcards
Protein derived from the greek word _____
proteios meaning “first
are the indispensable agents of biological function
- polypeptide structures consisting of one or more long chains of amino acid residues
Proteins
are the building blocks of proteins.
amino acids
The stunning diversity of the thousands of proteins found in nature arises from the _____ _____ of only 20 commonly occurring amino acids
intristic properties
Features of 20 commonny occuring amino acids
(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
Provide structural components
Structural
make muscles move
contractile
carry essential substances throughou the bodu
transport
store nutrients
storage
regulate body metabolism and the nervous system
hormone
catalyze biochemical reactions in the cells
enzyme
recognize and destroy foreign substances
protection
examples of structural class of protein
collagen (in tendons and cartilage)
keratin (in hair, skin, wool and nails)
example of contactile class of protein
myosin and actin (contract muscle fibers)
example of transport class of protein
Hemoglobin (transfers oxygen)
Lipoproteins (transports lipids)
example of storage class of protein
Casein (stores protein in milk)
Ferritin (stores iron in the spleen and liver)
example of hormone class of protein
Insulin (regulates blood glucose level)
Growth Hormone (regulates body growth)
example of enzyme class of protein
Sucrase (catalyzes the hydrolysis of sucrose)
Trypsin (catalyzes the hydrolysis of proteins)
Example of protection class of protein
Immunoglobulins (stimulate immune response)
Functions of proteins
- enzymes
- defense proteins
- Transport proteins
- Regulatory proteins
- Structural proteins
- Movement proteins
- Nutrient proteins
- are biological catalysts.
- Majority of the enzymes that have been studied are proteins.
- Reactions that would take days or weeks or require extremely high temperatures without enzymes are completed in an instant.
Enzymes
include antibodies (also called immunoglobulins) which are specific protein molecules produced by specialized cells of the immune system in response to foreign antigens.
Defense proteins
carry materials from one place to
another in the body.
Transfer proteins
The protein that transfers iron from the liver to the bone marrow, where it is used to synthesize the heme group for hemoglobin.
Transferrin
are responsible for transport and storage of oxygen in higher organisms
Hemoglobin - transport of oxygen
Myoglobin - storage of oxygen
control many aspects of cell function,
including metabolism and reproduction.
Regulatory proteins
- a hormone your adrenal glands make to help you prepare for stressful or dangerous situations
- ‘fight or flight’
Adrenaline
How does adrenaline works?
- makes your heart beat faster and your lungs breathe more efficiently.
- Causes your blood vessels to send more blood to your brain and muscles, increases your blood pressure, makes your brain more alert, and raises blood sugar levels to give you energy.
provide mechanical support to large animals and provide them with their outer coverings.
Structural Proteins
- a rare condition that causes fragile, blistering skin.
- a rare condition that causes fragile, blistering skin.
Epidermolysis bullosa (scientific name) and the butterfly babies
are necessary for all forms of movement.
Movement proteins
serve as sources of amino acids for embryos or infants.
Nutrient proteins
non-superposable to its mirror image due to the presence of an asymmetric carbon atom
Chiral molecule (chiral)
is reserved for those amino acids that
must be supplied in the diet for proper growth and development.
Essential Amino acids
Mnemonic for Essential amino acids
PVT. TIM HALL
The proteins of the body are made up of some combination of twenty different subunits
α-amino acids (Alpha-amino acids)
Neutral molecule with equal number of + and – charges
Zwitterion
Zwitterion from the german word
“Zwitter’” which means hybrid or hermaphrodite
The side chains of some amino acids are nonpolar. They prefer contact with one another over contact with water are said to be ____ _____
Hydrophobic Amino Acids (“water fearing”)
The hydrophobic side chains are often found generally found ______ in the _______ of proteins
-buried in the interior of the proteins.
Why are hydrophic amino acids buried?
- so they can associate with one another and remain isolated from water
9 Hydrophic Amino acids
PVT MALIG P
- Proline
- Valine
- Tryptophan
- Methionine
- alanine
- leucine
- isoleucine
- glycine
- phenylalanine
The side chains of the remaining amino acids are polar. Because they are attracted to polar water molecules, they are said to be
Hydrophilic amino acids
(“water loving”)
The hydrophilic side chains are often found on the ______ of _______.
-Surfaces of proteins
3 division of polar amino acid
- Polar, neutral amino acids
- Negatively charged amino acid
- Positively charged amino acid
have R groups that have a high affinity for water but are not ionic at pH 7
- Polar, neutral amino acid
Example of neutral amino acid
- Serine
- Threonine
- tyrosine, cysteine
- asparagine
- glutamine
have ionized carboxyl groups in their side chains. At pH 7, these amino acids have a net charge of −1.
- Negatively charged amino acid
Example negatively charged amino acid
- Aspartate and glutamate
These amino groups are basic because the side chain reacts with water, picking up a proton and releasing a hydroxide anion.
- Positively charged amino acid
Example basic amino acid
- Lysine
- arginine
- histidine
is an amide bond formed between the
—COO− group of one amino acid and the α-N+H3 group of another amino acid.
- The Peptide bond.
The molecule formed by condensing two amino acids.
- Dipeptide
The amino acid with a free α-NH3+ group
- Amino acid terminal or N-terminal amino acid or N-terminus
The amino acid with a free —COO− group is known as the
- Carboxyl or C-terminal amino acid residue or C-terminus.
The number of amino acids in small peptides is indicated by the _____
- Prefixes (di- two units, tri- three units, tetra- four units and so on)
At Physiological pH amino acid has Carboxyl group in ______
- –COO-
At Physiological pH amino acid has amino group in ______
- –NH3+
The pH point at which there is no net charge on the zwitterions is called
- isoelectric point (pI)
an amino acid is the pH at which it bears no net charge.
- The isoelectric point
applying a sample of the amino acid to specially treated paper or gel and applying an electric field at different pH values – a technique known as _______
electrophoresis
is the motion of dispersed particles or dissolved charged molecules relative to a fluid under the influence of a spatially uniform electric field
electrophoresis
Study slide 32 to 50
NO FLASHCARDS CREATED AT THIS AREA.
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<pI and migrates to the ____ ______ (____)
- NEGATIVE ELECTRODE (cathode)
The amino acid carries a NEGATIVE CHARGE at pH>pI and migrates to the ____ ______ (____)
- POSITIVE ELECTRODE (anode)
Study slide 53 to 65
NO FLASHCARDS CREATED AT THIS AREA.
Examples of small peptides
- Aspartame (Asp-Phe)
- Glutathione (Glu-Cys-Gly)
- Enkephalins (Tyr-Gly-Gly-Phe-Leu & Tyr-Gly-Gly-Phe-Met)
- Oxytocin
Sold under the trade names Nutrasweet and Equal
- is the artificial sweetener used in almost every diet food on the market today.
- Aspartame (Asp-Phe)
The tripeptide, produced by the body itself, is present in significant concentrations in most cells and is of considerable physiological importance as a regulator of oxidation reduction reactions.
- It functions as an antioxidant, protecting cellular contents from oxidizing agents such as peroxides and superoxides, which are highly reactive forms of oxygen often generated within a cell
- Glutathione (Glu-Cys-Gly)
natural painkillers produced in the body; bind to receptors in the brain to give relief from pain
- Enkephalins (Tyr-Gly-Gly-Phe-Leu & Tyr-Gly-Gly-Phe-Met)
stimulates uterine contractions in labor and vasopressin is an antidiuretic hormone that regulates blood pressure by adjusting the amount of water reabsorbed by the kidneys
- Oxytocin
The different structures of protein
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
amino acid sequence of the polypeptide chain
- A result of covalent bonding between the amino acids– the peptide bonds
- Primary structure
- When the primary sequence of the polypeptide folds into regularly repeating structures.
results from hydrogen bonding between the amide hydrogens (N—H) and carbonyl oxygens (C=O) of the peptide bonds.
- Secondary structure
Most common type of secondary structure
Coiled, helical.
- α-Helix (alpha helix)
Second most common secondary structure appears similar to folds of fabric.
- All the carbonyl O and amide H are involved in the H bonds with the chain nearly completely extended
- β-pleated sheet (beta-pleated sheet)
two possible orientations of β-pleated sheet
- Parallel if N-termini are head to head
- Antiparallel if N-terminus of one chain is aligned with the C-terminus of the other
- The three-dimensional structure, which is distinct from secondary structure.
- Globular tertiary structure forms spontaneously and is maintained by interactions among the side chains or R groups
- Tertiary structure
defines the biological function of proteins
- Tertiary structure
Types of interactions maintaining tertiary structure.
- Disulfide bridges
- Salt chains
- Hydrogen bonds
- Hydrophobic interactions
between two cysteine residues
- the only covalent bond, the strongest of the 3o bonds; link chains together and cause chains to twist and bend
- Disulfide bridges
(ionic interaction/electrostatic attraction) between ionic side chains –COO– and –NH3+
- Salt bridges
a weak bond between two molecules resulting from an electrostatic attraction between a proton in one molecule and an electronegative atom in the other.
- (H—O)
- Hydrogen bonds
two nonpolar groups are attracted by a mutual repulsion of water.
- Hydrophobic interactions
the arrangement of subunits or peptides that form a larger protein
The functional form of many proteins is not that of a single polypeptide chain but an aggregate of several globular peptides
- Quaternary structure.
a polypeptide chain having primary,
secondary, and tertiary structural features that is a part of a larger protein
- Subunit
Study slide 91 to 103
NO FLASHCARDS CREATED AT THIS AREA.
splits the peptide bonds to give smaller peptides and amino acids occurs in the digestion of proteins; occurs in cells when amino acids are needed to synthesize new proteins and repair tissues
- Protein hydrolysis
In the lab, the hydrolysis of a peptide requires a___ _ ___, ___, and ___.
- Acid or base, water, and heat
In the body, ___ catalyze the hydrolysis of proteins.
- Enzymes
Some practical aspects of protein denaturation
- Heat and UV
- Salts of heavy metal ions
- Organic compounds such as soap, detergents, phenol.
STUDY PROTEIN SEQUENCING BEFORE ADDING FLASHCARDS
STUDY PROTEIN SEQUENCING BEFORE ADDING FLASHCARDS
Procedures in determination of amino acid sequence (in order)
- hydrolysis - by acid, alkali, or enzyme
- identification of the products of hydrolysis
- fitting the pieces together as you would a jigsaw puzzle
the protein is completely hydrolyzed, but Trp, is destroyed completely and Ser, Thr, and Tyr are partially destroyed
Acid Hydrolysis
does not damage Trp, but destroys Arg, Cys, Thr, & Ser; and some amino acids are partly deaminated
-more disadvantageous but since it does not destroy Trp, it is used inquantitative determination of this amino acid
Alkali Hydrolysis
cuts peptide bonds on the carboxyl terminal side of methionine residues.
Cyanogen Bromide
enzymes that cleave external peptide bonds
Exopeptidases
sequentially cleaves peptide bonds, beginning at the N-terminal end of the polypeptide; the liberated amino acids are identified one by one
Aminopeptidases
sequentially cleaves peptide bonds beginning at the C-terminal end of the polypeptide
Carboxypeptidases
enzymes that cleave internal peptide bonds
Endopeptidases
cleaves peptide bonds at the carboxyl end of the two strongly basic amino acids: arginine and lysine
Trypsin
cleaves peptide bonds at the carboxyl end of the three aromatic amino acids: phenylalanine, tyrosine, & trptophan; and Leucine
Chymotypsin
cleaves on the carboxyl side of Gly and Ala.
Elastase
cleaves peptide bonds at the amino end of the three aromatic amino acids: phenylalanine, tyrosine, tryptophan; acidic amino acids, Asp and Glu; and Ile
Pepsin
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
Thermolysin
Other methods for determining the N-terminal end (chemical method)
- Sanger’s Method
- Edman Degradation
The key reagent in this method for identifying the N-terminus is 1-fluoro-2,4-dinitrobenzene
Sanger’s Method
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
