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146 Cards in this Set

  • Front
  • Back
The principal classes of biomolecules are:
proteins, carbohydrates, lipids, and nucleic acids
Proteins are polymers of:
amino acids
Every amino acid contains:
an amine group (-NH₂), a carboxyl group (-COOH), and an R group called a side chain all bonded to the same carbon atom.
The carbon that the amine group (-NH₂), a carboxyl group (-COOH), and an R group called a side chain are all bonded to is called:
the alpha carbon (α-carbon)
A large biological molecule made of many amino acids linked together through amide (peptide) bonds.
A molecule that contains both an amino group and a carboxylic acid functional group.
Amino acid
The variable group bonded to the central carbon atom in an amino acid; different in different amino acids.
Side chain (amino acid)
An amino acid in which the amino group is bonded to the carbon atom next to the -COOH group.
α-amino acid
The α-carbon is:
the central carbon in an amino acid to which the amine, carboxyl, and side-chain R groups attach.
An amide bond that links two amino acids together.
Peptide bond
Two amino acids, three amino acids, and many amino acids are called:
a dipeptide, tripeptide, and a polypeptide respectively
What reaction forms a peptide bond? What groups react?
The amine group of one amino acid replaces the hydroxyl group of the carboxylic group on another. An H from the amine and -OH from carboxylic acid form water.
The sequence of amino acids in a protein chain.
Primary structure
The regular and repeating spatial organization of neighboring segments of single protein chains.
Secondary Structure
The overall shape of a protein molecule produced by regions of secondary structure combined with the overall bending and folding of the protein chain.
Tertiary structure
The overall structure of proteins composed of more than one polypeptide chain.
Quaternary structure
What distinguishes one amino acid from another?
their different side chains
What are some different functions of proteins in the body?
-structure and support
-hormones and enzymes
-storage and transport
-protection (immunity)
All of the proteins in living organisms are made from _____ amino acids.
20 α-amino acids
19 of the amino acids differ in _______, but one of the them, _______ differs in:
19 of the amino acids differ in the side chain, but one of the them, proline differs in that it is a secondary amine whose N and α-carbon atoms are joined in a five-membered ring.
The 20 α-amino acids that make up proteins are classified as:
neutral, acidic, or basic, depending on the nature of their side chains.
Neutral amino acids are further divided into:
How many of the amino acids are neutral?
those with polar or non-polar side chains
15 are neutral
What is of central importance in determining the shapes and functions of proteins?
Intermolecular forces
Non-polar side chains are described as:
Polar, acidic, and basic side chains are described as:
Forces of attraction other than covalent bonds that can act between molecules or within molecules.
Noncovalent forces
"Water-fearing"; does not dissolve in water:
"Water-loving"; dissolves in water.
Amino acids contain both an acidic group (carboxyl group) and a basic group (amine group), can they undergo an intramolecular acid-base reaction?
yes, the result is a transfer of the hydrogen from the hydroxyl group of the carboxylic acid to the amine group.
The intramolecular acid base reaction of an amino acid forms a:
dipolar ion, an ion that has one positive charge (ammonium ion) and one negative charge (carboxylic acid anion).
Dipolar ions are known as:
What is the charge of zwitterions?
A neutral dipolar ion that has one positive charge and one negative charge.
Because they are zwitterions, amino acids have many of the physical properties of:
What are the properties of amino acids?
-can form crystals
-high melting points
-soluble in water, not soluble in hydrocarbons solvents
In acidic solutions, zwitterions:
ACCEPT protons on the carboxylic acid anion, leaving only the positively charged amine group.
In basic solutions, zwitterions:
LOSE protons on the amine cation, leaving only the negatively charged carboxylic acid anion group.
Draw the reaction of a NH₃⁺CH(R)COO⁻ + H⁺
Draw the reaction of a NH₃⁺CH(R)COO⁻ + OH⁻
Do amino acids ever exist in a completely un-ionized form in either the solid state or in aqueous solution?
THe charge of an amino acid molecule at any given moment depends on:
the particular amino acid and the pH of the solution.
Define the isoelectric point (pl)
The pH at which the net positive and negative charges are evenly balanced for a particular amino acid.
The point at which the net charge of all the molecules of a particular amino acid in a pure sample is zero.
isoelectric point (pl)
Is the (pl) the same for all amino acids?
No, the (pl) is different for each amino acid, due to differences in their side chains.
Pl influences:
protein stability and determines which amino acids in an enzyme participate.
The acidic and basic side chains are particularly important because:
at physiological pH, these groups are fully charged and can participate not only in ionic bonds within a protein chain but can also transfer H⁺ from one molecule to another during reactions.
Which amino acids are hydrophilic and which are hydrophobic?
The polar, acidic, and basic side chains are hydrophilic since they can interact with water.
The non-polar side chains are hydrophobic since they cannot interact with water.
Describe hydrolysis:
A reaction in which a bond or bonds are broken and the H- and -OH of water add to the atoms of the broken bond or bonds.
What reaction is involved in the formation of peptide bonds?
amide formation where: an H from the amine is added to the carboxyl group -OH forming water as the N-chain is added to the carbonyl group C.
Aspartic acid
Glutamic acid
Having right or left-handedness with two different mirror image forms that cannot be superimposed.
The opposite of chiral; having superimposable mirror images and thus no right or left-handedness.
Define a chiral carbon atom aka chiral center:
A carbon atom bonded to four different groups.
The two mirror image forms of a chiral molecule.
Enantiomers (optical isomers).
Define stereoisomers:
Isomers that have the same molecular and structural formulas but different spatial arrangements of their atoms.
Does the presence of a chiral atom always produce a chiral molecule?
Pairs of enantiomers always differ in:
their affects on polarized light and in how they react with other molecules that are chiral.
Pairs of enantiomers often differ in:
their biological activity, odors, tastes or activity as drugs.
Of the 20 alpha amino acids, how many are chiral?
19 of them; only glycine is achiral.
Even though the 19 chiral α-amino acids can exist as either D- or L- enantiomers, nature exclusively uses only:
L-amino acids for making proteins
Which amino acids have abbreviations that are not the first 3 letters?
Glutamine Gln
Asparagine Asn
Isoleucine Ile
Tryptophan Trp
How do you determine if a molecule is chiral?
Make a list of the different carbon atoms and the groups bonded to them. If a carbon has 4 different groups, it is chiral.
Define primary protein structure:
The sequence in which amino acids are linked by peptide bonds in a protein.
ie.. Alanine + Serine → Alanylserine but,
Serine + Alanine → Serylalanine
In the primary structure, the electrons of each carbonyl group double bond are shared to a considerable extent with:
the adjacent C-N bond (the α-carbon-nitrogen bond).
Does the C-N unit that shares electrons with the carbonyl group double bond carbons rotate?
No, this sharing of bonds makes it sufficiently rigid that there is no rotation.
One planar unit consists of:
the carbonyl carbon, -NH group bonded to it, and the two adjacent α-carbons.
Are the side chains on the same or opposite side of the backbone of the primary structure?
On opposite sides.
The amino acid with the free -NH₃⁺ group at the end of a protein.
Amino-terminal (N-terminal) amino acid.
The amino acid with the free -COO⁻ group at the end of a protein.
Carboxyl-terminal (C-terminal) amino acid
An amino acid unit in a polypeptide.
By convention, peptides and proteins are always written with the amino-terminal amino acid on the ______ and the carboxyl-terminal amino acid on the _______.
left; right
The individual amino acids joined in the chain are called:
How are peptides named?
Starting at the N-terminal amino acid and ending at the C-terminal amino acid, all residues are named in order. The residue name endings are changed from -ine to -yl for all except the C-terminal amino acid.
They can also be named by listing their 3-letter abbreviation in order, separated by hyphens.
ie... serine + tyrosine + glycine = seryltyrosylglycine or Ser-Tyr-Gly.
In L-forms of amino acids, the amino group is on the:
When drawing the 3-D primary protein structure of a L-hand form, the H atoms on the top are on the ____ side and point:
left side; away from you
When drawing the 3-D primary protein structure of a L-hand form, the H atoms on the bottom are on the ____ side and point:
right side; toward you
The planar unit square connects:
The α-carbon, carboxyl O, -NH group H, and second α-carbon.
Where there are ionized acidic and basic side chains, the attraction between their positive and negative charges creates:
salt bridges
Where there are interactions between hydrocarbon side chains, the attraction is from:
These interactions are called:
london-dispersion forces; hydrophobic
What is the one type of covalent bond in the formation of protein structure?
covalent sulfur-sulfur bonds.
covalent sulfur-sulfur bonds are formed between these residues:
between the thiol-containing side chains of two cysteine amino acids which form a sulfide bond.
What are the different types of bonds that determine protein structure?
-H bonds
-Salt bridges
-Hydrophobic interactions
-Sulfur-Sulfur bonds
An S-S bond formed between two cysteine side chains; can join two separate peptide chains together or cause a loop in a single peptide chain.
Disulfide bond
Describe the reaction of a disulfide bond:
-SH + -SH [O]⟶ S-S + HOH
Sulfide + Sulfide (with oxidizer) ⟶ Disulfide + HOH (two H's from each S add to an O from the oxidizer to form the HOH)
In the covalent disulfide bond between two cysteine residues, if they are in different protein chains, then:
the chains become linked together
In the covalent disulfide bond between two cysteine residues, if they are in the same protein chain, then:
a loop is formed in the chain
The regular and repeating structural patterns (ie.. α-helix, β-sheet) created by hydrogen bonding between backbone atoms in neighboring segments of protein chains.
Secondary protein structure
Secondary protein structure in which a protein chain forms a right-handed coil stabilized by hydrogen bonds between peptide groups along its backbone.
Alpha helix (α-helix)
Secondary protein structure in which adjacent protein chains either in the same molecule or in different molecules are held together by hydrogen bonds along the backbones, forming a flat sheet-like structure.
Beta-sheet (β-sheet
A tough, insoluble protein whose protein chains form fibers or sheets.
Fibrous protein
A water-soluble protein whose chain is folded in a compact shape with hydrophilic groups on the outside.
Globular protein
Define secondary protein structure:
The spatial arrangement of the polypeptide backbones of proteins.
The secondary structure includes two kinds of repeating patterns known as:
α-helix and β-sheet
In both α-helix and β-sheet patterns, what holds the polypeptide in place?
H bonding between backbone atoms
In both α-helix and β-sheet patterns, the H bonds connect:
the carbonyl oxygen atom of one peptide unit to the amide H atom of another.
an α-helix is:
and resembles:
A single protein chain coiled in a spiral with a right-handed (clockwise) twist. It resembles a coiled telephone cord.
What is the spatial arrangement of the H bonds and amino acid R-groups in the α-helix?
The H-bonds lie vertically along the helix and the amino acid R groups extend to the outside of the coil.
What is the spatial arrangement of the H bonds and amino acid R-groups in the β-sheet?
H-bonds connect different protein chains, which are fully extended, with their R-groups extending above and below the sheet.
Proteins are classified in several ways, one of which is to identify them as either:
fibrous or globular proteins.
How are the N-terminals and C-terminals arranged among the protein chains in a β-sheet?
They run in an antiparallel arrangement
Which structure is primarily responsible for the nature of fibrous proteins?
secondary protein structure
The way in which an entire protein chain is coiled and folded into its specific 3-dimentional shape.
Tertiary protein structure
A protein with the shape (secondary, tertiary, and quaternary structure) in which it exists naturally in living organisms.
Native protein
Secondary structure depends mainly on attraction between ___________, where tertiary structure depends mainly on attraction between ____________.
Secondary structure depends mainly on attraction between BACKBONE ATOMS, where tertiary structure depends mainly on attraction between AMINO ACID SIDE CHAINS THAT ARE FAR APART ALONG THE SAME BACKBONE.
Define a Simple protein:
A protein composed of only amino acid residues.
Define a Conjugated protein:
A protein that incorporates one or more non-amino acid units in its structure.
Which structure determines the overall shape of fibrous proteins? Which structure determines the overall shape of globular proteins?
Secondary structure determines the shape of fibrous proteins. Tertiary structure determines the overall shape of globular proteins.
A simple protein is made of nothing but __________, while a conjugated protein has:
A simple protein is made of nothing but amino acid residues, while a conjugated protein has something else in its structure, i.e... myoglobin which has a heme group in its structure.
The way in which two or more protein chains aggregate to form large, ordered structures.
Quaternary protein structure
Collagen and Hemoglobin both have this structure:
quaternary protein structure
The most abundant of all proteins in mammals is:
collagen; making up 30% or more of the total.
Define primary structure:
the sequence of amino acids connected by polypeptide bonds.
Define secondary structure:
the arrangement in space of the polypeptide chain (α-helix and β-sheet)
Define tertiary structure:
the folding of a protein into a specific 3-D shape
Define quaternary structure:
two or more protein chains assembled in a large 3-D structure.
Describe the bonds involved in each structure.
Primary = peptide bonds
Secondary = H-bonds between backbone carbonyl oxygen and amine hydrogens.
Tertiary = interactions between amino acid side chains, (in some cases disulfide bonds), that can be quite far apart along the backbone.
Quaternary = noncovalent interactions.
The reverse of protein synthesis is:
protein hydrolysis
Describe the reaction of protein hydrolysis:
Protein reacts with H³O⁺ or enzyme which breaks peptide bonds and adds an -OH group to the carboxyl carbon and an H⁺ to the amine.
The loss of secondary, tertiary, or quaternary protein structure due to disruption of non covalent interactions and/or disulfide bonds that leaves peptide bonds and primary structure intact.
Denaturation is accompanied by changes in:
physical, chemical, and biological properties.
Is solubility usually increased or decreased by denaturation?
What agents cause denaturation?
heat, mechanical agitation, detergents, organic solvents, extremely acidic or basic pH, and inorganic salts.
How does heat denature proteins?
It breaks side-chain interactions in globular proteins.
How does Mechanical agitation denature proteins?
stiffens the proteins
How do Detergents denature proteins?
disrupts hydrophobic side chains
How do Organic polar solvents denature proteins?
Polar solvents such as acetone and ethanol interfere with H bonding by competing for bonding sites.
How do Inorganic salts denature proteins?
by disrupting salt bridges