PROTEINS & NUCLEIC ACIDS Flashcards
HOW MANY PROTEINOGENIC AMINO ACIDS ARE THERE?
21 (seleno cysteine made from serine through post translational modification)
-most are L-α-amino acids as amino acids belong to optically active / chiral molecules
WHAT DOES AN AMINO ACID CONSIST OF?
-carboxylic group (deprotonated at physiologic pH), amino group (protonated at physiologic pH), side chain
ARE AMINO ACIDS AMPHOTERIC?
-yes
WHAT IS THE AMINO CARBON?
- this is the 2nd carbon of an amino acid chain, the carbon carriers the amino group and is chiral (exception of glycine)
HOW MANY POSSIBLE COMBINATIONS OF TRIPLETS FOR ENCODING AN AMINO ACID ARE THERE?
-64 different combinations of triplets (only 61 code AA – 3 are stop codons)
WHAT ARE THE PROPERTIES OF ACIDIC AMINO ACIDS?
-side chains have a -COOH group which can easily loose H+ and become negatively charged to COO-
-hydrophilic and polar
-when COO- accepts hydrogen the amino acid becomes a cation
-found on the outside of proteins that function in an aqueous environment and in the interior of membrane associated proteins
EG: GLUTAMIC ACID AND ASPARTIC ACID-
WHY IS PROLINE DIFFERENT TO OTHER AMINO ACIDS?
-Proline differs from other amino acids in that proline’s side chain and α-amino N form a rigid, five-membered ring structure. Proline, then, has a secondary (rather than a primary) amino group. It is frequently referred to as an imino acid. The unique geometry of proline contributes to the formation of the fibrous structure of collagen and often interrupts the α-helices found in globular proteins.
WHEN DOES AN AMINO ACID BECOME A ZWITTERION?
-has both a positive and negative charge
-specific pH at which it has a charge of 0 and becomes a zwitterion is called the isoelectric point
WHAT DOES THE SICKLE CELL DISEASE RESULT FROM?
-substitution of polar glutamate by nonpolar valine in the β subunit of hemoglobin
WHAT ARE THE CHARACTERISTICS OF BASIC AMINO ACIDS?
-NH2 group easily accepts H+ and becomes positively charged = protonated
-In a very basic environment NH3+ loses hydrogen and the amino acid becomes an anion
-At physiologic pH the side chains of lysine and arginine are fully ionized and positively charged. In contrast, histidine is weakly basic, and the free amino acid is largely uncharged at physiologic pH. However, when histidine is incorporated into a protein, its side chain can be either positively charged or neutral, depending on the ionic environment provided by the polypeptide chains of the protein
-found on the outside of proteins that function in an aqueous environment and in the interior of membrane associated proteins
EG: HISTIDINE, ARGININE, LYSINE
WHAT ARE THE ESSENTIAL AMINO ACIDS?
9
histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
WHAT ARE THE NON-ESSENTIAL AMINO ACIDS?
6
alanine, asparagine, aspartic acid, glutamic acid, and serine.
WHAT ARE THE CONDITIONAL AMINO ACIDS?
-essential only at certain life stages or in certain disease states
arginine, cysteine, glutamine, glycine, proline, and tyrosine.
HOW MANY AMINO ACIDS ARE PRESENT IN NATURE AND IN PROTEINS?
NATURE: around 300
PROTEIN: 20
WHAT ARE EXAMPLES OF MODIFIED AMINO ACIDS / NON PROTEIN AMINO ACIDS?
POST TRANSLATIONAL MODIFICATION: occurs in golgi apparatus and rough endoplasmic reticulum
-4-hydroxyproline: synthesized from proline
-5-hydroxylysine: synthesized from lysine
-Gamma-aminobutyric acid (GABA): synthesized from glutamic acid
-Gamm-carboxylglutamate: synthesized from glutamic acid
-Desmosine: synthesized from lysine
WHAT ARE THE HYDROPHOBIC / NON-POLAR AMINO ACIDS?
-Glycine, Alanine, Valine, leucine, Isoleucine, Methionine, Phenylalanine, Proline, Tryptophan
-R-chains in hydrophobic environments tend to be on exterior of protein
-R-chains in hydrophilic environments tend to cluster together in the interior of the the protein
WHAT ARE THE UNCHARGED, HYDROPHILIC, POLAR AMINO ACIDS?
-Cysteine, Serine, Threonine, Glutamine, Asparagine, Tyrosine
-zero net charge at neutral pH, although the side chains of cysteine and tyrosine can lose a proton at an alkaline pH
-Serine, threonine, and tyrosine each contain a polar hydroxyl group that can participate in hydrogen bond formation. (2nd hydroxyl)
-side chains of asparagine and glutamine each contain a carbonyl group and an amide group, both of which can also participate in hydrogen bonds.
-In proteins, the –SH groups of two cysteines can become oxidized to form a dimer, cystine, which contains a covalent cross-link called a disulfide bond (stabilizes albumin)
-polar hydroxyl groups can act as sites of attachments such as phosphate groups
-found on the outside of proteins that function in an aqueous environment and in the interior of membrane associated proteins
WHAT ARE THE GLUCOGENIC AMINO ACIDS?
-serve as precursors for gluconeogenesis
Glycine, Alanine, methionine, Aspartic acid
WHAT ARE THE KETOGENIC AMINO ACIDS?
-breakdown to form ketone bodies
Lysine and leucine
WHAT ARE BOTH GLUCOGENIC AND KETOGENIC AMINO ACIDS?
Isoleucine, Phenylalanine, Tryptophan and tyrosine
Ka and Kb values
-The larger the Ka, the stronger the acid, because most of the HA has dissociated into H+ and A-. Conversely, the smaller the Ka, the less acid has dissociated and, therefore, the weaker the acid
WHAT ARE THE ACIDIC AND BASIC PROPERTY OF AMINO ACIDS?
-Amino acids in aqueous solution contain weakly acidic α-carboxyl groups and weakly basic α-amino groups. In addition, each of the acidic and basic amino acids contains an ionizable group in its side chain. Thus, both free amino acids and some amino acids combined in peptide linkages can act as buffers
WHAT IS A BUFFER?
-solution that resists change in pH following the addition of an acid or base.
-created by mixing a weak acid (HA) with its conjugate base (A-). If an acid such as HCl is added to such a solution, A- can neutralize it, in the process being converted to HA. If a base is added, HA can neutralize it, in the process being converted to A-.
-buffering occurs within ±1pH unit of the pKa, and is maximal when pH = pKa, at which [A-] = [HA].
WHAT IS THE DISSOCIATION CONSTANT FOR THE CARBOXYL GROUP AND THE AMINO GROUP OF AN AMINO ACID CALLED?
COOH - = K1 = because molecule contains a NH3+ = K2 = second titratable group, much weaker than carboxyl group so lower K and therefore higher pKa
- At a low (acidic) pH, both of these groups are protonated
- Each titratable group has a pKa that is numerically equal to the pH at which exactly one half of the protons have been removed from that group.
(HENDERSON HASSELBACH)
WHY DO THE NATURE OF THE SIDE CHAINS DETERMINE THE ROLE OF AMINO ACIDS IN A PROTEIN?
-most alpha COO- and alpha NH3+ are combined together via peptide bonds in proteins and therefore cannot be used in a chemical reaction
WHAT IS THE HENDERSON HASSELBACH EQUATION?
-the quantitative relationship between the pH of a solution and the concentration of a weak acid (HA) and its conjugate base (A-)
IN WHICH ORDER IS GENETIC INFORMATION PASSED THROUGH AN AMINO ACID?
-from the N to C terminal
WHAT TYPE OF REACTION IS A PEPTIDE BOND?
-condensation reaction, -OH is lost from one carboxyl and a H is lost from the amino group of another amino acid resulting in the formation of water and a peptide bond
WHAT IS GABA A DERIVATIVE OF?
-glutamic acid
WHAT IS THE PRIMARY STRUCTURE OF PROTEINS?
-the sequence of amino acids in a polypeptide chain
-each chain has its own set of amino acids, assembled in a particular order
WHAT IS THE SECONDARY STRUCTURE OF PROTEINS?
-local folded structures that form within a polypeptide due to interactions between atoms of the backbone
-alpha helix and beta pleated sheet = both structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another
WHAT IS THE ZINC FINGER MOTIF?
-small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn 2+) in order to stabilize the fold.
-allows proteins to bind to DNA / RNA
WHAT IS THE LEUCINE ZIPPER?
-common three-dimensional structural motif in proteins formed by the dimerization of two specific alpha helix monomers bound to DNA/RNA.
WHAT IS THE TERTIARY STRUCTURE OF PROTEINS?
-overall three-dimensional structure of a polypeptide primarily due to interactions between the R groups of the amino acids
-globular (albumin) or fibrous (keratin, collagen, fibroin)
-R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces (WEAK-NON-COVALENT)
-important to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules
-Disulfide bonds, covalent linkages between the sulfur-containing side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary structure. They act like molecular “safety pins,” keeping parts of the polypeptide firmly attached to one another.
WHAT IS THE QUARTERNARY STRUCTURE OF PROTEINS?
-some proteins are made up of multiple polypeptide chains (SUBUNITS). When these subunits come together, they give the protein its quaternary structure.
-the same types of interactions that contribute to tertiary structure (mostly weak interactions, such as hydrogen bonding and London dispersion forces) also hold the subunits together to give quaternary structure
GIVE THE CHARACTERISTICS OF THE PROTEIN HEMOGLOBIN.
-allosteric protein
-heme is a prosthetic group of cytochromes
-binds O2 in lungs and transports to cells
-transports CO2 and H+ from tissue to lungs
-four heme groups surrounding a globin group structure giving a tetrahedral structure
-two alpha subunits and two beta subunits
-heme is composed of porphyrin to which an iron atom can attach to and bind oxygen
-four iron atoms in each molecule of hemoglobin, which accordingly can bind four molecules of oxygen. Globin consists of two linked pairs of polypeptide chains
WHAT ARE CHAPRONES AND CHAPERONINS?
-Chaperones refer to the proteins which assist the covalent folding or unfolding and assembly and disassembly of other macromolecular structures while chaperonins refer to the proteins which provide favorable conditions for the correct folding of denatured proteins, preventing aggregation
WHAT IS A PHOSPHODIESTER BOND?
bond via OH group of the 3´carbon of
deoxyribose of one nucleotide and phosphate of the 5´carbon of deoxyribose of the second nucleotide
-includes 2 ester bonds
-forms backbone of polynucleotide chain which is repeated deoxyribose and phosphate
-makes up the antiparallel orientation of the DNA strand – on one side there is a free OH group on 3rd carbon of pentose (3‘ end) on other side there is a free phosphate group on 5th carbon (5‘ end)
EG: they are antiparallel – one strand is 3‘ -> 5‘, other strand is 5‘ -> 3‘
NAME THESE SUGARS
LEFT = RNA (beta-D-ribose)
RIGHT = DNA (beta-d-2-deoxyribose)
WHAT OCCURS DURING CPG METHYLATION?
DNA methylated at CpG dinucleotides interferes with the binding of transcription factors
-it binds a class of methyl-binding proteins (MeCp2) that are in complex with
HDAC -> restores + charge of histones = tight chromatin structure
HMT -> adds methyl group to lysine in histones, which attracts HP1 protein that covers nucleosomes
RETT SYNDROME = DNA is methylated but histones are not modified
