Unit 1 - Chapters 1-6 Flashcards
In proteins, what “level” of structure refers to the three-dimensional arrangement of all the atoms in a single polypeptide chain?
Tertiary
Where can Z -DNA be found?
In G:C rich regions of DNA
What is the nucleoside comprised of?
Nitrogenous base and sugar
Nucleic acids absorb UV light. Do single or double strands absorb more light?
Single stranded (hypochromic shift)
The melting temperature depends on the G:C content. Is the Tm higher or lower for DNA with more G:C content?
It is higher with more G:C content
Under physiological conditions DNA is in A, B or Z form?
B - DNA
Which of the following “tags” is used as a signal for protein degradation?
- SUMO
- phosphorylation
- Ubiquitin
- Selenocysteine
- none of the above.
Ubiquitin
DNA contains both A:T and G:C base pairs, and each base pair contains a purine and a pyrimidine. Which of the bases are purines?
Adenine and Guanine
Hydrophobic interactions between non-polar molecules in aqueous solution result from the stability achieved when
they release “caged” water molecules as the hydrophobic surface area decreases.
In a nucleotide, when the nitrogenous base is positioned away from the ribose ring, the base is said to be in what position?
Anti
Which DNA structure contains Guanine in a syn conformation?
Z-DNA - C stays anti but whole C nucleoside (base and sugar) flips 180 degrees. Result is that G:C H bonds can be preserved in the transition from B-form to Z-form
Cholesterol is weakly amphipathic due to the presence of
OH group at C3
Buffers are solutions of weak acids and their corresponding conjugate bases that resist a change in pH. Buffers are most effective:
When there is an equal amount of A- and HA present
The hyperchromic effect refers to
the increase in absorption at 260 nm by DNA that has been denatured
Glycine and proline are usually present in a common protein secondary structural element.
β -bend - A β turn results in a tight 180° reversal in the direction of the polypeptide chain. Glycine is the smallest and thus most flexible amino acid, and proline can readily assume the cis configuration, which facilitates a tight turn.
The end of a polynucleotide (DNA) which possesses a free hydroxy group is the
3’ end
The end of a polynucleotide (DNA) which possesses a free phosphate group is the
5’ end
A non-protein, large organic molecule associated non-covalently with an enzyme is referred to as a
Prosthetic group
The amino acid cysteine plays an important role physiologically in protein structure because
It forms intra- or interchain disulfide bonds
Intrinsic membrane proteins are those that
are embedded within the lipid bilayer
What is the main difference between an aldose and a ketose?
Both, aldose and ketose are monosaccharides that can be differentiated as aldose is the monosaccharide that contains aldehyde group in its structure along with the carbon chain, whereas ketose is the monosaccharide that contains ketone group along with the carbon chain.
Identify the D and L configurations of glyceraldehyde.
The OH group on the sterigenic carbon farthest away from the aldehyde group points to the right, it is D configuration. These correspond to the configurations of glyceraldehyde.
Is Cysteine oxidized or reduced when it forms S-S bonds?
Oxidized
What is the H-bonding pattern in alpha helix?
The C=O binds to the N-H of residue i + 4
Identify where alpha helices appear on the Ramachandran plot below.
Right-handed around -60 phi and psi
Identify where Beta strands appear on the Ramachandran plot below.
About -120 to –60 phi and +120 to +160 psi
Why are glycine, cysteine and proline “special”?
Glycine is the smallest amino acid. Cysteine creates intra and inter disulfide linkages. Proline connects to the backbone twice forming a 5 - membered ring. It forms kinks in proteins.
What is the approximate pKa of Tyrosine?
10.1
What is the approximate pKa of Lysine?
10.5
What is the approximate pKa of Histidine ?
6.00
What is the approximate pKa of Arginine?
12.5
What is the approximate pKa of Aspartate?
3.7
What is the approximate pKa of Glutamate?
4.3
Which nitrogenous bases are pyrimidines?
Cytosine, Thymine and Uracil (RNA)
Which nitrogenous bases are purines?
Adenine and Guanine
Draw the structure of ATP
See structure
Draw Adenine
(Mnemonic: College Students in NC Never Cut Class (Six-membered ring) NC Never! (5 membered ring)
Adenine adds an amine - Think amine flag at top of six membered ring
See structure
Draw Guanine
(Mnemonic: College Students in NC Never Cut Class (Six-membered ring) NC Never! (5 membered ring)
Think Guanine has an amine but also needs a Correctional Officer
See structure
Draw Cytosine
(Mnemonic: College Students in NC Never Cut Class (Six-membered ring)
Think Cytosine copies Adenine with its amine and guanine with the Correctional Officer. All pyrimidines need Correctional Officers, but Cytosine only needs 1. The others need 2.
See structure
Draw Thymine
(Mnemonic: College Students in NC Never Cut Class (Six-membered ring)
Think Thymine doesn’t need a MINE it already has one. It needs 2 correctional officers because it has the “gas” to escape.
See structure - Gas is CH3
Draw Uracil
(Mnemonic: College Students in NC Never Cut Class (Six-membered ring)
Think Thymine but without gas to get away.
See structure - Gas is CH3
Where is the N-glycosidic bond between the sugar and a pyrimidine and purine?
On the number 1 N in pyrimidines and number 9 N (5 membered ring) on purines
Draw the structure of deoxyribose.
See structure
Draw the structure of tryptophan?
One carbon plus indole ring
What is a nucleotide comprised of?
A nucleotide has three characteristic components: (1) a nitrogenous (nitrogen-containing) base, (2) a pentose, and (3) one or more phosphates
How is the glycosidic bond formed between the sugar and nitrogenous base in DNA and RNA?
The N-β-glycosyl bond is formed by removal of the elements of water (a hydroxyl group from the pentose and hydrogen from the base), as in O-glycosidic bond formation.
Where is the N-glycosidic bond formed between the nitrogenous base and the sugar in RNA and DNA?
The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N-β-glycosyl bond to the 1’ carbon of the pentose, and the phosphate is esterified to the 5’ carbon.
What is another name for the sugars ribose and deoxyribose when they are nucleotides?
In nucleotides, both types of pentoses are in their β-furanose (closed five-membered ring) form.
Draw the structure of cAMP.
See structure
How is the phosphodiester linkage formed in DNA and RNA backbones?
The successive nucleotides of both DNA and RNA are covalently linked through phosphate-group “bridges,” in which the 5’ -phosphate group of one nucleotide unit is joined to the 3’-hydroxyl group of the next nucleotide, creating a phosphodiester linkage
Why are the phosphodiester bonds in DNA not rapidly hydrolyzed under alkaline conditions like RNA?
DNA does not have an OH on the 2’ carbon sugar. In RNA, water can pull the proton from the OH group on the 2’ carbon and hydrolyze the molecule.
The sequence of a single strand of nucleic acid is always written with the _______ end at the left and the ______end at the right — that is, in the _______ direction.
The sequence of a single strand of nucleic acid is always written with the 5’ end at the left and the 3’ end at the right — that is, in the 5’ - 3’ direction.
What is a short nucleic acid called?
A short nucleic acid is referred to as an oligonucleotide. The definition of “short” is somewhat arbitrary, but polymers containing 50 or fewer nucleotides are generally called oligonucleotides.
At what wavelength do nucleotides absorb UV light?
All nucleotide bases absorb UV light, and nucleic acids are characterized by a strong absorption at wavelengths near 260 nm
How does base stacking help to stabilize nucleic acids?
Base stacking involves hydrophobic stacking interactions. It also involves a combination of van der Waals and dipole-dipole interactions between the bases.
Base stacking helps to minimize contact of the bases with water, and base-stacking interactions are very important in stabilizing the three-dimensional structure of nucleic acids,
What is the most important complementary interaction between nucleic acids?
Hydrogen bonds involving the amino and carbonyl groups are the most important mode of complementary interaction between two (and occasionally three or four) complementary strands of nucleic acid.
What is the most important complementary interaction between nucleic acids?
Hydrogen bonds involving the amino and carbonyl groups are the most important mode of complementary interaction between two (and occasionally three or four) complementary strands of nucleic acid.
Draw the hydrogen bonds between Adenine and Thymine
See structure
Draw the hydrogen bonds between Guanine and Cytosine
See structure
Draw the hydrogen bonds between Adenine and Uracil
See structure
- Draw the side chain of Glycine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
Smallest amino acid
- See structure
- Nonpolar
- Gly, G
- Draw the side chain of Alanine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
- See structure
- Nonpolar
- Ala, A
- Draw the side chain of Valine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
- See structure
- Nonpolar
- Val, V
- Draw the side chain of Leucine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
- See structure
- Nonpolar
- Leu, L
- Draw the side chain of Isoleucine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
- See structure
- Nonpolar
- Ile, I
- Draw the side chain of Phenylalanine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
- See structure
- Nonpolar
- Phe, F
- Draw the side chain of Tryptophan
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
- See structure
- Nonpolar
- Trp, W
- Draw the side chain of Methionine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
2-S-1
- See structure
- Nonpolar
- Met, M
- Draw the side chain of Proline
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
- See structure
- Nonpolar
- Pro, P
- Draw the side chain of Serine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
One carbon + OH
- See structure
- Polar - uncharged
- Ser, S
- Draw the side chain of Threonine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
2 + OH
- See structure
- Polar - uncharged
- Thr - T
- Draw the side chain of Cysteine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
1 + SH
- See structure
- Polar - uncharged
- Cys, C
- Draw the side chain of Asparagine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
2 - End is part of amide
- See structure
- Polar - uncharged
- Asn, N
- Draw the side chain of Tyrosine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
- See structure
- Polar - uncharged
- Tyr, Y
- Draw the side chain of Glutamine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
3 - End is part of amide
- See structure
- Polar - uncharged
- Gln, Q
- Draw the side chain of Aspartate (aspartic acid)
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
2 - End is carboxylic acid
- See structure
- Polar - negatively charged (acidic)
- Asp, D
- Draw the side chain of Glutamate (glutamic acid)
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
3 - End is carboxylic acid
- See structure
- Polar - negatively charged (acidic)
- Glu, E
- Draw the side chain of Histidine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
5 membered ring with 2 NH
- See structure
- Polar -positively charged (basic)
- His, H
- Draw the side chain of Lysine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
4 + NH<span>3</span> on the end
- See structure
- Polar -positively charged (basic)
- Lys, K
- Draw the side chain of Arginine
- Classify as nonpolar, polar-uncharged, acidic or basic
- Provide the 3-letter abbreviation and 1 letter symbol
3 + NH + 1 bonded to 2 NH2 (1 NH2 double bonded)
- See structure
- Polar -positively charged (basic)
- Arg, R
You wish to engineer a protein to increase its thermal stability. One way to do this would be to
Substitute proline for other amino acids
The larger the difference in free energy, the greater the thermal stability.
∆G=∆H - T∆S, a smaller ∆S value leads to a flatter slope in the ∆G plot versus temperature close to the melting temperature and thus increases thermal stability of the protein. This is called entropic stabilization.
Sphingosine connected to a fatty acid via an amide bond makes up a lipid known as a
Cerebroside
Double stranded RNA would most likely form a structure similar to:
A DNA
What type of lipid is shown below?
Unsaturated fatty acid
Which of the following “tags” is used as a signal for protein degradation?
Ubiquitin
The free aldehyde of D-glucose can form a reversible intramolecular bond with either the hydroxyl group attached at carbon 4 or 5 to form what is known as a:
hemiacetal
Nucleic acids are polyanions because
The pK1 of the phosphate group is around 2
Which of the following is the major force that stabilizes the double helix of DNA?
base stacking interactions (van der Waals and hydrophobic)
Explain parallel beta-sheets and how to tell if an amino acid sequence has this structure in terms of hydrophobicity.
Parallel β-sheet is characterized by two peptide strands running in the same direction held together by hydrogen bonding between the strands.
Both strands are hydrophobic
Explain antiparallel beta-sheets and how to tell if an amino acid sequence has this structure in terms of hydrophobicity.
Antiparallel β-sheet is characterized by two peptide strands running in opposite directions held together by hydrogen bonding between the strands.
One strand is hydrophobic and the other is hydrophilic.
How can you detect a collagen helix in the primary amino acid sequence?
It consists of a triple helix made of the repetitious amino acid sequence glycine -X-Y, where X and Y are frequently proline or hydroxyproline.
How does CNBr cleave a polypeptide?
It cleaves on the carboxy side of Methionine.
How does trypsin cleave a polypeptide?
It cleaves on the carboxy side of Lysine or Arginine.
How does chymotrypsin cleave a polypeptide?
It cleaves on the carboxy side of the aromatic amino acids: Phenylalanine, Tyrosine and Tryptophan
How does carboxypeptidase cleave a polypeptide?
It cleaves amino acids with a free carboxy end, except arg, lys or pro
Acid hydrolysis changes Asn and Gln to which amino acids?
Asp and Glu
Linking two amino acids is a formed by what type of reaction?
Amino acids link by a condensation (loss of water) reaction (addition -elimination) in which the OH group is lost from the carboxylic acid (COOH) group of one molecule and a hydrogen atom from the amino (NH).
Digestion of amino acids is a formed by what type of reaction?
Amino acids are digested by a hydrolysis (addition of water) reaction in which the OH group is added to one amino acid and an H is added to another one.
Chiral type of amino acids found in proteins.
L- Amino Acids
Another name for dipolar molecules.
Zwitterions
Disulfide bonds are formed by pairs of which amino acid?
Cysteine
The amino acid with a pKa near neutral pH.
Histidine
When a peptide bond is formed, what molecule is also made?
Water
Where are proteins with extensive disulfide links likely to be found?
Extracellular
This amino acid residue disrupts the α helix because its side chain contains a unique ring structure that restricts bond rotations.
proline
Name of the plot that allows one to investigate the likely orientation of certain amino acid pairs.
Ramanchandran
The type of structure to which α helices, β sheets, and turns are referred.
Secondary structure
The overall structure of a protein is referred to as
tertiary structure
The amino acid that contains a weakly acidic “phenolic” group is
Tyrosine
is a fibrous protein and is the primary component of wool and hair.
Keratin
Every third residue in the protein collagen is
glycine
Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as
β mecaptoethanol
A protein is considered to be __________________ when it is converted into a randomly coiled structure without its normal activity.
Denatured
______________________ is the major fibrous protein present in skin, bone, tendon, cartilage, and teeth.
Collagen
Collagen contains _____________________, a modified amino acid.
Hydroxyproline
Agents such as ______________________ and guanidine hydrochloride denature proteins by disrupting the noncovalent interactions.
urea
_____________________________ refers to the spatial arrangement of subunits and the nature of their interactions
Quaternary
The ________________________ β-sheet structure occurs when the two strands are oriented in opposite directions (N → C).
antiparallel
What determines a protein’s function?
Structure
What charged group(s) are present in glycine at a pH of 7?
COO- and NH3+
At a pH of 12, what charged group(s) are present in glycine?
COO-
In what pH range is zwitterionic Alanine the predominate structure?
2-9
Which amino acids contain reactive aliphatic hydroxyl groups?
serine and threonine
Name three amino acids that are positively charged at a neutral pH.
Lys, Arg, His
Why is the peptide bond planar?
It contains partial double-bond character, preventing rotation.
The configuration of most α-carbon atoms of amino acids linked in a peptide bond is
Trans configuration
Where are Ω and β turns and loops often found?
on the surface of proteins
Alpha helices are disrupted by what type of amino acids?
- Proline - forms kinks in the helix
- Large numbers of bulky and/or branched chained amino acids due to steric hindrance
- Acidic or basic AA due to repulsion
Which of the following amino acid residues would most likely be buried in the interior of a water soluble, globular protein?
Asp, Ser, Phe, Lys, Glu
Phe
How does a protein’s amino acid sequence influence the tertiary structure?
A protein will spontaneously fold into a three-dimensional structure determined by the amino acid sequence.
What is the advantage of having 20 different amino acids available to form proteins?
The amino acids provide a rich diversity of functional groups, which can independently contribute to protein structure and function. In addition, many can be modified, increasing the diversity of functional groups.
How does the protein backbone add to structural stability?
The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone) groups. Hydrogen-bond formation between the hydrogen on the nitrogen and the oxygen support the protein conformation.
What is the “hydrophobic effect” as it relates to protein structure?
The three-dimensional structure of a water soluble protein is stabilized by the tendency of hydrophobic groups to assemble in the interior of the molecule.
The ratio of enzyme activity relative to total protein is called
specific activity
____________ A type of purification that is based on the attraction of the protein for a particular chemical group.
affinity chromatography
____________ can be added prior to gel electrophoresis to denature the proteins.
SDS
Exclusion gel or gel-filtration chromatography separates molecules on the basis of
__________________.
Size
In the Edman procedure for peptide sequence, phenyl isothiocyanate is used to selectively
remove the __________________ residue as a PTH-derivative.
N-terminal
Disulfide bonds in peptides and proteins are readily oxidized to cysteic acid residues by
treatment with __________________.
Performic acid
How do gel-filtration and ion-exchange chromatography differ?
Although both are used in purification, the properties of the column material determine how the separation is accomplished. Gel filtration is based on porous beads, and molecules are separated by size. In ion-exchange chromatography, the column material is charged with either positively or negatively charged molecules. Separation is based on the protein’s charge and affinity for the column media.
The information-carrying intermediates of translation.
mRNA
The flow of genetic information from DNA to protein is called ____________.
gene expression
Scientist who noted the A:T and G:C ratios in DNA are approximately 1:1.
Erwin Chargaff
The temperature at which half the DNA helical character is lost is referred to as ____________.
Tm
DNA renaturation after melting is called ____________.
Annealing
Organisms in which the flow of genetic information can be RNA®DNA.
retroviruses
Codons that specify the same amino acids are termed ____________.
synonyms
__________________ is the most abundant type of RNA in a cell.
rRNA
The phenomenon that stacked bases in double-helical DNA absorbed less UV light than the unstacked bases in single-stranded DNA is referred to as _________________.
: hypochromism or the hypochromic effect
The chemical forces that contribute to the stability of the DNA due to the base stacking present in the DNA helix are
van der Waals
Draw two nucleotides in DNA showing the linkage between the sugars linked.
See structure
What advantage do phosphodiesters have compared to other esters?
The negative charge serves to repel nucleophilic species such as OH-. Thus the phophodiester linkage is more stable because it is more resistant to hydrolytic cleavage.
Briefly describe the Meselson and Stahl experiment that indicated that DNA replication is semiconservative
Meselson and Stahl grew bacteria in the presence of 15N, or “heavy” nitrogen. They rapidly replaced the 15N media with 14N, or light nitrogen. DNA was extracted at various time intervals during the growth of the bacteria, representing different stages of replication (generations). They examined the DNA using density-gradient equilibrium sedimentation and observed that no “heavy” DNA was present in the first generation, but that the DNA was intermediate between light and heavy. After the second generation, there were equal amounts of intermediate and light. This confirmed that one strand of the parent DNA is present in each daughter strand of replicated DNA.
What does it mean that DNA is semiconservative?
DNA replication is a semi-conservative process, because when a new double-stranded DNA molecule is formed: One strand will be from the original template molecule.
___________________________ cleave DNA at sites with inverted repeat sequences referred to as palendromic sequences.
Restriction endonucleases
Complementary, single-strand overhangs that are produced by some restriction endonucleases are referred to as ___________________.
sticky ends or cohesive ends
The biological role of restriction enzymes in bacteria is to
Cleave foreign DNA
What do Southern, Northern, and Western blots detect, respectively?
DNA, RNA and protein
A number of tools are critical to gene exploration. Name at least four.
Tools include restriction enzyme analysis, blotting techniques (Southern and Northern), DNA sequencing, solid-phase synthesis of nucleic acid, PCR, and computer analysis.
Homologs are different species that perform similar or identical functions.
orthologs - - Human and Bovine Ribonuclease are Orthologs
Homologs are the same species that different functions.
paralogs - The growth factor angiogenin and ribonuclease are
Paralogs
Restriction enzymes are ________and do not work on the ends. They are all_______.
Restriction enzymes are endodeoxyribonucleases and do not work on the ends. They are all dimers.
Why do Cys, Gly, Pro and Trp have the greatest penalties for change.
Cysteine - disulfide bonds, glycine is smallest AA, Proline forms kinks and tryptophan is very large.
Homology is ultimately determined by _________
structure
Evolution requires
- A mechanism that generates change or
diversity - A selection for “fitness”
- Reproduction that enriches for the more “fit”
Explain how the hydrophobic effect drives the structure of three different biological molecules.
Base stacking of DNA allows the bases to minimize their contact with water which is the main effect of the hydrophobic effect.
Lipid bilayer membrane - the hydrophobic tails gather inside away from the aqueous environment of the cell.
Protein folding - hydrophobic residues hide inside the structure to limit contact with water.
Give an example of a molecule that has an alpha helix
α-Keratin of hair, feathers, nails (crosslinked by disulfide bonds)
Give an example of a molecule that has a beta conformation
silk
