Exam 1 Flashcards
What four elements make up 99% of all atoms in living organisms?
Carbon, Nitrogen, Oxygen, Hydrogen
What are the four major classes of biological molecules?
Proteins, Nucleic Acids, Lipids, Carbohydrates
Explain the central dogma of biology
DNA transcribed into RNA
RNA translated into Protein
DNA can also be replicated to inherit genetic information
although all cells in an organism have the same DNA, tissues differ due to selective _______
expression
the most common carbohydrate fuel
glucose
List the three roles of proteins in biological membranes
Control the permeability of molecules across the membrane
Relay information across the membrane
Generate biochemical energy using a molecular gradient across the membrane
Movement of particles due to the random fluctuations of energy content of the environment is known as
Brownian motion
What is meant by the phrase “water is a polar molecule?”
The electrons are not shared equally over the covalent bonds of the water molecule. This creates an electrical dipole over the molecule, with the oxygen atom being more electronegative and the hydrogen atoms being more positive.
Describe the hydrophobic effect and the driving force behind it
the hydrophobic effect is an organizing principle of non polar/hydrophobic molecules in an aqueous solution. there is an apparent attractive force between hydrophobic molecules that is spontaneous and driven by an increase in entropy. this entropy increase is due to the release of water molecules at the surface of the hydrophobic molecules as they come together
List the possible organizations of amphiphilic molecules in aqueous solution
bilayer membrane, micelle, vesicle
How is protein folding driven?
the nonpolar/hydrophobic residues are driven together by the hydrophobic effect to form the core of the protein’s 3D structure. As they come together water is excluded from the interior of the protein and the outer surface of the protein tends to contain more hydrophilic residues that will interact favorably with the aqueous solution.
Why are weak bonds important in biochem?
weak bonds allow for flexibility in biological molecules due to their transient nature. however, these weak interactions provide great strength in numbers
what is the distance range of a hydrogen bonds?
1.5 - 2.6 angstroms
atoms commonly found in biological molecules that are often hydrogen bond acceptor
oxygen & nitrogen
Describe the basis for the van der waals attractive force between two atoms
Non polar atoms without a partial or formal charge can induce a transient dipole. When these atoms are adjacent to one another at an optimal distance (3-4 angstroms) then complementary transient dipoles can provide a small attractive force between the atoms
Explain why pH is an important parameter of biological systems
The pH of the solution affects the electrostatic interactions among biological molecules. Because the numerous and important weak interactions (electrostatic, hydrogen bonds) among biological molecules rely on a charge component, these interactions will be altered if the pH is changed. This will have (negative) consequences for the function of these biological molecules if a stable pH cannot be maintained.
define pKa
a measure of ionization tendency. it is the pH at which an acid molecule is 50% protonated/50% deprotonated (or dissociated) into its conjugate base
an acid ionizes to form a proton and its
conjugate base
naturally occurring isomer in proteins (L or D)
L-isomer
Which amino acid has a pKa near neutral pH
histidine
Is valine an essential or nonessential amino acid for humans
essential
is aspartate negatively or positively charged at neutral pH
negatively charged
a dipolar ion (opposite charges on the same molecule)
zwitterionic
the amino acid with the smallest-size side chain allowing greatest flexibility in a protein is
glycine
which amino acid has a side chain that connects both the alpha carbon and the nitrogen of the amino group in the peptide bond
proline
an amino acid with a hydrophobic side chain containing a thioether
methionine
What is the three letter abbreviation for tryptophan
Trp
In what pH range is zwitterionic alanine the predominate structure
2-9
Interactions between side chains of Aspartate and Arginine at neutral pH would be
ionic
which amino acid has a carboxyl group in its side chain
glutamate
What is the advantage of having multiple functional groups in proteins?
the diversity of the physical and chemical properties of the functional groups contribute to the overall diversity of protein function
A gene is mutated such that the amino acids glycine and glutamate are now alanine and leucine, respectively. What are the potential results of each of these mutations? Assume that the mutations are not near each other in the primary sequence and have no impact on the other.
The glycine-to-alanine mutations are similar and will have little or no effect (unless the flexibility of the glycine is essential at that position). Glutamate and leucine have very different chemistries and will impact the function and structure of the protein, as one is charged and water soluble and the other is hydrophobic and nonpolar.
What are the three aromatic amino acids?
Tyrosine, Phenylalanine, Tryptophan
Serine, Threonine, and Tyrosine all have what in common?
hydroxyl functional groups
Which amino acid is responsible for stabilizing the structure of a protein by forming pairs of sulfhydryl groups?
Cysteine
Even though malnourished, children with Kwashiorkor display a distended stomach, giving the illusion of being full. Why does this happen
This is a nutritional state where there is an extremely low or poor protein intake in the diet. The osmolar shift of the blood, which is poor in protein content, causes water to flow into the tissues. Low protein content of the blood causes problems with fluid distribution in the body.
What is the difference between nonessential and essential amino acids?
Essential amino acids cannot be made by the body and must come from food
this molecule is made when a peptide bond is formed
water
this amino acid residue disrupts the alpha helix because its side chain contains a unique ring structure that restricts bond rotations
proline
the plot that allows one to investigate the likely orientation of certain amino acid pairs is called
Ramachandran plot
Due to the side group steric clash, almost all peptide bonds are _____ in their configuration
trans
Every third residue in the protein collagen is
glycine
Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as
Beta-mecaptoethanol
this beta-sheet structure occurs when the two strands are oriented in opposite directions
antiparallel
a protein is considered to be _____ when it is converted into a randomly coiled structure without its normal activity
denatured
do all cysteines participatein disulfide bond formation
no
what is the hydrogen bonding pattern for helices in proteins
i, i +4
which of the following amino acid residues would most likely be buried in the interior of a water-soluble, globular protein
phenylalanine
the folding of a protein into its native shape can be described as
a series of repeatable random events where the lowest energy structure is maintained
the amino acid sequence from the N-terminus to the C-terminus
primary structure
what is the predominant screw sense for helices in proteins
right-handed
How are the amino acid R groups arranged relative to the plane of a β-sheet structure?
The R-groups of amino acids in a β-sheet protrude perpendicular (above and below) the sheet plane.
what determines a protein’s tertiary structure
the amino acid sequence
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.
Why are amino acids with a branch at the β-carbon problematic for helices
The branched-chain R groups result in steric clashes within the compact structure of the α helix.
Why are all the theoretical combinations of phi and psi not possible
steric hindrances of the side chains make certain combinations and angles impossible
name of the modified amino acid in collagen
hydroxyproline
Molecular basis of scurvy
Scurvy is a deficiency in vitamin C, which humans must acquire from the diet, and causes defects related to collagen function in the body. The protein collagen contains the modified amino acid hydroxyproline. The enzyme that converts proline to hydroxyproline, prolyl hydroxylase, depends on Vitamin C for its activity. So, without Vitamin C, the proline in collagen cannot be efficiently converted to hydroxyproline, which leads to detrimental consequences in collagen structure and function.
Describe the Anfinsen ribonuclease experiment and what conclusions were drawn about protein folding.
Purified and active Ribonuclease A was treated with urea and β-mercaptoethanol to completely denature the protein. With these reagents all tertiary structure was lost and any disulfide bonds were reduced. At this point Ribonuclease lost all of its enzyme activity. The concentrations of these denaturants were slowly decreased (removed from solution) and the ribonuclease regained activity. The final renatured protein had the same characteristics as the original protein. Anfinsen concluded that the primary sequence of amino acids contained all of the necessary information to generate the three-dimensional tertiary structure of the enzyme.
proteins that can assume a new protein structure that is self-propagating
prions
