Molecular Bio Midterm #1 Flashcards
Lectures 1-11
what is a local energy minimum
a state with less energy than its surrounding neighbours in protein folding
what Is a chaperone
proteins that assist in proper folding of other proteins
what is a homodimer
two of the same proteins
what is a heterodimer
two different proteins
what is kinase
an enzyme used to add a phosphate group to an amino acid
what is a phosphatase
an enzyme used to remove phosphate groups from certain amino acids
5 post-translational modifications
methylation, acetylation, phosphorylation, glycosylation, hydroxylation
primary structure does what
encodes all information needed for proper protein folding
what are the two forces driving protein folding
hydrophobic and van der waals interactions
what does extreme electronegativity allow you to predict?
the type of bond that will form
what is separation of positive and negative charges called
electric dipole moment
how does electronegativity on the periodic table increase
left to right and bottom to top
what is the separation of positive and negative charges called
electric dipole moment
what are the three weak non-covalent bonds
hydrogen bonds, van Der Waals forces, hydrophobic interactions
hydrogen bond (of H-bond) is primarily what the of force?
an electrostatic force of attraction between a hydrogen atom which is covalently bonded to a more electronegative “donor” atom or group (Dn), and another electronegative atom bearing a lone pair of electrons – the hydrogen bond acceptor (Ac)
order the bond strength strongest to weakest
covalent, ionic, hydrogen and hydrophobic, van der waals
polar compounds are water soluble so they are…?
hydrophilic
non-polar compounds are not water soluble so they are..?
hydrophobic
do proteins have hydrophobic or hydrophilic regions and why
have both hydrophobic and hydrophilic regions due to structure and function once folded
5 functional groups
hydroxyl, amino, methyl, carboxyl, phosphate
why is cysteine chemically unique
cysteine is the only amino acid that can form covalent bonds
why is proline conformationally unique
part of essential things like collagen
why is glycine conformationally unique
R group is H- nothing else can fit and it is flexible (can fit in many different spots)
alpha carbons have what type of group
R- groups
what type of bond is formed between the c-terminus and the n-terminus
covalent peptide (C-N) partial double bond
is the peptide bond between the C-terminus and the N-terminus rotatable? why?
non-rotatable because carbon and oxygen are stuck at there respective sides
can other bonds rotate
the single bonds around the molecule are all rotatable
what is life
a chemical system capable of darwinian evolution
evolutionary processes depend on what
changes in genetic variability and allele frequencies over time
what are the three properties of life
multiplication, mutation, heredity
what we know about DNA
it is not the origin of like but provides stability and storage
RNA
reactive in a way DNA is not, capable of diversity, storage, and catalysis
which biomolecules are capable of diversity and storage but not catalyst?
RNA
life requires chemicals capable of what
storing information, replicating information, modifiability
what is RNA structure
highly evolved ribozyme
what is a ribozyme
RNA molecule that catalyzes things
p generation
parents used in a cross
F1 generation
progeny resulted from a cross in p gen
F2 generation
progeny resulting from a cross in the f1 generation
purebred
individual homozygous for a given trait or set of traits
hybrid
progeny resulting from a cross of parents with different genotypes
gene
section of DNA encoding a protein or functional RNA
allele
variant of the gene encoding a trait
phenotype
outward appearance of an organism
genotype
alleles contained in an organism
homozygous
having two identical copies of a allele for a gene
heterozygous
having two different alleles for a gene
dominant allele
allele expressed in the phenotype of a heterozygous organism
recessive allele
allele masked in the phenotype of a heterozygous organism
what does an atomic number stand for
number of proteins in its nucleus
how many bonds does H, O, N, and C need
H - 1
O - 2
N - 3
C - 4
what happens in a covalent bond
electrons are shared
what happens in ionic bond
electrons transferred
what is electronegativity
different affinities of the bonded atoms for electrons
what scale is electronegativity measured on
pauling scale
structural isomer
molecules with the same molecular formulas (number and type of atoms), but different bonding arrangements of atoms. They have different properties
what happens in extreme electronegativity
atom loses electron, and one becomes positive whereas the other becomes negative and forms an ionic bond
stereoisomers
molecules with the same molecular forms and bonding of atoms but different spatial arrangement. They have different properties
chiral molceule vs chiral molecule
a chiral molecule cannot be superimposed on its mirror image whereas an achiral molecule can be superimposed
what are the 4 unique amino acids
glycine, cystein, histamine, proline
how is a dihedral angle between two planes defined
defined by atoms 1,2, and 3 and atoms 2, 3, and 4 respectively
how are amide or peptide bond planes joined
joined by the dihedral bonds of the alpha carbon
how is a dihedral angle determined
between lines perpendicular to each plane
why are many possible conformations of an alpha carbon between two peptide planes are forbidden
few combinations are possible because of steric crowding/ hindrance
in an alpha helix, where does the hydrogen bond form
hydrogen on amide N forms a hydrogen bond with the carbonyl O of the 4th residue towards the N-terminus
amino acid residues in an alpha helix have conformations with what
ψ = -60° and ∅ = -45 to -50°
what is the N terminus
the nitrogen of the first amino group
what do helices exploit
maximum hydrogen bonding among groups
what is the N terminus
the nitrogen of the first amino group
when making a peptide bond where would you never add a new amino group
H2N
how are bonding strands in an antiparallel strand shown
straight
when making a peptide bond where would you add a new amino group
the OH of the first alpha carbon
how are bonding strands in a parallel strand shown
oblique (diagonal)
where does the R group of the helix pop out
towards the axis not outside
how do R groups alternate
up and down
how many angstroms are there per residue
3.5
how many angstroms are between R groups on the same side
7
where is the Phi angle around
the -N-CA- bond (where ‘CA’ is the alpha-carbon)
where is the psi angle around
around the -CA-C- bond.
what is a motif
particularly stable and common arrangements of multiple secondary structural elements (aka super secondary structures). motifs are structural but not necessarily functional characteristics
what is a domain
independent folding units with a defined function a domain can have one or more motifs
what is a protein
a functional polypeptide. it can have one or more domains
helical structures have R residues facing what way
outside
beta sheets (sheet motifs) have R residues facing what way
both inside and outside
what does a zinc finger motif do
reads DNA and shows alpha and beta
what is protein folding
the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil
all information needed for proper protein folding is encoded by what
primary structure
what are molten globules
compact, partially folded conformations of proteins that have near-native compactness, substantial secondary structure, dynamic tertiary structure and increased solvent-exposed hydrophobic surface area relative to the native state
what collapses during protein folding
postulated hydrophobic collapse
what is a local energy minimum
a dip that has less energy than its surrounding neighbours
what does a massive dip mean
protein has misfolded
what is methylation
addition of a methyl group
what is acetylation
addition of an acetyl group
what is phosphorylation
addition of a phosphate group
what is glycoslation
addition of a sugar molecule
what is hydroxylation
addition of a hydroxide (OH) group
what electronegativity range is non polar covalent
<0.4
what electronegativity range is polar covalent
0.4 - 1.8
what electronegativity range is ionic
> 1.8
what is alpha-keratin
key structural material making up scales, hair, nails, feathers, horns, claws, hooves, and the outlet layer of skin among vertebrates.
what is alpha-keratin found in
vertebrates
what is beta-keratin found in
birds and reptiles
what is collagen
a fibrous structural protein with modified amino acids. it is the main structural protein in the extracellular space in the various connective tissues in animal bodies
what percent of whole body protein does collagen make up
25% - 35%
what three consistencies can collagen tissues be
depending on degree of mineralization, can be rigid (bones), compliant (tendon), or have a gradient from rigid to compliant (cartilage)
how many amino acid residues does each collagen helix consist of
~1000
what post-translational modification needs vitamin C as a reactant
hydroxylation of Pro and Lys
what can cause wrinkles
collagen levels decreasing and cross linking not being rebuilt properly
what happens at carbon 1’
the carbon that leads to the base – the pyrimidine or purine base is linked here
what happens at carbon 2’
tell you if it’s a ribonucleotide or deoxynucleotide
- ribonucleotide will have one hydroxy and one hydrogen
- deoxy will have two hydrogens
what happens at carbon 3’
it has a hydroxy which in involved in the phosphodiester bond – related to the 3’ molecule of DNA
what happens at carbon 4’
nothing
what happens at carbon 5’
the phosphate is attached here
- bond between the phosphate of the 5’ and the hydroxy of the 3’ is formed here
what are the purine bases
adenine and guanine
what are the pyrimidine bases
cytosine, thymine (DNA), uracil (RNA)
what does a nucleoside have
base and a sugar
what does a nucleotide have
base, sugar, and phosphate
what are the base names
adenine, guanine, cytosine, thymine, uracil
what are the nucleoside RNA names
adenosine, guanosine, cytidine, thymidine, uridine
how do the nucleoside DNA names differ from the RNA names
“deoxy” is added onto the front the names but the names stay the same as in RNA
what are the three-letter abbreviations for nomenclature of bases
adenosine - AMP
guanosine - GMP
cytidine - CMP
thymidine - TMP
uracil - UMP
how do the three letter abbreviations change when talking about DNA
a “d” is added in front of the three letter abbreviations which stay the same
what is the orientation of the DNA molecule
5’ to 3’
why is DNA helical
protect the hydrophobic bases from water while exposing the backbone of the phosphodiester bonds
antiparallel orientation
one strand going 5’ - 3’ and the other going 3’ to 5’
what is the secondary structure of DNA
two antiparallel polynucleotide chains wound around the same axis with a sugar-phosphate backbone wrapped around the outside
