Biochem 1
pKa
-log Ka =
Free fatty acids
A common fuel
differential centrifugation
A method used to separate the components of cells on the basis of their size and density.
(pH = pka + log [A-/HA]) 10000/1
Aspirin has a pKa of 3.4. What is the ratio of base to acid in the blood (pH = 7.4)
(pH = pka + log [A-/HA]) 0.01/1
Aspirin has a pKa of 3.4. What is the ratio of base to acid in the stomach (pH = 1.4)
humans cannot synthesize them
Cis polyunsaturated fatty acids are essential components of our diets because _____
phospholipids glycolipids cholesterol
Common types of membrane lipids are
amino group on right
D amino acid
the pH at which a molecule or amino acid, exists in a neutral form or without a charge.
Define pI
Enzyme-linked immunosorbent assay
ELISA stands for
(as the denominator increases or the distance of the ions increase the electrostatic energy decreases. And as the distance of the ions decreases the electrostatic energy increases. Due to the nuclei of the atoms having a positive charges however there is only so close ions can get before they start to repel each other) the Coulombs law states that as the charges increase the force of the interaction or energy also increases. Thus as charges increase, so does the force of the interaction and as size increase the force decreases as the bigger the ions the more space it creates between each ion.
Explain how distance affects the force of attraction in IMFs
omega (ω)
Fatty acids can also be numbered from the methyl carbon atom, which is called the ___ carbon
0 due to Glu and Gly having two carboxylate anion and Arg and Glu having two protonated amine groups. (Met and Thr are neutral)
For the pentapeptide Glu-Met-Arg-Thr-Gly give the overall charge at a pH of 7
Gly
For the pentapeptide Glu-Met-Arg-Thr-Gly name the carboxyl-terminal residue
separating proteins by size. biggest come out first smallest come out last
Gel-filtration Chromatography
top
In SDS-PAGE, larger proteins stay towards the ____ and smaller proteins travel further.
parallel to the chain
In an alpha helix the hydrogen bonds are
isoelectric focusing. This gel is then attached to an SDS-PAGE gel, and electrophoresis is performed at a 90 degrees angle to the direction of the isoelectric focusing separation
In two-dimensional gel electrophoresis, proteins are separated in one direction by ____
detect antibodies produced in response to a pathogen by presenting a viral antigen as bait
Indirect ELISA
amino group on left
L amino acid
mucins
Like proteoglycans, ____ are predominantly carbohydrate. The protein is characteristically attached to the carbohydrate by N-acetylgalactosamine. often lubricants.
an increase in melting point
Longer fatty acid chains allow for more van der Waals interactions between the chains. Consequently, an increase in chain length will result in ____
Glycolipids
Membrane lipids composed in part of carbohydrates often seen on the outside of membranes
A bond formed between the anomeric carbon atom of glucose and an amine
N-glycosidic bond
Spectrophotometry
NADH can be detected by
A bond formed between the anomeric carbon atom of glucose and a hydroxyl group of another molecule
O-glycosidic bond (product is called a glycoside)
IONIZABLE IN BIOLOGICAL SYSTEM
ONLY 7 AMINO ACIDS ARE IONIZABLE DUE TO
isoelectric point
PI
acrylamide and bis-acrylamide
Polyacrylamide gel electrophoresis (PAGE) is made up of
differential centrifugation
Procedure for separating cellular components according to their size and density by spinning a cell homogenate in a series of centrifuge runs. After each run, the supernatant is removed from the deposited material (pellet) and spun again at progressively higher speeds.
Polyacrylamide gel electrophoresis (PAGE)
Protein fractionation technique in which the proteins are driven by an applied current through a gel composed of a small organic molecule (acrylamide) that is cross-linked to form a molecular sieve.
negative
SDS coats the protein with a ___ charge
glycolipids
The carbohydrate components of _____ are on the extracellular surface of the cell membrane, where they play a role in cell-cell interactions.
transferrin serum albumin alpha antitrypsin myoglobin cytochrome c
The following five proteins were separated by SDS-Polyacrylamide gel electrophoresis. Give the order of their migration from the top (the point of sample application) to the bottom of the gel alpha- antitrypsin 45,000 Da cytochrome c 13,400 Da myoglobin 17,000 Da serum albumin 69,000 Da transferrin 90,000 Da
met-leu-gly-lys trp-arg val-ser
The following peptide is digested with Trypsin, list the fragments generated Met-Leu-Gly-Lys-Trp-Arg-Val-Ser
Proteoglycans (lubercant joints)
The protein is attached to a particular type of polysaccharide called a glycosaminoglycan. By weight, ____ are mainly carbohydrate. play structural roles or act as lubricants.
Glycoproteins
The protein is the largest component by weight. ___ play a variety of roles, including as membrane proteins
high concentration of ketone bodies in the blood will generate an acidic environment thus stimulating peripheral chemoreceptors to increase respiratory rate. The body does this to reduce the amount CO2 in the body and bringing the pH back up. In addition it also allows the lungs to breath out acetone.
Uncontrolled diabetes can result in ketoacidosis, a condition in which metabolic acids such as B-hydroxybutyric acid (ketone body) build up. B-hydroxybutyric acid has a pKa that is below that of physiological pH. A characteristic of ketoacidosis is deep and rapid breathing. Why would ketoacidosis lead to this symptom?
double
Unsaturated have ___ bonds
nitrocellulose membrane
Western blot assay uses what membrane
cysteine
Which amino acid can stabilize protein structures by forming covalent cross-links between polypeptide chains
valine and isoleucine
Which amino acid residues are most likely to be found on the inside of a water soluble protein?
overlap peptides
Which of the following are used to sequence entire proteins?
MES pKa =6.15
You need to prepare a pH 7 buffer. Which reagent should you choose to make this buffer? - Citric acid pKa = 3.14 - CAPS pKa = 10.4 - MES pKa =6.15
speed and time
___ and ____ are factors that help separate material in a differential centrifugation
lipids
___ are defined as molecules that are not soluble in water, but are soluble in organic solvents.
DNA
___ determine the amino acid order in a protein
tertiary
___ structure is when it has folded in a 3D form. some active at this stage
sandwich
____ ELIZA produces higher resolution
potter homogenizers and French press function
____ and ____ sheer cell wall but does not affect proteins
lectins
____ are a group of proteins that specifically bind to glycoproteins and act as binding receptors for lipids
Saturated
____ fatty acids are less fluid
longer
____ fatty acids are less fluid
glycogen
____ has more branches opposed to starch which has very few if any branches
non reducing sugar
____ is a sugar which cannot serve as a reducing agent. An example is sucrose.
N
____ terminal is the beginning of the peptide
c
____ terminal is the end of the peptide
high pressure liquid chromatography
_____ allows proteins to pass through the column faster due to pressure. resulting in greater purity in less time
chaperonins
_____ are proteins that help new proteins to fold properly
Edman degradation
_____ is used to -analyze small proteins - selectively & sequentially removes the N terminal amino acid of the protein which is analyzed by mass spectroscopy removes one amino acid at a time if protein has a N terminal block (chemical modification) process does not work
Cerebrosides
______ are the simplest glycolipids.
cation exchangers
______ beads have negative charge and attract positive proteins
negative
a acidic protein or amino acid has an overall ______ charge
positive
a basic protein or amino acid has an overall ______ charge
greater
a basic protein will have a pI ___ than 7
Coomassie Blue staining (minimum of 0.3-1microgram protein)
a dye that stains proteins blue and allows them to be visualized
silver nitrate
a dye that stains proteins larger than 2-5 nanograms and allows them to be visualized
zwitterion
a molecule or ion having separate positively and negatively charged groups. overall neutral charge
hydrocarbon chain
aliphatic
nonpolar
aliphatic r groups are ____
dehydration
all macromolecules have covalent bonds formed by
contain regions that are polar and nopolar
amphipathic
Lower
an acidic protein will have a pI ____ than 7
isomers that differ at a new asymmetric carbon atom formed on ring closure
anomers
decreases
as double bond or cis increases melting point ___
hydrolyzes
by ____ we can get the amino acid composition
phosphate
by adding ___ to glucose it traps it in the cell. glucose on its own will leave the cell.
energy, structure, component of nucleic acids, cellular markers
carbohydrate functions
energy (immediate glucose) storage (glycogen) (plants store glucose as starch)
carbohydrates benefits
both aim to purify or isolate proteins. PAGE discriminates proteins by shape and charge. SDSPAGE linearizes proteins and gives them a negative charge thus differentiating them only by weight
compare and contract SDS PAGE to PAGE
phospholipids (amphipathic)
complex lipids (additional phosphate group. hydrophobic and hydrophilic portions)
The diffusion of small solutes through a selectively permeable membrane.
dialysis
mirror images
enantiomers
the break down of cell wall
enzymatic digestion
pregnancy test, drug tests,
examples of ELIZA
speed, length of time, weight and liquid that protein is in
factors that affect ultracentrifugation
1953 (insulin)
first protein sequenced in
free fatty acids, triacylglycerols phospholipids glycolipids steroids
five classes of lipids
dipolar ions
free amino acids in solution at neutral pH exist as ___
the protein is made up of multiple proteins
hemoglobin has 4 subunits creating more than one lines in gel because ___
pH = pKa + log [B]/[A]
henderson hesselbalch equation
less
high melting point of lipids = ___ fluidity
a mixture of all of the components of the cell, but no intact cells.
homogenate
time and speed
how does differential centrifugation target different intra cell organelles
compounds that dissolve easily in water. generally charged or polar
hydrophilic
nonpolar molecules such as lipids and waxes
hydrophobic
size
in Polyacrylamide gel electrophoresis (PAGE) altering the concentration of acrylamide and bis-acrylamide the ___ of the pores can be adjusted.
second
in a 5 ring structure the ___ carbon needs to be free
first
in a 6th ring structure the ____ carbon need to be free to open
110
in average, 1 amino acid = ___ Daltons
Alfa, beta
in fatty acid carbons atoms, Carbon atoms 2 and 3 are also referred to as ___and ___, respectively
increase chaos or disorder
increase entropy
alfa amylase primary antibody mouse anti-alfa amylase IgG secondary antibody goat anti-mouse IgG alkaline phosphatase linked
indirect ELIZA process
the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles
intermolecular force
noncovalent reactions
intermolecular force is also known as
uses a charged column and a variably saline eluent. negative and neutral chargers come through the column first. positives charged proteins stick to column
ion exchange chromatography
have the same molecular formula but different structures
isomers
same chemical formula different properties
isomers
reducing agent
linear sugar carbons can participate in oxidation reaction acting as a _____
energy, insulation, protection, steroid hormones, lipid soluble vitamin storage, membrane formation
lipid functions
sonification detergent potter homogenizers French press
methods to lysis cell to remove specific protein
serine, ethanolamine, choline, inositol
most common R groups attached to phospholipids
L amino acid
mostly ____ (L/D) amino acid found inside the human body
the amino acids is acyclic amino group
no amino free end resulting in no reaction to fluorescent means ___
same
once the concentration gradient solution reaches the ____ density in the gradient, it stops moving
positive charge
pH < pI = net
negative charge
pH > pI = net
unprotonated
pH above pka
isoelectric point
pH at which a molecule has no net charge. (where we see zwitterion)
protonated
pH below pKa
0
ph = pI net charge is
- amino acid composition (PI and solubility) - amino acid sequence (localized solubility) - number of amino acids (size)
protein structure / function is effected by
the entire set of proteins expressed and modified by a cell under a particular set of biochemical conditions.
proteome
Protein precipitation caused by an increase in the salt concentration.
salting out (ammonium sulfate fractionation)
solid
saturated fats are ___ at room temperature
Fats with the maximum number of hydrogens (no double bonds)
saturated fats are ____
triglycerides
simple lipid (only alcohol and fatty acids)
increases
specific activity _____ as purity increases
atoms are connected in the same order but differ in spatial arrangement
stereoisomers
same bonds different spatial arrangement
stereoisomers
Polycyclic hydrocarbons with a variety of functions.
steroids
smaller
the _____ the size of the beads in chromatography the higher the purity
nuclei repels
the closer the distance the stronger the interaction until
entropy
the increase in ____ of the system is largely responsible for the ease of dissolving salts in water
better
the longer the chromatography the _____ the purity
specific activity
the ratio of enzyme activity to protein concentration
Separates proteins in two steps, first by isoelectric points and then by molecular weights.
two-dimensional gel electrophoresis
liquid
unsaturated fats are ___ in room temperature
glycoproteins, proteoglycans, mucins
what are the three main classes of glycoproteins
dithiothreitol (DTT) or B-mercaptoethanol break disulfide bonds and non covalent bonds, linearizing the protein
what does SDS-PAGE do?
ionic bonds, hydrogen bonds, disulfide bonds, LDS, R groups
what factors influence the folding of amino acids
dipole-dipole
what is the type of interaction does the dotted line represent
steric hindrance (OH next to OH)
why is alfa D Glucopyranose les favorable than beta D Glucopyranose
glycogen is insoluble and dies not cause a osmolarity reaction while glucose dissolves in water and moves water into the cell.
why is glucose stored as glycogen in cells?
