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?