Exam 1

Ohio University , Daewoo Lee

what are the two hallmarks of Alzheimer’s Disease?

senile plaque, neurofibrillary tangles

a patient with senile plaque and neurofibrillary tangles likely has what neurodegenerative disease?

Alzheimer’s

what happens in prion-like propagation of pathogenic tau in neurodegenerative diseases?

self-assembly - a natively unfolded Tau creates several new misfolded Tau proteins (β-structure)

seeded assembly - Tau^FL seeds bond to Tau^FL

what is biochemistry?

the branch of science that explores the chemical processes within and related to living organsims

what are the four main chemical components of the human body?

carbohydrates, lipids, amino acids/proteins, biomembranes, nucleic acids (DNA/RNA)

what are the major chemical processes in the human body?

cell development, enzyme activity, membrane transport mechanisms, homeostasis, blood coagulation (clotting), oxygen transport, neurotransmitter function, aging, etc.

how can biochemists understand and solve biological problems at the molecular level?

using chemical knowledge and techniques

biochemistry focuses on what happens inside cells, studying components like ….?

proteins, lipids, and organelles

biochemistry also looks at _________________, for example during growth or fighting illness

how cells communicate with eachother

biochemistry covers a range of scientific disciplines, including…?

genetics, genomics, microbiology, neurobiology, medicine, etc

if chemistry is the science of matter, than biochemistry is the science of _________.

living matter

what diseases are considered “biochemistry in every day life” according to Dr. Lee’s slideshow?

cardiovascular, pulmonary diseases (e.g. atherosclerosis); neurodegenerative diseases (e.g. alzheimers)

how is biochemistry used in food?

biochemical fertilizers, tolerance to biotic and antibiotic stresses

how is biochemistry used in the fashion industry?

biotechnological applications in the textile industry, spider silk - strong, flexible, and lightweight properties → using bioreactor to produce in large quantities

how does free radical biology interact with medicine?

Reactive Oxygen Species (ROS)

cardiovascular, pulmonary diseases (atherosclerosis)

neurodegeneratice diseases (alzheimers)

aging biology

reproduction (fertility)

more!

what common lipid causes cardiovascular disease by building up plaques in arteries?

cholesterol

true or false: cholesterol is bad for you

false, too much cholesterol is bad for you, but cholesterol is necessary for survival

the liver produces cholesterol, which can then become…?

cell membrane, sex hormones, bile acids, vitamin D

____ adds cholesterol to plaque

low density lipoprotein

____ removes cholesterol from plaque

high density lipiprotein

there are four major classes of biological macromolecules, what are proteins main functions?

structure and function within the cell

there are four major classes of biological macromolecueles, what are the main functions of carbohydrates?

energy metabolism

there are four main classes of biological macromolecules, what are the main functions of lipids?

biomembrane and energy storage

there are four major classes of macromolecules what are the main functions of nucleic acids?

storage and transmission of genetic information

what are chemical bonds?

the formation of chemical compounds in biological systems

what are the two BROAD categories of chemical bonds?

covalent and non-covalent

of covalent and non-covalent bonds, which one has subtypes? what are they?

non-covalent: ionic interaction, hydrogen bonds, van der Waals, hydrophobic interactions

what is the strongest type of chemical bonds?

covalent bonds

what is a covalent bond?

formed by electron sharing between two adjacent atoms

what is the typical distance of a C-C covalent bond?

1.54 Å

what is the typical bond energy of a C-C bond?

355 kJ mol^-1

what law allows us to calculate the energy of electrostatic interaction? what is the formula for this law?

Coulomb’s law, E=kq₁*q₂/r²

electrostatic interactions in water have a bond distance of _______

3 Å

electrostatic interactions in water have a bond energy of _______

5.86 kJ mol^-1 or 1.4 kcal mol^-1

Hydrogen bonds occur between a(n) __________ atom and a hydrogen ____________________

electronegative, covalently bonded to another electronegative atom

hydrogen bonds vary in distance from ___Å to ___Å

1.5 to 2.6

hydrogen bonds cary in bond energies from ____ to _____ kJ mol^-1

4-20 (1-5 kcal mol^-1)

what are van der Waals interactions?

when two atoms are sufficiently close so that transient asymmetry in electron distribution in one atom induces complementary asymmetry in a neighboring atom and the neighbors attract each other

van der Waals interactions are [STRONG / WEAK], with bond energies from ____ to ____ kJ mol^-1

weak, 2 to 4

rank the four types of chemical bonds from shortest to longest

covalent bonds, H-bonds, ionic bonds, van der Waals

rank the four types of chemical bonds from lowest to highest bond energy

van der Waals, H-bond/Ionic bonds (interchangeable, H-bonds are 4-20 and Ionic are 5.86), covalent bonds

are water molecules polar or non-polar? explain

polar, they have a partial positive charge (on the hydrogens) and a partial negative charge (on the oxygen)

water is highly _______, a large number of hydrogen bonds are formed in liquid water and maximum hydrogen bonds are form in crystalline ice

cohesive

which state of water has the most hydrogen bonds?

crystalline ice

what is the hydrophobic effect?

nonpolar molecules in water can be driven together by the increase in entropy of water.

when non-polar molecules are driven together by the increase in entropy of water, this connection is called the _______

hydrophobic effect

acid-base reactions involve the addition/removal of a(n) _______

H⁺ ion

pH is a measure of the ______ concentration, and is defined by _______

H⁺, pH = -log [H⁺]

H⁺ and OH^- ions are formed upon the dissociation of ________

H₂O

a ___________ resists changes in the pH of a solution

acid-base conjugate pair

HA ←→ ___ + ____

H⁺ (acid), A^- (conjugate base)

an acid base conjugate pair acts as a ______, which is most effective at a pH near its pKa

buffer

at what pH is a buffer most effective?

a pH near its pKa

what is the pKa of sodium acetate?

4.75

what is the formula that describes the proton remocal from any molecule HA?

K_a=[H⁺][A^-] ÷ [HA] → K_a is the dissociation constant

what is the formula for pKa? what does it represent?

pK_a = -log(K_a), indicates the susceptibility of proton removal

log(K_a) = log (___) + log (_________)

[H⁺], [A^-]÷[HA]

what is the Henderson-Hasselbalch equation?

pH = pKa + log([A^-]÷[HA])

weak acids are most effective as buffers at pH _____

near their pKa

the chemical basis of the denaturation is the ______ of base pairing

disruption

why does high pH cause issues with base pairing?

H-bond donors are lost, so H-bonds can no longer form

what is the pI?

Isoelectric Point, the pH at which a molecule carries no net electrical charge, or is electrically neutral

how do you calculate the pI with two pKa values?

average them

how do you calculate the pI with more than two pKa values?

take the pKa values that surround the zwitterion, and average those

when pH is raised, which group on an uncharged will be deprotonated first?

-COOH group

when pH is raised, what group on an uncharged amino acid will be deprotenated second?

NH3⁺

what is protein moonlighting?

proteins may have a second job, what job a protein performs is dependent on situation and location

proteins are linear polymers composed of _______

amino acids

proteins have a wide variety of f_____ g______

functional groups

proteins can __________ one another and with other macromolecules to form complexes

interact with

proteins can interact with one another and with other macromolecules to form ______

complexes

some proteins are _____(such as collagen), while others are ______

rigid, flexible

a protein is a _______ made up of amino acids

biopolymer

amino acids are __________ for proteins

building blocks

what is the name for the central carbon of an amino acid?

alpha (ɑ) carbon

what are the four branches off of the alpha carbon of an amino acid?

amino group, hydrogen, carboxyl group, side chain

what is the pKa of the carboxyl (COOH) group on an amino acid?

3

what is the pka of the amino group (NH₃) on an amino acid?

9

what is the only non-chiral amino acid?

glycine

amino acids are ______, which means they have both an acid and a base group

amphoteric

what does amphoteric mean?

has both an acid and a base group

amino acids have two isomers, the ___ and the ____. the ____ is more naturally prevalent

L isomer and D isomer, L isomer

what are the four main groups of amino acids?

1. hydrophobic amino acids with non-polar R groups

2. polar amino acids, but uncharged

3. positively charged amino acids with R groups that have a positive charge at physiological pH (basic)

4. negatively charged amino acids with R groups that have a negative charge at physiological pH (acidic)

the amino acid cysteine can create _______, which are a common mechanism used in nature to stabilize many proteins

disulfide bridges

the phosphorylation of amino acids is important for ________________ of enzyme activity

activation and inhibition

what does it mean for an amino acid to have a readily ionizeable side chain?

can donate or accept protons to facilitate reactions as well as to form ionic bonds

when writing out an amino acid, the N terminus is on the [RIGHT / LEFT] and the C terminus is on the [RIGHT / LEFT]

Left, right

amino acids are linked by ________ bonds

peptide

peptide bond formation involves the linking of two amino acids, accompanied by the loss of _______

a water molecule

the reaction that links two amino acids is called ________, and is catalyzed by _______

hydrolysis, proteases

peptide bonds are _____ and _______

planar, rigid

how many atoms lie in the same plane of a polypeptide?

6

in most cases, the _________ form of the peptide bond is strongly favored. this is because the other form experiences ___________

trans, steric clashes

aspartame (Asp-Phe) is used as an artificial sweetener. how does this fact prove that properties of polypeptides change with amino acid sequence?

neither Phe nor Asp is sweet, and the opposite combination (Phe-Asp) is also not sweet

what two amino acids make up aspartame?

Asp-Phe

a proteins primary structure is widely defined as…?

sequence of a chain of amino acids

the secondary level of protein structure is widely defined as…?

the sequence of amino acids linked by hydrogen bonds

the tertiary level of protein structure is widely defined as…?

certain attractions are present between alpha helices and beta pleated sheets

the quaternary level of protein structure is broadly defined as…?

a protein consisting of more than one amino acid chain

what are the two possible forms that are a part of secondary structure?

alpha helix, beta sheet/beta pleated sheet