Biochemistry Exam 1

Biochemistry

The fundamental understanding of the molecular basis for the functioning and malfunctioning of living tissue, including the study of the building blocks of life

Buffer

A chemical pair, typically a weak acid and its conjugate base, that helps maintain a specific environment required for healthy cell function

pH

pH is a measure of hydronium ion (H3O+) concentration

Strong Acid Dissociation

Acids that dissociate completely (~100%) when added to water, such as Hydrochloric Acid (HCl)

Weak Acid Dissociation

Acids that dissociate only partially (

What type of logarithm is used in the pH scale?

Logarithm base 10 (log10)

What does a change of 1 pH unit represent in terms of [H3O+]?

A 10-fold change

What does a change of 2 pH units represent in terms of [H3O+]?

A 100-fold change

What does a change of 3 pH units represent in terms of [H3O+]?

A 1000-fold change

pKa Definition (Titration)

The horizontal inflection point on a titration curve (0.5 equivalents of base) where a group is 50% protonated and 50% deprotonated

pH=pKa when 50% disassociation occurs

Henderson-Hasselbalch Equation

The formula pH = pKa + log10([Conjugate Base]/[Acid]), used to calculate biological pH or relative acid-base concentrations

Ka

acid disassociation constant (how strong an acid is)

H30+ x Conj Base/ Conj Acid= Products/ Reactants

what is Ka of a strong acid

large number (in millions)

What is the Ka of a weak acid?

small number

pKa of a strong acid

-6.3 SMALL

pKa of a weak acid

4.8 LARGE

how do you measure Ka/pKa

titration of a weak acid with a strong base (1 equivalent of a strong base is the amount necessary to completely neutralize a strong or weak acid)

what is the ratio needed to titrate a weak/strong acid with a strong base

1:1

pH

weak acid protonates

pKa>pH

weak acid deprotonates

Effective Buffer Range

A buffer system is most effective at resisting pH changes within ±1 pH unit of its pKa

what are the factors that make a buffer good

pH range

having ALOT of the buffer

amino acid structure

amino group (NH2), carboxyl group (COOH), R group

why is there a range of pKa's for amino/carboxyl groups for different amino acids

environment/interaction with the R-groups makes a difference

Isoelectric Point (pI)

The specific pH at which a molecule, such as an amino acid, carries no net electrical charge; it is marked by a vertical inflection point on a titration curve (in the middle)

why is pI significant

this is where a buffer becomes ineffective

titration of glycine

there is no dissociable R-group, just 1 acid and 1 base

-causes there to be two ideal pKa's for glycine because of the dissociation of either titratable species

what do we see for ionizable species with glycine

# equivalents of OH- = # of ionizable species (pKa)

causes a strict order based off the pKa that COOH goes first then NH3+

glutamic acid titration

has 3 equivalents of strong OH- which are required to titrate the 3 ionizable groups of glutamic acid so ends up having 3 effective buffering ranges

Histidine Buffering

One of five amino acids with buffering side chains (pKa ~6.0); it allows hemoglobin to function as a buffer during gas transport

is histidine a good buffer when not bound

no its pKa is too low but when bound to hemoglobin its a good buffer

Blood pH Homeostasis

In healthy individuals, blood pH is strictly maintained within a narrow range of 7.35 to 7.45

Primary Blood Buffers

Biological pH in the blood is regulated by carbonic acid/bicarbonate (pKa 6.1), proteins like hemoglobin (pKa ~6.8), and phosphoric acid/phosphate (pKa 7.2)

Saliva pH Range

Healthy saliva typically ranges from pH 6.2 to 7.5; it is an "open system" influenced by factors like diet, medication, and disease

why is saliva important in the mouth

contains multiple buffers which helps neutralize acid

is a natural lubricant to help reduce abrasions

contains minerals

is a natural rinsing agent for plaque

has antimicrobial properties to help limit bacterial colonization

xertostomia

lack of saliva that causes dry mouth

can adversely affect oral health

what causes xerostomia

consequence of some diseases (sjogrens or diabetes 1 or 2)

side effect of certain medications

Critical Saliva pH

The threshold of 5.5; if saliva pH drops below this, tooth enamel begins to demineralize, increasing cavity risk

what minerals does saliva contain to help with early decay

calcium/phosphate

is phosphate higher in saliva or blood

saliva

Stimulated Saliva Buffering

gustatorily stimulated, significantly increases the concentration of bicarbonate in saliva, making it a more effective buffer than resting saliva

GERD

gastroesophageal reflux disease, treated with diet/lifestyle changes, medications for acid reduction, and sugar free gum to help stimulate saliva reproduction

acidosis

alkalosis

> pH 7.45, net gain of base in body fluids

how does bicarbonate and carbonic acid regulate blood pH

bicarbonate:carbonic acid

20:1 ratio

how can a reduction in bicarbonate influence blood pH

it lowers the pH causing borderline acidosis

how can an increase in bicarbonate influence blood pH

it raises the pH causing borderline alkalosis

what system regulates CO2 in blood

respiration

what type of pH regulation does respiration do in the blood

quick regulation and becomes a minor contribution overall to blood pH

what system regulates acid and bicarbonate (HCO3-) in the blood

kidneys

what type of regulation does kidney do in the blood

slower pH regulation and becomes a major contribution to pH of blood

respiration response to acidosis

increased respiration rate, which causes blood co2 to decrease and blood h2co3 to lower and increased pH to create homeostasis

respiration response to alkalosis

a decreased respiration rate causes a blood co2 to increase and blood h2co3 to increase and lowers pH to crease homeostasis

what is the kidneys response to acidosis

it lowers blood acid and increases hco3 and increases pH

what is the kidneys response to alkalosis

it increases blood acid and decreases hco3 and lowers pH

Respiratory Acidosis

Excessive acid in body fluids caused by a buildup of CO2 in the blood due to hypoventilation

what are common causes of respiratory acidosis

Neuromuscular disorders, chest muscle weakness, chest deformities/injuries, chronic lung disease, and sedative drug abuse

Metabolic Acidosis

Excessive acid buildup or bicarbonate loss (which is acid gain)

metabolic acidosis causes

diabetic acidosis (if there is no sugar in the blood the body uses fats which creates ketones which are acids)

hyperchloremic acidosis (loss of bicarbonate and increased chloride)

lactic acidosis (lactic acid build up)

kidney disease

aspirin poisoning

Respiratory Alkalosis

Excessive base in body fluids caused by insufficient CO2 in the blood

what causes respiratory alkalosis

anxiety (hyperventilation)

lack of O2 from high altitude

Metabolic Alkalosis

Excessive base caused by acid loss or bicarbonate gain

what causes metabolic alkalosis

dehydration which causes changes in body's water distribution

repeated vomiting

excessive sweating

abuse of diuretics

diarrhea

kidney disease (can cause either)

Peptide Bond Formation

A covalent amide linkage formed through a condensation reaction (releasing H2O) between the alpha-carboxyl group of one amino acid and the alpha-amino group of another

Peptide Bond Character

It possesses partial double bond character, making the bond rigid and restricted in rotation, which keeps the atoms in a single plane

what causes peptide bond structure to be rigid

the alpha carbon and the plane that the peptide bonds they end up depend on R-groups

Trans vs. Cis Configuration

Most amino acids prefer the trans configuration to avoid steric clash (~1,000:1 ratio)

which amino acid is the exception to the the trans configuration favoring

proline because the side chain comes back and is covalently linked to amide

Phi (φ) and Psi (ψ) Angles

Phi is the rotation around the Ca-N bond and Psi is the rotation around the Ca-C bond; these angles help dictate secondary structure

what dictates protein function

protein structure which in turn is dictated by amino acid structure

Primary Protein Structure

The linear sequence of amino acids in a polypeptide chain, determined by the DNA sequence

Secondary Protein Structure

Local structural elements like alpha-helices, beta-strands/sheets, and beta-turns, stabilized by hydrogen bonds between main chain atoms

Alpha-helix Characteristics

A right-handed corkscrew structure (~4 residues/turn)

stabilized by H-bonds between amide protons (n+4) and carbonyl oxygens (n) MAIN CHAIN ATOMS

present in globular and fibrous proteins

which amino acids do alpha-helices not normally contain

glycine and proline

why is glycine not normally found in secondary structures

it has a small R group (H)

causes it to be really flexible

common in loops and required for beta turns

Beta-strand

Beta-strands are extended structures (~2.3x longer than alpha-helices)

open phi and psi angles

usually associated with other strands to form beta sheet

stabilized by main chain atoms

beta sheets

created of multiple beta strands

can be parallel or anti parallel

amide protons of one strand hydrogen bond to the carbonyl oxygens of the second strand

stabilized by main chain atoms

which is more stable: parallel or anti-parallel beta sheets

parallel

Beta-turn

A 4-amino acid motif (often X-Pro-Gly-X) that allows a polypeptide to reverse direction; Proline and Glycine are essential for these tight corners

which form of proline creates beta turns

cis formation

which positions in a beta turn is usually hydrogen bonded

position 1 and 4

Proline as "Helix Breaker"

Because its imino side chain is covalently linked to the amide nitrogen, it lacks an amide hydrogen for H-bonding and disrupts regular secondary structures

which two amino acids are required for beta turns

glycine (allows the turn to still connect to the rest) and proline (causes the turn)

what stabilizes primary structure

covalent linkage between adjacent amino acids

tertiary Protein Structure

The 3D arrangement of secondary elements in a single polypeptide, caused by hydrophobic effect that has a thermodynamic explanation

thermodynamic explanation of tertiary structures

local folding begins in secondary structure usually spontaneously (-delta G), some may require help from chaperones, delta S of water helps to drive tertiary structures because of the hydrophobic effect, environment really matters

so delta S of water is favorable and delta H of protein is favorable

free energy equation

delta g (free energy) = delta h (enthalpy) - TdeltaS (entropy)

what do tertiary proteins usually have a role in

extra-cellular systems

what stabilizes tertiary/quartenary protein structure

stabilized by R-group interactions including H-bonds, van der waals, electrostatic forces, and disulfide bonds

Quaternary Protein Structure

The specific 3D association of multiple discrete polypeptide subunits (e.g., hemoglobin), the polypeptides may be the same or different, causes allostery within these proteins

allostery

regulation of the activity of a protein by the binding of an effector molecule to a site other than the active site

Thermodynamics of Folding

Driven by a decrease in free energy (ΔG); while protein entropy decreases, the hydrophobic effect increases water entropy (ΔS), making the process spontaneous and rapid

Hydrophobic Effect

The tendency of nonpolar side chains to cluster in the protein interior to minimize contact with water, serving as the primary driver of folding

what can errors in protein folding cause

disease like alzheimers, CF, mad cow disease, inherited emphysema, and certain cancers

what can influence final structure of protein folding

posttranslational modification and chaperones (atp), disulfide isomerase, and cis-trans isomerase, and temperature

Protein Modularity

The organization of proteins into domains, allowing structurally similar catalytic sites to work on different substrates via distinct specificity sites

why does protein modularity matter

helps drive evolution

Serine Protease Catalytic Triad

A functional module in enzymes like trypsin consisting of POLAR aa.- Aspartate (D102), Histidine (H57), and Serine (S195- which usually doesn't normally ionize) involved in a charge relay system

what does trypsin cut after

lys and arg

what does chymotrypsin cut after

phe, tyr, trp (large hydrophobic)