Biochemistry Exam 1 - Spring 2023

Organic Chem and Digestion

Bones are made of what?

Protein, Carbohydrates, and many minerals

What are discs made of?

Water, Protein, and Carbohydrates

What are nerves made of?

Lipids, carbohydrates, protein, vitamins, & minerals

Plasma Membrane

Lipid bilayer, separates cell contents from exterior, controls movement in and out of cell

Cytoplasm

Highly organized network inside cell, liquid portion called cytosol, many biochemical processes occur here

Nucleus

Information center of cell, DNA & RNA synthesis (transcription)

Mitochondria

Produces 90% of energy for cell, has 2 membranes, has some genetic info here.

Endoplasmic Reticulum

2 Parts:

Smooth ER - Produces lipids -- think smooth like butter

Rough ER - Studded with ribosomes that make protein

Golgi Complex

Makes proteins from RER more specific and sorts them

Secretory Granule

Vesicle budded off from golgi complex, waits for extracellular signal to fuse with plasma membrane and release contents

Endosome

Vesicle formed from contents taken in by cell (endocytosis)

Lysosome

Contains digestive enzymes

Peroxisome

Contains oxidative enzymes used to protect cell

Which cell organelle is responsible for synthesizing lipids?

Smooth ER

Which organelle is the digestive system of the cell?

Lysosome

What are the 2 ways to evaluate cells?

In vitro - Experiments performed in glass

*helps determine cellular mechanisms, doesn’t tell the whole story*

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In vivo - Experiments done in whole, living organisms

*Difficult to control all variables*

99% of mass of cell is made of what?

Hydrogen, oxygen, nitrogen, and carbon.

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*the lightest elements form the strongest bonds*

What are the 4 universal classes of biomolecules?

Proteins → Made of amino acids, signaling molecules, receptors, enzymes, structure, immunity.

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Nucleic Acids → Information keepers of the cell; deoxyribonucleic acid (DNA) & ribonucleic acid (RNA)

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Lipids → Important for membranes; energy storage

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Carbohydrates → Made of sugar, important source of energy; cell recognition.

What is a functional group?

A compound’s structure and function (aka personality) is determined by the functional groups it contains.

What are the 4 types of hydrocarbons?

Alkanes - only has single bonds

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Alkenes - has a double bonded carbon

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Alkynes - has a tripple bonded carbon

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Aromatics - contains 6 carbons with alternating single and double bonds in circle.

Alcohol

Contains a hydroxyl group (OH)

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ex. Ethanol

Aldehyde

Contains a carbonyl on the *end* of the molecule

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O=C-H

Ketone

Contains a carbonyl in the *middle* of the molecule

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C=O

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Ex. Propan__one__ or acet__one__

Carboxylic Acid

Contains a carbonyl and hydroxyl at the *end* of the molecule

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O=C-OH

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Carboneal & Alcohol

Pentanoic Acid

COOH

What do you do when acids are ionized?

Replace “-ic acid” with “ate”

Ester

Acid + Alcohol

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Carbonyl and oxygen in the *middle* of the molecule

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O-C=O

What does it mean to be esterified?

Contains an ester bond

Ether

Reaction of 2 alcohols

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Oxygen connecting 2 carbon chains

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R-O-R

What is Organic vs Inorganic

Organic → Contains hydrocarbon (C & H)

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Inorganic → Does NOT contain hydrocarbon

Why is configuration and conformation important?

The 3D structure is determined by a molecule’s configuration and conformation

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The 3D structure determines how it will interact or “fit” with other biomolecules

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Configuration is the spatial arrangement of atoms based on presence of double bonds or chiral centers

Stereochemistry - Chirality

If they are not superimposable, they have a chiral center - Carbon with 4 different groups bonded to it.

Isomer Types

Structural Isomers → Same formula, different order of attachment

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Stereoisomers → Same formula & order of attachment, different 3D arrangement

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What are the two types of Stereoisomers?

Entantiomers → Nonsuperimposable mirror images

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Diastereomers → NOT mirror images

What are the two types of Diastereomers?

Geometric Isomers → Different rotation around a double bond

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Epimers → Different rotation around 1 carbon (C1)

Oxidation & Reduction

Where are oxidation reactions found in?

Metabolism

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Formation of heart disease (LDL oxidation)

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Cancer (oxidation of DNA can initiate cancer)

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Aging (oxidation can damage tissues and cause wrinkles)

Reduction Example

Dehydration

Removal of water → Water is a product!

Hydration

Addition of water across a double bond.

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Water is a reactant!

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Double bond is broken by water to form a single bond. Product is a secondary alcohol

Hydrolysis

Water is used to break a single bond.

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Water is a reactant!

Digestion of all macronutrients occurs via what?

Hydrolysis

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Carbs, lipids, and proteins must all be digested prior to absorption.

What is the formation of soap from vegetable oil called?

Saponification

What is Methylation?

Addition of a methyl group

Phosphorylation

Addition of a phosphate group

Phosphorylation

ATP to ADP

What is equilibrium?

Reaction where the forward and reverse reaction are occurring at the same rate resulting in no net change in amounts of reactants & products

What is steady state?

Rate of intake or synthesis occurs at the same rate that it is being used up

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maintaining steady state (constant blood glucose or oxygen concentration) requires constant investment in energy.

What is the first law of thermodynamics?

Energy is neither created nor destroyed → Energy is transferred within the system.

Endergonic Vs Exergonic

Endergonic = Requires energy

Delta G = positive

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Exergonic = Energy releasing

Delta G = negative

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*for a reaction to spontaneously occur, we want the sum of delta G to be negative*

What is Energy Coupling?

When two molecules are combined and their combined charges equate a charge. If that combined charge is negative, then the reaction will happen spontaneously (exergonic).

Catabolic vs Anabolic Pathways

Enzymes speed up chemical reactions.

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Catabolic = Breakers

Anabolic = Builders

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Catabolic + anabolic = metabolic

*Metabolic enzymes are highly regulated*

What is the 3 legged stool of Evidence-Based Clinical Practice (EBCP)

Clinical Expertise + Patient Values + Current Best Evidence

How do you appraise clinical trials?

See image

Measurement of Risk

Absolute Risk (AR) → True incidence of disease, also called risk difference

Subtraction - (control/100) minus (trial/100)

ex. 40/100 - 30/100 = .10 = 10%

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Relative Risk (RR) → Aka risk ratio, measure of probability of risk. Only used in cohort studies.

Division - (trial/100) divided by (control/100)

ex. 30/100 / 40/100 - .75 = 1-.75 = .25 = 25%

Interpreting RR

If RR = 1

No association, risk in exposed = risk in non-exposed

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If RR>1

Positive association (increased risk), risk in exposed > risk in non-exposed

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If RR

Interpreting OR

If OR = 1

No association, exposure is not related to disease

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If OR >1

Exposure is positively related to disease, positive association (increased risk)

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If OR

How to tell if a result is significant?

What to look for?

Confidence Interval (CI) → 95% CI says that I’m 95% sure that the actual result falls in the calculated range.

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If the CI crosses the referent number, it is not significant. It can touch or come near line, but cannot cross it. If it crosses 1, it is not significant.

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ex. (1.02-1.65) = significant

(.99 - 1.25) = NOT significant

What is Number Needed to Treat (NNT)?

How many patients need to receive the treatment for one patient to benefit. You want a small NNT.

Correlation vs Causation

Correlation

Can find an association.

NOT cause & effect

Closer correlation coefficient is to 1, the greater the association

Results from cohort studies

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Causation

Can tell true cause and effect

Only determined by randomized control trials

Water

The most abundant substance in living systems

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Human body is \~65% water by weight, typical call is 70% water

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Electronegativity can also help determine which element is more polar and less polar - called dipoles

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Biomolecules are held together by strong (covalent) interactions

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*Water’s ability to form weak (non-covalent) interactions is extremely important to function*

Although weak, there is stability in numbers.

Transient weak changes allow for dynamic interactions.

Types of Interactions

Covalent and Noncovalent

Covalent → True Bonds; determined by electronegativity difference

Noncovalent → Not true bonds, but intermolecular forces (IMF)

Hydrogen Bonds

*Not true bonds, attractive forces between compounds*

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Between H and O or N

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Important in the double helical structure of DNA and 3D folding of proteins

Electrostatic Interactions

Forces between ions (cations and anions)

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Can be attractive or repulsive

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Charged molecules dissolve readily in water

Hydrophobic Interactions

Between nonpolar compounds

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Hydrophobic molecules cluster together in a polar solution

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Called “Hydrophobic effect”

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Not because they like each other

Due to highly ordered structure of water surrounding nonpolar clusters

What drives the formation of the lipid bilayer in membranes?

Hydrophobic Interactions

What drives the folding of proteins as they associate in the interior of the protein?

Nonpolar amino acids in protein.

Van der Walls Interactions

Aka London Dispersion Forces (LDF)

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Weakest of all the attractive forces

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Interaction between 2 uncharged compounds in close proximity

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Found in all polar and nonpolar compounds

Passive (simple) Diffusion

Molecules move from high to low concentration gradient

Osmosis

Diffusion of water molecules from a higher to lower water concentration

Facilitated diffusion

Moves from high to low concentration gradient with help of transport protein

Hypotonic

Solution with a lower solute concentration

Hypertonic

Solution with a higher solute concentration

Isotonic

Equal solute concentrations

How do cells remain isotonic?

Large amounts of albumins and other proteins in blood

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Cells being able to actively pump Na+ and other ions out of cells

Cell Permeability

See image

How are weak acids measured?

By the acid dissociate constant (Ka)

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Stronger acids have a bigger Ka (more likely to dissociate)

Weaker acids have smaller Ka (less likely to dissociate)

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pKaa = -logKa

When pH = pKa, there is equal amounts of a weak acid and its conjugate base.

pKaa General Rules

pKaa is a lab determined number that is relatively constant

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pH will change substantially throughout body fluids

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If pH is below pKaa = H is still attached.

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If pH is at pKa = half attached, half lost.

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If pH is above pKaa = H is lost.

Biochemical Acids

Acids are substances that can donate H+ to lover the pH

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Volitile acids - can be turned into a gas & eliminated through lungs

*most important is carbonic acid*

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Nonvolatile acids - cannot be turned into gas, must be eliminated through kidneys

*end products of carb, protein, and lipid metabolism*

Biochemical Bases

Bases are substances that can accept a H+ to increase the pH

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Most important base in vivo = bicarbonate (HCO3-)

Primarily regulated by the kidneys

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Fruits and vegetables are also basic in nature when metaboliced.

pH Imbalances

Acidosis

Accumulation of acid or loss of base

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Alkalosis

Accumulation of base or los of acid

Buffers

Usually a weak acid and its conjugate base

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A buffer is anything that can reversibly bind protons (H+)

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Chemical solution designed to resist a change in pH despite addition of acids or bases

What is the buffer for extracellular fluid?

Bicarbonate-carbonic acid buffer system

What is the buffer for intracellular functions?

Protein buffer system (ex. hemoglobin in RBC), phosphate buffer

What is the buffer for kidneys

Phosphate buffer system and bicarbonate-carbonic acid buffer system

Chemical buffers in body fluids

Bicarbonate/carbonic acid system, phosphate buffering and proteins

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Takes seconds to minutes

Respiratory Buffers

Regulate CO2 concentrations

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Takes minutes

Kidney buffering systems

Excrete acidic or basic urine

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Takes hours to days

T/F - Acid production increases the free H+ pool, thus decreasing the pH

True

T/F - Base production pulls free H+ from the pool, thus increasing the pH

True

Proteins are amphoteric, what does that mean?

They can act as an acid or a base

Phosphate Buffers

Intracellular

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Found inside all cells

Resits changes in pH between 5.9 and 7.9

How do you buffer an excessive acid?

Base and protein

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Carboxylate and protein

How do you buffer and excessive base?

Acid and protein

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Amine and protein

Bicarbonate buffering system

Respiratory & renal pH regulation

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Respiratory buffers → control concentrations of carbon dioxide

Renal buffers → control concentration of H+ or bicarbonate

Respiratory Control of Bicarbonate Buffer System

Lungs and brain stem control CO2 concentrations by dictating breathing rate = Respiratory buffers

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Increase in CO2 signals the brain to increase breathing rate

Decrease in CO2 signals the brain to decrease breathing rate

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Too much CO2 = Respiratory Acidosis

Too little CO2 = Respiratory Alkalosis

Metabolic Acidosis

Caused by any other mechanism other than increased CO2

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Usually due to loss of bicarbonate or excessive nonvolatile acids

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major causes: Diarrhea, kidney disease, lactic acid production, ketoacidosis, alcoholism

Metabolic Alkalosis

Excessive bicarbonate production

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Can be due to fluid imbalance or other mechanisms

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Major causes: Vomiting, chronic antacid use

Gastrin

Released from G cells of antrum, duodenum, jejunum

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Distention, vagus nerve impulse, sight/smell/thought all stimulate release

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Stimulates HCl secretions, mucosal growth, pepsinogen secretion, increases gastric motility.

Secretin

Released from S cells of the duodenum, jejunum, ilium

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Releases acidic chyme in duodenum

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Effects the stomach by releasing pancreatic bicarbonate, decreases HCl secretions, opposes gastrin