BIOCHEM MIDTERM 1
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UNIT 1 FOUNDATIONS OF BIOCHEMISTRY INTENDED LEARNING OUTCOMES
Explain the interdisciplinary and multidisciplinary nature of biochemistry, and its role to the medical profession;
Describe how molecules that make up life are organized in the cell;
Describe the different properties of the 4 major classes of biomolecules, and how these properties reflect their fitness to living conditions;
Explain the functions of the different organelles of the cells;
Explain similarity and difference between organic chemistry and biochemistry;
Illustrate structure of common organic compounds using expanded, condensed, and skeletal structures;
Categorize different organic compounds based on functional groups;
Explain the importance of functional groups in predicting the physical properties of organic compound;
Explain how the physical properties of water affect its role as the major biochemical solvent;
Classify substances as acids and bases based on the Bronsted-Lowry definition;
Relate the chemistry of buffers to the buffering capacity of the blood.
UNIT OUTLINE
Topic Page
I. The Nature of Biochemistry 5
II. Cellular Foundation
A. The Molecular Organization of Life 6
B. The Biomolecules
C. The Cell
III. Chemical Foundation
A. The Origin of Organic Chemistry
B. Chemical Bonding 14
C. Bonding in Organic Compounds
D. Classification of Organic Compounds Based on Functional Groups
IV. Water As Biochemical Solvent
A. Physical Properties of Water 27
B. Acids, Bases, and Buffers
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Supramolecular Complexes
Interactions among macromolecules
Inorganic precursors (18-64 daltons): Carbon dioxide, Water, Ammonia, Nitrogen(N,), Nitrate(NO,")
Supramolecular complexes are formed by various members of macromolecules
Examples of supramolecular assemblies: enzyme complexes, ribosomes, chromosomes, cytoskeletal elements
Structural integrity maintained by noncovalent forces
Noncovalent forces include hydrogen bonds, ionic attractions, van der Waals forces, and hydrophobic interactions
Organelles
Entities present in the cell
Membrane bounded cellular inclusions
Dedicated to important cellular tasks
Examples: Nucleus, Mitochondria, Chloroplasts, Endoplasmic reticulum, Golgi apparatus, Vacuole
Cells
Basic unit of life
Smallest entities capable of displaying attributes associated with living states
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Biomolecules
Specialized organic compounds in living systems
Classified into 4 major divisions: carbohydrate, lipids, proteins, and nucleic acids
Structurally composed of smaller units called building blocks
Building blocks: monosaccharides, fatty acids and glycerol, amino acids, nucleotides
Carbohydrates: main source of energy, structural roles
Lipids: component of cell membrane, energy storage, palatability to food
Proteins: involved in cell recognition, catalysis, transport, and structural functions
Nucleic Acids: responsible for protein synthesis, heredity
Elemental Composition of Biomolecules
Biomolecules are carbon compoundsPage 5
Biomolecules are informational
Biomolecules have a sense to their structure
Sequential order of building blocks can specify information
Polysaccharides are often composed of repeated monosaccharides
Proteins and nucleic acids have unique sequences
Biomolecules have characteristic three-dimensional architecture
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Proteins have intricate complexity
Proteins can turn, fold, and coil in three dimensions
Establish specific, highly ordered architecture
Biomolecules are involved in series of chemical reactions for energy
Energy transformations occur through sequential series of reactions
Reactions release or store useful energy
Cellular metabolism
Example: Production of energy from glucose
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Two major types of cells: prokaryotic and eukaryotic
Prokaryotic cells have no well-defined nucleus
Prokaryotes are mostly bacteria
Eukaryotic cells have a nucleus and organelles
Eukaryotes are animals, plants, fungi, and protists
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Nucleus:
Enclosed in a double membrane
Communicates with the surrounding cytosol via nuclear pores
Contains nuclear chromatin that contains the organism's genome
Genes within the chromatin are made of DNA
DNA stores the organism's entire encoded genetic information
During cell division, chromatin condenses into chromosomes
Nucleolus:
Produces ribosomes
Ribosomes move out of the nucleus and take positions on the rough endoplasmic reticulum
Ribosomes are critical in protein synthesis
Cytosol:
"Soup" within which all other cell organelles reside
Most of the cellular metabolism occurs in the cytosol
Full of proteins that control cell metabolism
Cytoplasm:
Collective term for cytosol and organelles suspended within the cytosol
Centrosome:
Area in the cell where microtubules are produced
Plant and animal cell centrosomes play similar roles in cell division
Plant cell centrosome is simpler and does not have centrioles
During animal cell division, centrioles replicate and the centrosome divides
Result is two centrosomes, each with its own pair of centrioles
Centrosomes move to opposite ends of the nucleus and microtubules grow into a "spindle"
Spindle is responsible for separating replicated chromosomes into daughter cells
Centriole (animal cells only):
Ring of nine groups of fused microtubules
Part of the cytoskeleton
Arranged perpendicular to each other in the complete animal cell centrosome
Golgi Apparatus:
Membrane-bound structure with a single membrane
Stack of membrane-bound vesicles
Important in packaging macromolecules for transport
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Secretory Vesicle
Cell secretions (e.g. hormones, neurotransmitters) are packaged in secretory vesicles at the Golgi apparatus
The secretory vesicles are then transported to the cell surface for release
Cell Membrane
Every cell is enclosed in a membrane, a double layer of phospholipids (lipid bilayer)
The membrane acts as a protective barrier to the uncontrolled flow of water
The membrane is made more complex by the presence of numerous proteins
Proteins include receptors for odors, tastes, and hormones, as well as pores responsible for the controlled entry and exit of ions
Mitochondria
Mitochondria provide the energy a cell needs
They are the power centers of the cell
Mitochondria are membrane-bound organelles with a double membrane
The inner membrane is highly convoluted, forming folds (cristae) that greatly increase the surface area
Food (sugar) is combined with oxygen on the cristae to produce ATP - the primary energy source for the cell
Vacuole
A vacuole is a membrane-bound sac that plays roles in intracellular digestion and the release of cellular waste products
Vacuoles are generally small in animal cells and large in plant cells
In plant cells, vacuoles store nutrients and waste products, help increase cell size during growth, and regulate turgor pressure
Cell Wall (plant cells only)
Plant cells have a rigid, protective cell wall made up of polysaccharides (usually cellulose)
The cell wall provides and maintains the shape of plant cells and serves as a protective barrier
Turgor pressure in plant cells is responsible for the crispness of fresh vegetables
Chloroplast (plant cells only)
Chloroplasts contain chlorophyll responsible for the plant's green color and the ability to absorb energy from sunlight
Chloroplasts convert water and carbon dioxide into sugars through photosynthesis
Ch
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Synthesis and transport of proteins
Ribosomes are packets of RNA and protein
Play a crucial role in protein synthesis
Comprised of a large subunit and a small subunit
Messenger RNA moves along the ribosome
Transfer RNA adds amino acid molecules to the protein chain
Role of cytoskeleton
Helps maintain cell shape
Important for cell motility
Organized network of three primary protein filaments
Microtubules, actin filaments, and intermediate fibers
Chemical foundations
Organic chemistry deals with carbon compounds
Biomolecules are made up of carbon compounds
Focus on aspects of organic chemistry relevant to living cells
Origin of organic chemistry
Originally thought organic compounds were different from inorganic compounds
Vitalism theory believed only living things could create organic compounds
Friedrich Wohler disproved vitalism theory by synthesizing urea in the lab
Organic compounds can be created from inorganic substances
Organic compounds contain carbon, regardless of origin
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Chemical bonding
Chemical bonds formed when atoms are held together
Atoms form bonds to achieve stability
Valence electrons are involved in chemical bonds
Atoms become stable when valence shell contains 8 electrons (Octet Rule)
Ionic bond
Results from interaction of metals with nonmetals
Metal atom gives off valence electrons, forming a cation
Non-metal atom accepts the electrons, forming an anion
Chemical bond formed by electrostatic attraction between the ions
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Types of chemical bonds
Ionic bond
Formed between ions with different charges
Example: Sodium chloride (NaCl)
Sodium (metal) gives off one electron, chlorine (non-metal) gains that electron
Formation of sodium ion (cation) and chloride ion (anion)
Attraction between sodium and chloride ions is ionic bond
Compounds with ionic bonds are usually crystalline with high melting point
Mostly soluble in water and dissociates into ions
Covalent bond
Formed between nonmetals
Chemical bond formed when non-metal atoms share electrons
Example: Hydrogen molecule (H2)
Electron clouds of hydrogen atoms overlap, forming a covalent bond
Substances with covalent bonds are usually gases, liquids, or solids with low melting points
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Electronegativity and Bond Polarity
Electronegativity is the measure of an atom's attraction for shared electrons in a bond
Electronegativity values range from 0 to 4
Trends in electronegativity:
Increases across the row of the periodic table (excluding noble gases)
Decreases down a column of the periodic table
Electronegativity values indicate whether electrons in a bond are equally shared or unequally shared
Identical atoms bonded together have equally shared electrons and a nonpolar bond
Different atoms with similar electronegativity values have nonpolar bonds
Bonding between atoms of different electronegativity values results in unequal sharing of electrons and a polar bond
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The direction of polarity in a bond is indicated by an arrow
Head of the arrow points toward the more electronegative element
Tail of the arrow, with a perpendicular line drawn through it, is positioned at the less electronegative element
Alternatively, symbols o+ and 5- indicate unequal sharing of electron density
5- means partial negative charge (more electronegative)
+ means partial positive charge (less electronegative)
A polar bond has an electronegativity difference between two atoms greater than or equal to 0.5 units
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Bonding in Organic Compounds
Major elements in organic compounds: carbon, hydrogen, oxygen, nitrogen, sulfur, and halogens
These elements form covalent bonds with carbon
Each non-metal should have 8 bonds around it based on the Octet Rule
Table showing the total number of bonds and their distribution for each element
Sample Problems
Problem 1: Is the given structure valid?
Problem 2: Which of the two given structural formulas is valid?
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Structure analysis of the given examples
Invalid structure due to carbon having only 3 bonds instead of 4
Valid structure with each element satisfying the required number of bonds
Invalid structure with oxygen having 3 bonds instead of 2
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Classification of Organic Compounds Based on Functional Groups
Over 50 million known organic molecules
Organic compounds can be categorized into families based on structural features
Members of a given family often exhibit comparable chemical behavior
Functional Groups
Most organic molecules have C - C and C - H single bonds
Structural features used to classify organic compounds into families
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C - C and C - H single bonds are strong, nonpolar, and inert
Heteroatoms (O, N, S, halogens) and multiple bonds (double or triple) confer reactivity on organic molecules
These structural features are called functional groups
Functional groups have predictable reactivity and properties
C-C and C-H bonds form the carbon backbone to which functional groups are bonded
Functional groups can help distinguish one organic molecule from another
Functional groups behave the same regardless of the size of the carbon skeleton
The carbon and hydrogen portion of the molecule is often abbreviated as R
Examples:
Ethane has no functional group
Only C-C and C-H single bonds
Ethanol has a hydroxyl group (-OH)
Two carbons and five hydrogens in the carbon backbone
Properties of ethanol are different from ethane
Cholesterol also has a hydroxyl group
Similar chemical properties to ethanol
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Hydrocarbons are organic compounds containing only carbon and hydrogen
Hydrocarbons are subdivided into different subgroups based on the type of carbon-carbon bond
Alkanes
No multiple bonds between carbon atoms (single bonds only)
Example: ethane
Carbon atoms involved in single bonds with each other
Can also form rings known as cycloalkanes
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Alkynes
Hydrocarbons containing at least one carbon-carbon triple bond
Indicated by the -yne ending in the family name and specific compound names
Functional group of alkynes
Simplest alkyne is ethyne (acetylene)
Ethyne is used as fuel for welding torch
Arene
Special class of hydrocarbon containing a special type of ring
Most common example is benzene ring
Compounds containing such rings are known as aromatic compounds
Benzene has different properties from alkenes
Benzene allows for the movement of carbon-carbon bond electrons around the ring
Compounds with benzene ring can be functional group and known as phenyl
Compounds containing C - Z single bond
Z can be o, N, or S
Creates a polar bond with partial positive charge on carbon atom
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Alkyl Halides
Compounds where a halogen replaces a hydrogen from a hydrocarbon
Generic formula R - X where X = halogen
Examples: ethyl chloride, 2-fluoropropane
Chlorofluorocarbons (CFCs) are alkyl halides and damage the ozone layer
Alcohols
Compounds containing a hydroxyl group (-OH) attached to a saturated carbon
Generic formula R - OH
Examples: methanol, ethanol
Alcohols can be classified as primary, secondary, or tertiary based on degree of substitution
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Tertiary amine
Nitrogen is attached to 3 organic groups
Example: trimethylamine (H3C - N CH3 CH3)
Compounds containing C = 0 group
Carbonyl group is a polar group
Aldehydes and Ketones
Carbonyl group of aldehyde is bonded to one hydrogen atom and one carbon atom
Carbonyl group of ketone is bonded to 2 carbon atoms
Examples of aldehydes: acetaldehyde, benzaldehyde
Examples of ketones: acetone, ethyl methyl ketone
Carboxylic acids, Esters, and Amides
Carboxyl group is a supra-functional group
Compounds containing carboxyl groups are known as carboxylic acids
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Esters and amides are derivatives of carboxylic acids
Ester is formed when -OH of carboxyl is replaced with an ether-like group (-O - R')
Amide is formed when -OH of carboxyl is replaced with an amino group (-NH2)
Examples of carboxylic acids: acetic acid, butyric acid, benzoic acid
Examples of esters: ethyl acetate, ethyl butyrate
Examples of amides: formamide, acetamide
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Water as biochemical solvent
Living organisms are mostly made up of water
Water accounts for 60-95% of living cells
Water acts as transport medium, helps maintain temperature, and acts as solvent in biochemical reactions
Water balance in the body
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Electronegativity difference in C-H bond in hydrocarbons is small, making the bond nonpolar
Water molecules attract each other through hydrogen bonding
Hydrogen bond is a non-covalent interaction formed between a hydrogen donor and a hydrogen acceptor
Water can act as both a hydrogen donor and a hydrogen acceptor
A water molecule has the potential to form 4 hydrogen bonds
Hydrogen bonding in water is cooperative
Hydrogen bonding in water leads to strong intermolecular attractions and unique properties
High boiling point, melting point, heat of vaporization, and surface tension
Water can dissolve organic biomolecules through hydrogen bonding
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Ionic and polar substances dissolve in water
Water molecules align themselves around ionic substances through ion-dipole interaction
Polar substances can be hydrated by water through dipole-dipole interaction
Polar substances may also participate in hydrogen bonding, enhancing solubility
Non-polar substances do not dissolve in water
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Non-polar substances and water mix together separate into layers
Non-polar substances cannot form dipole-dipole interaction or hydrogen bond with water
Non-polar substances can interact with each other through hydrophobic interaction
Water molecules tend to interact with other water molecules rather than with non-polar molecules
Water molecules exclude non-polar substances forcing them to associate with each other
Hydrophobic effect is critical for folding of proteins and self-assembly of biological membranes
Amphipathic molecules form micelles and bilayers
Amphipathic molecules are both hydrophilic and hydrophobic
Amphipathic molecules have a non-polar hydrocarbon tail and an ionic or polar end
Amphipathic molecules dispersed in water result in the formation of structurally ordered aggregates
Aggregates can be in the form of micelles or bilayers
Micelles are globules of amphipathic substances with hydrophilic heads at the surface and non-polar tails in the center
Bilayers are sheets in which the polar groups face the aqueous phase
Both micelles and bilayers are stabilized by the hydrophobic effect
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Acids, Bases, and Buffers
Biological molecules have functional groups that act as acids or bases
Bronsted-Lowry definition: acid donates a proton, base accepts a proton
Acid-base reaction: HA (acid) + B (base) -> A (conjugate base) + BH+ (conjugate acid)
Specific examples
Acetic acid (CH3COOH) donates H+ to water, making it an acid
Water accepts H+ and is therefore a base
Acetate is the conjugate base of acetic acid
Hydronium ion (H3O+) is the conjugate acid of water
Ammonia (NH3) accepts H+ from water, making it a base
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Buffers are used to resist pH changes
Buffers maintain pH even after the addition of small amounts of acid or base
Buffer system is composed of a weak acid and its conjugate base
Examples of buffer mixtures: acetic acid and acetate, formic acid and formate, carbonic acid and bicarbonate, phosphoric acid and dihydrogen phosphate
Buffers work by reacting with added acid or base
If acid is added, it reacts with the conjugate base to form the weak acid
If base is added, it reacts with the weak acid to form water and the conjugate base
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Bicarbonate Buffer System is important for maintaining pH in living systems
Blood pH range is between 7.35-7.45
Acidosis occurs when blood pH is low, alkalosis occurs when blood pH is high
Bicarbonate Buffer System equation: CO2 + H2O -> H2CO3 -> H+ + HCO3
Key organs involved in the buffer system are the lungs and the kidneys
Buffer system responds to changes in H+ concentration by changing the partial pressure of CO2
In acidosis, concentration of H2CO3 increases and CO2 is expired through exhalation
In alkalosis, concentration of HCO3 increases and CO2 is converted to H2CO3 in the capillaries of the lungs
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Acidosis and alkalosis can be classified as respiratory or metabolic
Respiratory acidosis occurs when there is an increase in CO2, resulting in more H+ and lower blood pH
Respiratory alkalosis occurs when there is a decrease in CO2, resulting in lower H+ and higher blood pH
Metabolic acidosis occurs when there is a decrease in HCO3, resulting in more H+ and lower blood pH
Metabolic alkalosis occurs when there is an increase in HCO3, resulting in lower H+ and higher blood pH