Introduction Flashcards
What is biochemistry? What fields of chemistry does it incorporate? What is it the basis of
The chemistry of living organisms (molecular level)
Organic (carbon), Inorganic (metal ions), Physical, Analytical
Basis for cellular biology and biology/medicine
What 4 elements are considered for the biochemistry of the eye?
Genetics
Nutrition
Environment
Lifestyle
What is the extracellular matrix? What does it aid in facilitating for the cell?
Large network of proteins and other molecules that surround, support, and give structure to cells (in a tissue)
Cell attachment/movement
Cell communication
What are two cell properties that can determine cell shape? (ex: RPE)
Molecular makeup and cytoskeleton
What are the monomers of protein, carbohydrate, lipid, and Nucleic acid?
Amino acid
Monosaccharide
Glycerol (fatty acid)
Nucleotide
Is water a polar or nonpolar molecule?
Polar
Does water act as a solute or solvent?
Solvent
How does water accelerate biochemical reactions?
Provides ions
Act as transport medium
What is the opposite of dehydration?
Edema (fluid retention in tissues)
Describe the structure of water. What bonds hold it together?
2 hydrogen atoms and 1 oxygen atom
Bound by covalent bonds
Describe the structure of an atom.
Nucleus- positively charged, contains protons and neutrons
Surrounded by electron shell
Overall is neutral
Describe the distribution of charge in water.
Hydrogen has 1 proton and 1 electron
Oxygen has 8 protons and 8 neutrons and 8 electrons (2 in the inner shell, 6 in the outer)
Describe the orientation of the water molecule. (Bonds, sharing of electrons). What is the bond angle?
Each hydrogen atom shares an electron pair with oxygen
Polar covalent bond
Bond angle is 104.5
What dictates the shapes of the water molecule? What property does the bend provide water with?
The shapes of the outer electron orbitals of the O-atom
Polar/ dipole
Does the water molecules have equal sharing of electrons? If not, which atom is stronger? What is formed as a result of this sharing?
Unequal sharing
The oxygen atoms attracts electrons more strongly than hydrogen
Electric dipoles are formed (two positive H, one negative O)
What kind of bonds are between water molecules? What causes these bonds? Are these bonds strong or weak?
Hydrogen bond (electrostatic attraction between oxygen of one water and hydrogen of another)
The dipole character of water causes this
Weak bonds
Can polar and non polar mix? Can polar molecules combine and why? Can nonpolar molecules combine and why?
Only polar/polar and nonpolar/nonpolar mix
Polar molecules mix because they are hydrophilic (salt, ions)
Nonpolar molecules will not mix because they are hydrophobic (fat, oil)
Does hydrogen attract positive or negative ions? What does oxygen attract?
Positive H attracts negative ions
Negative O attracts positive ions
What are amphipathic (amphiphilic) compounds? What are some examples?
Contain regions that are polar (hydrophilic) and regions that are nonpolar (hydrophobic)
Ex: proteins, pigments, phospholipids of membranes
Describe micelle formation.
The smallest hydrophobic area that form when the non-polar regions cluster together
What is an example of water as a solvent and transport medium in the eyes?
Tears prevent dryness, protect from irritants and also transport oxygen and nutrients
Different tears have different compositions
Where is the water content in the eye from highest to lowest?
Vitreous
Cornea
Sclera
According to the Bronsted-Lowry theory are which of acids and bases are donors/ acceptors?
Acids are proton (H+) donors (givers)
Bases are proton acceptors (takers)
What affects do acids have on H+ concentration and pH? Which are more biologically important: weak or strong acids?
Acids increase H+ concentration and lower the pH
Weak
What affects do bases have on H+ concentration and pH? Which are more biologically important: weak or strong bases?
Basis decrease H+ concentration and increase the pH
Weak
At what temperature is water equilibrium reached?
25 Celsius (room temp)
H2O(l) ⇄ H+(aq) + OH− (aq)
What is the pH scale? What does it measure? What is the classification of hydrogen and hydroxide ions?
Expresses the acidity or alkalinity of a solution on a logarithmic scale
Hydrogen concentration
Hydrogen is acidic
Hydroxide (OH-) id basic
How is pH calculated?
pH Calculation: pH = -log10 [H+ concentration]
What are amphoteric substances? Examples?
Can act as acids or bases
Amino Acids- basic amine group, acidic carboxyl group
What are the two types of buffers? What are their functions?
A mixture of weak acids and their salts of strong bases (or) A mixture of weak bases and their salts of strong acids.
Maintain normal pH of biological systems
Neutralize small quantities of acid or bases
What is buffer capacity?
The amount of cid or base that can be added to a buffer before changing its pH
How does blood function as a buffer? What kind of buffer system? What does it eliminate? Describe the reaction that occurs.
Bicarbonate buffer system (carbonate weak acid and bicarbonate conjugate base)
Eliminate CO2 and protons from plasma
H+ added to blood (ex: from lactic acid) bind to bicarbonate ion, increases carbonic acid, increases CO2 in blood plasma and lungs
What is normal blood pH? What condition occurs when it get too low or too high?
7.35 to 7.45
0.2 pH units lower than normal: acidosis
Increase of pH of 0.2 and more: alkalosis
What is the Henderson-Hasselbalch equation used to calculate? What does the value K represent?
PH of a buffered solution
K=equilibrium constant
What is respiratory acidosis?
Increase of carbonic acid concentration as a result of asthma or pneumonia
What are used to adjust buffers? What are two examples?
Acids and bases
NAOH and HCl
Describe carbon. Atomic number? Metallic or nonmetallic? How many electrons are available to form covalent bonds? What is this called?
6
Nonmetallic
Tetravalent- 4 electrons available, one carbon atom can form a total of 4 covalent bonds
Describe the orientation of the carbon atom. How many p, n , and e? What kind of attachment can they form? What is it called when carbon bonds to itself? What elements does carbon bind to?
6 electrons in the shell
6 protons and 6 neutrons in nucleus
Cantenation (bonds to itself)
Can form chains, branched chains, and rings
Binds to H, N, O, S
What is the basis of all biomolecules?
Carbon
What happens when carbon is combined with O and H? N and S? Phosphorus?
Sugars and fats form
Amino acids and proteins form
DNA and RNA (Nucleic acids), ATP, and chemical code carriers of life form
What are the 3 main types of strong chemical bonds?
covalent bond (electron share, single, double, triple)
ionic bond (electrostatic attraction between two oppositely charged ions, electron transfer)
metallic bond
What is the difference between polar covalent and nonpolar covalent bonds?
Nonpolar is between atoms that are the same
Polar is between atoms that are different
What are the 4 types of non covalent (weak) interactions among biomolecules in aqueous solvents?
Hydrogen bonds
Ionic interactions (attraction and repulsion)
Hydrophobic interactions
Van der Waals interaction (close proximity)
What are intermolecular forces? What are they defined by? Give and example.
Interaction between molecules (nonbonding)
Functional groups define the type and strength of interactions
Ex: Hydrogen bonds are interactions between an electronegative atom (O or N) and a hydrogen atom (H)
What is the difference between intramolecular and intermolecular forces? Which are weak, which are strong? Give 3 examples of each.
Intramolecular is within a molecule, strong, ex: covalent, ionic, metallic
Intermolecular is between 2 molecules, weak, ex: hydrogen, dipole-dipole, London dispersion
What are functional groups? What do they participate in? What atoms do they include?
Groups of atoms that contribute to the chemical characteristics of a molecule and their chemical reactions.
Participate in predictable reaction
Can contain O, N, S, and P
