Biochemistry Test 1 Flashcards
Why are cells considered the fundamental unit of life?
They make up every aspect of life.
What are the three domains of living organisms?
Archaea, Bacteria, Eukarya
Plasma Membrane
thin, flexible, hydrophobic barrier around the cell; composed of lipids and proteins; contains transport proteins, receptor proteins, and membrane enzymes
Cytoplasm
internal volume enclosed by the plasma membrane; composed of cytosol
Cytosol
highly concentrated solution; contains enzymes, RNA, amino acids, nucleotides, metabolites, and inorganic ions
What are the four major classes of biomolecules and what are they used to build?
- Proteins: enzymes, structural elements, signal receptors, transporters
- Nucleic Acids: DNA and RNA; store and transmit genetic information, some RNA molecules have structural and catalytic roles in supramolecular complexes
- Polysaccharides: polymers of simple sugars; energy rich fuel stores; structural components of cell walls; extracellular recognition elements that bind to proteins on other cells
- Lipids: water insoluble hydrocarbons; structural components of membranes, energy rich fuel stores, pigments, intracellular signals
What does it mean that living organisms exist in a dynamic steady state (avoiding equilibrium) with their surroundings?
Living organisms stay in a dynamic steady state, never reaching equilibrium. The laws of Thermodynamics state that living organisms extract energy from their surroundings and use it to maintain homeostasis.
Where do cells store information needed to build proteins and carry out self-replication and self-assembly? What biomolecule is used to store the information?
DNA; Nucleic Acids
Mutation
change in nucleotide sequence
Wild Type
normal; unmutated
The textbook claims life arose by chance over long periods of time from pools of chemicals. What are some objections to this model for the origin of life?
The laboratory that the experiments were ran in are unable to replicate the real world. There are not perfectly pure chemicals in the real world and the climate is not controlled like it is in the lab.
The textbook assumes that genetic similarity is only (or best) explained by common descent. What is another possible explanation for genetic similarity?
Genetic similarity could exist due to common design instead of common descent. Common design shows that the reasoning for the similarity could be because it was the best way, not just the only one.
Why is the origin of life a “chicken or egg question”?
It is a chicken or an egg question because no one is sure what organism came first. “No chicken without the egg. No egg without the chicken”
What is meant by saying the biological molecules are interdependent?
The biological molecules are interdependent due to Causal Circularity: product of one part of the process is used in the next part of the process.
What is a hydrogen bond?
The electrostatic interaction between the oxygen on 1 H2O molecule with the hydrogen on a second H2O molecule
How many hydrogen bonds are formed in ice vs. liquid H2O?
Ice: 4 H bonds
Liquid: 3.4 H bonds
Polar
Hydrophilic, or water loving, soluble in water
Nonpolar
Hydrophobic, poorly soluble in water
Amphipathic
containing both polar and nonpolar domains
Hydrophobic
non polar, insoluble in water
Hydrophilic
polar or charged, dissolve easily in water
Van der Waals Interactions
weak intermolecular forces between molecules as a result ofc each inducing polarization in the other
Osmolarity
the product of the vann Hoff factor (i) and the solute’s molar concentration (c)
Osmosis
water movement due to osmotic pressure
Hypertonic
higher osmolarity than the cytosol
Hypotonic
lower osmolarity than the cytosol
Isotonic
equal osmolarity to the cytosol
What does it mean for water to be a solvent?
Water has the ability to dissolve multiple different salts easily
How are biological molecules stabilized by relatively weak interactions?
the most stable structure usually maximizes weak interactions
By breaking and forming bonds quickly
How are biological molecules stabilized by relatively weak interactions?
-the most stable structure usually maximizes weak interactions
What is the Keq and what is the equation for it?
- Keq is the equilibrium constant that tells what the position of equilibrium is
- products/reactants
- [H][OH]/[H2O]
What is the Kw and how can that be used to derive pH?
- Kw is the ionization constant of water
- At neutral pH the ion product of water is 1x10-14 M
- Due to the concentrations of both H+ and OH-
What are some acidic vs basic fluids?
- Acidic: gastric juice, lemon juice, coke, vinegar
- Basic: household ammonia, household bleach, NaOH
What are acidosis and alkalosis?
- Acidosis: pH of blood is below 7.4
- Alkalosis: pH of blood is above 7.4
What is an ionization constant?
-The tendency for any acid to lose a proton and form its conjugate base is defined by the equilibrium constant for the reversible reaction
What is the relationship between ionization constant and strength of an acid or base?
- The stronger the ionization constant, the stronger the acid=low pKa
- The weaker the ionization constant, the weaker the acid=high pKA
What is a buffer?
resist change of pH in a solution; consists of a weak acid and its conjugate base
How can a weak acid and its conjugate base act as a buffer?
-From the book: “Whenever H+ or OH− is added to a buffer, the result is a small change in the ratio of the relative concentrations of the weak acid and its anion and thus a small change in pH. The decrease in concentration of one component of the system is balanced exactly by an increase in the other. The sum of the buffer components does not change; only their ratio changes.”
How does the bicarbonate system maintain physiological pH?
- It works in the blood and is effective at a pH near 7.4 (normal for blood)
- H_2 CO_3⇆H^++HCO_3^-
- H_2 CO_3^- acts as a proton donor and HCO3- acts as a proton acceptor
What are the main features of amino acids?
- Carboxyl group
- Amino Group
- R group that is unique to every amino acid
- Alpha carbon with four amino acids
What are the main groupings of amino acids based upon R-group?
- Nonpolar, Aliphatic
- Aromatic
- Polar, uncharged
- Positively charged
- Negatively Charged
What R groups can act as acids, bases, or both?
-Positively charged R groups
What effect do local factors have on pKa of R-groups?
If in an acidic environment, R-groups are more likely to have a more acidic pKa or vice versa for bases
What is the isoelectric point (pI)? What does it mean when applied to amino acids? When applied to proteins?
-pI: the pH at which a solute has no net electric charge and thus does not move in an electric field
-When applied to amino acids:
pH=pI net charge is zero
pH>pI net charge is negative
pH
What is a peptide bond?
A covalent bond formed through condensation. Between the carboxylic acid group and the amine group carbons
What are the N-terminus and the C-terminus?
- N-terminus: amino terminus(front/start of amino acid)
- C-terminus: carboxy terminus (back/end of amino acid)
What is a prosthetic group in a protein?
A prosthetic group is the non-amino acid part of a conjugated protein (such as sugars, lipids, and metals.
What terms are used to describe proteins that contain other molecules (like lipids, sugars, and metals)
- Conjugate Proteins: contain permanently associated chemical components
- Lipoproteins: contain lipids
- Glycoproteins: contain sugars
- Metalloproteins: contain specific metals
