Biochemistry Exam 1

Define biochemistry.

the study of biomolecules and systems of molecular levels, often in-vitro (outside of cellular environment)

List 4 applications of biochemistry.

• medications/pharmaceuticals

• agriculture

• information about pathogens/disease

• commercial products

List the 4 most abundant elements in the human body.

• carbon

• hydrogen

• oxygen

• nitrogen

What percentage of the human body consists of H₂O?

70%

What are trace elements?

elements that are, in small amounts, required for life and used as co-factors in proteins

List 5 examples of trace elements.

• Zn

• Fe

• Mn

• Co

• Cu

What are essential ions important for?

cell-signaling and neurophysiology

List 5 examples of essential ions.

• Na⁺

• K⁺

• Mg²⁺

• Ca²⁺

• U^-

Identify the functional group.

carbonyl

Identify the functional group.

carboxyl

Identify the functional group.

amine

Identify the functional group.

sulphydryl

Order the elements from elements to ecosystem.

• elements/functional groups

• biomolecules

• macromolecules

• metabolism

• cells

• organisms

• ecosystem

Specify biomolecules v.s. macromolecules.

biomolecules: amino acids, simple sugars (ie: glucose), fatty acids, nucleotides

macromolecules: proteins, carbohydrates, lipids, DNA/RNA

Define the central dogma.

how information is transferred between DNA, RNA, and proteins

What is the process that converts DNA to RNA?

transcription

List the 5 types of RNA.

• mRNA (messenger RNA)

• rRNA (ribosomal RNA)

• tRNA (transfer RNA)

• miRNA (micro RNA)

• snRNA (small nuclear RNA)

What process is each type of RNA involved in?

• mRNA - protein synthesis (template)

• rRNA - protein synthesis

• tRNA - protein synthesis

• miRNA - gene expression, protein synthesis, and RNA regulation

• snRNA - RNA processing

What is the process that converts RNA to proteins.

translation

Define genome.

complete set of DNA of an organism

Define transcriptome.

collection of RNA products produced by DNA transcription

Define proteome.

collection of proteins produced from mRNA translation

Define metabolome.

collection of metabolites

Describe the nature and location of non-covalent interactions.

weak and take place in aqueous environments

What is the function of non-covalent interactions?

plays an important role in structure and function

List the examples of non-covalent interactions.

• hydrogen bonding

• ionic interactions

• salt bridges

• van der waals

• hydrophobic interactions

What is hydrogen bonding?

a hydrogen covalently bonded to an electronegative atom (O or N) that is then close in proximity to another electronegative atom which then undergoes hydrogen bonding

What is the purpose of hydrogen bonding of H₂O with proteins?

critical role in enzyme active site

What are ionic interactions?

interactions between oppositely charged species

What is the hydration layer that forms due to ionic interactions?

a group of water molecules that surround and stabilize an ion

Draw the hydration layers for cations and anions.

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Define crystal lattice.

an arrangement of repeating positive and negative ions held together by ionic bonding

Define salt bridges.

combinations of hydrogen bonding and ionic interactions

Define Van der Waals interactions.

attractions caused by temporary partial charges that form when electrons are unevenly distributed around atoms (they are in constant motion even in nonpolar molecules)

Explain the distance factors of Van der Waals interactions.

too far: weak attraction

optimal: van der waals interactions

too close: strong repulsion

Draw the graph corresponding to potential energy and distance of atoms involved.

What is the relationship between potential energy and stability?

the lower the potential energy, the more stable

Quantify the optimal Van der Waals distance.

slightly greater than the length of a covalent bond

Define the hydrophobic effect.

the tendency of nonpolar molecules or nonpolar regions of molecules to cluster away from water

What is the purpose of the hydrophobic effect?

energetically favorable because of reduced surface area

Identify each layer’s non-covalent interaction.

1. salt bridge (ionic interaction + hydrogen bonding)

2. hydrogen bonding

3. hydrophobic effect (C-H is nonpolar)

4. hydrogen bonding

5. salt bridge

What is Keq? What is the equation?

the equilibrium constant which tells you the relative amounts of reactants and products during equilibrium

Keq = [products]/[reactants]

What is Kw? What is the equation?

the ionization constant of water which tells you the relationship between H⁺ and OH^- in water at equilibrium

Kw = [H⁺][OH^-]

What is the standard value for Kw?

@ 25 C, Kw = 1×10^-14 M²

Explain how you determine that the pH of water is 7.

if Kw = 1×10^-14- and the concentrations of H⁺ and OH^- are the same as seen in the reaction H₂O < - > H⁺ + OH^-, then the concentration of H⁺ is sq rt of 1×10^-14 and pH is -log(concentration of H⁺)

What is the pH equation in reference to H+ concentration?

pH = -log[H⁺]

What is pH?

the concentration of hydrogen ions (H⁺)

What does pH measure?

acidity of a solution

What is the pOH equation?

pOH = -log[OH^-]

What are the equations (log version and nonlog version) that relate pH and pOH?

log: -log[H⁺] + -log[OH^-] = -log(10^-14)

non-log: pH + pOH = 14

Differentiate between acids and bases.

acids: donate protons

bases: accept protons

Describe strong acids and bases.

dissolve fully in H₂O

List an example of each.

strong acid: HCl → H⁺ + Cl^-

strong base: NaOH → Na⁺ + OH^-

Find the concentration of H⁺ and OH^- in .02 M NaOH

[OH^-] = 2×10^-2 M

[H⁺] = 5×10^-13

Calculate the concentration of H⁺ and OH^- in .02 M HCl. What is the pH?

[OH^-] = 5×10^-13

pH = 1.70

Describe solutions >7 and <7.

>7 = basic solutions

<7 = acidic solutions

Describe biological systems.

• contain weak acids and bases

• pH = 7

• can form buffer systems

Describe weak acids and bases.

no full disassociation

What is Ka? What is the equation for Ka?

the acid disassociation constant which describes the affinity of the acid for dissociable H⁺

Ka = [H⁺][A^-]/[HA]

What is the pKa equation?

pKa = -log(Ka)

Describe the relationship between Ka, pKa and strength of an acid.

high Ka, low pKa, strong acid

low Ka, high pKa, weak acid

When can we use the Henderson-Hasslebach equation?

when we want to calculate pKa of a weak acid of a particular pH if the concentrations of the weak acid (HA) and its conjugate base (A^-) are experimentally determined

What is the Henderson-Hasslebach equation?

pH = pKa + log[A-]/[HA]

What is the relationship between pH and pKa if the concentrations of the weak acid (HA) and its conjugate base (A^-) are the same?

pH = pKa because the log of 1 is 0

Draw a titration graph.

What is the buffering region?

the horizontal point of the titration curve which is where there is substantial amounts of both HA and A^-

Describe where a buffer works most effectively.

within ± 1 pKa, so if pKa is 5, the buffering region is 4-6

List the relevant percentages at points A-E.

• A: 100% H₃PO₄

• B: 50% H₃PO_4, 50% H₂PO_4^-

• C: 50% H₂PO_4^-, 50% HPO₄^2-

• D: 50% HPO₄^2- , 50% PO₄^3-

• 100% PO₄^3-

Calculate the concentration of lactic acid is pH of solution is 5.1, lactate concentration is 0.2 M and pKa of lactic acid is 3.9.

.013 M

Define proteins.

polymers/assemblies of amino acids

Briefly describe how proteins are built.

amino acids bond covalently through amide/peptide bonds to form proteins

How large is a peptide?

less than 40 amino acids in length

How many amino acids are found in nature?

20

Draw the general structure of an amino acid.

What differentiates the 20 amino acids?

the R group or side chain

Describe the chirality of amino acids.

all amino acids are chiral except for glycine because its r group is just another H

List the four categories of amino acids.

• nonpolar, hydrophobic, aliphatic

• polar, uncharged

• aromatic

• charged

  • positive

  • negative

List the 7 amino acids that are in the nonpolar, hydrophobic, aliphatic category

• glycine

• alanine

• proline

• valine

• leucine

• isoleucine

• methionine

What do newly synthesized proteins always begin with?

methionine

glycine

alanine

proline

valine

leucine

isoleucine

methionine

List the 5 amino acids in the polar, uncharged category.

• serine

• cystine

• threonine

• aspargine

• glutamine

serine

threonine

cysteine

asparagine

glutamine

What are serine and threonine often involved in?

hydrogen binding with each other and water

Where are serine and threonine often found and why?

on the surface of proteins where they can interact w/ water

What amino acids undergo phosphorylation?

serine and threonine

What enzymes perform phosphorylation?

kinases

How do kinases add a phosphate group (phosphorylation)?

by converting ATP into ADP

Where is the phosphate group added onto serine and threonine?

replaces the H on the OH which is then donated to the surrounding solution

What enzyme removes the phosphate group?

phosphatase

What does phosphatase release?

inorganic phosphate (Pi)