Exam 1

Molecular Hierarchy of Structure (smallest to largest)

Monomeric units → Macromolecules → Supramolecular complexes → the cell & its organelles

Unfavorable Reactions

Anabolic process

• “building” small → big things

• Requires energy (endergonic)

• Non-spontaneous +G or G>0

Favorable Reactions

Catabolic process

• “breaking” big/complex → simple units

• Releases energy (exergonic)

• Spontaneous -G or G<0

Catalyst

A compound that increases rate of chemical reaction (i.e. enzymes)

• Lower activation free energy (G)

• Do not alter G

Enzymatic catalysis offers:

1. Acceleration under mild conditions

2. High specificity

3. Possibility for regulation

Central Dogma of Biochemistry

DNA —transcription→ mRNA —translation→ unfolded hexokinase

Water

Critical determinant of structure & function of proteins, nucleic acids, and membranes

Structure of water molecule

The electronegativity of the oxygen atom allows it to serve as both a hydrogen bond donor and acceptor

Hydrogen Bonds

Strongest when the bonded molecules allow for linear bonding patterns; ideally 3 atoms involved are in a line

Hydrogen Bonding in Water

Up to 4 H-bonds per water molecule gives water its:

• high boiling point

• high melting point

• large surface tension

Ice: Water in a Solid State

Hexagonal ice contains maximal hydrogen bonds/water molecules, forcing water molecules into equidistant arrangement → ice has lower density than liquid water (ice floats)

Water: Good solvent

Charged & polar substances

• amino acids & peptides

• small alcohols

• carbohydrates

Water: Poor solvent

Nonpolar substances:

• nonpolar gases

• aromatic moieties

• aliphatic carbon-based chains

Hydrophobic solutes

Low entropy → thermodynamically unfavorable = low solubility

Hydrophobic effect

One of the main factors behind:

• protein folding

• protein-protein association

• formation of lipid membranes

• binding of steroid hormones to their receptors

Osmotic Pressure

Water moves from areas of high water concentration (low solute concentration) to areas of low water concentration (high solute concentration)

Hypotonic

Water moves in → cell swells → eventually bursting

• Occurs in low solute concentration

Hypertonic

Water moves out → cell shrinks

• Occurs in high solute concentration

K_a constant

more acidic = more dissociation

Ka = products / reactants

pK_a

Low pKa = the stronger the acid

Low pKa = increase in -logK_a

Good buffer

pH = pK_a where mixture is 50:50

Henderson-Hasselbalch Equation

pH = pK_a + log([conj. base] / [weak acid])

Amino Acid Classification

1. Nonpolar, aliphatic (non-aromatic)

2. Nonpolar, aromatic

3. Polar, uncharged

4. Polar, positively charged

5. Polar, negatively charged

Nonpolar, aliphatic R groups (7)

1. Glycine

2. Alanine

3. Proline

4. Valine

5. Leucine

6. Isoleucine

7. Methionine

Nonpolar, aromatic R groups (3)

1. Phenylalanine

2. Tyrosine

3. Tryptophan

Polar, uncharged R groups (5)

1. Serine

2. Threonine

3. Cysteine*

4. Asparagine

5. Glutamine

• These AA side chains can form hydrogen bonds

* Cysteine can form disulfide bonds

Positively charged R groups (3)

1. Lysine

2. Arginine

3. Histidine

Negatively charged R groups (2)

1. Aspartate (aspartic acid)

2. Glutamate (glutamic acid)

Zwitterion

Net neutral charge; in which a single molecule has both a positive and negative charge

Isoelectric points (pI)

Only where Zwitterion is present

• AA is least soluble in water

• AA does not migrate in electric field

pI = (pK₁ + pK₂) / 2

Cation form

low pH

Anion form

high pH

Multi-point titration curve

• If +AA → avg w/ basic form

• If -AA → avg w/ acidic form

Condensation reaction

Reaction in which a molecule of H2O is removed

Internal amino acids

No charge on carboxyl & amine groups; charges are neutralized in peptide bonds

Terminal end amino acids

Have charges; free amine and carboxyl group

• N-terminal (amino terminal end)

• C-terminal (carboxyl terminal end)

Naming Peptides

Always read/name peptides from N-terminal → C-terminal

Proteins are comprised of:

Polypeptides (covalently linked-amino acids) + possibly:

• cofactors - functional non-amino acid component

• coenzymes - organic factors

• prosthetic groups - covalently attached cofactors

A series of enzymatically catalyzed chemical reactions that are all related is referred to as a:

a) metabolic pathway

b) feedback inhibition

c) coordinated set

d) allosteric reaction

e) central dogma

Metabolic pathway

Of the following structures found inside a eukaryotic organism, which are the largest?

a) macromolecules

b) cells

c) monomeric units

d) organelles

e) supramolecular complexes

Cells

All of the following statements are true regarding catalysts except:

a) catalysts increases the rate of reaction

b) catalysts lower the activation free energy of a reaction

c) all are true

d) catalysts increase standard delta G

FALSE. catalysts increase standard delta G

All of the following are characteristics of living matter except:

a) the ability to respond to surroundings

b) the ability to create energy

c) a high degree of complexity

d) the interactions of components being coordinated

e) the capacity for self-replication

FALSE. the ability to create energy

If you place a cell in hypertonic environment, you would expect:

a) none

b) water to move into the cell

c) the cell to burst

d) no net water movement

e) water to move out of the cell

Water to move out of the cell

Two atoms that are physically involved in a hydrogen bond could be:

a) carbon & hydrogen

b) hydrogen & hydrogen

c) hydrogen & oxygen

d) oxygen & oxygen

e) nitrogen & oxygen

Hydrogen & oxygen

Ice is ___ than liquid water b/c ___

a) less dense; liquid water maintains more hydrogen bonds than frozen water

b) denser; frozen water cannot hydrogen bond

c) denser: frozen water maintains more hydrogen bonds than liquid water

d) less dense; frozen water maintains more hydrogen bonds than liquid water

e) denser; liquid water maintains more hydrogen bonds than frozen water

less dense; frozen water maintains more hydrogen bonds than liquid water

As the pH of a solution shifts away from the isoelectric point of an amino acid, the net charge on the amino acid becomes:

a) more negative

b) more positive

c) closer to neutral

d) either more negative or positive

e) stronger

either more negative or positive

The formation of a peptide bond is classified as a ____ reaction because ____ is removed in the process.

a) dehydrogenation; hydrogen

b) condensation; water

c) deoxygenation; oxygen

d) deamination; an amino group

e) decarboxylation; a carboxyl group

condensation; water

Which of the following is a technique used to isolate proteins based on isoelectric point and by size?

a) isoelectric focusing

b) nucleotide sequencing

c) 2D gel electrophoresis

d) SDS PAGE

e) affinity chromatography

2D gel electrophoresis

Which of the following statements is expected to be TRUE when a peptide consisting of six amino acids with uncharged R groups is placed in a neutral pH

a) the total net charge of the peptide is positive

b) there are six peptide bonds in the peptide

c) the amino and carboxyl group of each amino acid contributes charge

d) the total net charge of the peptide is negative

e) the amino and carboxyl termini of the polypeptide are charged

the amino and carboxyl termini of the polypeptide are charged

The general name for the class of proteins that is responsible for helping other proteins fold into proper conformation is ___ proteins.

a) passenger

b) transcription

c) chaperone

d) renaturation

e) translation

chaperone

Which of the following statements regarding protein denaturation is false?

a) Denatured proteins can be renatured when returned to physiological conditions

b) Protein denaturation can be caused by organic solvents

c) Protein denaturation can be caused by extreme pH

d) The melting temperature of a protein is defined as the temperature where the protein is 50% denatured

e) NONE

NONE - all are true

The secondary proteins structure of a ____ B sheet is relatively ___ because the hydrogen bonds holding it together are linear.

a) bent; parallel

b) antiparallel; strong

c) parallel; weak

d) parallel; strong

e) antiparallel; weak

antiparallel; strong

Proteins in their fully-functional shape found under physiological conditions are said to be in their ___ fold/structure/conformation.

a) intrinsic

b) denatured

c) native

d) natural

e) inherent

native

_____ occurs when the binding of one ligand increases the binding affinity for additional ligands in a multi-subunit protein.

a) Lock & key

b) Induced fit

c) Positive cooperativity

d) Negative cooperativity

e) Intermediate stabilization

Positive cooperativity

The binding site of a protein is complementary to a specific ligand due to which potential characteristic of the binding site?

a) its charge

b) its shape

c) all are correct

d) its hydrophobicity

e) its size

ALL are correct

A small molecule that decreases the activity of an enzyme by temporarily binding to the protein at the allosteric site is termed a(n):

a) noncompetitive inhibitor

b) competitive or noncompetitive inhibitor

c) covalent inhibitor

d) irreversible inhibitor

e) competitive inhibitor

noncompetitive inhibitor

Enzyme regulation can be based on all of the following except:

a) due to covalent modification

b) negative allosteric regulation

c) due to permanent amino acid substitution

d) positive allosteric regulation

e) reversible

due to permanent amino acid substitution

V_max for an enzyme-catalyzed reaction:

a) is determined by the amount of substrate supplied

b) is the rate observed when the concentration of substrate is equal to the K_m

c) none are correct

d) will always increase when substrate concentration increases

e) decreases in the presence of a competitive inhibitor

NONE are correct

Which of the following does NOT describe one reason why enzymes are more efficient catalysts for cells as compared to inorganic catalysts?

a) enzymes work equally well under all environmental conditions

b) enzymes maintain the capacity for regulation

c) enzymes do not get used up during chemical reactions

d) enzymes have greater reaction specificity

e) enzymes have higher reaction rates

Enzymes work equally well under all environmental conditions

All of the following are true regarding enzyme inhibition except:

a) it can be induced by very high substrate concentration

b) it can be based on allosteric regulation

c) it can be irreversible

d) it can be due to covalent modification

e) it can be reversible

It can be induced by very high substrate concentration

Glycogen and starch are similar in that they both:

a) contain only unbranched heteropolysaccharides

b) made up of solely of glucose

c) have low molecular weights

d) are used for very long-term energy storage

e) are both found in plants

made up of solely of glucose

A large polymer carbohydrate molecule that contains more than one type of monomeric units would be categorized as a:

a) linear polysaccharide

b) disaccharide

c) branched-chain polysaccharide

d) homopolysaccharide

e) heteropolysaccharide

heteropolysaccharide

When breaking down the disaccharide maltose into two glucose monosaccharides, ___ is required for the reaction to proceed.

a) carbon monoxide

b) carbon dioxide

c) hydrogen

d) oxygen

e) water

water

The main energy storage polysaccharide in plants is ____, whereas the main storage polysaccharide in animals is ____

a) glycogen; cellulose

b) glycogen; starch

c) starch; glycogen

d) cellulose; starch

e) starch; cellulose

starch; glycogen

Both glucose and fructose are considered ____ monosaccharides, however only fructose is a(n) _____.

a) triose; ketose

b) pentose; aldose

c) hexose; ketose

d) hexose; aldose

e) pentose; ketose

hexose; ketose

The primary lipid-based energy storage molecule in the human body is

a) glycolipids

b) phospholipids

c) triacylglycerols

d) sphingolipids

e) cholesterols

triacylglycerols

Which of the following characteristics would you expect to find in a fatty acid with a relatively low melting point?

a) saturated bonds

b) long hydrocarbon chain

c) cis-unsaturated bonds

d) trans-unsaturated bonds and/or saturated bonds

e) trans-unsaturated bonds

cis-unsaturated bonds

Which of the following molecules is a component of the lipid-based compounds found on the surface of red blood cells that help determine blood type groups?

a) phosphoglycerol

b) glycogen

c) cholesterol

d) sphingosine

e) glycerol

sphingosine

Of the nitrogen-rich bases found within nucleic acids in a cell there are ____ pyrimidines and ____ purines.

a) 3;3

b) 3;2

c) 2;2

d) 2;3

e) 4;4

3;2

Which of the following DNA bases is most likely to form dimers when exposed to UV light?

a) thymine or uracil

b) uracil

c) adenine

d) thymine

e) guanine

thymine

Which of the following statements are false regarding dGMP and ADP?

a) dGMP and ADP contain different pentose sugars

b) dGMP and ADP are both found in DNA

c) dGMP and ADP have a different number of phosphates attached

d) dGMPand ADP are both nucleotides

e) dGMP and ADP contain different nitrogen-rich bases

dGMP and ADP are both found in DNA

When comparing two polynucleotides, the polynucleotide with the lower melting point

a) must contain more nucleotides

b) must contain fewer nucleotides

c) either contains fewer nucleotides and/or has less G/C basepairs

d) must contain more G/C basepairs

e) must contain fewer G/C basepairs

either contains fewer nucleotides and/or has less G/C basepairs

Which statement is NOT true of naturally occurring DNA?

a) the amount of A always equals the amount of T

b) adjacent deoxyribose nucleotides on individual strands are connected by phosphodiester bonds

c) each of the bases show up in equal numbers

d) the two complementary strands run antiparallel

e) three hydrogen bonds form between G and C bases

each of the bases show up in equal numbers

A PCR reaction requires all of the following except

a) all four deoxyribonucleotides

b) a plasmid

c) target DNA

d) oligonucleotide primer(s)

e) heat-stable DNA polymerase

a plasmid

Which of the following is NOT considered one of the major steps of DNA cloning?

a) insert the recombinant vector into host cell

b) inset the gene into the vector

c) lyse the host cell to determine if recombinant DNA has been inserted correctly

d) select a suitable carrier DNA (vector)

e) cut the source DNA at the boundaries of the gene

lyse the host cell to determine if recombinant DNA has been inserted correctly