BSC 300: Ch. 1-3

Key terms from chapter 1-3

What are the 4 main types of biological noncovalent interactions?

1. Ionic (electrostatic interactions)

2. Hydrogen bonds (nonbonding electron hydrogen attraction)

3. Van der Waals (transiet dipole interactions)

4. Hydrophobic effect interactions (reduces contact with water)

T/F: it takes the same amount of energy to break a bond as what is released when the bond is formed

T

Are polar molecules hydrophillic or hydrophobic?

Hydrophillic

Are nonpolar molecutes hydrophillic or hydrophobic?

Hydrophobic

What is electronegativity?

The ability of an atom to attract electrons towards itself forming a polar covalent bond

What are functional groups?

Groups of atoms giving organic molecules different characteristics and properties

Noncovalent bonds are responsible for the _____ interaction between cellular macromolecules

Transient

Within noncovalent bonds, the multipoint contacts additive provides what 3 specificity in molecular interactions?

1. Selectivity in biological associations

2. Conformation of macromolecules

3. Formation of complexes between macromolecules

Within noncovalent bonds, the multipoint contacts additive produces _____ structures

Stable

Ionic bonds are attractions between charges atoms and are _____ in the presence of water, and may be _____ within large biological molecules

Weakened, significant

Hydrogen bonds occur when _____ bound hydrogen has a partial positive charge and attracts electrons of a second atom

Covalently

Hydrogen bonds determine the structure and properties of _____

Water

Hydrophobic attractions between nonpolar molecules are due to transient dipole formation. What type of noncovalent bonding is this an example of?

Van der Waals interactions

_____ interactions occur when nonpolar molecules associate and minimize their exposure to polar molecules

Hydrophobic

Proteins are polymers of _____ and form a diverse group of macromolecules

Amino acids

Nucleic adics are polymers of _____ that store and transmit genetic information

Nucleotides

_____ include simple sugars and sugar polymers

Carbohydrates

Lipids are a diverse group of _____ molecules

Nonpolar

_____ are made of glycerol linked by 3 ester bonds the 3 _____

Fats, fatty acids

What reaction resuls from the polymerization of 2 monomers by forming a covalent bond?

Dehydration (condensation)

_____ reactions are responsible for the breakdown or cleavage of a covalent bond by incorperating water

Hydrolysis

Amino acids only differ in their _____

Side chains (R group)

Key Term: Amino acids are linked together by _____ bonds into a _____ chain

Peptide, polypeptide

R groups may be what 3 things?

1. Polar charged

2. Polar uncharged

3. Nonpolar

Polar charged amino acids contain R groups that act as stronger organic _____ or _____

Acids, bases

Polar uncharged amino acids are _____ acidic or basic and are _____ charged at pH 7

Weakly, not

Amino acids with nonpolar R groups are _____

Hydrophobic

Amino acids with nonpolar R groups generally lack _____ & _____

O, N

Amino acids with nonpolar R groups _____ interact with water or form electrostatic bonds

Cannot

What are the 3 unique amino acids?

1. Glycine

2. Proline

3. Cysteine

What makes the amino acid glycine unique?

W

What makes the amino acid proline unique?

What makes the amino acid cysteine unique?

Name the purines (2 ring structure) in DNA and RNA

Adenine and guanine

Name the pyrimidines (single ring structure) in DNA and RNA

Cytosine and thymine in DNA

Cytosine and uracil in RNA

Nucleosides consist of

Nucleostides consist of

What is the difference between nucleosides and nucleotides?

In the classic double-stranded DNA complex A is linked to T by _____ hydrogen bonds

2

In the classic double-stranded DNA complex G is linked to C by _____ hydrogen bonds

3

Of the 2, is AT-rich or GC-rich DNA more stable?

GC-rich is more stable due to the 3 hydrogen bonds

What is the general chemical formula of a charbohydrate?

(CH₂O)_n

_____ serve as energy storage molecules or stuctural molecules

Carbohydrates

Glycosidic bonds are —___—___—___— links between sugars

— C — O — C —

In carbohydrates _____ are used as a source of readily available energy

Disaccharides

In carbohydrates _____ are found bound to a cells surface proteins and lipids and may be used for cell recognition

Oligosaccharides

What are the 3 major types of lipids we will be focusing on?

1. Fatty acids

   1. Saturated (lack C=C double bonds)

   2. Unsaturated (have 1 or more C=C double bonds that give the chain kinks)

2. Sterols (4 ring structure)

3. Phospholipids (amphipathic)

K_eq = Product / Reactant

when…

Forward and reverse rates are equal

Cell linked reactions are at a _____ not equilibrium

Steady state

Dissociation constant (K_d) is a measure of…

Noncovalent interactions

Cytoplasm has a pH of…

7.2 - 7.4

Lysosome has a pH of…

4.5

At equilibrium, what is the equation for molar concentrations (M)?

k₁[A][B] = k₂[C][D]

When K_eq = 1, the reaction is at…

Equilibrium

If cells biochemical reactions are at equilibrium what happens?

Cell death

T/F: Macromolecules can have distinct binding sites for multiple ligands

T

Large macromolecules can have multiple distinct independent or interdependent binding cites

Changes in pH affect the _____ state and _____ of proteins

Ion, function

Kinetic energy: Thermal

The flow of energy from a region of higher temperature to lower temperature

T/F: Thermal energy is a major player in cellular activity

F

Kinetic energy: Radiant

Kinetic energy of photons, or waves of light

ex. Photosynthesis

Kinetic energy: Mechanical

Major form of kinetic energy in biology

ex. Reorganization of the cytoskeleton

Kinetic energy: Electric

Energy of moving electrons or charged particles

ex. Transport of charged ions across the cell membrane; electrically active neurons

Potential energy: Chemical

Potential energy: Concentration gradients

Potential energy: Electric

Transduction

The conversion of energy from one form to another

What is the first law of thermodynamics?

The law of conservation of energy

What is the second law of thermodynamics?

Events in the universe tend to proceed from a state of higher energy to a state of lower energy towards equilibrium

What is entropy?

A measure of randomness or disorder

The second law of thermodynamics is only absolute in a _____ (no external energy)

Closed system

The first and second laws of thermodynamics can be expressed mathmatically as…

ΔH = ΔG + TΔS

If ΔG = 0 the reaction is…

At equilibrium

If ΔG < 0 the reaction is _____ and enegetically favorable

Exergonic

If ΔG > 0 the reacion is _____ and energentically unfavorable

Endergonic

What equation do we use to tell if a reaction will be spontaneous?

ΔG = ΔH - TΔS

If ΔG is negative, the reaction will be energetically _____

Favorable

If ΔG is positive, the reaction will be energetically _____

Unfavorable

Is this an exergonic or endergonic reaction?

Exergonic

Is this an exergonic or endergonic reaction?

Endergonic

Reactions with K’_eq > 1 have _____ ΔG and are _____ reaction favorable

Negative, forward

Reactions with K’_eq < 1 have _____ ΔG and are _____ reaction favorable

Positive, reverse

Reactions with K’_eq = 1 have _____ ΔG and are _____ reaction favorable

0, equally (equilibrium)

Catalysis does NOT influence the _____ of a reaction

Thermodynamics

Key Concept: Cellular reactions with +ΔG occur because of what 3 things?

1. The ratio of reactants to products is kept low enough to drive the forward reaction

2. Input of energy; coupled reactions

3. The use of activated carrier molecules

In coupled reactions, the product of the 1^st reaction becomes…

The reactant or substrate for a 2^nd reaction