Test 1 Biochemistry

Amine

Functional Group of Amine

Alcohol

Functional Group of Alcohol

Thiol

Thiol Functional Group

Ether

Ether

Aldehyde

Functional Group of Aldehyde

Ketone

Ketone Functional Group

Carboxylic acid

Functional Group of Carboxylic Acid

Ester

Ester Functional Group

Amide

Functional Group of Amide

Imine

Imine Functional Group

Disulfide

Disulfide Functional Group

Diphosphate ester

Diphosphate Ester Function Group

Phosphate ester

Phosphate Ester Function Group

Phosphate diester

Phosphate Diester Function Group

Carbon

Most abudant element in the human body (61.7%)

DNA and RNA

Two types of nucleic acids

Deoxyribonucleic acid (DNA)

consists of a double helix of polymers made up of deoxyribose, phosphate, and four bases (A, G, C, and T)

Nucleic acid

Information molecules of the cells

Carbohydrates

Fuels and informational molecules. Glucose is stored as glycogen in animals. Important signal molecules

Ribonucleic acid (RNA)

single-stranded polymer made up of ribose, phosphate, and the bases A, G, C, and U

Catalyst

a substance that promotes a chemical reaction without itself undergoing a net change

Nucleus

Site of most DNA and RNA Syntheiss. Storage of genetic information. Bound by a double membrane. Largest organelle in eukaryotic cells

Endoplasmic reticulum

Used for manufacturing, modification and transport of cellular materials. Two types: smooth ER and rough ER

Smooth ER

Site of lipid synthesis

Rough ER

site of protein synthesis via ribosomes

Lysosomes

Responsible for degrading cell components that have become obsolete
for the cell or organism. Internal pH ~5 (very acidic). Enzymes in lysosomes degrade polymers into their individual building blocks

Golgi Apparatus

Flattened vesicles of lipid/protein/sugar - Usually found near smooth ER and nucleus - Involved in protein and fat processing and trafficking to other organelles (e.g. lysosomes, plasma membranes). Distribution and shipping department for cell materials.

Mitochondria

Has a double membrane (inner and outer). Place where most oxidative energy production occurs = “powerhouse” of the cell. Forms ATP – converts oxygen and nutrients to energy. Small, typically the size of a bacterium. Depends on need for energy- muscle cells have a lot.

Cytoplasm/Cytosol

Viscous aqueous environment (not free flowing). Contains small molecules, nutrients, salts, soluble proteins. Highly organized environment 20%-30% is protein- very concentrated. A major site of cellular metabolism (e.g. glycolysis)

System

the specific part of the universe you choose to study

Surroundings

the rest of the universe

Open system

allows exchange of energy and matter

Closed system

allows only exchange of energy

Isolated system

no exchange of matter or energy

First Law of Thermodynamics

Energy is conservd

Work (w)

F x D

Exothermic process

a process that gives off heat. q is negative

endothermic process

a process that absorbs thermal energy as heat. q is positive

Enthalpy (H)

-U + PV

-the total heat content of a system, calculated as the internal energy plus the product of pressure and volume

Spontaneous processes

proceed without any outside assistance.

nonspontaneous

One that does not occur under a specific set of conditions

Entropy (S)

-measure the degree of randomness

-kbLnW

Second Law of Thermodynamics

The total entropy (a measure of disorder or randomness) of an isolated system always increases over time, and any spontaneous process is irreversible.

Spontaneous

ΔSuniv > 0

Nonspontaneous (in forward direction direction)

ΔSuniv < 0

spontaneous in the forward direction

∆G < 0

nonspontaneous in the forward direction

∆G > 0

Noncovalent

Does not involve sharing of electrons, and are individually much weaker than a single covalent bond

Ionic interactions

Electrostatic interactions between permanently charged or polar species

Van der Waals forces

Weak, noncovalent interactions between all atoms, regardless of polarity; individually weak but collectively important for stabilizing macromolecular structures such as proteins.

Dipole interactions

Noncovalent interactions between polar molecules, where the partially positive (δ⁺) region of one molecule interacts with the partially negative (δ⁻) region of another. Greater dipole moments produce stronger dipole-dipole interactions.

Hydrogen bond

A specialized type of dipole interaction involving H, typically between two electronegative atoms—usually O or N—where one is bonded to H. Strongest when the bonded molecules are oriented to maximize electrostatic interaction (ideally the three atoms involved are in a line). Relatively weak and fleeting.

Hydrogen Bond Donor

Specialized dipole interaction involving H and usually O or N. O–H and N–H can donate; C–H typically cannot.

Hydrogen Bond Acceptor

Interacts with the H involved in the hydrogen bond. Usually O or N.

Solvation shell

A layer of water molecules surrounding a charged or polar solute, formed by favorable interactions between water’s partial charges and the solute.

Hydrophobic effects

The association or folding of non- polar molecules in the aqueous solution. Does not arise because of some attractive direct force between two non-polar molecules. Molecules are often hydrocarbons

Amphiphiles

Molecules that have both hydrophilic and hydrophobic portions

Proton jumping

Rapid proton movement through water caused by hydronium ions switching partners.

Equilibrium expression for water ionization

Keq​=[H2​O][H+]/[OH−]​

Keq

equillibrium constant

expression for ion product of water

Kw​=[H+][OH−]

Kw

Ion product of water ([H+][OH−]=1.0×10^-14)

pH equation

pH=−log[H+]

pH + pOH

=14 at 25°C

Acid (Bronsted-Lowry)

Donates H⁺

Base (Bronsted-Lowry)

Accepts H⁺

Strong acids

Completely dissociate

Weak acids

dissociate only partially in water.

Ka

dissociation constant for acid base reaction

pKa

logarithmic way to express Ka: =-log Ka

Buffers

Resist change in pH when small amounts of acid or base is added. A mixture that contains significant amounts of both weak acid and its conjugate base

Buffering region

the flat zone of a titration curve

pH=pKa

50% of the weak acid (HA) is ionized

pH<pKa

majority of the weak acid is in unionized status

Nucleotide

Energy currency (ATP), drives protein synthesis (GTP), metabolic carriers (UDP → sugars, CDP → lipids, NAD/CoA → ADP intermediates), second messengers (cAMP/cGMP), and building blocks of DNA/RNA.

DNA

stores and transmits biological information to the next generation.

rRNA

Component of ribosomes.

mRNA

Intermediate in protein synthesis.

tRNA

Adapter molecule that translates information in mRNA into a specific amino acid sequence

ncRNA

Has a wide variety of functions, such as forming the spliceosome.

Ribose

deoxyribose

Purine bases

Adenine (A) and Guanine (G)

Pyrimidine

Cytosine (C), Thymine (T), Uracil (U)

N-Glycosidic Bond

Connects the pentose sugar to the nitrogenous base. The bond forms at N1 in pyrimidines and N9 in purines.

Adenine