biochem packets

what type of molecule has both hydrophilic and hydrophobic parts?

amphipathic

List the FIVE fundamental concepts of biochemistry

1. Is observational & experimental science

2. All branches life from common ancestor

3. Is interdisciplinary science

4. life obeys laws of physics

5. life obeys the laws of chemistry

palmitic acid

phosphatidyl serine

cholesterol

triacylglycerol

lipids

cellulose

glucose

sucrose

fructose

starch

polysaccharide

carbohydrates

insulin

thrombin

trypsin

myoglobin

urease

antibodies

proteins

ethanol, urea, sodium ion

other

linkage for amino acid

peptide

linkage for carbohydrates

glycosidic

linkage for nucleotides

phosphodiester

Nucleus

Contains DNA; DNA is wrapped around proteins

nuclear envelope

surrounds the nucleus

nucleolus

Where rRNA is synthesized and ribosome subunits are assembled

cytoplasm

Cytosol & organelles; provides a medium for chemical reactions and supports organelles

cytoskeleton

structural framework of the cell; provides structure, shape, movement, and intracellular transport

smooth endoplasmic reticulum

makes lipids, detoxification, storage of calcium ions

lysosome

contains digestive enzymes

perixosomes

houses enzymes involved in oxidation reaction *not part of endomembrane system

golgi apparatus (cis=receiving, trans=opposite)

Modifies, sorts, and packages proteins and lipids from the ER for secretion or delivery to organelles

1. lysosome

1. organelle recycling facility; digestion, waste removal

vacuole (both in animal and plant cells)

Storage organelle

the endomembrane system does not include _______ , _______ , or _______ but does include _____ ________

mitochondria

chloroplasts

peroxisomes

plasma membrane

types of noncovalent interactions weakest to strongest

1. Charge–charge (salt bridges in proteins)

2. Charge–dipole (ions interacting with polar molecules, e.g., ions in water)

3. Hydrogen bond (H with O/N) ***strong

4. Dipole–dipole (polar compounds in water)

5. Dipole–induced dipole (polar induces temporary dipole in nonpolar molecule)

6. Charge–induced dipole (ion induces temporary dipole in nonpolar molecule)

7. Dispersion / London forces (weak, nonpolar interactions)

4 types of intermolecular forces

• 1) London dispersion forces (Van der Waals forces)

  • Weakest, present in all molecules, caused by temporary fluctuations in electron density.

• 2) Dipole–dipole interactions

  • Between polar molecules with permanent dipoles.

• 3) Hydrogen bonds

• 4) Ion–dipole interactions

  • Between an ion and a polar molecule

H bond donor vs H bond acceptor

• Donor = gives H

• Acceptor = receives H (through lone pair)

Explain where the polarity of water comes from

O more EN than H→ pulls electron density closer to O than H

Maximum number of hydrogen bonds one water molecule can have with neighboring water molecules:

4

Electrolytes dissolve readily in water because of:

• Ion–dipole interactions between the ions and polar water molecules

Ionic compounds can be readily dissolved in water because the high dielectric constant of water screens and decreases the:

Electrostatic force between oppositely charged ions

micelles

spherical aggregates of amphipathic molecules

how does soap remove grease from surfaces:

• form micelles around hydrophobic grease/oil

• The hydrophobic tails interact with grease, and the hydrophilic heads interact with water, allowing the grease to be solubilized and washed away

The ________________ effect describes the tendency for hydrophobic molecules to aggregate by excluding water:

hydrophobic

The average charge on an amino acid below its pI will be:

positive

the net charge on an amino acid at its isoelectric point (pI) is:

Zero (neutral)

Attractions of oppositely charged functional groups in proteins are called:

Salt bridges (ionic interactions)

Many proteins interact with DNA at physiological pH because:

DNA is negatively charged (phosphate backbone), and many proteins have positively charged amino acid side chains (lysine, arginine) that bind via electrostatic interactions

adenine

thymine

uracil

cytosine

guanine

nucleotides

Charge on each repeating unit in DNA or RNA:

negative

Ions that neutralize this charge inside the cell:

Positively charged ions (cations) such as Na⁺, K⁺, Mg²⁺.

Complementary base pairing in dsDNA determines the __________ helix formation from two

____________________ strands

double, antiparallel

• Purines (A, G) are larger, ____-ring structures.

• Pyrimidines (T, C) are smaller, ____-ring structures.

• Pairing a purine with a pyrimidine keeps the helix diameter uniform, essential for the stable double helix.

2, 1

Which of the following does NOT describe the secondary structure of DNA as proposed by

Watson and Crick?

A) The two strands of the double helix are stabilized by hydrogen-bonding between A and T and

between G and C.

B) The two strands of the double helix run in opposite directions.

C) The phosphate deoxyribose backbones of the helix are on the outside.

D) The base pairs are stacked on one other with their planes at 180o to the helix axis

D

Consecutive base pairs in a dsDNA interact by ____________________________ interactions.

The nonpolar faces of the stacked bases are in the ___________ of the double helix,

_________________ from the surrounding aqueous environment, contributing to the overall

stability of the DNA structure. This is known as the hydrophobic effect.

• Base stacking (van der Waals)

• interior (core)

• shielded

Single-stranded RNA molecules can have extensive regions of ____________ ____________ _____________

Intramolecular base pairing

The melting point, Tm, of a dsDNA is the

temperature at which the mixture contains ____%

_______ and _____% dsDNA.

The Tm is an important parameter in setting up the

temperature sequence of ____________

50, 50, PCR

A DNA vs B DNA

Nucleic acids absorb strongly at UV range because their _____________ _____________ _____________ have _____________ double bonds.

aromatic nitrogenous bases, conjugated

The concentration of a dsDNA sample can be

calculated using the absorbance measured at

_______ nm, and knowing that an

A260 of 1.000 equals 50 μg/mL

260 nm

for various dsDNA fragments the Tm ________________ with increasing G C content.

Explain why

increases

• More GC pairs → stronger hydrogen bonding and base stacking interactions → higher thermal stability → higher Tm.

list and describe the weak interactions that hold the dsDNA helix together

• Hydrogen bonds between complementary base pairs (A–T: 2 H-bonds, G–C: 3 H-bonds)

• Base stacking / van der Waals interactions between consecutive bases

• Hydrophobic effect: Nonpolar faces of bases are buried inside the helix, away from water

• Electrostatic interactions: Phosphate backbone interacts with cations (Na⁺, Mg²⁺) to neutralize negative charges

The phosphodiester bonds in DNA are linked between the:

3′ hydroxyl (–OH) of one deoxyribose to the 5′ phosphate (–PO₄) of the next deoxyribose.

Expression of genetic information involves first ___________ then ___________ .

transcription, translation

DNA replication inside the cell creates an __________ copy of its DNA. The process involves DNA

helicase to unwind the ____________ helix, creating a _________________ fork. Then, DNA

___________________________ (enzyme) builds 2 new DNA strands using the original strands as

_____________________

exact, double, replication, polymerase, templates

PCR is used for:

—> purpose of each component

amplifying a given sequence of dna