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 (strongest → weakest)

1) h bond

2) charge charge

3) dipole dipole

4) charge induced dipole

5) dipole induced

6) van der waal

4 types of intermolecular forces

Weakest→ strongest

• 1) London dispersion forces (Van der Waals)

  • due to temporary polarity in the molecules because of unequal electron distribution

• 2) Dipole–dipole interactions

  • Due to permanent polarity in the molecules due to their structure

• 3) Hydrogen bonds

  • Very strong dipole-dipole attraction; H is attached to N, O

• 4) Ion–dipole interactions

  • Between an ion and a polar molecule ( water )

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)

Salt bridge

attractions of oppositely charged functional groups

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% ssDNA

50%

PCR

A DNA vs B DNA

A DNA: open in center (present in low humidity, double stranded RNA, DNA-RNA hybrids), base pairs on side

B DNA: closed in center, twist angle = 36 degrees

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

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

1) H bonds (a-t=2, g-c=3)

2) induced dipole: between consecutive bases

3) hydrophobic effect: bases release solvation water molecules as they stack

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

isoelectric point

pH where amino acid has no charge

draw ATP vs DATP

primary, secondary, tertiary structure

primary: linear nucleotide sequence of a polynucleotide chain

secondary: α-helix and β-sheet formed by hydrogen bonds

tertiary: Overall 3D shape of a single protein chain

quaternary: Assembly of multiple protein chains into one functional unit

concentration of a dsDNA sample can be calculated knowing that

A260 of 1.000 equals 50 micrograms/mL

B DNA is a _______-handed helix made of ___(#) ________ strands that are held together by __________ bonds in the _____-__________ and __________-__________ base pairs.

One helical turn of B-DNA has _____ (#) base pairs that are ______ within the helix and are almost __________ to the helical axis

The diameter of the dsDNA cylinder is _____ Angstrom

The distance between consecutive base pairs is ______ Angstrom

There is a twist angle of ___ degrees between stacked base pairs

the phosphate groups are located on the _______ of the dsDNA

right-handed, 2, polynucleotide, hydrogen, A–T, G–C

10, stacked, perpendicular

20 Å, 3.4 Å, 36 degrees

outside

restriction endonucleases are useful in gene cloning because they ____ DNA at ____ and ____ sequences. Ligases _______ dna molecules by forming __________ bonds between the dna fragments

cut, specific, palindromic

join, phosphodiester

PCR is a laboratory technique used for _____________ a given sequence of _____________

amplifying, DNA

Explain the role for each component of a PCR:

___________ ___________: template containing the target sequence to be amplified

___________: single-stranded DNA sequences; provide a starting point for DNA synthesis

___________: building blocks (A, T, G, C) that DNA polymerase uses to synthesize new DNA strands

___________: maintain optimal pH and salt conditions

___________ ___________: heat-stable DNA polymerase that synthesizes new DNA strands by adding dNTPs to primers

___________: cofactor required for DNA polymerase activity; stabilizes the dNTPs and the enzyme-DNA complex

genomic DNA

primers

dNTPs

buffer

Taq Polymerase

Mg²+

acetic acid

formic acid

6 strong acids

1. HCl

2. HBr

3. HI

4. HNO₃

5. H₂SO₄

6. HClO₄

8 strong bases

1. LiOH

2. NaOH

3. KOH

4. RbOH

5. CsOH

6. Ca(OH)₂

7. Sr(OH)₂

8. Ba(OH)₂

Ka equation

[H+][A-]/HA