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Biochem > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

• Diversity of Life

A

o Vertebrate animals, invertebrates, plants, protists, bacteria, and viruses (?)
o All life forms are composed of inert molecules that obey physical and chemical laws that describe nonliving things

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2
Q

• To be alive:

A

o Has to be a defined collection of molecules that interact with each other through chemical means

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3
Q

• 3 characteristics to distinguish living from nonliving

A

o Degree of chemical complexity and organization
• Living = high degree of both
o Ability to extract, transform, and use energy from environment to maintain structures and do work
o Ability to precisely self-replicate and self-assemble

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4
Q

• Biochemistry is

A

to explain diversity and complexity in unifying chemical terms
o All organisms are amazingly similar at the cellular and chemical level
o Biochemistry describes in molecular terms the structures, mechanisms, and chemical processes shared by all organisms

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5
Q

• Practical Applications of this knowledge

A

o Medicine
o Agriculture
o Nutrition
o Industry

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6
Q

• Though all organisms share a fundamental UNITY in biochemistry terms, there are actually

A

very few generalizations that are completely correct for every organism under every condition

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7
Q

• All known cells grouped in 2 categories

A

o Prokaryotic: no true nucleus
• Eubacteria (true)
• Archaebacteria (extremophiles)
o Eukaryotic true nucleus present
• Fungi, protists, plants, animals

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8
Q

• Evidence suggest that eukaryotes evolved from

A

the same branch that gave rise to the Archaebacteria
o We are more closely related to extreme bacteria than regular bacteria

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9
Q

• Difference between Prokaryotes and Eukaryotes

A

o Cell Size: Prokaryotes smaller than Eukaryotes
o —-Genome (+/- histones, location): Euk. Located in nucleus; Pro located in space (nucleoid region – not an organelle) inside prok.
• Euk. Have specific proteins (histone proteins) that bind to DNA
• Prok. Doesn’t have histon proteins
o Cell Division (fission vs. mitosis): Prok – fission; Euk. – Mitosis
o Membrane-bound Organelles: Prok. Do not have membrane-bound organelles; Euk. Have many types of them
o Nutrition: Prok. Obtain nutrition through absorption; Euk. Absorption and ingestion
o Energy Metabolism (+/- Mitochondria): Prok. No mitochondria to act in synthesis of ATP (do it differently); Euk. Have mitochondria
o Cytoskeleton: Pro lack substantial cytoskeleton; Euk cytoskeleton very complex made of microfilaments and microtubule network
o Intracellular Movement: must have cytoskeleton to work
• Generated by cytoskeleton
• Prok. Can’t do it but they can do diffusion movement
• Euk. Can do both

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10
Q

o —Give 2 or 3 examples of nonmembrane bound organelles and their functions

A
  • Ribosomes: site of protein synthesis
  • Microtubules
  • Microfilaments
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11
Q

o —Give 2 or 3 examples of single membrane organelles and their functions

A
  • Vacuoles
  • ER
  • Golgi
  • Lysosomes
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12
Q

o —Give 2 or 3 examples of double membrane organelles that have 2 bilayers and 4 leaflets and their functions

A
  • Mitochondria – site of ATP production
  • Nucleus – site of DNA storage in Eukaryote
  • Chloroplast
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13
Q

o Rough ER in some cases has ribosomes on membrane

A
  • ** Do not use function of ribosome
  • Function is to take newly translated protein and modify the protein
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14
Q

o A cell wall is not the same as a cell membrane

A
  • No cell wall in animals, only cell membranes
  • In plants, cell membrane is surrounded by cell wall
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15
Q

• Organelle means

A

little organ; specific defined structure that is found in cytoplasm that is going to perform a specific function

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16
Q

• C, H, O, and N account for about

A

99% of the weight of biological molecules

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17
Q

• There are 4 major groups of biological macromolecules

A

o Proteins
o Carbohydrates
o Lipids
o Nucleic Acids

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18
Q

• What was the origin of all this carbon, hydrogen, oxygen, and nitrogen?

A

o Masses of hydrogen from a particle explosion would collect to the point of clusters and the overall gravity was so great it caused a compression and a fussion (nuclear fussing of two atoms to create a new atom) reaction was started creating Helium (stars)
o Then Helium fused, etc.
o Stars burned out and collapsed and explode and scatter all the elements that were present in the star is spewed out into space which also has mass and then gravity took those elements and created rocky mass (Earth)

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19
Q

• —Polyampholytes

A

o Molecules having many acidic and basic groups (Ex. PROTEINS)

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20
Q

• —Polyelectrolytes

A

o Molecules that carry multiples of only one type of charge
• Cationic (Multiple (+) charges) OR Anionic (Multiple (-) Charges)
• Ex. NUCLEIC ACIDS

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21
Q

• —Functional Groups

A

o Functional groups are the reactive groups on molecules
o The hydrocarbon backbones of those molecules are very stable
• FIGURE 1-15, PAGE 12
• ENOL GROUP IS INCORRECT IN 5TH EDITION OF TEXTBOOK
o —KNOW ALL FUNCTIONAL GROUPS FROM FIGURE 1-15 EXCEPT ENOL GROUP
• He will draw some and ask for names or he will give names and ask us to draw or supply the missing name or structure

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22
Q

• —INTERACTION BETWEEN MOLECULES

A

Weak and Strong

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23
Q

Weak interactions

A

• Typically less than 1/20th the strength of a covalent bond
• Occur thru short-range, non-covalent forces
• A) Hydrogen Bonds (Look up)
• –N–H O–
• Always involve hydrogen
• B) van der Waals Forces
• Weak attraction between any 2 atoms due to their fluctuating (unstable) electrical charges
• van der Waals REPULSION (strong) occurs if 2 atoms are brought close together
• C) Hydrophobic Forces
• Water will force hydrophobic groups together. This lessens the disruptive effect on the H-bonded water lattice.
• Bunch together in the middle of the protein to stay away from water
• D) Ionic Bonds
• Ionic interactions occur between either fully charged or partially charged groups
• In the absence of water, ionic forces are very strong
o EX. NaCl crystal
• Ionic bonds are WEAK in aqueous solution as the charged groups are shielded from each other by water molecules
• Opposite charges attract
• Ionic bods are weakened even more by the presence of salts. Salt atoms form COUNTERIONS around the major charged groups.
• Salt ions that weaken the positive charge are counterions which shield the positive charge from interacting with other ions
• Despite weakening by water and counterions, ionic bonds are important in biological systems
o EX) Binding of substrates in active site

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24
Q

Strong Interactions

A

• A) COVALENT BONDS (only strong bond)
• Much stronger than any of the interactions previously mentioned
• Consists of a shared pair of electrons between two atoms
• Reactants are either:
o NUCLEOPHILES: electron rich
o Or ELECTROPHILES: electron deficient
• Biologically important nucleophiles typically contain O, S, or N
o Ex) R—O(-) with the oxygen being the nucleophile
• Biologically important electrophiles include:
o H+
o Metal Cations (Cu+, Zn+, etc.)
o Some types of cofactors (particularly derivatives of vitamins B1 and B6

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25
Q

o —5 Common Reactions that Occur in Cells

A
  • —He will draw one or two of the reactions and ask us to identify which reaction he has drawn
  • —He is sending an email with examples
  • Group Transfer: substrate group transferred from one molecule and linked to another
  • Oxidation-Reduction: Adds oxygen or removes hydrogen or remove electrons = Oxidation; Add hydrogen or electrons or removed oxygen = Reduction
  • Rearrangement: Not adding or subtracting anything, just rearranging atoms into a different arrangement of molecule
  • Cleavage: Chops a molecule in two
  • Condensation: Two smaller molecules condensing to make one larger one with water always being a product as well as the larger molecule made
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26
Q

o The 5 most common reactions and many others must have medium suitable for their occurrence.

A

o WATER is a suitable medium for many biologically relevant reactions
• It serves as a reaction matrix (place for reactions to happen)
• It allows for molecular mobility (allows reacting molecules to be free giving the functional groups the opportunity to get close to each other so that the reaction will happen)
• One of the two places in cells where reactions occur
• Second place is literally within the membrane bilayer
• Any reaction that is hydrophilic is in water
• Any reaction that is not soluble in water react in a hydrophobic environment which is in the membrane bilayer

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27
Q

o The physiochemical properties of water are ideal for biochemical reactions

A
  • Low freezing point
  • High boiling point
  • High heat of vaporization
  • High surface tension
  • These properties indicate a relatively high degree of attraction between water molecules and a high internal cohesion
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28
Q

o The strong intermolecular forces are due to

A

the distribution of electrons in the water molecule

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29
Q

o Each H shares a pair of electrons with the O. Strong electronegativity of O tends to

A

withdraw those electrons from H. This results in charge asymmetry (H is partially positive and O is partially negative).

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30
Q

o Water molecules are electrostatically attracted to

A

each other and hydrogen bonding occurs

31
Q

o H-bonding accounts for the cohesiveness of water

A

o Water is an excellent solvent due to its ability to form H-bonds and its dipolar character

32
Q

o Flickering Cluster

A

when water molecules lock into position with other water molecules it forms a lattice of water molecules briefly and then they tumble out of the lattice and reform with other molecules and continues on and on…

33
Q

• Substances that are capable of forming H-bonds are

A

soluble in water as are ionic compounds

34
Q

o HYDROPHOBIC:

A

found between the fatty phospholipid tails; water fearing

35
Q

o HYDROPHILIC:

A

water loving; molecules that are soluble in water

36
Q

o AMPHIPATHIC:

A

molecules that are both hydrophobic and hydrophilic; part of the molecule exhibits one and the other part exhibits the other
• Phospholipid molecules: have a head (hydrophilic) group attached to a phosphate that is attached to glycerol which is attached to fatty tails (hydrophobic)

37
Q

• Water molecules can ionize to form

A

HYDRONIUM and HYDROXYL ions
o HYDRONIUM: H3O+; carry a positive charge
o HYDROXYL: -OH; carry a negative charge
o H2O + H2O → H3O + OH-

38
Q

• Water can act as both an acid and a base

A
39
Q

• In water, hydrogen ion concentration equals

A

hydroxyl ion concentration
o [H+] = [OH-}
o [ ] means concentration of
o Hydrogen ion concentration is expressed as pH
o pH=-log[H+]
o Physiological pH ranges between 6.5 – 8.0
o Physiological pH means range of pH in cells of living things
o There can be exceptions where ranges are lower or higher (i.e. mouth – more basic: pH greater than 8; stomach – pH around 3)

40
Q

o Molar concentration:

A

pH of 0 means there’s 100 concentration; pH of 1 means there is 10-1 concentration

41
Q

o The more hydrogen ions put into something, the more

A

acidic it becomes

42
Q

o pOH

A

hydroxyl concentration; pOH 14 means 10-14 concentration

43
Q

o Acids are proton

A

Donors

44
Q

Bases are proton

A

Acceptors

45
Q

o STRONG acids and bases dissociate completely

A

• For example: HCl dissociates completely to H+ + Cl-

46
Q

o A weak acid will PARTIALLY dissociate to form its corresponding base which is called a CONJUGATE BASE

A
  • For example: HCOOH (formic acid) → HCOO- (formate) + H+
  • Formic = acid; Formate = Conjugate Base; H+ = proton
  • HA → A- + H+ (represents the reaction)

o WEAK acids and bases are most often encountered in biochemistry

47
Q

o Equilibrium constants for ionization reactions are typically called

A
48
Q

o The dissociation constant Ka for a weak acid is expressed

A

• Ka= [H+] [A-]
[HA]

49
Q

o As the value of Ka increases

A

the greater the tendency for dissociation to occur

50
Q

o The STRENGTH of weak acids is expressed as:

A

pKa = -log Ka
• The smaller the pKa value, the STRONGER the acid
• The larger the pKa value, the WEAKER the acid

51
Q

o The Henderson-Hasselbalch Equation (NO CALCULATIONS)

A
  • pH = pKa + log [A-]/[HA]
  • The pKa is the midpoint of the titration curve for the acid
  • At the midpoint of the titration of the acid pH=pKa
  • Establishes what the relationship is between pH and pKa
52
Q

o Buffers take advantage of the fact that in the pH range near the pKa, the pH will change only slightly when additional acid or base is added

A
  • Buffer region: little to no change in pH if additional acid or base is added
  • Buffers resist pH change when near pKa value
  • If you didn’t know the pKa do a titration, find the midpoint of the curve
53
Q

o Buffers are

A

mixtures of weak acids and their conjugate bases

54
Q

o Why is buffering important in cells and tissues?

A

• Buffering systems in blood stream don’t allow blood to become to acidic

55
Q

o Why is it important to buffer biochemical reactions?

A

• Every enzyme functions best within a certain pH; in the presence of a buffer, the pH is not driven down allowing maximum results

56
Q

o AMPHOLYTES are

A

molecules having both acid and basic pKa values associated with them

57
Q

• Glycine

A

• H2N –CH2 – COOH
• pKa1 = 2.34 (carboxyl group) (ionizable group)
o pKa value tells us when the ionization occurs???
• pKa2 = 9.60 ( amino group) (ionizable group)?

58
Q

• The pH where the net charge = 0 is the

A

ISOELECTRIC POINT

59
Q

The Isoelectric point does not refer to the structure, it only refers to the

A

the pH value where the net charge = 0 (can be a range)
• Normally doesn’t ask where the isoelectric point is
• Just know what it is!

60
Q

• NH3CH2COOH (pH 1.0: =1 charge) ←→ NH3CH2COO- (pH 6.0: 0 charge ←→ Zwitterion) ←→ NH2CH2COO- (pH 14.0: -1 charge)

A

• Glycine is solubilized in water, and adjusted the solution so the pH is around 1.
• ***Look at the structure and say is the pH bigger than the pKa for that ionic species?
o EX. Amino: pH is not bigger; not protonated; its going to carry 3 hydrogens giving it an overall positive charge
o EX> Carboxyl: pH is not bigger; that group is not ionized it will be fully protonated
o We take the same solution and titrate the pH up to make it less acidic until the pH is 6.0: ask the same question
• Amino: NO
• Carboxyl: YES; it ionizes and loses its hydrogen (see bold part of reaction where COOH loses the H)
o Take the same solution, add more base to it and force pH up to say 14. Ask same question
• Amino: YES; it ionizes and loses a hydrogen going from NH3 to NH2 (see underlined part of reaction)
• Carboxyl already ionized
o All three structures are still glycine, its just exhibiting a different structure
o NH3: N has positive charge and glycine overall positive charge
o NH3 + and COO- there is no overall charge
o NH2 and COO- there is a -1 charge
o Zwitterion: means no charge on the ionic species

61
Q

Deci

A

10^-1

62
Q

Centi

A

10^-2

63
Q

Milli

A

10^-3

64
Q

Micro

A

10^-6

65
Q

Nano

A

10^-9

66
Q

Pico

A

10^-12

67
Q

Femto

A

10^-15

68
Q

o Buffer Calculation

——-Example: Describe how you would prepare 500 mL of 400 mM Tris-HCl buffer pH 7.5. The molecular weight of Tris is 121.1

A

• Tris is the base in powder form; must be weighed out
• Add HCl separately
• 1) Determine what weight of Tris is needed to yield a 400 mM solution when it is dissolved in a final volume of 500 ml.
• MEMORIZE: Molarity= (wt. in grams/Molecular Weight)/ Liters
• 0.4M = (x/121.1)/(.5L/1)
o .4M = (x/121.1)(1/.5L)/ (.5L/1)(1/.5L)
o .4M = x/60.55
o .4M (60.55) = x
o x = 24.22 g of Tris needed

69
Q

• —Proportionality
o What volume of 400 mM Tris-HCl pH 7.5 and what volume of H2O are needed to prepare 200mL of 100mM Tris-HCl pH 7.5?

A

• Formula: (C1)(V1) = (C2)(V2)
• (400mM)(?) = (100mM)(200mL)
o 400x = 20,000
o X = 50 mL 400mM Tris-HCl
o 150mL water

70
Q

• —Buffer Calculations
o Example: Describe how you would prepare 500 mL of 400 mM Tris-HCl buffer pH 7.5. The molecular weight of Tris is 121.1

A

• 1. Determine what weight of Tris is needed to yield a 400 mM solution when it is dissolved in a final volume of 500 mL
• M = (Wt. in Grams/Molecular Wt.)/Liters
• .4M = (X/121.1)/(0.5L/1)
o X = 24.22 g of Tris needed
• 2. Dissolve 24.22 g of Tris in about 300 mL of water. Place solution on calibrated pH meter. Add small volumes of HCl until pH reads 7.5. Pour (transfer) solution into a graduated cylinder and add water to 500 mL.
o Hepes NaOH or KOH = common buffer in biochemistry
• Hepes is acidic because NaOH is a base
• Therefore you weigh out the Hepes and titrate NaOH to adjust pH
o Units:
• 0.4 mol/L = (x/121.1 g/mol)/(0.5L/1) = Grams

71
Q

Oxidation-Reduction

And

Rearrangement

A
72
Q

Group Transfer

A
73
Q

Cleavage and Condensation

A
74
Q
A

Biochem (11 decks)

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