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Lecture 1 & 2 Flashcards

1
Q

Current biochemical generalization regarding living things:

1) Life requires ____, viruses are _____
2) Biochemical reactions require ____
3) The information of life is transmitted in the ____
4) The Central Dogma of life information flow is ___

A

1) Life requires LIFE, viruses are NOT LIVING
2) Biochemical reactions require CATALYSTS
3) The information of life is transmitted in the GENOME
4) The Central Dogma of life information flow is DNA -> RNA -> PROTEIN

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2
Q

Gibb’s Free Energy formula:

A

∆G = ∆H - T∆S

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3
Q

What is Gibb’s Free Energy defined in terms of?

A

defined in terms of Enthalpy (heat) and Entropy (disorder) at a given temperature (kelvin)

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4
Q

∆G<0 =

A

∆G<0 = spontaneous, reaction releases energy

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5
Q

∆G>0 =

A

∆G>0 = non spontaneous, reaction absorbs energy

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6
Q

∆G=0 =

A

∆G=0 = equilibrium, no energy change

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7
Q

What does spontaneous say about the rate?

A

NOTHING

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8
Q

If ∆H is - and ∆S is +, what will the reaction look like?

A

the reaction is both enthalpically favored (exothermic) and entropically favored

it is spontaneous (exergonic) at all temperatures

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9
Q

If ∆H is - and ∆S is -, what will the reaction look like?

A

the reaction is enthalpically favored BUT entropically opposed

it is spontaneous only at temperatures below T = ∆H/∆S

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10
Q

If ∆H is + and ∆S is +, what will the reaction look like?

A

the reaction is enthalpically opposed (endothermic) BUT entropically favored

it is spontaneous only at temperatures above T = ∆H/∆S

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11
Q

If ∆H is + and ∆S is -, what will the reaction look like?

A

the reaction is both enthalpically and entropically opposed

it is non spontaneous (endergonic) at all temperatures

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12
Q

Some of the most important reactions in biochemistry are:

A

non spontaneous, they require energy

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13
Q

How do you make non spontaneous reactions go?

A
  • couple the non spontaneous reaction with a spontaneous reaction that produces more energy than needed to make the non spontaneous reaction go
  • ATP the cell’s energy source reaction releases 30.5 kg/mol
  • energy release from ATP
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14
Q

In the reaction of converting ADP back to ATP, the reaction is powered by what?

A

powered by a proton gradient where the body is never at equilibrium

(at equilibrium, there are no gradients)

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15
Q

What happens at equilibrium?

A

reactions near equilibrium can operate in either direction

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16
Q

What is Le Chatelier’s Principle?

A

a chemical system, once at equilibrium will respond to a stress or change in the environment to reduce the stress

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17
Q

Exothermic

A

products have lower energy

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18
Q

Endothermic

A

products have higher energy

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19
Q

At equilibrium-

A

-the concentrations of all species remain constant over time
-both forward and reverse reactions occur BUT at the SAME RATE

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20
Q

For something to be at equilibrium, what is the rule of products and reactants and their rate?

A

there is no rule that products = reactants BUT rather that the rate of the forward and reverse reactions are equal

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21
Q

We are carbon-based life forms, what are some things that contain a majority of carbon atoms?

A

proteins
nucleic acids
carbohydrates
lipids

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22
Q

PROTEINS

Atoms:
Building Blocks:
Forms polymers? type of blood:
Intra-molecular interactions:
Functional role in cells:

A

Atoms: C, H, N, O, S

Building Blocks: Amino Acids

Forms polymers? type of bond: Yes, Peptide bonds

Intra-molecular interactions: Covalent (S-S), H-bonds, charge based, van Der Waal’s

Functional role in cells: Enzymes, structural proteins, sensors, receptors, etc.

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23
Q

NUCLEIC ACID

Atoms:
Building Blocks:
Forms polymers? type of blood:
Intra-molecular interactions:
Functional role in cells:

A

Atoms: C, H, O, P, N

Building Blocks: Nucleotides

Forms polymers? type of blond: Yes, phosphodiester bonds

Intra-molecular interactions: H-bonds, stacking interactions

Functional role in cells: Storage of genetic information, enzymes, ribosomes

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24
Q

CARBOHYDRATES

Atoms:
Building Blocks:
Forms polymers? type of blood:
Intra-molecular interactions:
Functional role in cells:

A

Atoms: C, H, O, N

Building Blocks: Simple sugars

Forms polymers? type of blond: Yes, glycosidic linkages - of various types

Intra-molecular interactions: H-bonds

Functional role in cells: storage of energy, structural, recognition, interactions

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25
Lipids Atoms: Building Blocks: Forms polymers? type of blood: Intra-molecular interactions: Functional role in cells:
Atoms: C, H, O Building Blocks: Fatty acids, glycerol Forms polymers? type of blood: No, forms various di-, tri-, glycerides Intra-molecular interactions: Van Der Waal's Functional role in cells: Membranes, signaling, energy storage, small molecule hormones
26
What are the four important classes of biomolecules?
1) proteins (amazing diverse polymers - hemoglobin 2) carbohydrates - glucose 3) lipids 4) nucleic acids
27
DNA provides what for proteins?
DNA provides the protein template
28
What are proteins a series of and what can they do?
Proteins are a series of LINKED AMINO ACIDS that can FOLD into functional structures
29
Lysozyme
-enzyme -part of the innate immune system -protects infection from Gram-positive bacteria (Salmonella, E. coli, and Pseudomonas) -found in tears
30
What are the four important carbohydrates?
glucose ribose deoxyribose cellulose
31
Which important carbohydrate is this?
Glucose
32
Which important carbohydrate is this?
Ribose
33
Which important carbohydrate is this?
Deoxyribose
34
Which important carbohydrate is this?
Cellulose
35
What is the blue, and what is the yellow part of this lipid?
Blue: polar head, hydrophilic Yellow: non polar tail, hydrophobic
36
What do membrane proteins do?
interact with the environment
37
How do membrane proteins interact with the environment?
ion/water/small molecule transport -cell signaling, cytokines, hormones, receptors
38
A DNA strand has direction, the 5' and 3' ends have what different groups?
5' end: terminal phosphate group 3' end: terminal hydroxyl group
39
What cells contain - no nucleus -intracellular membrane -usually unicellular
prokaryotic cells
40
What kind of model organisms do biochemists focus on for their studies?
prokaryote cells (escherichia coli)
41
Examples of eukaryote cells
humans mice rats yeast arabidopsis drosophila (fruit fly)
42
Which cell contains membrane-bound organelles?
eukaryotic cell
43
Examples of membrane-bound organelles in a eukaryotic cell:
nucleus ER Golgi mitochondria lysosomes peroxisomes chloroplasts
44
Cells are crowded. What do crowding effects do to diffusion rates?
crowding effects REDUCE diffusion rates in the cell
45
Proteins are gene products created by what?
Proteins are gene products created by the ribosome by translating mRNA
46
What are considered the "cell's workhorses"?
Proteins
47
A large, linear molecule made up of repeating units.
Polymer
48
Proteins are amazing _____.
Proteins are amazing HETEROPOLYMERS (different amino acids)
49
Proteins are made of how many amino acids?
20 amino acids
50
Mulder derived the chemical formula of an animal substance (protein). He used ___ ____ to produce _____ the building blocks of proteins (we know them today as amino acids).
Mulder derived the chemical formula of an animal substance (protein). He used ACID HYDROLYSIS to produce "GRUNDSTOFF" the building blocks of proteins (we know them today as amino acids).
51
What are proteins made by and what does it contain?
made by the ribosome which contains amino acids and RNA
52
What are proteins a chain of?
amino acids corresponding the gene's base-pair sequence
53
What does the sequence of amino acids in proteins determine?
determines how the proteins are folded and their function
54
The peptide bond is a ___ structure.
The peptide bond is a PLANAR STRUCTURE.
55
Why are these two structures planar structures?
-the N and carbonyl C are sp2 hybridized -both can resonate yielding the planar structure -peptide plan spans the chain between two alpha carbons
56
What are the six atoms in the peptide plane?
Cx3 - carbon N - nitrogen O -oxygen H - hydrogen
57
What does the function of a protein depend on?
depends on its structure
58
Where is the peptide plane?
-look for sp2 atoms -look for N and C double bonded to O
59
What does the sequence of amino acids direct?
directs the peptide chain to spontaneously 'fold' into the "native-lowest energy" structure of the protein
60
What are the mysterious forces that drive protein folding?
1) electrostatic (charge interactions) 2) hydrophobic effects - oil and water don't mix
61
What are the electrostatic (charge interactions)?
-salt bridges (pH dependent) & ionic bonds -hydrogen bonds -van der Walls interactions
62
How is a hydrogen bond formed?
by sharing a hydrogen between two dipoles (due to an asymmetric distribution of electrons between atoms with different electronegativities (H
63
Are hydrogen bonds pH dependent?
NO not pH dependent
64
Hydrogen donor
the atom with a higher affinity for, and is covalently attached to the H -has a partial positive charge
65
What are common donor atoms?
O N S ALMOST NEVER C
66
Hydrogen acceptor
an atom that contributes a lone pair of electrons to the H- bond -has a partial negative charge
67
What is formed by sharing a hydrogen UNEQUALLY between two dipoles?
hydrogen bond
68
What are dipoles?
molecular dipoles are due to an asymmetric distribution of atoms with different electronegativities (H
69
Rules of hydrogen bond strength:
1) the H-A distance (closer =stronger) 2) the D-H-----A angle (180 degrees is the strongest)
70
van der Waals interaction
1-the electron shell represents the electron density function of the atom -random fluctuations of the electrons can produce a dipole
71
Induced Dipole in a VDW Contact
the orbitals of two molecules will establish resonance at close distances and behave as weak dipoles
72
Non-covalent interactions contributions to folding and stability? (what are the 3 and their kJ/mol)
1) Salt Bridge -20 to -40 kJ/mol 2) H-Bond -2 to -20 kJ/mol 3) VDW -0.4 to -4 kJ/mol
73
How does water interact with proteins?
via Dipole-charge interactions
74
When water is interacting with proteins, what does it compete with?
water competes for intrapeptide H bonds and salt bridges (desolvation of polar or charged groups costs energy)
75
The energetic cost of desolvation implies what?
implies that- intrapeptide H-bonds and Salt Bridges contribute LITTLE to the stability of a folded protein
76
Why is delta G of peptide H-bond/salt bridge formation close to zero?
1) competition with water 2) often the intrapeptide bond geometry is less than ideal
77
What must be done first to form an inter peptide H-bond?
you must first break water H-bonds
78
The hydrophobic effect
Liquid water averages: 3.4 H-bonds Ice averages : 4 H-bonds
79
Ice H-bonds are stronger despite the loss in entropy. How does the "hydrophobic effect explain this?
Stronger H-bonds because water is a great DONOR when it is being 'protonated' (increases partial +) Stronger H-bonds because water is a great acceptor when it is being 'deprotonated' (increases partial -)
80
What is surface tension due to?
an ice-like ordering of water at the surface
81
Solvation of hydrophobics
-unfavorable due to the increased order (lower entropy) of the water molecules
82
Solvation energy
-proportional to the volume of the clathrate (large clathrate = more order)
83
What is the hydrophobic effect (explained)?
-driven by the entropy of water -is proportional to the decrease in surface area of the ordered water
84
How do non-covalent interactions contribute to folding and stability?
H-bonds and salt-bridges provide specificity, and are a necessary consequence of folding they have a SMALL contribution to stability
85
What drives protein folding?
electrostatic (charge interactions) -salt bridges & ionic bonds (20-40 kJ/mol -H-bonds (2-20 kJ/mol) -van der Walls interactions (0.4-4 kJ/mol) -hydrophobic effects (3-10 kJ/mol)
86
Why is a micelle our first model for protein folding and structure?
1) hydrophobic interior and hydrophilic surface 2) it is self-forming
87
How do amino acids pack together?
pack together like puzzle pieces to fill the interior of a protein
88
What are the structures of micelles and soluble proteins due to?
due to the hydrophobic effects
89
What is the pH scale?
14 = pH + pOH
90
What is the Henderson-Hasselbalch Equation?
91
What is a buffer?
a weak acid or base, used to maintain a specific pH by absorbing or releasing protons according to the Le Chatelier's principle
92
What determines the buffering range?
pKa
93
What does pKa tell us?
tells how strongly the acid/base wants the proton
94
at pH below the pKa what happens?
the group will be PROTONATED (HA) -KEEPS THE PROTON
95
at pH above the pKa what happens?
the group will be DEPROTONATED (A-) -LOSES PROTON
96
What is the pKa of water?
15.7
97
What does the pKa of water really mean?
water wants to REALLY REALLY keep its proton (pH is below pKa) -water rarely dissociates to donate a proton (SUPER RARE)
98
What does pKa predict?
predicts the leaving group
99
How does pKa predict the leaving group?
leaving group will be the conjugate acid with the LOWEST pKa
100
What do you need to know about pKa?
-determines buffering range -tells how strongly the acid/base wants the proton -predicts what the leaving group will be - AA ionizable groups will be positive if pHpKa
101
How do we maintain our physiological pH?
the pH of the blood is regulated primarily by the CO2 -carbonic acid - bicarbonate buffer system
102
What is the pH of Human blood plasma?
about 7.4
103
What is the CO2-carbonic acid-bicarbonate buffer system?
at low pH (tissue) excess acid (H30+) in the body is neutralized by HCO3- -equilibrium shifts left at high pH (lungs) the excess base (OH-) reacts with the carbonic acid (H2CO3) -equilibrium shifts right
104
How effective is the CO2-bicarbonate buffering system?
highly effective

BCMB (6 decks)

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