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BIOB 260 > Study Guide > Flashcards

Study Guide Flashcards

not gonna lose my mind 💪

1
Q

When were cells first discovered/who discovered them?

A

1660s by
Robert Hooke and Anton van
Leeuwenhoek .

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2
Q

Cell Theory

A

All organisms are made of cells and cells come from pre-existing cells (life reproduces)

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3
Q

Spontaneous Generation

A

Cells randomly appear, not from reproduction/previous cells

KNOW: Pasteur’s broth experiment

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4
Q

Pasteur’s Experiment

A

Swan-neck vs. Boat neck

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5
Q

Basics of DNA

A

Double stranded helix
4 Nucleotide bases
Phosphate backbone
Carries information for reproduction/growth

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6
Q

Central Dogma

A

DNA ————> mRNA ————-> Protein
Transcription Translation

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7
Q

What are the building blocks of life?

A
  1. Amino Acids
  2. Nucleotides
  3. Lipids
  4. Saccharides
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8
Q

ATP
~Function~

A

The energy currency of the cell

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9
Q

ATP
~Structure~

A

Three phosphate groups, Ribose, and Adenine

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10
Q

Evolution

A

change in characteristics of a population over time

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11
Q

Natural Selection

A

process that drives evolution
Heritable traits that are more desirable (better survival or reproduction) are passed onto offspring.

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12
Q

Viruses

A
  1. DNA/RNA - Double or single stranded
  2. No plasma membrane
  3. No transcription : even if a viral polymerase is present, transcription of viral genomes
    requires nucleotides provided by host
    cells
  4. No translation
  5. No metabolic capabilities
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13
Q

Requirements for life

A
  1. CELLS
  2. REPRODUCTION
  3. INFORMATION
  4. ENERGY
  5. EVOLUTION
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14
Q

96% of atoms in the Human Body

A

Hydrogen (H), Carbon (C), Nitrogen (N), and Oxygen (O)

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15
Q

99% of atoms in the Human Body

A

H,C,N,O, Phosphorous (P) and Sulfur (S)

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16
Q

Valance Electrons to know

A

H- 1
C- 4
N- 5
O- 6
P- 5
S- 6

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17
Q

Electronegativity

A

O>N>S ≅C ≅H ≅P

A measure of an atom’s ability to attract shared electrons to itself.
generally : increases from left to right across a period and decreases down a group

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18
Q

Hydrophilic

A

Will/wants to bond with water
Ionic or Polar

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19
Q

Hydrophobic

A

Will not bond with water
Nonpolar
Likely : Carbon Chains

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20
Q

Solution

A

homogeneous mixture of a solute and
solvent

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21
Q

Aqueous Solution

A

solute dissolved in water

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22
Q

Why is water a good solvent?

A

Polar - Hydrogen bonding
Hydrophilic

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23
Q

Why is water bent?

A

Two lone pairs

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24
Q

Cohesion

A

attraction between like molecules

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25
Q

Surface tension

A

cohesive force at surface of liquid

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26
Q

Adhesion

A

attraction between unlike molecules
Usually between a liquid and solid surface

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27
Q

Is Liquid water or Ice denser?

A

Liquid, less hydrogen bonding more packed

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28
Q

Specific Heat

A

amount of energy to raise temperature 1 degrees C.
* H-bonds must break before heat is transferred
* This gives water a high capacity to absorb energy (heat).

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29
Q

Heat of Vaporization

A

amount of energy to change 1 gram of H2O
from liquid to gas.
* Water has a high heat of vaporization because of hydrogen bonds.

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30
Q

Molarity

A

Moles Solute/ Liters Solution

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31
Q

Acid

A

Donates Proton (H+)
Below pH 7

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32
Q

Base

A

Accepts Proton (H+)
Above pH 7

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33
Q

Buffers

A

Minimize changes in pH
Ex: weak acids
Exist most functionally within their pKa

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34
Q

pKa

A

Weak acid and conjugate base are in
equal amounts

pH below pKa -> more H+
pH above pKa -> less H+

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35
Q

Is water a good buffer

A

No.
concentration of weak acid/conjugate base is too small

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36
Q

1st Law of Thermodynamics

A

Energy is neither created nor destroyed

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37
Q

Potential Energy

A

Amount of stored energy (hasn’t happened)

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38
Q

Kinetic Energy

A

Movement (as happening)

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39
Q

Types of Kinetic Energy

A
  1. Mechanical Energy
  2. Heat Energy
  3. Sound Energy
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40
Q

Energy

A

capacity to do work or supply heat

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41
Q

2nd Law of Thermodynamics

A

Entropy (disorder) increases during a spontaneous reaction
Can increase in the surroundings when heat, light, or sound are given off

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42
Q

What makes a reaction
spontaneous?

A
  1. If the products have lower
    potential energy than the reactants.
  2. Products have more entropy
    (microstates) than reactants.
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43
Q

Amino Group

A

NH3

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44
Q

Carboxyl

A

CHO2

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45
Q

Carbonyl

A

CHO, CO

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46
Q

Hydroxyl

A

OH

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47
Q

Phosphate

A

PO4

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48
Q

Sulfhydryl

A

SH

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49
Q

Monomers

A

Single Building Blocks that make up polymers

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50
Q

Function of Proteins

A
  1. Enzymes
  2. Structure (cell skeleton)
  3. Movement
  4. Signaling
  5. Transport
  6. Defense
  7. Central dogma
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51
Q

Amino Acids

A

(20)
Building blocks of proteins

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52
Q

Types of Amino Acid Groups

A

Amino group
Alpha carbon
Carboxyl
Hydrogen
R-Group (where they differ)

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53
Q

Basic Structure of Amino Acids

A

NH3 + C2 + H20 + OH + Rgroup

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54
Q

Protonated
(Structure + Definition)

A

H+ included

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55
Q

Deprotonated
(Structure + Definition)

A

No H+

56
Q

pKa of Carboxylic Acid

A

1.8-2.8

57
Q

pKa of Amino Groups

A

8.7-10.7

Below pKa-> NH3+
Above pKa-> NH2

58
Q

Polar Uncharged Amino Acids

A

Serine, Tyrosine

Threonine, Asparagine, Glutamine

59
Q

Polar Charged Amino Acids

A

Aspartate, Lysine

Glutamate, Arginine, Histidine

60
Q

Non-Polar Amino Acids

A

Glycine, Alanine, Valine, Cysteine

Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline

61
Q

Serine Structure

A
62
Q

Tyrosine Structure

A
63
Q

Aspartate Structure

A
64
Q

Lysine Structure

A
65
Q

Glycine Structure

A
66
Q

Alanine Structure

A
67
Q

Valine Structure

A
68
Q

Cysteine Structure

A
69
Q

Peptide Bonds

A

Between N and C, double bond characteristics
Backbone joining amino acids
Chains are flexible bc of oscillating single bonds on each side

70
Q

N and C terminus

A

N-Terminus : Amino Group
C- Terminus : Carboxyl Group

71
Q

Amino Acid’s Work

A

Active Site of an enzyme - Catalytic Residues
Mechanisms of a reaction
Histidine is the most common amino acid in active sites !!

72
Q

Active Site (Definition)

A

Pocket where substrate binds on enzyme
Substrate

73
Q

Types of Amino Acid Substitutes

A

Conservative + Radical

74
Q

Conservative Substitutes

A

Amino acids would have similar properties
Ex : Non-polar substituted with a non-polar of similar size

75
Q

Radical Substitutes

A

Amino acids would have very different
properties
Ex : Non-polar substituted with polar

76
Q

Protein Structure Hierarchy

A
  1. Primary - sequence of amino acids
  2. Secondary - alpha (α) helices or beta (β) pleated sheets
  3. Tertiary - 3D folding of the enzyme
  4. Quaternary - Multiple proteins working together
77
Q

Protein Structure Bond Hierarchy

A
  1. Primary - peptide bond
  2. Secondary - hydrogen bond
  3. Tertiary - hydrogen bond, hydrophobic interactions, Van der waals, Covalent, Ionic
  4. multiple polypeptides working together
78
Q

Subunits

A

sugars, amino acids, nucleotides

79
Q

Macromolecules

A

Globular proteins and RNA

80
Q

Macromolecular Assemblies

A

Ribosomes

81
Q

Ribosomes

A

Organelle
>50 proteins
Nucleic acids + sugars

82
Q

Folded protein energy

A

Less potential energy

83
Q

Denatured protein

A

loses secondary + tertiary structure

h bonds break, s-s (disulfide) bonds bridge

84
Q

Molecular Chaperones

A

Heat Shock Proteins
Large quantities as a result
Help proteins fold
bind hydrophobic regions

85
Q

Prion Disease

(Definition, Propagation, resistance)

A

Infectious proteins
Beta pleated

*Normal prions = PrP c
Function unknown
Alpha helix *

Propagate :
inherited, ingested, spontaneous

Resistant :
Heat, detergents

86
Q

Type of Bond holding Amino Acids

A

Peptide bonds

87
Q

Type of Bond holding Nucleotides

A

Phosphodiester Linkage

88
Q

Break Amino Acids into “Single Units”

A

R groups, Carboxyl, Hydrogen, Amine

89
Q

Break Nucleotides into “Single Units”

A

5 Carbon Sugar, Phosphate backbone, nitrogenous base

90
Q

Synthesis Direction of Amino Acids

A

N –> C

91
Q

Synthesis Direction of Nucleotides

A

5’ –> 3’

92
Q

Function of Carbohydrates

A

Energy !
Support cell wall/exoskeleton structure
Form more complex structures

93
Q

Function of “on” “off”

A

Enzymes/Proteins are dynamic / flexible
* They can be turned “on” or “off” via small modifications:
Add/delete a phosphate group (from ATP)
* Interact/bind with ions (Ca+2) other proteins, molecules
Allows cells to regulate and change with the cellular environment
send/respond to internal and external cues

94
Q

Diffusion

A

Constant random motion
* Spontaneous movement of ions and molecules
* Disrupts original position

95
Q

Concentration Gradient

A

“ladder” created by difference in solute concentrations
example of disruptive diffusion

96
Q

Net movement

A

rom high-concentration regions to low-concentration regions
Example of disruptive diffusion

97
Q

Concentration Gradients + Diffusion + Equilibrium
(Sketch)

A
98
Q

Osmosis

A

Diffusion of Water
Water moves from regions of low solute to regions of high
solute

99
Q

Hypertonic Solution

A

Water moves out of the cell via Osmosis
Cell shrinks

100
Q

Hypotonic Solution

A

Water moves into cell via Osmosis
Cell grows

101
Q

Isotonic Solution

A

No Net Movement
Cell remains

102
Q

Fluid Mosaic Model

A

Membranes are a dynamic and fluid mosaic of proteins and phospholipids
made up of Peripheral / Integral membrane proteins

103
Q

Peripheral membrane protein

A

bind to membrane lipids without passing through
found on interior or exterior of cell

104
Q

Integral membrane protein

A

Proteins that span membrane
segments facing both interior and exterior surfaces

105
Q

Types of Passive Transport

A

Diffusion
Osmosis
Proteins: Channel and Carrier

106
Q

Types of Active Transport

A

Proteins: Pumps

107
Q

Channel Proteins

A

passive (no energy required) / facilitated diffusion
Movement with the chemical gradient
Molecules flow from high concentration to low concentration. Ions flow from areas of like charge to unlike charge.
Pores
Ex: ions- Na + , K + , Cl-
Aquaporins- water
Concentration gradient

108
Q

Carrier Proteins

A

passive/facilitated diffusion
Movement with the chemical gradient
pick up + transport
Shape change - does not require energy

109
Q

Protein Pumps

A

require energy
Movement against the chemical gradient
* Energy comes from the transfer of a phosphate group from ATP (usually) *
Shape Change!
Ex: Na/K

110
Q

Facilitated Diffusion

A

transmembrane proteins assist passive movement of substances that would not readily cross the plasma membrane

111
Q

Active Transport
(Definition)

A

Requires energy to pump ions and molecules against their gradient

112
Q

Electrochemical Gradient

A

Ions build up on one side of the membrane
Establish both concentration gradient and charge gradient

113
Q

Aquaporins

A

Highly selective
Shape of protein is responsible for selecting
Hydrophilic amino acids that line the pore for polar molecules
Other side = hydrophobic
Amino acids in pore act as a filter

114
Q

Why do you need aquaporins if water
freely diffuses across the membrane?

A

Quicker / more efficient
The cell membrane has a limited permeability to water and thus aquaporins are necessary to move large amounts of water across the membrane

115
Q

Channel Protein Substitutions

A

Glycine for Asparagine
Proline and Leucine for Tyrosine and Tryptophan

116
Q

Gated protein channels

A

Open or close in response to a signal (on or off)
Signal could be binding of a substance or change of electrical
potential

117
Q

Cystic Fibrosis - Channels

A

Chlorine channel- impacts cells that produce mucus, sweat, and digestive juices

  • Defective Cl- channel prevents Cl from leaving the cell,
  • creates a hypertonic solution
  • the water stays inside the cell with the Cl- instead of leaving to dilute the mucus layer
118
Q

Sodium (Na) Potassium (K) Pump
(Sketch)

A

Na+ has a concentration gradient into the cell
Na+/K+ pump maintains the concentration gradient
* Membrane has more channels to move K+ than Na+ *
Energy converted from ATP to electrochemical gradient

119
Q

Secondary Active Transport

A

Using the concentration gradient created by the Na+/K+ pump
ATP is not directly used, but was necessary for the gradient to be maintained

120
Q

Secondary Active Transport - Co-transporter

A

The concentration gradient of Na+ allows Glucose to be transported against the Secondary Active Transport (Na+ K+) gradient

121
Q

The Endosymbiotic Theory

A

Mitochondria – aerobic prokaryote that once lived separately was engulfed by a Eukaryotic cell.
Chloroplasts- photosynthetic bacteria that was engulfed.

122
Q

Evidence for Endosymbiotic Theory

A

mitochondria and chloroplasts have circular, single stranded DNA
Single stranded, circular DNA is found exclusively in prokaryotes
lack of histones in mitochondria and chloroplast

123
Q

ER Signal Sequence

A
124
Q

Extracellular compartments (ECM)

A

Rich in proteins and carbohydrates
Collagen- Fibrous component
Proteoglycans- “filler”
Proteins attached to many carbohydrates.
* Gives structure, support, communication
Resists tension and compression *

125
Q

Extracellular Matrix
(Humans or Animals)

A

Animal !
bind using Integral membrane proteins

126
Q

Collagen

A

1/3 protein in human
made by the rough ER, processed in the Golgi, and secreted by exocytosis

127
Q

Residue of Glycine

A

A glycine residue is every third amino acid in collagen
chains

128
Q

**Protein Kinase

A

Definition: Enzyme that binds another protein and ATP.
Function: Transfers the 3rd phosphate group from ATP to OH group.
Substrates: Acts on Tyrosine, threonine, and serine residues.
Example: Involved in signal transduction pathways.

129
Q

Review of Enzyme-Linked Receptors

A

Description: Receptor binds signal and activates by phosphorylation.
Intermediate Activator: Ras.
Activation Cascade: Involves kinase phosphorylation cascade.

130
Q

Signal Response

A

Short-term Effect: Activates or deactivates a target protein.
Long-term Effect: Induces a change in gene expression.

131
Q

Signal Deactivation

A

Importance: Essential for cellular homeostasis.
Rapid Mechanisms: Hydrolysis of GTP to GDP + Pi.
Conversion of cAMP and cGMP to inactive forms.
Re-sequestration of Ca2+.
Dephosphorylation of active proteins by phosphatases.

132
Q

Deactivation of cAMP & cGMP

A

Enzymes: Catalyze the hydrolysis of the 3’ carbon phosphate bond.
Regulation: Controls signal transduction.
Result: Inactivation of secondary messengers.

133
Q

Signal Transduction Cascade

A

Activation Process:
Ligand binds to receptor.
Receptor activates G protein.
G protein activates enzyme.
Enzyme triggers phosphorylation cascade.
Phosphorylated proteins mediate cellular response.

134
Q

When Signaling Goes Awry

A

Consequences:
“Always on” receptors due to mutations.
Mutations in deactivation enzymes lead to disease, like cancer.
Inactivating mutations prevent receptor-ligand binding.

135
Q

Interactions between Signal Pathways**

A

Crosstalk: Integration of diverse signals received by a cell.
Parallel Pathways: GPCRs and Receptor Tyrosine Kinases (RTKs) activate similar intracellular pathways.
Mechanism: Phosphorylation of target proteins.

BIOB 260 (5 decks)

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