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Biology > Biology DAT Ch. 1-5 > Flashcards

Biology DAT Ch. 1-5 Flashcards

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1
Q

Matter

A

Anything that takes up space and has mass

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2
Q

Element

A

Purest substance that has physical/chemical properties, cannot be broken down

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3
Q

Atom

A

Smallest unit of matter with chemical properties

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4
Q

Molecule

A

one or two atoms joined together

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5
Q

Intramolecular forces

A

attractive forces holding atoms within a molecule

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6
Q

Intermolecular forces

A

forces that exist between molecules & affect physical properties of the substance

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7
Q

Monomers

A

single molecules that can be polymerized

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8
Q

Polymers

A

substance made up of monomers

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9
Q

Carbohydrates

A

Carbon, hydrogen, and oxygen (CHO). Come in forms of monosaccharides, disaccharides, and polysaccharides

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10
Q

Monosaccarides

A

carbohydrate monomers with the empirical formula (CH2O)n. n indicating the number of carbons.

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11
Q

Ribose

A

5 carbon monosaccarides

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12
Q

Fructose

A

6 carbon monosaccarides

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13
Q

Glucose

A

6 carbon monosaccarides

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14
Q

Disaccharides

A

Two monomers joined together by a glycosidic bond. This bonds is created by dehydration reaction.

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15
Q

Dehydration (condensation) reaction

A

Water molecule leaving, thus covalent bond is formed

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16
Q

Hydrolysis reaction

A

Water molecule added and covalent bond is broken

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17
Q

Sucrose

A

glucose + fructose

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18
Q

Lactose

A

galactose + glucose

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19
Q

Maltose

A

glucose + glucose

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20
Q

Starch

A

energy storage for plants and is a (alpha) bonded polysaccharides.

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21
Q

Glycogen

A

energy storage for humans and is a (alpha) bonded polysaccharide. Is much more branched than starch.

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22
Q

Amylose

A

linear starch

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23
Q

Amylopectin

A

branched starch

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24
Q

Cellulose

A

structural component of plant cell well, its b (beta) bonded polysaccharides. Linear strands are packed rigidly in parallel.

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25
Q

Chitin

A

component of fungi cell wall and insect exoskeleton, bonded by b (beta) polysaccharides, with nitrogen added to each monomer

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26
Q

Polysaccharides

A

multiple monomers bonded by glycosidic bonds in a long polymer

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27
Q

Proteins

A

contain hydrogen, carbon, oxygen, and nitrogen (CHON). These combine to form amino acids, which link up to form polypeptides.

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28
Q

Polypeptides

A

(proteins) polymers of amino acids linked by peptide bonds through dehydration and hydrolysis reactions. It forms an amino acid chain with two end terminals on opposite sides.

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29
Q

Amino acids

A

20 different, each have a different R-group

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30
Q

N-terminus

A

(amino terminus) the polypeptides side that ends with the last amino acid’s amino group

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31
Q

C-terminus

A

(carboxyl terminus) the polypeptide side that ends with the last amino acid’s carboxyl group

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32
Q

Protein structure

A

primary, secondary, tertiary, and quaternary structure

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33
Q

Protein classification

A

globular, fibrous, intermediate

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34
Q

Protein denaturation

A

temperature change, pH change, and salt concentration

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35
Q

Protein functions

A 
storage
immunity
receptors
enzymes
hormones
motion
structure
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36
Q

Protein composition

A

conjugated (amino acids + other components) and simple (amino acids)

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37
Q

Primary structure

A

sequence of amino acids

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38
Q

Secondary structure

A

alpha and beta pleated sheets formed by hydrogen bonding due to intermolecular forces between polypeptide backbone

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39
Q

Tertiary structure

A

3D structure due to interactions between R-groups. Hydrophobic and hydrophilic. Disulfide bonds are created by covalent bonding between R-groups of two cysteine amino acids.

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40
Q

Quaternary structure

A

multiple polypeptides chains coming together to form one protein

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41
Q

Storage

A

reserve of amino acids

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42
Q

Hormones

A

provide signaling throughout the body to regulate physiological processes

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43
Q

Receptors

A

Proteins in cell membrane which bond to signal molecules to trigger changes inside the cell

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44
Q

Motion

A

movement generated for a cells or of an entire organism

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45
Q

Structure

A

Provide strength and support to tissues

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46
Q

Immunity

A

Prevention and protection against foreign invaders

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47
Q

Enzymes

A

acts as a biological catalyst, binding to the substrate (reactants) to convert them into products

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48
Q

Catalyst

A

increases reaction rate by lowering activation energy, it reduces energy in the transition state. They do not shift chemical reaction & do not affect spontaneity

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49
Q

Transition State

A

unstable intermediate between reactants and products

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50
Q

Active site

A

site on enzyme where substrate binds, it is specific

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51
Q

Specificity constant

A

measures how efficient the substrate binds with the enzyme and converting it to a product

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52
Q

Induced fit theory

A

the active site changes shape to fit the substrate when it binds, also known as “lock and key” model

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53
Q

Ribozyme

A

RNA molecule that acts as an enzyme

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54
Q

Cofactor

A

non-protein molecule that helps enzymes perform its reaction

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55
Q

Coenzyme

A

An organic cofactor such as vitamins. (inorganic=metal ions)

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56
Q

Holoenzymes

A

cofactor + enzyme

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57
Q

Apoenzymes

A

enzyme + NO cofactor

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58
Q

Prosthetic groups

A

cofactor tightly or covalently bonded with its enzyme

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59
Q

Competitive inhibition

A

competitive inhibitor competes with substrate for the active site binding. Adding more substrate would increase enzyme reaction rate.
Km = increases
Vmax = stays the same

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60
Q

Noncompetitive inhibition

A

noncompetitive inhibitor does not compete for active site but instead binds on allosteric site, thus modifying the active site. Adding more substrate would NOT increase enzyme reaction rate.
Km = stays the same
Vmax = decreases

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61
Q

Allosteric site

A

other site on enzyme that is not the active site

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62
Q

Enzyme kinetics plot

A

can be used to visualize how inhibitors affect enzymes

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63
Q

Michaelis Constant (Km)

A

substrate concentration at which velocity is 50% of vmax

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64
Q

Vmax

A

maximum reaction of velocity

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65
Q

Saturation

A

occurs when all active sites are occupied, so the rate of reaction does not increase anymore despite increasing substrate concentration

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66
Q

Lipids

A

Carbon, hydrogen, and oxygen (CHO), they have long hydrocarbon tails making them very hydrophobic

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67
Q

Triacyglycerol

A

a lipid molecule with a glycerol backbone and 3 fatty acids linked by ester linkages

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68
Q

Ester linkages

A

links glycerol back bone and the 3 fatty acids

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69
Q

Glycerol backbone

A

3 carbon and 3 hydroxyl groups

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70
Q

Saturated fatty acids

A

no double bonds and as a result pack TIGHTLY (solid at room temperature)

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71
Q

Unsaturated fatty acids

A

double bonds by monounsaturated fatty acids and polyunsaturated fatty acids

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72
Q

Cis-Unsaturated fatty acids

A

have kinks that cause the hydrocarbon tails to bend, thus do not pack tightly

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73
Q

Trans-Unsaturated fatty acids

A

have straighter hydrocarbon tails so they pack more tightly (unhealthy)

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74
Q

Phospholipids

A

lipid molecule that have glycerol backbone, one phosphate group, and 2 fatty acids, causing it to be amphipathic, thus spontaneously assembling into a lipid bilayer

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75
Q

Cholesterol

A

lipid molecule that has 4 fused hydrocarbon rings. It is amphipathic. It is the most common precursor to steroid hormones. It helps with membrane fluidity

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76
Q

Steroid hormones

A

cholesterol is its precursor, 4 hydrocarbon rings

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77
Q

Cholesterol is starting material

A

material for vitamin D and bile acids

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78
Q

Membrane fluidity

A

temperature: increase of temp = increase of fluidity
cholesterol = holds membrane together at HIGH temp and keeps membrane fluid at LOW temp
degree of unsaturation

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79
Q

Lipoproteins

A

allow the transportation of lipid molecules into the blood stream due to out coat of phospholipids, cholesterol, and proteins

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80
Q

Low-Density Lipoproteins (LDLs)

A

“Bad Cholesterol”

low protein density, delivers cholesterol to peripheral tissues, and vessel blockage can occur

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81
Q

High-Density Lipoproteins (HDLs)

A

“Good Cholesterol”

high protein density, delivers and takes cholesterol away from peripheral tissues to the liver to make bile (reduces blood lipid levels)

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82
Q

Waxes

A

Hydrophobic protective coating, simple lipids that have long fatty acids connected to monohydroxy alcohols through ester linkages

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83
Q

Carotenoids

A

Pigments, lipid derivatives containing long carbon chains with conjugated double bonds and 6 membered rings at each end.

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84
Q

Nucleic acids

A

Carbon, hydrogen, oxygen, nitrogen, and phosphorus (CHONP). Nucleotide monomers that build into DNA or RNA polymers.

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85
Q

Nucelosides vs Nucleotides

A

Nucleoside
- ribose sugar and nitrogenous base
Nucleotide
- ribose sugar, nitrogenous base, and phosphate group

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86
Q

Deoxyribose sugar

A

contain hydrogen at the 2’ carbon

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87
Q

Ribose sugar

A

contain hydroxyl group at the 2’ carbon

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88
Q

Purines

A

A, G (two rings)

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89
Q

Pyrimidines

A

C T and U (one ring)

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90
Q

Phosphodiester bonds

A

connect the phosphate group of one nucleotide at the 5’ carbon to the hydroxyl group at the 3’ carbon. A series of phosphodiester bonds create the sugar-phosphate backbone with a 5’end free phosphate and a 3’end free hydroxyl.

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91
Q

Nucleic acids polymerizaion

A

proceeds as nucleoside triphosphate are added to the 3’ end of the sugar-phosphate backbone

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92
Q

DNA

A

double stranded, antiparallel double helix, two complementary strands with opposite directionalities (5’ and 3’ end) twist around each other.

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93
Q

RNA

A

single stranded after being copied from DNA during transcription, U replaces T and binds to A.

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94
Q

Modern Cell Theory

A
  1. All lifeforms have one or more cells.
  2. The cell is the basic structural, functional, and organizational unit of life.
  3. All cells from from other cells (cell division).
  4. Genetic information is stored and passed down through DNA
  5. An organism’s activity is dependent on the total activity of its independent cells.
  6. Metabolism and biochemistry (energy flow) occurs within cells
  7. All cells have the same chemical composition within organisms of similar species.
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95
Q

Central Dogma of Genetics

A

information is passed through DNA –> RNA –> Protein

exceptions: reverse transcriptase and prions

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96
Q

RNA world hypothesis

A

states that RNA dominated Earth’s primordial soup before there was life. RNA developed self-replicating mechanisms and later could catalyze reactions such as protein synthesis to make more complex macromolecules. Since RNA is reactive and unstable, DNA later became way of reliably of storing genetic information.

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97
Q

A-T bond

A

2 hydrogen bonds

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98
Q

G-C bond

A

3 hydrogen bonds

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99
Q

Cell membrane

A

is made up of phospholipids, cholesterol, and proteins

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100
Q

Membrane proteins

A

are either integral or peripheral membrane proteins

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101
Q

Integral (transmembrane) proteins

A

Transverse the entire bilayer, thus it is amphipathic. Assist in transport and cell signaling.

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102
Q

Peripheral membrane proteins

A

is found outside the bilayer, thus it is hydrophilic. Assist with cell recognition, receptor, adhesion.

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103
Q

Receptor

A

Trigger secondary responses within cell for signaling

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104
Q

Adhesion

A

attaches cells to other things (e.g. other cells).

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105
Q

Cellular recognition

A

proteins which have carbohydrate chains (glycoproteins). Used by cells to recognize other cells.

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106
Q

Glycoproteins

A

any of a class of proteins that have carbohydrate groups attached to the polypeptide chain. They form hydrogen bonds with the water molecules surrounding the cell and thus help to stabilize membrane structure.

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107
Q

Fluid Mosaic Model

A

describes how the components that make up the cell membrane can move freely within the membrane (fluid). Thus, the cell membrane contains many different kinds of structures (mosaic).

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108
Q

3 types of transport across the cell membrane

A

Simple diffusion, facilitated diffusion, and active transport.

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109
Q

Simple diffusion

A

flow of small, uncharged non-polar substances (e.g. O2 and Co2) across the cell membrane from high to low without using energy.

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110
Q

Osmosis

A

simple diffusion that involved water molecules

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111
Q

Facilitated transport

A

integral proteins allow larger, hydrophilic molecules to cross the cell membrane; uniporters, symporters, or antiporters, channel proteins, carrier proteins, passive diffusion, porins and ion channels

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112
Q

Channel proteins

A

Integral protein open tunnel from both sides of bilayer

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113
Q

Carrier proteins

A

Integral protein that binds to a molecule on one side to change the shape to bring it to the other side

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114
Q

Passive diffusion

A

performed by channel proteins,, bring molecules down their concentration gradient without energy use (similar to simple diffusion but a protein channel is used). E.g. porins and ion channels

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115
Q

Active transport

A

substances that travel against their concentration gradient and require the consumption of energy by carrier proteins.

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116
Q

Sodium-potassium pump

A

us a primary active transport that uses ATP hydrolysis to pump molecules against their concentration gradient. It establishes membrane potential.

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117
Q

Secondary active transport

A

uses free energy released when other molecules flow down their concentration gradient (gradient established by primary active transport) to pump the molecule of interest across the membrane.

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118
Q

Cytosis

A

refers to the bulk transport of large, hydrophilic molecules across the cell membrane and requires energy (active transport mechanism).

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119
Q

Endocytosis

A

cell membrane wrapping around an extracellular substance, internalizing it into the cell via vesicle or vacuole. Phagocytosis, pinocytosis, and receptor-mediated endocytosis.

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120
Q

Phagocytosis

A

cellular eating around solid objects

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121
Q

Pinocytosis

A

cellular drinking around dissolved materials (liquids)

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122
Q

Receptor-mediated endocytosis

A

requires binding of dissolved molecules to peripheral membrane receptor proteins, which initiates endocytosis.

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123
Q

peripheral membrane receptor proteins

A

initiates endocytosis, binds to dissolved molecules for receptor-mediated endocytosis

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124
Q

Exocytosis

A

opposite of endocytosis, releasing material to the extracellular environment through vesicle secretion

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125
Q

Organelles

A

cellular compartments enclosed by phospholipids bilayers (membrane bound) located in the cytosol.

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126
Q

Cytosol

A

aqueous intracellular fluid

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127
Q

Cytoplasm

A

cytosol + organelles

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128
Q

Prokaryotes

A

do not have organelles but have other adaptation such as keeping their genetic material in a region called the nucleoid.

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129
Q

Nucleus

A

primarily functions to protect and house DNA. DNA replication and transcription occurs here (DNA –> mRNA).

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130
Q

Nucleoplasm

A

is the cytoplasm of the nucleus

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131
Q

Nuclear envelope

A

membrane of the nucleus. Two phospholipids bilayers (outer and inner) with a perinuclear space in the middle

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132
Q

Nuclear pores

A

holes in the nuclear envelope that allows molecules to travel in and out of the nucleus

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133
Q

Nuclear lamina

A

provides structural support for the nucleus, as well as regulating DNA and cell division

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134
Q

Nucleolus

A

is a dense area that is responsible for making rRNA, and producing ribosomal subunits.

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135
Q

ribosomal subunits

A

rRNA + proteins

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136
Q

Ribosomes

A

not an organelle but work as small factories that carry out translation (mRNA –> protein). Composed of ribosomal subunits.

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137
Q

Eukaryotic ribosomal subunits

A

(60s + 40s) to assemble in the nucleoplasm and form a complete ribosome in the cytosol of 80s.

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138
Q

Prokaryotic ribosomal subunits

A

(50s + 30s) to assemble in the nucleoid and form the complete ribosome in the cytosol 70s.

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139
Q

Free-floating ribosomes

A

ribosomes make proteins that function in the cytosol

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140
Q

Rough ER

A

ribosomes make proteins that are sent out of the cell or to the cell membrane. Rough ER is continuous with the outer membrane of the nuclear envelope. Proteins synthesized by the embedded ribosomes are sent into the lumen for modifications (glycosylation).

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141
Q

Smooth ER

A

Not continuous. Its main function is to synthesize lipids, detoxify cells, and produce steroid hormones.

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142
Q

Golgi apparatus

A

made up of cisternae (flattened sacs) that modify and package substances. Vesicles come from the ER and reach the cis face of the Golgi and leave from the trans face.

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143
Q

Lysosomes

A

membrane-bound organelles that break down substances taking through endocytosis. They contain acidic digestive enzymes that function at low pH. They carry out autophagy and apoptosis.

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144
Q

Autophagy

A

breakdown of the cell’s own machinery for recycling

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145
Q

Apoptosis

A

programmed cell death

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146
Q

Transport vacuoles

A

transport material between organelles

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147
Q

Food vacuoles

A

temporarily hold endocytosed food and later fuse with lysosomes

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148
Q

Central vacuoles

A

large in plants and have a specialized membrane called tonoplast that helps maintain cell rigidity by exerting turgor. Functions in storage and material breakdown.

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149
Q

Storage vacuoles

A

stores pigments, starches, and toxic substances

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150
Q

Contractile vacuoles

A

found in single-celled organisms and works to actively pump excess water out

151
Q

Endomembrane system

A

works to modify, package, and transport proteins and lipids that are entering and exiting the cell. Nucleus, ER, golgi, lysosomes, vacuoles, and cell membrane.

152
Q

Peroxisomes

A

contain an enzyme called catalase that performs hydrolysis, and break down stored fatty acids and help with detoxification. These processes generate hydrogen peroxide , which is toxic because produces ROS.

153
Q

Reactive oxygen species (ROS)

A

damage cells through free radicals

154
Q

Catalase

A

enzyme that breaks down hydrogen peroxide into water and oxygen.

155
Q

Mitochondria

A

powerhouse of the cell, generates ATP for energy use through cellular respiration

156
Q

Chloroplast

A

found in plants and some protist, carries out photorespiration

157
Q

Centrosomes

A

found in animal cells containing a pair of centrioles, oriented at 90 degree angles to one-another. They replicate during the S phase of the cell cycle so that each daughter cell after cell division has one centrosome.

158
Q

Microtubule organizing centers (MTOCs)

A

present in eukaryotic cells and organize microtubule extension during cell division.

159
Q

Cytoskeleton

A

provides function and structure within the cytoplasm; microfilaments, intermediate filaments, and microtubules

160
Q

Microfilaments

A

smallest, are composed of 2 actin filaments. Involved in cell movement and can quickly assemble and disassemble.

161
Q

Microfilament functions

A

cyclosis, muscle contraction, and cleavage furrow

162
Q

Cyclosis

A

cytoplasmic streaming, stirring of the cytoplasm, organelles and vesicles travel on microfilament tracks

163
Q

Cleavage furrow

A

during cell division, actin microfilaments form contractile rings that split the cell.

164
Q

Muscles contraction

A

actin have directionality, allowing myosin motor proteins to pull on them for muscles contraction

165
Q

Intermediate filaments

A

structural support, keratin and lamins in nuclear lamina

166
Q

Microtubules

A

largest, structural integrity to cells, they are hollow and have walls made of tubulin protein dimers

167
Q

Centrioles

A

hollow cylinders made of 9 triplets of microtubules (9x3 array)

168
Q

Cilia and flagella

A

have 9 doublets of microtubules with two singles in the center (9+2 array) and are produced by a basal body

169
Q

Basal body

A

formed by the mother centriole and produce cilia and flagella

170
Q

Mother centriole

A

older centriole after S phase replication

171
Q

Extracellular matrix (ECM)

A

provides mechanical support between cells

172
Q

Proteoglycan

A

type of glycoprotein that have a high proportion of carbohydrates

173
Q

Collagen

A

most common structural protein and organized into collagen fibrils (secreted by fiboblasts)

174
Q

Integrin

A

transmembrane protein that facilitates ECM adhesion and signals to cells how to respond to the extracellular environment (growth, apoptosis, etc.)

175
Q

Fibronectin

A

protein that connects integrin to ECM and helps with signal transduction

176
Q

Laminin

A

influence cell differentiation, adhesion, and movement, it is a major component of the basal lamina.

177
Q

Cell walls

A

are carbohydrate-based structures that act like a substitute ECM because they provide structural support to cells that either do not have or have minimal ECM. Present in plants (cellulose), fungi (chitin), bacteria (peptidoglycan), and archaea.

178
Q

Glycocalyx

A

glycolipid/glycoprotein coat found mainly on bacterial and animal epithelial cells. Helps with adhesion, protection, and cell recognition.

179
Q

Cell-matrix junctions

A

ECM –> cytoskeleton

focal adhesions and hemidesmosomes

180
Q

Focal adhesions

A

ECM connects via integrins to actin microfilament inside the cell

181
Q

Hemidesmosomes

A

ECM connects via integrins to intermediate filaments inside the cell

182
Q

Cell-cell junctions

A

connect adjacent cells

183
Q

Tight junctions

A

form water-tight seals between cells to ensure substancecs pass through cells and not between them

184
Q

Desmosomes

A

provide support against mechanical stress. connects neighboring cells via intermediate filaments

185
Q

Adherens junctions

A

similar in structure and function to desmosomes, but connects neighboring cells via acting filaments

186
Q

Gap junctions

A

allow passage of ions and small molecules between cells

187
Q

Middle lamella

A

plant cell, sticky cement similar in function to tight junctions

188
Q

Plasmadesmata

A

plant cell, tunnels with tubes between plant cells, allows cytosol fluids to freely travel between plant cells.

189
Q

Isotonic solutions

A

same solute concentration as the cells placed in them

190
Q

Hypertonic solutions

A

have higher solute concentration than the cells placed in them, causing water to leave the cell and it shrinking

191
Q

Hypotonic solutions

A

have a lower solute concentration than the cells place in them, causing water to enter the cell (cell swells up), lysis is the bursting of a cell when too much water enters

192
Q

Metabolism

A

refers to metabolic pathways (a series of chemical reactions) that are happening in an organism.

193
Q

Catabolic

A

breaking down larger molecules for energy

194
Q

Anabolic

A

using energy to build larger macromolecules

195
Q

To break down carbohydrates for energy, cells must…

A

utilize aerobic or anaerobic cellular respiration

196
Q

Adenosine triphosphate (ATP)

A

is an RNA nucleoside triphosphate. It contains adenosine nitrogenous base linked to a ribose sugar and 3 phosphate groups. It is the cellular energy currency because of the high energy bonds between the phosphates groups. These bonds release energy by hydrolysis, breaking the bonds.

197
Q

Reaction coupling

A

the process of powering energy-requiring reactions with energy releasing reaction. It allows unfavored reaction to be powered by a favorable one, making the net Gibbs free energy negative, exergonic, spontaneous

198
Q

Mitochondria structure

A

inner (with cristae) and outer membrane, intermembrane space, and matrix

199
Q

Endosymbiotic theory

A

states that aerobic bacteria were internalized as mitochondria while the photosynthetic bacteria became chloroplasts. Size similarities and the fact that mitochondria and chloroplasts contain their own circular DNA and ribosomes.

200
Q

Aerobic cellular respiration

A

is performed to phosphorylate ADP into ATP, by breaking down glucose and moving electrons around. It involves 4 catabolic processes: glycolysis, pyruvate manipulation, krebs cycle, and oxidative phosphorylation.

201
Q

Glycolysis

A

Glucose –> 2 ATP + 2 NADH + 2 Pyruvate

Takes place in the cytosol and does NOT require oxygen

202
Q

Substrate-level phosphorylation

A

the process used to generate ATP in glycolysis, transferring a phosphate group to ADP directly from a phosphorylated compound.

203
Q

Glycolysis phase 1

A

Hexokinase uses one ATP to phosphorylate glucose into glucose-6-phosphate, which cannot leave the cell.

204
Q

Glycolysis phase 2

A

Isomerase modifies glucose-6-phosphate fructose-6-phosphate.

205
Q

Glycolysis phase 3

A

Phosphofructokinase uses a second ATP to phosphorylate fructose-6-phosphate into fructose-1,6-biphosphate.

206
Q

Glycolysis phase 4

A

Fructose-1,6-biphosphate is broken into dihydroxyacetone phosphate (DHAP) and
glyceraldehyde-3-phosphate (G3P), which
are in equilibrium with one another.

207
Q

Glycolysis phase 5

A

G3P proceeds to the energy payoff phase so DHAP is constanly converted into G3p to maintain equilibrium. 1 glucose molecule will produce 2 G3P that continue into the next steps.

208
Q

Glycolysis phase 6

A

G3P undergoes a series of redox reactions to produce 4 ATP through substrate-level-phosphorylation, 2 pyruvate and 2 NADH.

209
Q

Pyruvate manipultions

A

2 pyruvate –> 2CO2 + 2NADH + 2 acetyl CoA

210
Q

Pyruvate dehydrogenase

A

is an enzyme that carries out the pyruvate manipulation; decarboxylation, oxidation, and Coenzyme A

211
Q

Pyruvate dehydrogenase phase 1

A

Decarboxylation: pyruvate molecules move from the cytosol into the mitochondrial matrix (except for prokaryotes), a carboxyl group is removed from pyruvate, releasing carbon dioxide.

212
Q

Pyruvate dehydrogenase phase 2

A

Oxidation: two-carbon molecule is converted into an acetyl group, giving electrons to NAD+ to convert it into NADH

213
Q

Pyruvate dehydrogenase phase 3

A

Coenzyme A: CoA binds to the acetyl group, producing acetyl CoA

214
Q

Krebs cycle

A

2 acetyl CoA –> 4 CO2 + 6 NADH + 2 FADH2 + GTP

Occurs in the mitochondrial matrix

215
Q

Krebs cycle phase 1

A

Acetyl CoA joins oxaloacetate (4 carbon) to form citrate (6 carbon)

216
Q

Krebs cycle phase 2

A

Citrate undergoes rearrangements producing 2 CO2 and 2 NADH

217
Q

Krebs cycle phase 3

A

After the loss of 2 CO2, the resulting 4 carbon molecule produces 1 GTP through substrate level phosphorylation

218
Q

Krebs cycle phase 4

A

The molecule will now transfer electrons to 1 FAD+, which is reduced into 1 FADH2

219
Q

Krebs cycle phase 5

A

The molecule is converted back to oxaloacetate, thus gives electrons to produce 1 NADH

220
Q

Oxidative phosphorylation

A

Electron carriers (NADH + FADH2) + O2 –> ATP + H2O

221
Q

ETC goal

A

regenerate electron carriers and create an electrochemical gradient to power ATP production. The mitochondrial inner membrane is the ETC for eukaryotes while cell membrane is for prokaryotes

222
Q

Oxidative-reduction (redox) reactions

A

four protein complexes I-IV are responsible for moving electrons through a series in the ETC.

223
Q

Electrochemical gradient

A

As the series of redox reactions occurs, protons are pumped from the mitochondrial matrix to the intermembrane space, making it highly acidic

224
Q

Complex I

A

NADH is more effective and drops electrons off, regenerating NAD+

225
Q

Complex II

A

FADH2 drops electrons off at this second protein, regenerating FAD+, this results in less pumping of protons due to the bypassing of complex I

226
Q

Chemosmosis goal

A

Use the proton electrochemical gradient (proton-motive force) to synthesize ATP

227
Q

ATP synthase

A

is a channel protein that provides hydrophilic tunnel to allow protons to flow down their electrochemical gradient (back into the mitochondrial matrix). The spontaneous movement of protons generates energy that is used to convert ADP + Pi –> ATP, a condensation reaction that is endergonic, +∆G

228
Q

NADH produces

A

3 ATP (NADH from glycolysis produces less)

229
Q

FADH2 produces

A

2 ATP

230
Q

Glycolysis stage

A

Net products: 2 ATP & 2 NADH

Net yield ATP: 2 ATP & 4-6 ATP

231
Q

2 pyruvate oxidations stage

A

Net products: 2 NADH

Net yield ATP: 6 ATP

232
Q

2 Krebs cycles stages

A

Net products: 2 GTP, 6 NADH, 2 FADH2

Net yield ATP: 2 ATP, 18 ATP, 4 ATP

233
Q

Total net ATP yield during aerobic respiration

A

36-38 ATP

234
Q

Fermentation

A

does not require energy, anaerobic pathway, only relies on glycolysis by converting the produced pyruvate into different molecules in order to oxidize NADH back to NAD+, thus glycolysis can continue to make ATP. Occurs in the cytosol.

235
Q

Two types of fermentation

A

Lactic acid and alcohol fermentation

236
Q

Lactic acid fermentation

A

uses the 2 NADH from glycolysis to reduces the 2 pyruvate into 2 lactic acid, thus NADH is oxidized back to NAD+ so that glycolysis may continue, this happens in muscle cells and occurs in red blood cells, which do not have mitochondria for aerobic respiration

237
Q

Cori cycle

A

is used to convert lactate back into glucose once oxygen is available again, it transports the lactate to liver cells, where it can be oxidized back to into pyruvate, it can then be used to form glucose, its an ideal energy generation

238
Q

Alcohol fermentation

A

uses 2 NADH from glycolysis to convert the 2 pyruvate into 2 ethanol, NADH is oxidized back to NAD+ so that glycolysis may continue, this process has an extra step; decarboxylation of pyruvate into acetaldehyde, which is only then reduced by NADH into ethanol.
pyruvate -CO2-> acetaldehyde -NAD+-> ethanol

239
Q

Obligate aerobes

A

only perform with oxygen present

240
Q

Obligate anaerobes

A

can only undergo anaerobic respiration or fermentation, oxygen is poison to them

241
Q

Facultative anaerobes

A

can perform either anaerobic or aerobic respiration or fermentation but prefers oxygen because it generate the most ATP

242
Q

Microaerophiles

A

can only undergo aerobic respiration but cannot handle too much oxygen it can be harmful

243
Q

Aerotolerant organisms

A

only undergoes anaerobic fermentation but oxygen is not toxic

244
Q

Alternative sources of energy generation

A

fats, carbohydrates, and proteins

245
Q

Glycogenolysis

A

when carbohydrates enter during glycolysis. It describes the release of glucose-6-phosphate from glycogen, a highly branched polysaccharide of glucose. Disaccharides can undergo hydrolysis to release two carbohydrate monomers, which can enter glycolysis.
glyogen –> glucose-6-phosphate

246
Q

Glycogenesis

A

the reverse process - the conversion of glucose into glycogen to be stored in the liver when energy and fuel is suffiecent

247
Q

Fats

A

are present in the body as triglycerides, lipase are required to first digest fats into free fatty acids and alcohols, these digested pieces the can be absorbed by enterocytes to reform triglycerides.

248
Q

Lipolysis

A

process of digesting fats into free fatty acids and alcohols

249
Q

Enterocytes

A

absorb digested pieces in the small intestine to reform triglycerides

250
Q

Adipocytes

A

cells that store fat (triglycerides) and have hormone sensitive lipase to help release triglycerides back into circulation as lipoproteins or as free fatty acids bounded to albumin

251
Q

Lipase

A

enzyme that helps release triglycerides back into circulation as lipoproteins or free fatty acids

252
Q

Albumin

A

a protein that is bound to free fatty acids

253
Q

Chylomicrons

A

are lipoprotein transport structures formed by the fusing of triglycerides with proteins, phospholipids, and cholesterol. They leave enterocytes and enter lacteals.

254
Q

Lacteals

A

small lymphatic vessels that take fats to the rest of the body.

255
Q

Proteins as an energy source

A

is less desirable because the processes to get them into cellular respiration take considerable energy and proteins are needed for essential functions in the body

256
Q

Oxidative deamination

A

removal of NH3, then proteins can be broken down into amino acids, then shuttled to various parts of cellular respiration

257
Q

Ammonia

A

is toxic, so it must be converted into uric acid or urea depending on the species and excreted from the body. Humans convert ammonia into urea which is then excreted as urine.

258
Q

Free fatty acids

A

undergo beta-oxidation to be converted into acetyl-CoA, it requires an initial investment of ATP, but then is cleaved to yield two-carbon acetyl CoA molecules (that can be used in the Krebs cycle) and electron carriers (NADH or FADH2)

259
Q

Glycerol

A

molecule that travels to the liver, it can undergo a conversion to enter glycolysis or make new glucose via gluconeogensis at the liver

260
Q

Heterotrophs

A

get energy from what they eat

261
Q

Autotrophs

A

make their own energy (food)

262
Q

Photosynthesis

A

creates chemical energy that is transferred through food-chains, reduces atmospheric carbon dioxide, and releases oxygen.
6CO2 + 6H2O –> C6H12O + 6O2
photosynthesis + solar energy—>
chemical energy

263
Q

Photons

A

are light energy that are used to synthesize sugars (glucose) in photosynthesis.

264
Q

Carbon fixation

A

is the process of taking inorganic carbon (CO2) and converts it into organic glucose. Photosynthesis takes electrons from photolysis and excites them using solar energy, thus these electrons are using to power carbon fixation

265
Q

Photolysis

A

splitting of water molecules

266
Q

Epidermis

A

out layer of the cells that provides protection and prevents water loss

267
Q

Palisade mesophyll cells

A

right below the upper layer of the epidermis, has most of the chloroplast here

268
Q

Spongy mesophyll cells

A

bottom of the leaf, has moderate chloroplast here, the leaf has a lot of space here due to gas movement.

269
Q

Stomata

A

are pores underneath the leaf for gas to enter and exit

270
Q

Guard cells

A

surround the stomata and control their opening and closing

271
Q

Choloroplasts

A

similar to mitochondria but found in plants and photosynthetic algae (not in cyanobacteria)

272
Q

Parts of a chloroplast

A

outer membrane, intermembrane, inner membrane, stroma (fluid material fills are inside inner membrane, calvin cycle), thylakoids (within stroma, light dependent reactions occur, granum is the entire stack, lamella is the junction in between), thylakoid lumen (interior of the thylakoid and H+ ions accumulate)

273
Q

Light dependent reactions

A

located in the thylakoid membrane, harnesses light energy to produce ATP and NADPH that is later used in the Calvin cycle

274
Q

Photosystems

A

contain pigments such as chlorophyll and carotenoids that that absorb photons

275
Q

Reaction center

A

special pair of chlorophyll molecules in the center of these proteins: photosystem II (680) and photosystem I (700) that are used in photosynthesis

276
Q

Non-cyclic photophosphorylation

A

is carried about by light dependent reactions

277
Q

Non-cyclic photophosphorylation step 1

A

water is split, passing electrons to photosystem II and releasing protons into the thylakoid lumen

278
Q

Non-cyclic photophosphorylation step 2

A

Photons excite in the reaction center of photosystem II, passing electrons to a primary electron acceptor

279
Q

Non-cyclic photophosphorylation step 3

A

The primary electron acceptor sends the excited electrons into the electron transport chain (ETC). During redox reactions within the ETC, protons are pumped from the stroma to the thylakoid lumen. The electrons are then deposited into the photosystem I

280
Q

Non-cyclic photophosphorylation step 4

A

Photons excite pigments in the photosystem I, energizing the electrons in the reactions center to be passed to a primary electron acceptor

281
Q

Non-cyclic photophosphorylation step 5

A

the electrons are sent to a short ETC that terminates with NADP+ reductase, and anzyme then reduces NADP+ to NADPH using electrons and protons.

282
Q

Non-cyclic photophosphorylation step 6

A

The accumulation of protons in the thylakoid lumen generates an electrochemical gradient that is used to produce ATP using ATP synthase (chemiosmosis), as H+ moves from the thylakoid lumen back into the stroma

283
Q

Cyclic photophosphorylation

A

happens when photosystem I passes electrons back to the first ETC, causing more proton pumping and more ATP production, while not NADPH is generated

284
Q

The Calvin cycle

A

known as the light independent reactions, it does not directly use light energy, but it can only occur of the light dependent reaction is providing ATP and NADPH. It takes place in the chloroplast stroma of plant mesophyll cells, it fixes CO2 that enters the stomata.
6CO2 + 18 ATP + 12 NADPH + H+ –> 18 ADP + 19 Pi + 12 NADP+ + 1 glucose

285
Q

The Calvin cycle step 1

A

Carbon fixation: carbon dioxide combines with 5-carbon ribulose -1,5-bisphosphate (RuBP) to form 6-carbon molecules, which quickly break down into 3-carbon phosphoglycerates (PGA). This reaction is catalyzed by RuBisCo.

286
Q

The Calvin cycle step 2

A

Reducation: PGA is phosphorylated by ATP and
subsequently reduced by NADPH to form
glyceraldehyde-3-phosphate (G3P).

287
Q

The Calvin cycle step 3

A

Regeneration: Most of the G3P is converted

back to RuBP.

288
Q

The Calvin cycle step 4

A

Carbohydrate synthesis: some of the G3P is

used to make glucose.

289
Q

RuBisCo

A

in addition to fixing carbon dioxide into RuBP, can also cause oxygen to bind to RuBP in a process called photorespiration

290
Q

Photorespiration

A

occurs in the stroma, producing a 2-carbon molecule phosphoglycolate that is shuttled to peroxisomes and mitochondria for conversion into PGA. Fixed carbon is lost as carbon dioxide in the process, overall there is a net loss of fixed carbon atoms and no new glucose would be made.

291
Q

C2 photosynthesis

A

aka photorespiration, since 2-carbon phoshoglycolate is produces

292
Q

Hot and dry stomata

A

is close to prevent water loss, thus oxygen accumulates and CO2 is used up. RuBisCo binds oxygen and photorespiration occurs.

293
Q

C3 photosynthesis

A

normal photosynthesis, where a 3-carbon PGA is produced

294
Q

C4 photosynthesis

A

produces 4-carbon oxaloacetate, occurs in plants living in hot environments.

295
Q

Spatial isolation

A

of CO2 to prevent photorespiration

296
Q

Alternative photosynthetic pathways

A

C3, C4, and CAM photosynthesis

297
Q

C4 photosynthesis step 1

A

PEP carboxylase fixes CO2 into a three carbon PEP molecule, producing oxaloacetate, which
is converted into malate in the mesophyll cell

298
Q

C4 photosynthesis step 2

A

Malate is transferred to bundle sheath cells, which have lower concentrations of oxygen.

299
Q

C4 photosynthesis step 3

A

Malate is decarboxylated to release CO2, spatially isolating where CO2 is fixed byRuBisCo. The only drawback is that pyruvate is also produced and needs to be shuttled back to mesophyll cells using ATP energy.

300
Q

C4 photosynthesis step 4

A

Pyruvate is converted back into PEP.

301
Q

CAM photosynthesis

A

uses temporal isolation of CO2 to prevent photorespiration in hot environments

302
Q

CAM photosynthesis step 1

A

During the day, stomata are closed to prevent transpiration (evaporation of water from
plants).

303
Q

CAM photosynthesis step 2

A

During the night, stomata are open to let carbon dioxide in. Just like in C4 photosynthesis, PEP carboxylase fixes CO2
into PEP, producing oxaloacetate and afterwards malate. However, malate is stored in vacuoles instead of being shuttled to bundle sheath cells.

304
Q

CAM photosynthesis step 3

A

During the next day, the stomata are closed again and malate is converted back into oxaloacetate, which releases CO2 and PEP. Thus, CO2 accumulates in the leaf for use in the Calvin cycle through temporal isolation.

305
Q

Photoautotrophs

A

can take light energy and convert it into chemical energy via Photosynthesis

306
Q

Genome

A

all DNA in a cell

307
Q

Chromosomes

A

separate DNA molecules that make up the genomes

308
Q

Homologous chromosome pairs

A

two different versions of the same chromosome number. One from mom and one from dad.

309
Q

Sister chromatids

A

identical, attached copies of a single chromosomes, forming dyads

310
Q

Dyads

A

replicated chromosomes containing sister chromatids that look like an “X”

311
Q

Centromeres

A

regions of DNA that connect sister chromatids in a dyad

312
Q

Kinetochores

A

proteins on the sides of centromeres that help microtubules pull sister chromatids apart during cell division

313
Q

Karyokinesis

A

division of the nucleus

314
Q

Cytokinesis

A

physical division of the cytoplasm and cell membrane

315
Q

Parent cell

A

one parent cell produces two daughter cells after division

316
Q

Ploidy

A

describes the number of chromosomes sets found in the body.

317
Q

Diploid

A

humans, contain two sets of chromosomes (46 chromosomes, 23 pairs) one from each parent

318
Q

Haploid

A

gametes, only contain one chromosome set (23 chromosomes)

319
Q

Sex chromosomes

A

one pair in the human body that determine sex

320
Q

Autosomes

A

22 pairs in the human body that aren’t sex chromosomes

321
Q

Gametes

A

haploid cells, egg and sperm

322
Q

Germ cells

A

diploid cells that divide by meiosis to produce gametes

323
Q

Gametocyte

A

eukaryotic germ cell that can either divide to form more gametocytes or produce gametes

324
Q

Somatic cells

A

body cells excluding the gametes, diploid in humans

325
Q

Cell cycle

A

is divided into interphase (G1, G0, S, and G2) and the M phase. 90% of the cell cycle happens during interphase. M phase is where karyokinesis and cytokinesis occur.

326
Q 
Go
Sam
Go
Make 
Cake
A 
Gap phase 1 (G1)
Synthesis phase (S)
Gap phase 2 (G2) 
Mitosis of M phase
Cytokinesis of M phase
327
Q

Gap phase 1 (G1)

A

cell grows in preparation for cell division and checks for favorable conditions. If favorable, the cell will enter S phase. If unfavorable it will enter G0 phase.

328
Q

G0 phase

A

cells still carry out their functions but halt in the cell cycle, cells that do not divide are stuck here

329
Q

Synthesis phase (S)

A

cell replicates its genome and centrosomes here and moves to G2 phase when completed.

330
Q

Gap phase 2 (G2)

A

cell continues to grow and prepare for cell division by checking DNA for any errors after replication, also checking for mitosis promoting factor (MPF), which needs to be an adequate amounts for cell cycle continuation. Organelles replicated here.

331
Q

Microtubules Organizing Centers (MTOCs)

A

made of protein tubulin, are responsible for forming spindle apparatus which guides chromosomes during karyokinesis, organizing microtubule extension

332
Q

Microtubules in the spindle apparatus:

A

Kinetochore, astral, and polar microtubules

333
Q

Kinetochore mircotubules

A

extend centrosomes and attach to kinetochores on chromosomes

334
Q

Astral microtubules

A

extend from centrosomes to cell membrane to orient the spindle apparatus.

335
Q

Polar microtubules

A

extend from the two

centrosomes and connect with each other. Pushes centrosomes to opposite ends of the cell.

336
Q

Centrioles

A

Centrioles are hollow cylinders made of nine triplets of microtubules (9x3 array).

337
Q

Centrosomes

A

organelles that contain a pair of centrioles oriented at 90 degree angles to one another (attached by interconnecting fibers), they replicate during the S phase of the cycle so that each daughter has one centrosome

338
Q

Pericentriolar material

A

surrounds the centrioles and is responsible for microtubules nucleation (anchoring tubulin to start microtubule extension).

339
Q

M-phase

A

is the stage in the cell cycle where karyokinesis and cytokinesis occurs.

340
Q

Mitosis

A

is a type of karyokinesis (nuclear division) that involves a diploid parent cell dividing into two diploid daughter cells.

341
Q

Prophase

A

chromatin condenses into

chromosomes (X-shaped dyads). The nucleolus and nuclear envelope disappear. Spindle apparatus forms.

342
Q

Metaphase

A

the spindle apparatus guides

the chromosomes to the metaphase plate (midpoint of cell) in single file.

343
Q

Anaphase

A

kinetochore microtubules
shorten to pull sister chromatids apart. Now, the sister chromatids are considered separate
chromosomes. Chromosome number doubles.

344
Q

Telophase

A

chromosomes have segregated

and nuclear membranes reform. In addition, nucleoli reappear and chromosomes decondense into chromatin.

345
Q

Cytokinesis

A

is the physical separation of the

cytoplasm and cell membrane into two daughter cells.

346
Q

Plant cell cytokinesis

A

cells, cytokinesis begins in telophase with the formation of a cell plate. The cell plate is
created by vesicles from the Golgi apparatus and ends up producing the middle lamella (cements plant cells together).

347
Q

Animal cell cytokinesis

A

cytokinesis begins in late anaphase with the formation of a cleavage furrow. The cleavage furrow is a contractile ring of actin microfilaments and myosin motors that pinches the cell into two.

348
Q

Cell cycle influences

A

cell division through limitations to growth and regulations to prevent cancerous growth.

349
Q

Functional limitations

A

surface to volume ratio and genome to volume ratio

350
Q

Surface to volume ratio

A

cell division occurs when volume is too large because cells rely on the surface area of their cell membrane for transport of material. Decrease in S/V leads to division.

351
Q

Genomes to volume ratio

A

cell division occurs when volume is too large for cells to support with its limited genome. Decrease in G/V leads to division.

352
Q

Cell specific regulations

A

cell specific checkpoints, cyclin-dependent kinases (CDKs), growth factors, density dependent inhibition, anchorage dependence.

353
Q

Cell specific checkpoints

A

G1 restriction point (checks for favorable conditions to grow,
enters G0 phase if unfavorable), and end of G2 (checks accuracy of DNA replication and MPF levels), and M checkpoint (during metaphase, checks for chromosomal attachment to spindle fibers).

354
Q

Cyclin-dependent kinases (CDKs)

A

phosphorylate certain substrates to signal cell cycle progression. Activated by cyclin, a protein that cycles through stages of synthesis and degradation.

355
Q

Growth factors

A

bind to receptors in the plasma membrane to signal for cell division.

356
Q

Density dependent inhibition

A

halting cell division when density of cells is high.

357
Q

Anchorage dependence

A

dividing only when attached to an external surface.

358
Q

Mitosis increases the number of

A

cells in an organism

359
Q

Binary fission

A

used by archaea, bacteria, and certain organelles to reproduce. Organisms will replicate their genome while cell division is happening (no S phase for DNA replication). And no spindle
apparatus.

360
Q

Meiosis

A

produces four haploid daughter cells from one diploid parent cell. It does this by repeating the steps of karyokinesis twice. Meiosis can be divided into meiosis I (homologous chromosomes separate) and meiosis II (sister chromatids
separate).

361
Q

Meiosis I

A

(reductional division) produces two haploid daughter cells through separation of homologous chromosomes.

362
Q

Prophase I

A

chromatin condenses into
chromosomes (X-shaped dyads). Also nucleolus and nuclear envelope will disappear. Homologous chromosomes pair
up and crossing over occurs.

363
Q

Homologous chromosomes pair up and crossing over during:

A

Synapsis - the pairing up of homologous chromosomes to form tetrads (aka bivalents).
Synaptonemal complex - protein
structure that forms between
homologous chromosomes during synapsis.
Tetrads (bivalents) - pair of two
homologous chromosomes each with two sister chromatids.
Chiasmata - where chromatids
physically crossover during synapsis, causing genetic recombination.
Genetic recombination - exchange of DNA between chromosomes to produce genetically diverse offspring.

364
Q

Metaphase I

A

tetrads randomly line up

double file on metaphase plate, also contributes to genetic diversity.

365
Q

Anaphase I

A

kinetochore microtubules
shorten to separate homologous
chromosomes from each other. Will not begin unless at least one chiasmata has formed within each tetrad.

366
Q

Telophase and Cytokinesis I

A

after tetrads have been pulled to opposite poles, nuclear membranes reform. In addition, nucleoli reappear and
chromosomes decondense into
chromatin. Cleavage furrow formed in animal cells and cell plate formed in plant cells.

367
Q

Meiosis II

A

is very similar to mitosis because sister chromatids are separated. Two haploid cells divide into four haploid daughter cells.

368
Q

Prophase II

A

chromatin condenses into
chromosomes (X-shaped dyads). Also nucleolus and nuclear envelope will disappear. Spindle apparatus forms. No crossing over.

369
Q

Metaphase II

A

chromosomes line up single file at the metaphase plate just like in mitosis.

370
Q

Anaphase II

A

kinetochore microtubules

shorten to pull sister chromatids apart. Sister chromatids become separate chromosomes and chromosomes number doubles

371
Q

Telophase and Cytokinesis II

A

nuclear membranes reform, nucleoli reappear, and chromosomes decondense into chromatin. Four haploid daughter cells are produced in
total.

372
Q

Mitosis chromosomes and chromatid numbers:

A

During the S phase of the cell cycle, a human’s 46 chromosomes are duplicated. Afterwards, there are still 46 chromosomes but also 92 chromatids.

373
Q

Meiosis I chromosomes and chromatid numbers:

A

During S phase. This results in the same total numbers - 46 chromosomes and 92 chromatids. Each cell will have 23 chromosomes and 46 chromatids.

374
Q

Meiosis II chromosomes and chromatid numbers:

A

sister chromatids are

separated, resulting in 23 chromosomes (23 chromatids) in each daughter cell. These cells are haploid.

Biology (3 decks)

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