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biology- cell & molec Flashcards

1
Q

catabolism

A

break down

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2
Q

anabolism

A

build up

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3
Q

oxidation

A

loss of electrons

more bonds to oxygen

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4
Q

reduction

A

gain of electrons

more bonds to hydrogens

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5
Q

enzymes

A

protein catalysts

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6
Q

Vmax

A

enzymes processing substrate as fast as they can

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7
Q

active site

A

site where enzyme binds

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8
Q

inhibitors

A

bind to wrong active sites that slow down reactions

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9
Q

competitive inhibition

A 
inhibitor and substrate compete for the enzyme
doesn't change vmax (rate)
new Km (concentration) value increases
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10
Q

non-competitive inhibition

A
  • inhibitor can bind to the enzyme at the binding site at the same time as the substrate but not to the active site
  • doesn’t bind to active site but somewhere else
  • binding happens but reaction doesnt
  • vmax decreases
  • km unchanged
  • EI and EIS complexes enzymatically inactive
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11
Q

uncompetitive inhibition

A

inhibitor cannot bind to the free enzyme, only to the ES complex
the complex formed is enzymatically inactive
rare kind of inhibition
may happen in multimeric enzymes

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12
Q

mixed inhibition

A

like noncompetitive
EIS complex has residual enzymatic activity
does not follow the MIchaelis-Menten Equation

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13
Q

enzymes work by lowering the _____

A

activation energy and increase the rate of reaction

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14
Q

enzymatic catalyzed reactions form products faster, making reactions reach their ______ more rapidly

A

equilibrium

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15
Q

T/F enzymes are not conumed by the reactions they catalyze

A

true

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16
Q

how do enzymes differ from other catalysts

A

they are highly specific for their substrates due to their complementary shape, charge, and hydrophilic/hydrophobic characteristics

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17
Q

michaelis-menten equation

A

v=(vmax [S])/(km + [S])

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18
Q

cooperativity

A

when a substrate binds to one enzymatic sub-unit/binding site, which induces the rest of the subunits to be stimulated and become active

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19
Q

example of cooperativity

A

hemoglobin shows positive cooperativity for oxygen because it is more accepting to oxygen after one oxygen molecule binds
-transports 4 oxygen subunits while myoglobin only transports 1 subunit

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20
Q

what demonstrates cooperativity?

A

ligands

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21
Q

negative cooperativity

A

as ligands bind to the protein, the protein’s affinity for the ligand decreases

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22
Q

types of enzyme regulation

A
  1. allosteric
  2. phosphorylation
  3. zymogens
  4. cofactors
  5. association with other peptides
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23
Q

allosteric regulation

A

other molecules bind to enzyme in places other than active site
-ex: feedback inhibition

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24
Q

phosphorylation

A

adding a phosphate group

  • covalent modification (make covalent bond)
  • ser, thr, tyr residues can be phosphorylated by kinases (using ATP hydrolysis) or phophorylases
  • phosphatases pull phosphate off
  • phosphorylation can either activate or inhibit an enzyme depending upon the enzyme
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25
Q

zymogens

A

inactive precursors that become active upon proteolytic cleavage
-ex: proteins cleave in stomach

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26
Q

cofactors

A

involvement of metal ions or organic molecules (coenzymes)

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27
Q

association with other peptides

A

individual peptides come together to form a bigger one

-one of the peptides will have a regulatory feature that regulates catalytic activity

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28
Q

gibbs equation

A

G=H-TS

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29
Q

delta G is negative means

A

spontaneous reaction

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30
Q

delta G positive means

A

not spontaneous

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31
Q

thermodynamics

A

tells you if a reaction will happen or not

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32
Q

H - and S +

A

spontaneous at all temps

exothermic

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33
Q

H means

A

enthalpy

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34
Q

S means

A

entropy

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35
Q

H + S -

A

nonspontaneous at all temps

endothermic

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36
Q

H + S +

A

spontaneous at all high temps

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37
Q

H - S -

A

spontaneous at all low temps

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38
Q

standard conditions

A

1 atm
1 molar gas
all reactants and products present at 1 M concentration

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39
Q

Q

A

products/reactatns

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40
Q

what happens to delta G if you shift the equilibrium to the right

A

more negative

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41
Q

shift equilibrium to left?

A

more positive

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42
Q

catalyst

A

lowers activation energy
provides an alternate pathways
helps get to equilibrium faster
can work in both directions

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43
Q

what does adding a catalyst do to delta G?

A

doesnt change it at all

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44
Q

what is the only thing that can change delta G

A

temp

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45
Q

path of glucose catabolism (aerobic)

A
  1. glucose
  2. glycolysis (cytosol)
  3. pyruvate (mitochondrial matrix)
  4. acetyl coA
  5. TCA (kreb’s) cycle (mitochondrial matrix)
  6. electron transport chain (mitochondrial inner membrane)-oxidative phosphorylation
  7. ATP synthase
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46
Q

yield for glycolysis

A

per glucose:
2 ATP (net)
2 NADH
2 pyruvate

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47
Q

what does glucose use in glycolysis? what is the cost?

A

2 ATP, 4 ADP, 2 NAD+

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48
Q

anaerobic catabolism of glucose

A
  1. glucose
  2. glycolysis (cytosol)-substrate level phosphorylation
  3. 2 pyruvate
    3a. reduces to lactate using NADH—> NAD+
    3b. OR reduces/ferments to ethanol and CO2 using NADH—> NAD+
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49
Q

mitochondrial structure

A

outer membrane, intermembrane space, inner membrane, matrix

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50
Q

commitment step in glycolysis

A

fructose-6-phosphate turns into fructose-1,6-biphosphate
ATP—>ADP
irreversible step

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51
Q

Pyruvate dehydrogenase complex (PDC or PDH complex)

A

responsible for bringing glycolysis into Krebs

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52
Q

yield of krebs

A 
per acetyl coA:
GTP=ATP
3 NADH
2 CO2
FADH2
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53
Q

start of krebs

A

acetyl coA + oxalo-acetate—-> citrate

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54
Q

how many oxidation steps of krebs

A

4

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55
Q

ADP

A

low energy
turns catabolism on
biosynthesis inhibited

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56
Q

ATP

A

high energy
turns catabolism off and anabolism on
biosynthesis activated

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57
Q

gluconeogenesis

A

production of glucose
reverse of glycolysis
occurs mainly in liver (but also kidneys)

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58
Q

glycogen metabolism

A
  • glucose polymer for glucose storage in the liver and muscles
  • insulin activates glycogen synthesis
  • glucagon and epinephrine promote degradation
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59
Q

cori cycle

A

lactate transported to the liver for conversion back to glucose

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60
Q

formula for catabolism of glucose

A

C6H12O6 + 6 O2—> 6 CO2 + 6H2O

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61
Q

where do the electrons come from to deposit in the electron transport chain

A

oxygen and turn into H2O

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62
Q

oxidations in electron transport chain

A

NADH–NAD+

FADH2–FAD

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63
Q

what has a high H+ concentration in the electron transport chain

A

intermembrane space

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64
Q

what has a low H+ concentration in the electron transport chain

A

matrix–higher pH

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65
Q

path of electron transport chain from NADH

A
  1. NADH —> NAD+
  2. complex 1
  3. coQ
  4. complex 3
  5. cytochrome C
  6. complex 4
  7. oxygen making water
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66
Q

path of electron transport chain from FADH2

A
  1. FADH2—>FAD
  2. complex 2
  3. coQ
  4. complex 3
  5. cytochrome C
  6. complex 4
  7. oxygen making water
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67
Q

what powers ATP synthase

A

electrochemical potential from electron transport chain

voltage gradient

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68
Q

NADH=

A

2.5 ATP

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69
Q

FADH2=

A

1.5 ATP

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70
Q

dietary uptake of lipids

A

triacylglycerides use lipases (in lumen of small intestine) and turn into monoacylglyerides and fatty acids (translported into electrocytes) and then turn into triacylglycerides then using chylomicrons (packaged with choleserol) turn into adipose tissue

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71
Q

what breaks triacylglyerides apart?

A

lipases

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72
Q

what stores more energy–fats or carbohydrates

A

fats

73
Q

liver turns glyerol into what

A

glycolysis or gluconeogenesis

74
Q

fatty acids turn into what

A

acetyl coA to CAC cycle

75
Q

what is the body’s response to fasting, exercise, or stress?

A

glucagon and epinephrine activate the triacylglyerides to be converted to fatty acids and glyerol by hormone-sensitive lipases

76
Q

adipose tissue to energy production path

A

triacylglycerides converted to fatty acids and glycerol by hormone-sensitive lipases

  • activated by glucagon and epinephrine in response to fasting, exercise, or stress
  • glycerol transported to the liver for glycolysis or gluconeogenesis
  • fatty acids transported through the bloodstream to tissues in need (heart and primary muscles)
77
Q

beta oxidation activated by

A

hooking up fatty acid with acetyl coA

78
Q

oxidations in beta oxidation

A
  1. FAD turns into FADH2

2. NAD turns into NADH

79
Q

virus

A
  • nonliving
  • parasitic
  • structure-nucleic acids encased in a protein capsid (enveloped or nonenveloped)
  • genome-linear or circular (dsDNA, ssDNA, dsRNA, or ssRNA)
  • relatively small genomes that can often be read in different reading frames
  • typically uses host’s replication, transcription, and translation machineery
  • much smaller than prokaryotic or eukaryotic cells
80
Q

bacteriophage

A

head with capsid protein coating and contains genome

tail punctures and injects DNA into bacteria

81
Q

animal virus

A

envelope outside
capsid protein with coat containing genome
endocytosis thru cell membrane
not all have envelope

82
Q

lytic cycle

A
  1. adsorption-bind cell surface via tail (host cell specific interactions)
  2. penetration-puncture cell wall and membrane and inject genome into host cell
  3. hydrolase (a viral gene product) is produced and degrades the host’s genome
  4. replication of the viral genome (many copies) and synthesis of much capsid protein
  5. assembly of new virus particles
  6. production of lysozyme to degrade the cell wall resulting in cell lysis and release of virus particles
    * *disadvantage of this cycle–kills host cell and eventually kills them all
83
Q

lysogenic cycle

A
  1. adsorption-bind cell surface via tail (host cell specific interactions)
  2. penetration-puncture cell wall and membrane and inject genome into host cell
  3. integration of the phage genome into the host genome
  4. dormancy-viral genes not expressed by viral genome is transmitted to all progeny during cell division
  5. activation- excision of viral DNA and entrance into lytic cycle
84
Q

bacteriophage life cycles

A

lytic or lysogenic

85
Q

how do viruses of eukaryotes enter and exit the cell

A

they have a lipid bilayer envelope and enter the host cell via endocytosis and exit by budding out of the host cell

86
Q

host cells contain what that will degrade the viral DNA

A

restriction enzymes

87
Q

bacteria do what to distinguish their own DNA from foreign DNA

A

methylate their own DNA

88
Q

transduction

A

transer of genetic material via a virus in the lysogenic cycle

89
Q

virus types

A
  1. +RNA virus
  2. -RNA virus
  3. retroviruses
90
Q

+RNA

A

genome is single stranded (ssRNA) which can serve directly as mRNA
-must code for an RNA-dependent RNA polymerase for viral replication

91
Q

-RNA

A

viral genome is ssRNA which is anti-sense (-) and therefore complementary to the mRNA coding for viral genes

  • must code for an RNA-dependent RNA polymerase and include this polymerase in its capsid to be infectious
  • needs enzyme in capsid
92
Q

retrovirus

A

-have enzyme called reverse transcriptase which converts +RNA to dsDNA
then incorporates itself into the host’s genome
-must encode an RNA-dependent DNA polymerase (reverse transcriptase)
-specificity

93
Q

prokaryotes

A
  • no nucleus
  • no membrane bound organelles
  • no mitosis
  • one chromosome–dna in cytoplasm
  • coupled transcription and translation
94
Q

cell wall of prokaryotes made out of

A

peptoglycand

95
Q

eubacteria vs archaebacteria

A

eubacteria–true bacteria

archaebacteria–separate domain, eukaryotes more related, extreme conditions

96
Q

classifications of bacteria

A
  1. cocci (spherical)
  2. bacilli (rod)
  3. spirilla (spiral shaped)
97
Q

gram positive bacteria

A

stain dark purple during gram staining

have cell membrane and cell wall (peptidoglycan)

98
Q

gram negative bacteria

A

stain pink during gram staining

have cell membrane, cell wall, and outer lipopolysaccharide layer (LPS) (contains endotoxins)

99
Q

flagellar propulsion

A

bacterial flagellum used by motile bacteria for locomotion
decide what direction to move in using chemotaxis–either toward chemoattractants or away from chemorepellants (sensed by chemoreceptors)
-powered by ATP hydrolysis

100
Q

bacterial growth

A

fission

reproduction simply through growth, DNA replication, and cell division

101
Q

4 phases of bacterial growth

A
  1. lag phase
  2. log phase
  3. stationary phase
  4. death phase
102
Q

endospores

A

dormant form produced by some bacteria under harsh conditions

  • have a thick peptidoglycan coat and can survive through extreme conditions
  • can survive boiling
103
Q

aerobes

A

can survive in an oxygen environment

104
Q

anaerobes

A

do not require oxygen to survive

105
Q

facultative anaerobes

A

can carry out metabolic processes with or without oxygen

can use oxygen as final electron acceptor

106
Q

conjugation

A

way for bacteria to share genetic information adding to diversity
common way of conferring antibiotic resistance genes

107
Q

fungi

A

some unicellular (yeast)
most are multicellular
eukaryote (nucleus and organelles)
cell wall made of chitin

108
Q

asexual reproduction of fungi

A
  1. budding–a fungi cell simply grows out of an existing fungal cell until distinct
  2. spore formation–produced by mitosis, spore will germinate under favorable conditions to become active
109
Q

sexual reproduction of fungi

A
  1. 2 haploid gametes
  2. fusion to become dikaryon
  3. fusion of nuclei
  4. diploid zygote made
  5. meiosis
  6. haploid progeny
110
Q

nucleus

A
  • storage of DNA, site of transcription
  • surrounded by nuclear envelope (2 lipid bilayers) through which nuclear pores regulate traffic of large molecules
  • contains the nucleolus (dark spot which is the site of rRNA synthesis
111
Q

ribosomes

A

translation of mRNA into proteins (present in both pro- and eukaryotes)

112
Q

rough ER

A

ER associated with ribosomes that is involved in synthesis and glycosylation of peptides to form glycoproteins destined for secretion or integration into the membrane

113
Q

smooth ER

A
  • synthesis of lipids (membrane) and hormones often for export from the cell
  • breakdown of toxins in liver cells
114
Q

golgi apparatus

A

modification (glycosylation) and packaging of proteins into vesicles for secretion or transport to cellular destinations (like lysosomes)

115
Q

mitochondria

A
  • site of ATP synthesis via ATP synthase as a result of oxidative phosphorylation (PDC, Krebs, and electron transport chain)
  • site of fatty acid catabolism (beta oxidation)
  • have their own DNA (circular) and ribosomes for self-regulation
116
Q

lysosomes

A
  • contains acid hydrolases (digestive enzymes) and have pH=5
  • degradation of old organelles or phagocytosed materials
  • produced from the golgi apparatus
  • not present in plant cells
117
Q

perioxosomes

A
  • involved in the breakdown (involving hydrogen peroxide) of many substances including fatty acids, amino acids, and various toxins
  • carry out the glyoxalate cycle in germinating plant seeds
118
Q

centrioles

A

source of the spindle apparatus used for cell division (acts as microtubule organizing center)
not present in plant cells

119
Q

vacuoles

A

fluid filled membrane bound vesicles used for transport, storage of nutrients and other substances, pumping excess water out of a cell, and cell rigidity (in plants)

120
Q

chloroplasts

A

site of photosynthesis in plant cells

121
Q

animal cells have what that plant cells dont

A

lysosomes and centrioles

122
Q

plant cells have what that animal cells dont

A

cell walls, chloroplasts, and a central vacuole

123
Q

bacteria cell walls material

A

peptidoglycans

124
Q

archaebacteria cell walls material

A

polysaccharides (not peptidoglycans though)

125
Q

fungi cell walls material

A

chitin

126
Q

plant cell walls material

A

cellulose

127
Q

animal cell walls material

A

none!

128
Q

PDC and krebs cycle occur in

A

mitochondrial matrix

129
Q

ETC complexes are located

A

in inner membrane of mitochondria

130
Q

protons are pumped (actively) from _____ to the ______

A

mitochondrial matrix to the intermembrane space

131
Q

ATP synthase located in the ____ and synthesizes ATP on ______

A

inner membrane and matrix side

132
Q

protein trafficking

A

signal peptide recognized by signal recognition particle (SRP)

  • binds to SRP and translation haulted and takes it to rough ER
  • threads peptides into ER lumen
  • signal peptide cleaved
  • if peptide is destined for secretion, entire peptide ends up in ER
133
Q

2 destinations of protein trafficking

A
  1. plasma membrane (integral membrane or secreted)

2. organelles (ex. lysosomes, ER)

134
Q

fluid mosaic model

A
  • different components free to diffuse throughout membrane, 2D
  • composed of phosphpolipids, glycolipids, and cholesterol
  • cholesterol adds rigidity to the membrane
  • unsaturated fatty acids increase membrane fluidity
135
Q

what can cross the plasma membrane

A

hydrophobic molecules and small polar molecules (uncharged)

ex: CO2, O2, lipids, some drugs

136
Q

membrane proteins

A
  1. transmembrane protein-spans the entire membrane and includes channel proteins, carrier proteins, porins
  2. integral membrane protein- anchored to and embedded in the membrane
  3. peripheral membrane proteins- adhere to membrane surface via electrostatic interactions
137
Q

cell receptors

A

recognition glycoproteins on the cell surface that interact with hormones or other molecules and relay signals to the cell

138
Q

function of plasma membrane

A
  • separates living thing from environment
  • gradient
  • resting membrane potential
  • isolate nutrients from environment
139
Q

channel proteins

A

liquid membrane permiable to small, polar molecules and hydrophobic molecules

  • form a barrel across membrane that allows different ions in/out
  • very specific
  • ions must bind first
  • need hydrophobic proteins on side
140
Q

carrier proteins

A

bind to whatever theyre supposed to transport on one side and then undergo a conformational change and go to the other side

141
Q

porin

A

protein that forms a giant hole in membrane
allow diffusion to take place
not specific
not common in animal cells

142
Q

membrane proteins are glycosylated at

A

golgi and rough ER

143
Q

what play a big role in signaling

A

polysaccarides
ligand will bind to it
always on exterior of cell receptor

144
Q

adhesion proteins

A
  1. gap junctions- allow exchange of nutrients and cell-to-cell communication (ex. cardiac muscle cells)
  2. tight junctions- completely encircle cells and seals the space between them to prevent leakage (ex. intestinal cells)
  3. desmosomes- ‘spot welds’ between cells that adhere them to one another and give mechancal strength and anchored to the cytoskeletons of each cell (ex. skin cells)
  4. plasmodesmata- narrow channels allowing the exchange of nutrients in plant cells
145
Q

glycocalyx

A

carbohydrate coating on the cell wall of some bacteria and the plasma membane of some animal cells
-functions in adhesion, barrier to infection, or cell-cell recognition

146
Q

passive transport

A
  • don’t require ATP
  • go down WITH concentration gradient
  • simple diffusion right across membrane
  • facilatated diffusion-larger polar things using porin, carrier, channel proteins
147
Q

active transport

A
  • requires ATP
  • go against/up concentration gradient
  • primary-transport directly coupled to ATP hydrolysis (Na/K pump)
  • secondary- solute being transported is not directly coupled with ATP hydrolysis; creates concentration gradient by pumping a solute across and then it will couple the actual one with ATP hydrolysis (Na/glucose transporter)
148
Q

sodium potassium pump

A
  • more Na on outside of cell
  • more potassium inside of cell
  • primary active transport
  • pumps 3 Na out
  • brings 2 K in
  • resting membrane potential=-70 mV
  • Na/glucose pump brings more Na in only if it brings glucose with it (secondary active transport)
149
Q

cell signaling and second messengers

A
  1. ligand binds G-protein receptor (conformational change)
  2. G-protein receptor activates G-protein which binds GTP (exchanges GTP for GDP)
  3. G-protein activates Adenylate Cyclase (ATP –> cAMP)
  4. cAMP acts as a second messenger activating a series of proteins and transcription factors
150
Q

plasmolysis

A

osmosis in hypertonic solution (higher in solute concentration, relative to cell)
-cell shrivels up

151
Q

cytolysis

A

osmosis in hypotonic solution (lower in solute concentration)
-destruction of cell/ bursts

152
Q

isotonic

A

cell and solute have same concentration

153
Q

endocytosis

A

taking something within cell

154
Q

phagocytosis

A

cell taking in solids

155
Q

pinocytosis

A

cell dissolving stuff

156
Q

receptor mediated endocytosis

A

cell surface already has pits coated with receptors

sends signals that cause endocytosis to take place

157
Q

cytoskeleton filaments (largest to smallest)

A
  1. microtubules–made from tubulin (monomer) in a 9+2 arrangement; “railroad” for intracellular transport; found in the spindle apparatus of mitosis and in flagella and cilia
  2. intermediate filaments-support and maintain the shape of the cell
  3. microfilaments-made from actin and involved in cellular motility, muscle contraction, and cytokinesis
158
Q

cell cycle (interphase)

A

G1-protein and nucleic acid synthesis to prepare for replication; production of organelles
S- DNA replication
G2-continued growth in preparation for mitosis

159
Q

mitosis

A
  1. prophase-chromosomes condense; nuclear envelope disappears, polarization of centrioles
  2. metaphase-chromosomes line up on metaphase plate; spindle fibers attach at centromeres
  3. anaphase-spindle fibers pull sister chromatids apart towards centrioles; cleavage furrow begins forming
  4. telophase-nuclear membranes reform; completion of cytokinesis
160
Q

cellular metabolism uses _____ to make ______

A

fuel to energy

161
Q

photosynthesis

A

uses sun’s energy to make carbohydrates by reducing CO2

-exact opposite of cellular respirtation

162
Q

light reactions

A
  • require light
  • goal-make energy
  • H2O —-> O2
  • NADP+—>NADPH (reducing agent)
163
Q

dark reactions

A
  • dont require light
  • ATP—> ADP
  • CO2—>carbohydrates
164
Q

location of photosynthesis

A

in chloroplasts of plants–membrane bound organelles
inner and outer membrane
**thylakoid membrane, full of chlorophyll (light absorbing molecules)

165
Q

location of dark reactions

A

stroma

166
Q

chlorophylls absorb ____ and _____

A

red light (600-700 nm) and blue light (400-500 nm)

167
Q

antennae chlorophyll molecules pass light energy to _____

A

reaction centers

168
Q

photophorphorylation

A

photosystems are part of an electron transport chain that creates a proton gradient
-the proton gradient powers ATP synthase

169
Q

light reaction path

A
  1. PS II P680–water turned into O2
  2. PQ (plastoquinon)
  3. Cyt b6/f complex
  4. PC
  5. PS I P700
  6. Fd (ferodoxin)
  7. FNR
  8. thylakoid membrane
  9. atp synthase
170
Q

final electron carrier of photosynthesis

A

NADPH

171
Q

lots of H+ on what side of thylakoid membrane

A

lumen

172
Q

less H+ on what side of thylakoid membrane

A

stroma

173
Q

location of light reactions

A

lumen of thylakoid

174
Q

go through how many rounds of dark reaction (calvin cycle) to get product?

A

3

175
Q

product of dark reaction

A

glyceraldehyde-3-phosphate used to make carbs and glycolysis

176
Q

RuBisCo

A

major enzyme used in dark reactions
starts off reaction
one of the most abundant enzymes on planet

177
Q

carbon fixation

A

turning carbon dioxides into sugars

costs a lot of ATP and NADPH which you get from light reactions which get their energy from the sun

178
Q

3 CO2—->

A

1 glyceride-3-phosphate

DAT (1 decks)

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