Exam 3 Flashcards
1
Q
What kind of reaction is used when you are using ADP to build up ATP?
A
An anabolic reaction
2
Q
What kind of reaction is used when you are breaking down ATP to ADP?
A
A catabolic reaction
3
Q
What is hydrolysis?
A
ATP that is released in water
4
Q
What happens to the water in a hydrolysis reaction?
A
The water temperature rises
5
Q
What are enzymes made out of?
A
Proteins
6
Q
What do enzymes bind to?
A
To substrates
7
Q
What part of the enzyme do substrates bind to?
A
The active site
8
Q
What shape/form is the active site?
A
The same as the substrate that binds with the enzyme (it is complementary)
9
Q
How do substrates bind to an active site?
A
By non-covalent attractions (non-covalent bonds)
10
Q
What are some types of non-covalent bonds?
A
ionic bonds, hydrogen bonds, Vander wall attractions
11
Q
What is induced fit?
A
When enzymes change shape to maximize interactions between amino acids and substrates
12
Q
What is catalysis?
A
Converting the substrate to the product in the enzyme
13
Q
What is the cycle of enzyme activity?
A
E + S forms ES then to forms into EP then it lets go of P and becomes E + P ( E = enzyme, P = product, S = substrate) LOOK AT PICTURE IN THE PICTURE TAB
14
Q
In enzyme activity what does energy need to overcome to get to the product?
A
It needs to overcome the energy barrier
15
Q
What is activation energy in enzyme activity?
A
The amount of energy needed to overcome the energy barrier that leads to the next lower stable state
16
Q
What is the transition state in enzyme activity?
A
Input of activation energy
17
Q
What is free energy change?
A
It is the free energy of the products minus the free energy of the reactants
18
Q
What electrical charge will free energy always be?
A
Negative
19
Q
What provides the activation energy that is needed to overcome the energy barrier?
A
Enzymes
20
Q
Why are enzymes used the most to provide activation energy to overcome the energy barrier?
A
Because it doesn’t rely on chance collision, carries out specific reactions
21
Q
Why isn’t thermal energy used that much to provide activation energy to overcome the energy barrier?
A
Because in lower temps they don’t have enough force or speed to bind together so the molecules bounce off each other.
In higher temps they do have enough force and speed to bind together but the probability of it happening is really low. It relies on Chance collision. And molecules/cells can die because of high temps.
22
Q
What different factors affect enzyme effectiveness?
A
Temperature
PH levels
Substrate concentration
Presence of Co factors
presence of inhibitors
23
Q
What are enzyme cofactors?
A
Any non-protein molecule or ion that is required for the proper functioning of the enzyme
24
Q
How does temperature affect enzyme activity?
A
High temperature speeds up the reaction
Low temperature slows down the reaction
25
How does the PH levels affect enzyme activity?
PH levels need to be at the optimal level for the enzyme to be at it's most effective point. If the PH levels are above or below the optimal level then the enzyme activity decreases.
26
How does substrate concentration affect enzyme activity?
Increasing substrate increases enzyme activity to a certain point until all the enzymes are bound to a substrate.
Decreasing substrate decreases enzyme activity
27
How does the presence of cofactors affect enzyme activity?
The increase of cofactors will increase the enzyme activity
The decrease of cofactors decreases enzyme activity drastically
28
How do enzymes work?
Enzymes work by lowering the activation energy required
Enzymes speed up the reaction by lowering the activation energy
29
What are the different types of inhibitors?
Competitive inhibitors, Allosteric regulation
30
What is the function of a competitive inhibitor?
They fight the substrate to the active site and turn off the enzyme
31
What is the function of an allosteric reaction?
They bind to the regulatory site of an enzyme and they turn on the enzyme and help with its function that it needs to perform
32
What function is performed for allosteric inactivation?
Binds to the regulatory site of an enzyme and turns off the enzyme so it can not perform its function
33
What is cooperation in an enzyme?
It is where a substrate binds to one of the active sites in an enzyme and puts all the other active sites in their active form. (basically make all of the other active sites the same)
34
What is feedback inhibition in an enzyme?
It is where the product of the enzyme acts as an inhibitor and goes back into the same enzyme and helps to control it (either turns it on or turns it off)
35
What is the active site?
The place where substrates bind to the enzyme
36
What is the regulatory site?
Where the allosteric activators and allosteric inhibitors bind to the enzyme and either turn it on or off.
37
What do cells need energy for?
chemical, mechanical, transport work
38
What is reduction?
the gaining of electrons
39
What is oxidation?
the losing of electrons
40
What are redox reactions?
The transfer of electrons between electrons
41
What follows electrons?
hydrogens
42
What are the 3 differences between reduction and oxidation?
Look for a change in the charge
Look for a change in the number of hydrogens
Look for a change in the number of oxygens
43
What are the reduced forms in each scenario?
Fe=+2 VS Fe +
NH3 VS N2
CH4 vs CO2
Fe+, NH3, CH4
44
What are the two ways that energy can be transferred?
1. they jump down to the end and bind to the oxygen and explode
2. they move step by step and release little bit of energy at a time (cellular respiration)
45
What carries out cellular respiration?
enzymes
46
What is the function of NADH+ and FAD?
to carry electrons to the electron transport chain
47
When NAD+ and FAD are carrying the electrons to the electron transport change. What do they turn into?
NADH and FADH2
48
What does glycolysis start off with?
glucose
49
where does glycolysis take place?
in the cytosol of the cell
50
what are the 2 stages in glycolysis?
The investment stage, the energy payoff stage
51
What happens in the investment stage in glycolysis?
It uses 5 different enzymes, has to receive 2 ATPs to start the process, and NADH+ comes in and takes the electrons and turns into NADH
52
What happens in the payoff stage in glycolysis?
Produces 4 ATP's but only get a net gain of 2 ATPs, and get the molecule pyruvate
53
What are the inputs of glycolysis?
glucose (1), ATP (2), NAD+ (2)
54
What are the products of glycolysis?
pyruvates (2), ATP (4), NAD+ (2)
55
What is the role of Coenzyme A in pyruvate oxidation?
To make the molecule more reactive so it can interact with other molecules
56
Where does pyruvate oxidation take place?
in the matrix of the mitochondria
57
How do the pyruvates get into the matrix of the mitochondria to start the pyruvate oxidation process?
They use a transport protein
58
What does the pyruvate oxidation process start with?
2 pyruvates
59
What are the steps of the pyruvate process?
CO2 is cut off from the pyruvate, electrons are stripped and taken by NAD+ which turns into NADH, Coenzyme A attaches to from acetyl CoA
60
What are the inputs in the pyruvate oxidation process?
pyruvates, NAD+, CoA
61
What are the products in the pyruvate oxidation process?
CO2 (2), acetyl CoA (2), NAD+ (2)
62
Where does the citric acid cycle take place?
in the mitochondrial matrix
63
What does the citric acid cycle start with to begin it's process?
Acetyl CoA
64
What type of electrons does FAD take to the electron transport chain?
electrons that have less energy
65
What type of electrons does NAD+ take to the electron transport chain?
Electrons that have more energy
66
What are the steps of the citric acid cycle?
Acetyl- CoA (2 carbons)is joined with Oxaloacetate (4 carbons) to make citric acid (6 carbons). Coenzyme A is released, Citric acid is oxidized in a series of oxidation reactions, 2 CO2 are released , GTP is made into ATP
67
What are the inputs in the citric acid cycle?
Acetyl-CoA, NAD+ (3), FAD (1), GTP +PI
68
What are the products in the citric acid cycle?
NADH (3), CO2 (2), GTP (1ATP), FADH2 (1)
69
Where does the electron transport chain take place?
in the mitochondrial membrane
70
What does the electron transport chain start with to start the process?
NADH, FADH2
71
What are the steps of the electron transport chain?
NADH and FADH2 transfer electrons to complex 1 (then turn back into NADH+ and FAD), Electrons are passed through the electron transport chain in this order. 1. complex 1 2. Coenzyme Q 3. Complex 3 4. cytochrome C 5. complex 4, With every transfer electrons give off energy (that energy is used to pump electrons, and establish a proton gradient)
72
What are the inputs of the electron transport chain?
NAD+
FADH2
O2
3-4 H+ (hydrogen ions)
ADP +Pi (inorganic phosphate)
73
What are the outputs of the electron transport chain?
NAD+
FAD
H2O
Proton gradient
3-4 H+ (hydrogen ions
ATP
74
What is chemiosmosis?
Where hydrogen ions and ADP + PI move down their gradient, through a channel in ATP synthase
75
How can chemiosmosis function? (what energy is used to do chemiosmosis?)
potential energy is used to do the work
76
What is the enzyme called in chemiosmosis?
ATP synthase
77
Where does chemiosmosis take place?
In the mitochondrial membrane
78
What moves through the ATP synthase in chemiosmosis?
ADP + pi, and hydrogen ions
79
What does Pi stand for?
inorganic phosphate
80
How many ATPs does chemiosmosis often times produce?
28 ATPs
81
How many ATPs does glycolysis produce?
2 ATP
82
How many ATPs does the citric acid cycle produce?
2 ATP
83
How many ATPs does cellular respiration often times produce?
32 ATPs
84
What is anaerobic respiration and what are the steps of it?
It goes through the same exact cycle/steps of cellular respiration. BUT it DOES NOT use oxygen as the electron acceptor.
85
How can cellular respiration produce so much ATP?
It uses oxygen as it's electron acceptor
86
What is the electron acceptor in cellular respiration?
Oxygen
87
What other molecules are used as the electron acceptor in anaerobic respiration?
Sulfate and nitrate
88
Why is anaerobic respiration less effective than cellular respiration?
because they end up producing less protons and fewer ATP is produced
89
What is fermentation and it's steps?
A different way of getting energy, the do glycolysis but do not have an electron transport chain. So to get NAD+ back to NADH they dump/give their electrons to the pyruvate molecules.
90
How much ATP is gained in fermentation?
2 ATP
91
What other molecules can be used for cellular respiration?
Proteins, carbs, fats
92
What is deamination?
It is where amino acids are used in cellular respiration. Where N3H breaks off from the amino acid chain and goes through cellular respiration
93
How are fats used in cellular respiration?
The fat is broken down into glycerol and fatty acids and used in cellular respiration
94
What are photoautotrophs?
Organisms that get their energy from light and their organic carbon from themselves
95
What are chemoautotrophs?
Organisms that get their energy from chemical molecules (inorganic molecules) and their carbon from themselves. Eat other things to get their energy
96
What are photoheterotrophs?
Organisms that get their energy from light and their inorganic carbon from eating other things
97
What are chemoheterotrophs?
Organisms that get their energy from eating things and their inorganic carbon from eating other things as well
98
What are some examples of chemoheterotrophs?
Animals, humans
99
What are some examples of photoautotrophs?
Plants, algae
100
What are some examples of chemoautotrophs?
Organisms in the deep blue sea
101
What are some examples of photoheterotrophs?
Some kinds of bacteria
102
What is photosynthesis?
Transforming the energy of sunlight into chemical energy that is stored in sugars and other organic molecules
103
Where does photosynthesis take place in Eukaryotic, and prokaryotic cells?
Eukaryotes: In the chloroplast
Prokaryotes: In-folded membrane systems within the cell
104
What is light?
A form of electromagnetic energy
105
What determines how much energy is in a specific type of light?
The wavelengths in the light
106
How do you measure wavelengths?
From peak to peak or from troph to troph. (top to top or bottom to bottom)
107
What kind of wavelengths have more energy?
The shorter or more compact the wavelength is the more energy it has
108
What type of light is the main contributor in photosynthesis?
Visible light
109
What are pigments?
A molecules that reflects, transmits or absorbs light
110
What do plants use pigments for?
To absorb light
111
How can we see the color green?
Because the molecules absorb all of the other colors in ROYGBIV and reflect the color green so we can see that color
112
How can we see the color purple?
Because the molecules absorb all of the other colors in ROYGBIV and reflect the color purple so we can see that color
113
What is chlorophyll a?
The key light capturing pigment in photosynthesis
114
What are chlorophyll b and carotenoids?
They are accessory pigments to chlorophyll a (they help chlorophyll a in photosynthesis)
115
What happens when a photon strikes an isolated pigment?
An electron absorbs the energy from the photon and rises up to the excited state (a high energy level) then since it has no where to go it falls back down and gives off light and heat.
116
STUDY THE PHOTOSYSTEM
STUDY THE CALVIN CYCLE (watch those bioman videos and do interactive homework)
117
What happens to the protons in the photosystem?
They are being pumped from the stroma to the thylakoid system and then used to make ATP
118
What type of reactions are NAD used for?
Catabolic reactions (cellular respiration)
119
What type of reactions are NADPH used for?
Anabolic reactions mainly for the photosystems and the Calvin cycle (photosynthesis)
120
What does the calvin cycle need to have to start the cycle?
Carbon dioxide (CO2)
121
What does the calvin cycle produce?
Glucose (sugar)
122
What was the study that Gregor Mendel conducted?
He studied garden peas and cross pollenated them. He created the laws of inheritance
123
What was the study that Nettie Stevens conducted?
Studied meal worms. And found out that there were 2 chromosomes that varied by gender. Male = XY & Female = XX.
124
What was the study that Walter Sutton & Theodor Boveri conducted?
They studied grasshoppers and sea urchins. And observed chromosome replication during meiosis. And that chromosomes are related with inheritance.
125
What was the study that Thomas Hunt Morgan conducted?
He studied fruit flies and did breeding studies. He demonstrated that altered genes were sex-linked.
126
What was the study that Frederick Griffith conducted?
He studied pneumonia and injected the R strain and the S strain into rats. He injected the living S strain in the mouse and the mouse died. He injected the living R strain in the mouse and the mouse lived. He injected the dead S strain in the mouse and the mouse lived. He mixed living R strain and dead S strain and injected it into the mouse and then the mouse died. And by doing this he discovered the transforming factor
127
What was the study that scientists in the 1940s conducted?
They found out that chromosomes are made of both DNA and proteins. And that DNA consists of 4 bases and that proteins had 22 amino acids. And said DNA was too basic to make a code of a living organism.
128
What was the study that Erwin Chargaff conducted?
He studied the bases of DNA. And that A=T & G=C. and that DNA is not uniform and different living organisms can have different amounts of bases in their DNA. (example humans have less of the DNA base A than a sea urchin).
129
What was the study that Alfred Hershey and Martha Chase conducted?
They studied the virus bacteriophage T2. Fond out that it only consists of DNA and protein. And that DNA in the virus only goes into the bacterial cell.
130
What was the study that Rosalind Franklin conducted?
She studied X-ray pictures of DNA. Found the shape and the size of the individual DNA molecules. Found that DNA is in a double helix form.
131
What was the study that James Watson and Francis Crick conducted?
They made a DNA model from the pictures of Rosalind Franklin (that they stole).
132
What is the structure of DNA?
it contains a phosphate group, deoxyribose or ribose, and a nitrogenous base (ATGC) (a purine or a pyrimidine). And it is anti parallel (3 prime and 5 prime one way and then the opposite on the other).
133
What is the natural base paring of this DNA sequence?
A
T
G
C
A
C
T
A
C
G
T
G
134
How does DNA replication work?
At the beginning the DNA forms replication forks and replication bubbles. Inside the bubbles they form the semi conserved strands. (the DNA strands that are replicating the DNA). And it ALWAYS replicates from 5 prime to 3 prime (the top strand on the inside goes to the right and the bottom goes to the left).
135
What is the leading strand?
The strand on the inside that is continuous
136
What is the lagging strand?
The strand that goes in the opposite direction as the leading strand
137
What is the function of Helicase in DNA replication?
Opens up the template for DNA replications (the unzipper)
138
What is the function of Topoisomerase in DNA replication?
It cuts the DNA helix to relive the tension then it glues it back together (the chiller)
139
What is the function of SSBP (single stranded binding proteins) in DNA replication?
It stabilizes the single strand form of DNA (the stabilizer)
140
What is the function of DNA primase in DNA replication?
It reads the sequence and places RNA primers along the strand (the inhibitor)
141
What is the function of DNA polymerase I in DNA replication?
Adds bases of DNA where RNA has been cut out (the fixer)
142
What is the function of DNA polymerase III in DNA replication?
Synthesizes the leading and the lagging strands (the copier)
143
What is the function of DNA ligase in DNA replication?
Glues two DNA bases together (the gluer)
144
What type of errors happen in DNA replications?
pairing errors, DNA damaging (by UVU light, radiation), Chemical mutagens (by base analogs which look like a DNA base but don't act like one)
145
How can errors in DNA replication be made good again?
Proof reading by DNA ploymerase
146
How does proofreading work?
The nuclease comes in and cuts the nucleic acids int the DNA and leaves a gap then DNA polymerase I comes in a puts in new DNA bases then DNA ligase glues those bases together
147
What was the study Archibald Garrod performed?
Basically he developed the one gene = one enzyme hypothesis
148
What was the study that George Beadle and Edward Tatum perform?
They exposed bread mold to X- rays. And each enzyme lacked a different enzyme. It supported the one gene = one enzyme hypothesis.
149
What did scientist change the one gene= one enzyme hypothesis to?
one gene = one polypeptide
150
Complex enzymes are made out of?
Multiple polypeptide chains
151
What do genes code for?
ALWAYS for RNA and sometimes for proteins
152
What is the coding strand?
The top strand of the DNA and has the same sequence as RNA polymerase
153
What is the template strand?
Is the bottom strand of DNA and is the strand that RNA polymerase reads
154
What is the role of RNA polymerase?
It comes into the DNA and reads the template strand. to make a copy of it. As it is reading it instead of pairing the the A's with T's it pairs it with U's and vice versa
155
How do you read the table of RNA codons?
The first letter us the letter on the left row the second is on the top and the third is on the right row
156
Organisms that live in a hot spring, what DNA bases are they most likely to favor in their DNA?
G & C because they have 3 bonds instead of A & T which has 2 bonds
157
What is the promotor in DNA transcription in bacterial & eukaryotic cells?
It marks the beginning of a gene so RNA polymerase can come and start the process
158
What is the initiation in DNA transcription in bacterial cells?
Where the promoter marks the beginning of the gene for RNA polymerase and starts unwinding the DNA strand
159
What is the initiation in DNA transcription in bacterial cells?
Where RNA polymerase starts off by unwinding the DNA and starts the process
160
What is the elongation in DNA transcription in bacterial & Eukaryotic cells?
Where RNA polymerase reads the template strand and makes a RNA transcript
161
What is the termination in DNA transcription in bacterial & Eukaryotic cells?
Where the RNA polymerase completes the RNA transcript and goes off from the DNA
162
What is the initiation in DNA transcription in & Eukaryotic cells?
The RNA polymerase cannot recognize the start point so it needs the transcription factors to lasso it into the start point then it turns it on by adding a phosphate then finally RNA polymerase can start the copying of the template strand
163
What is the photosystem and what does it do?
Basically it depends on light. Light hits photosystem 2 which excite the electrons and moves them through the electron transport chain to photosystem 1. As it is going through the electron transport chain hydrogens go through the membrane and chill there. Then when the electrons are in photosystem 1 they wait for light to hit photosystem 1 then they go through the electron transport chain and are picked up by nadp + which turns into nadph and are taken to the Calvin cycle.
164
What are the 3 steps of processing in RNA?
5 prime cap
Splicing (removal of the introns)
3 prime poly A tail
165
What are frameshift mutations?
Shifts the reading frame
166
What is the reading frame?
(reading frame = group of three DNA bases)
167
What are insertion mutations?
adds one or more bases to a group of 3 bases and changes the rest of the bases along the line
168
What are deletion mutations?
Removes one or more bases and changes the rest of the bases along the line
169
What are point mutations?
A single nucleotide base changes in DNA sequence but does not ruin the rest of the bases in the line
170
What are missense mutations?
A single amino acid change happens within the protein and doesn’t change the rest of the amino acid bases in the line
171
What are nonsense mutations?
Creates a premature stop codon in the amino acid chain. Turns an amino acid into a stop codon
172
What are silent mutations?
Change in a nucleotide that does not change the amino acid (doesn't have an effect on the end product of the protein)
173
What are differential gene expressions?
Expression of different genes by cells with the same genome
174
Why do we have differential genes?
Allows cells to respond to changes in the environment
Allows cells to differentiate
175
How does bacteria cells respond to change?
Feed-back inhibition, Product of pathway stops it's own production (when production gets too much it stops (tryptophan) the production of the original enzyme)
it is a Rapid response
176
What is transcription regulation?
Product of pathway stops (tryptophan) transcription and doesn’t make mRNA
it is a Slow response
177
What are operons in transcription regulation?
2 or more genes whose products function in a common pathway that are controlled by a single promoter and operator
178
What is the operator and its function in transcription regulation?
Binding site for the repressor protein
(on/off switch)
179
What is the repressor protein and what is its function?
Prevents RNA polymerase from transcribing or from binding
180
What is the active form of a repressor protein?
it inhibits (stops) the expression of the operons
181
What is the inactive form of a repressor protein?
It allows the mRNA to do the transcribing it doesn't stop it
182
What is the function of a corepressor?
It binds to the repressor protein that activates it to bind to the operator
183
What is the role of the trp operon?
To produce trytophan
184
What is the default state of the trp repressor?
Inactive
185
What is the corepressor in the trp operon?
Tryptophan
186
What is the state of the trp repressor when the corepressor is bound to it?
Active
187
What is the state of the trp operon when the corepressor binds to the repressor?
Inactive
188
What conditions cause trp operon to be repressed?
When there is enough tryptophan already
189
When will the cell de-repress the trp operon?
When there is not enough tryptophan
190
What is the role of the lac operon?
To break down lactose
191
What is the default state of the lac repressor?
Active
192
What is the corepressor in the lac operon?
Lactose
193
What is the state of the lac repressor when the corepressor binds to it?
Inactive
194
What is the state of the lac operon when the corepressor binds to the repressor?
Active
195
What conditions cause the lac operon to be repressed?
When there is no lactose present
196
When will the cell de-repress the lac operon?
When lactose is present
197
What is negative and positive gene regulation?
Negative = Operons are switched off by the active form of their respective repressor proteins
Positive = A protein interacts with the DNA and transcription turns on
198
Explain the positive gene regulation in lac operon.
When the glucose levels are low in the lac operon, cAMP binds to the inactive CRP then activates the CRP and the lac operon will be turned on
199
Explain the negative gene regulation in lac operon.
It's the normal way like you just explained bc you're so smart haha
200
Explain the negative gene regulation in the trp operon
It's the normal way like you just explained bc you're so smart haha
201
What happens in gene regulation and chromatin?
Tightly packed means genes are hidden and not available (Heterochromatin) and loosely packed means genes are not hidden and available (Euchromatin)
202
What groups tighten chromatin and what groups loosen them?
Acetylation group = loosens chromatin
Phosphorylation group = loosens chromatin
Methylation group = condenses chromatin
203
How are genes expressed when there is a lot of methylation, not a lot of methylation, and when there is a normal amount of methylation?
More methylation = no expression
Less or no methylation = high expression
Normal amount of methylation (some methylation) = normal expression
204
What are specialized transcription factors?
They enhance the activity of the gene or silence it, they do not bind to the promoter. Either bind before the promoter or after the promoter
205
What are general specialized transcription factors?
They do the same thing and bind to the promoter
