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Biology 6B > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

What is the induced fit model?

A

as substrate binds to the enzyme, the fit bends so that the substrate induces protein to be the correct shape and allows the reaction to occur

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2
Q

substrate-action-“ase”

ex: glucose phosphorylase

A

the naming of an enzyme

ex: an enzyme that adds phosphate to glucose

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3
Q

what is an isoenzyme?

A

a different version of an enzyme made by different organs and tissues that have the same activity

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4
Q

What regulates enzyme activity? (5 factors)

A
  1. Mass action: the concentration of substrates and products
  2. The concentration of enzymes: more enzymes = more binding
  3. Alteration of enzyme structure: Activation, Temperature, pH
  4. Cofactors and Coenzymes
  5. Inhibitors
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5
Q

Law of mass action

A

reversible reactions will be driven from the
side of the equation where concentration is higher to the side where the concentration is lower
ex: H20+CO2 ⇆ H2CO3

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6
Q

Will adding more substrate increase reaction time?

A

YES BUT ONLY UNTIL SATURATION: Adding more substrates will increase reaction time until all the enzymes are saturated, meaning there will be a plateau of speed when enzyme is saturated

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7
Q

What will increase the reaction time?

A

Adding more enzyme

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8
Q

What is the reason behind zymogens?

A

zymogens are inactive enzymes that are used for urgent processes, like in digestion, to have them in stock when needed

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9
Q

how to activate zymogens?

A

The part of the polypeptide that is blocking the active site is hydrolyzed “cut” of

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10
Q

What does an enzyme need to bind correctly to a substrate?

A

correct 3-D shape, correct polar and non-polar groups, correct distribution of charges

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11
Q

What destroys “denatures” an enzyme’s shape?

A

Heat and Acid (pH)

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12
Q

What are Cofactors?

A

A mineral that binds to an enzyme that (temporarily) alters the shape to make the active sites available to different substrates

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13
Q

What are Coenzymes?

A

Organic molecules derived from water-soluble vitamins that make reactions more likely to occur by changing the shape of a substrate

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14
Q

What are Competitive Inhibitors?

A

a shape that partially fits in the active site that blocks substrate from binding to enzyme

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15
Q

What are Allosteric Inhibitors?

A

binds to different parts of the enzyme that change its shape meaning that the active site no longer will fit that substrate

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16
Q

What is Ligand?

A

Something that binds to a binding protien

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17
Q

What are the 3 characteristics that all binding proteins have in common?

A
  1. Specificity: bind to a narrow range of ligands
  2. Saturation: a bigger concentration gradient is not going to affect the speed of reaction
  3. Competitive Inhibition: alternative ligands will compete with the normal ligand for the active site, therefore, inhibit the normal activity of that binding protein
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18
Q

What are coupled reactions?

A

Catalysis of one reaction allows the catalysis of a second reaction by a different active site on the same enzyme (both reactions have to occur for either to occur)

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19
Q

What is Exergonic?

A

[Exer = Out] releases energy, products have less potential energy than the reactants
A –> B + C + heat
heat is a product = energy is released

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20
Q

What is Endergonic?

A

Requires energy, The products of reaction has more potential energy than the reactants, absorbs free energy from the environment
ex: in cells ATP is usually the source of energy for an endergonic reaction

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21
Q

What is a coupled bioenergetic reaction?

A

the energy released by the exergonic reaction is used to power the endergonic reaction

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22
Q

What is a spontaneous change?

A

The released free energy can be harnessed to do work

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23
Q

More free energy (higher G)

A

less stable and greater work capacity

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24
Q

Less free energy (lower G)

A

more stable and less work capacity

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25
What is the relation of an Exergonic reaction to ATP?
Removes phosphate from ATP and releases energy | A-P-P --> P
26
What is the relation of an Endergonic reaction to ATP?
Transfer of phosphate to glucose and stores energy | A-P-P+P
27
What is a Catabolic pathway?
breaking down of macromolecules | Releases energy that may be used to produce ATP
28
What is an Anabolic pathway?
building up of macromolecules. | Requires energy from ATP
29
What is the structure of ATP?
three phosphates, attached to ribose, attached to an adenine nucleotide
30
What is Hydrolysis?
breaking bonds with the addition of water | ex: breaking the bonds that join the phosphate groups in an ATP molecule
31
List the pyrimidines
cytosine, thymine, and uracil (in RNA)
32
List the Purines
Adenine and Guanine
33
What are the 3 components of the DNA nucleotide?
3 phosphates, a pentose sugar, and a nitrogenous base (G,A,T,C)
34
Where is the phosphate located on a DNA nucleotide?
the 5' carbon of the sugar
35
Which direction does a nucleic acid polymer run?
5' to 3'
36
What is Anti-Parallel?
both strands run in different directions 5'-3' 3'-5'
37
What type of bond holds together nitrogenous bases?
hydrogen bonds
38
What type of bonds holds together DNA's sugars?
phosphodiester bonds
39
What pairs with A in DNA?
T
40
What is the complementary pair with A in DNA? How many hydrogen bonds hold it together?
T with 2 H bonds
41
What is the complementary pair with G in DNA? How many hydrogen bonds hold it together?
C with 3 H bonds
42
What is the semiconservative model?
Each strand serves as a template for a new strand. Each daughter cell gets one original template strand and one complementary strand
43
What needs to happen for DNA to be read?
Hydrogen bonds need to unzip DNA and then reform between new strands
44
What is the DNA template model?
the old strand acts as a template that tells the machinery how to make the new strand
45
What are the enzymes of DNA replication?
1. DNA Helicase: UNZIPS DNA 2. DNA Polymerase: catalyzes the building polymer of DNA (ADDS new nucleotides to the 3' end) and also helps in proof-reading 3. DNA Ligase: JOINS the pieces together
46
Which direction is DNA added?
only added to the 3' end
47
What is the difference between the leading strand of DNA vs the lagging strand?
the leading strand can be built continuously (5'->3') whereas the lagging strand is built in fragment called Okazaki fragments that are joined (ligated) later
48
What is primase?
Starts the DNA replication process by laying down a primer which is RNA complementary to the exposed DNA (needed before DNA polymerase) (primase before every Okazaki fragment and one primase on the leading strand)
49
What is the origin of replication?
a special site on a DNA strand where the two strands being and replication starts (think replication bubble)
50
purine have ___ rings
2 rings
51
pyrimidines have _____ rings
1 ring
52
true or false | the DNA sugar has OH - H on its carbon
True DNA has only 2 oxygen atoms on its pentose sugar
53
true or false | the DNA sugar has OH - OH on its carbon
False, this describes RNA
54
What enzyme proofreads and replaces any incorrect nucleotides?
DNA Polymerase
55
What limits the number of times DNA can be replicated? What is the loophole to this fact?
The ends of eukaryotic chromosomal DNA get shorter with each round of replication due to the There overhang of DNA left which gets digested Telomers “tie off” the ends to protect them from unraveling or degrading
56
Do telomeres get shorter as we age?
Yes
57
What does Telomerase do?
in germ cells, telomerase catalyzes the lengthening of telomeres so no genes are lost in gametes
58
How does Telomerase extend DNA?
extends DNA ends by using its own built-in RNA template
59
What is the difference between DNA and RNA molecules?
DNA is usually double-stranded, whereas RNA is usually single-stranded
60
How many oxygen atoms are on RNA?
three oxygen atoms | OH-OH
61
What is gene expression?
taking a bit of DNA (gene) → make a working copy of that gene → taking that copy to a workshop "ribosome" → use the copied instructions to build a protein
62
What is a gene?
a unit of hereditary either asexually or sexually | a gene is a tiny bit of DNA
63
What is the structure of a gene?
a short sequence of DNA nucleotides | one chromosome carries hundreds of genes
64
What is the function of a gene?
Each gene codes for a different polypeptide
65
What is the central dogma of biology?
DNA ← (replication) ← DNA → transcription → RNA → translation → proteins → structural proteins, carrier, enzymatic/hormonal
66
What is mRNA?
mRNA uses the information in genes to create a blueprint for making proteins mRNA is made from DNA
67
Describe the process of gene expression
DNA synthesizes mRNA (a copy of genes) in the nucleus → mRNA leaves the nucleus into the cytoplasm → the ribosome then uses the info in mRNA to build a polypeptide out of amino acids
68
what are the complementary base pairs in RNA?
A→U G→C | wherever there is a T in DNA a U will be used in RNA
69
What are the 2 stages of gene expression?
Transcription: DNA is used as a template to transcribe a complimentary copy of RNA Translation: RNA goes into a ribosome to construct a protein
70
What are the steps of transcription?
a specific gene is turned on → (initiation) Starts at Promoter: DNA region before a gene → (Elongation) copy of RNA → (termination) Ends at Terminator: DNA region at the end of a gene
71
Describe the initiation process of RNA transcription
RNA polymerase binds to the promoter region of DNA and separates the two double strands of the DNA template and initiates RNA synthesis
72
Describe the elongation process of RNA transcription
polymerase moves down DNA 3' -> 5' and elongates RNA by adding new RNA nucleotides on newly synthesized end. DNA is unwound and the RNA transcript is elongated (synthesized) 5' -> 3' (only adds on the 3' end). After transcription DNA is reformed (only separated while in polymerase bubble)
73
What are transcription factors?
Proteins that bind to the promoter. Facilitate binding of polymerase
74
Describe the termination process of RNA transcription
The RNA transcript is released, and the polymerase detaches from the DNA
75
Where is the promoter located
upstream 25 baes from the gene
76
Where is the promoter located and how can you recognize it?
upstream 25 baes from the gene you can recognize it from the TATA box
77
How many bases are unzipped in RNA transcription?
10-20 bases at a time
78
How is RNA transcription terminated in prokaryotes?
Transcribed RNA forms “GC hairpin" which causes RNA polymerase to fall off terminating transcription
79
How is RNA transcription terminated in Eukaryotes?
The Polyadenylation signal (rich in A's and T's from DNA) tells an enzyme to clip off the RNA transcript, w RNA polymerase still continues to transcribe downstream for a bit before disconnecting.
80
What is the processing of “primary transcript” in RNA
it's the modification of transcripted RNA with the addition of the 5' cap and the poly-A tail this only happens in eukaryotes and helps the RNA to last longer in the cytoplasm (this can help to use more information)
81
What is RNA splicing?
introns (inserted region within the gene with no info) are cut out and the exons can be spliced together to make the correct gene
82
What are introns?
intervening sequences – non-coding regions of DNA within a gene
83
What are codons?
3 RNA nucleotides in a row used as "words" | each codon represents a specific amino acid
84
What is the purpose of translation? Where does it take place?
the sequence of mRNA codons determines the sequence of amino acids in the polypeptide it takes place in the ribosome
85
What do tRNA's do?
tRNAs translate the sequence of 3-base nucleotide “words” (codons) into a sequence of amino acids in a polypeptide
86
What is an anticodon?
A triplet sequence on tRNA that base pairs with a mRNA codon
87
What does aminoacyl-tRNA synthetase do?
Joins a specific amino acid to a specific tRNA
88
Describe the Initiation of Translation
mRNA binds to ribosome at start codon (AUG) tRNA binds to mRNA (anticodon to codon)
89
Describe the Elongation of Translation
tRNA binds to A site, Adjacent amino acids linked, tRNA in P site leaves, Ribosome moves to the next codon
90
Describe the Termination of Translation
When the ribosome reaches the stop codon, a releasing factor (protein) binds to the codon instead of a tRNA, Polypeptide is released from tRNA, Ribosome is then released from mRNA
91
What are mutations?
Changes in the DNA which results in changes to RNA which changes the protein
92
What is a point mutation?
change in a single base pair
93
What is a substitution mutation?
one base pair is replaced by a different base pair
94
What is a deletion mutation?
removal of at least one nucleotide in a gene
95
What is an insertion mutation?
addition of genetic material
96
What is a Frameshift mutation?
insertion or deletion to make the codon more than three nucleotides changes the whole downstream sequence!
97
What is a silent mutation?
a mutation that codes for the same thing so no change from the mutation
98
What is a missense mutation?
Makes a different version of a polypeptide - wrong codon
99
What is a nonsense mutation
does not have a code for what that spells out - no polypeptide

Biology 6B (2 decks)

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