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Microbiology 2125 > Unit 3- Phylogeny, Metabolism, and Genetics > Flashcards

Unit 3- Phylogeny, Metabolism, and Genetics Flashcards

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1
Q

Define parsimony

A

the shortest possible tree that explains the data is considered best

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2
Q

What is parsimony’s utility in the sciences generally

A

It helps ensure data is presented efficiently without filler or jargon

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3
Q

What are the 3 different types of secondary structures of proteins?

A

Random Coils, Alpha Helices, and Beta Pleated sheets

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4
Q

Uracil is found only in

A

RNA

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5
Q

Thymine is found only in

A

DNA

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6
Q

What is the direction DNA is replicated in?

A

5’ to 3’ on its respective strand

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7
Q

what is the Central Dogma of Biology?

A

DNA-> RNA-> Proteins

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8
Q

What are the different types of genomic DNA found in Eukaryotes?

A

Nuclear, Mitochondrial, Chloroplast

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9
Q

What is the purpose of the cladistic method and phylogenetic systematics

A

The cladistic method visually shows the evolutionary and phylogenetic history of organisms. It illustrates mutation and speciation events

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10
Q

Define Phylogeny

A

the natural relatedness between groups of living things

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11
Q

Distinguish between Character and Character-State

A

Characters are traits which help identify organisms, which can be phenotypic, genotypic, biochemical, or molecular. The character-state (0,1,2,3,4) Helps identify whether or not the trait is ancestral or derived (0 vs 1,2,3,4)

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12
Q

What is the difference between ancestral and derived character-states?

A

Ancestral states are those which are original to the common ancestor and not changed. Derived states (1, 2, etc.) are those which have changed from the common ancestor

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13
Q

What is the significance of an outgroup?

A

An outgroup shows one organism with all ancestral traits and is used as a means of mutation/speciation identification within a taxon data matrix

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14
Q

Define Monophyletic

A

A Group of organisms classified in the same taxon and share a common ancestor

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15
Q

Define Parsimony

A

The Simplest explanation for data is most likely to be correct

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16
Q

What is the difference between a character by taxon data matrix, a cladogram, and a Venn Diagram

A

a Taxon Data Matrix is a grid which represents character changes by evolutionary history with an outgroup and the corresponding speciation events A Cladogram shows in visual tree form, how organisms speciated from a common ancestor over time A Venn Diagram is a visual representation of comparing and contrasting traits for different organisms

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17
Q

Explain how mutations (nucleotide substitutions and insertions/deletions) change DNA sequences

A

Frameshift mutations could cause an early or late stop codon(Insertion/deletion) and a substitution could be a silent or missense mutation

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18
Q

What is the significance of R-Groups? How do they make Amino Acids different?

A

R Goups’ placement in a formula indicates that the group attached to that site varies from one compound to another

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19
Q

Protein’s Primary structure

A

Amino Acid Chains

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20
Q

Protein’s Secondary Structure

A

beta Pleated sheets, Alpha Helices, and Random coils

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21
Q

Protein Tertiary Structure

A

Secondary structures bonded by disulfide bonds (3D state)

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22
Q

Protein Quaternary Structure

A

More than 1 polypeptide, has subunits, and features the 1st 3 structure types

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23
Q

What is a protein’s native conformation?

A

3-D correct state of a protein. If it’s altered, it’s considered denatured

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24
Q

What is a protein subunit

A

A single protein molecule that assembles with other protein molecules to form a protein complex

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25
What is the significance of active sites with regard to enzyme function?
Active site binds to the substrate to catalyze a reaction
26
What is the significance of Allosteric sites with regard to enzyme function?
The altered activity of an enzyme due to the bonding of a molecule to a region other than the active site
27
what effect do factors such as pH, temperature, salt concentration and the presence of activators or inhibitors have on enzyme function?
They all have the ability to denature the protein and cause loss of function
28
What is Enzyme/Protein denaturation?
Alteration of native conformation and function by breaking bonds
29
Define Cofactor
An Enzyme accessory, usually a metallic Ion
30
Define a Coenzyme
Serves as transient carriers of specific atoms or functional groups during metabolic reactions. They operate in conjunction with an enzyme
31
What is the difference between competitive/noncompetitive enzyme inhibitors
Competetive enzyme inhibitors bind to the active site Noncompetitive enzyme inhibitors bond off the active site, but change conformation of the protein
32
What is a spontaneous reaction?
A reaction that does not require an enzyme to catalyze it
33
What is a nonspontaneous reaction?
A reaction that requires an enzyme and ATP to catalyze the reaction
34
What is an endergonic reaction
A reaction that absorbs surrounding energy
35
What is an Exergonic reaction
A reaction that releases energy into the surroundings
36
Why are enzymes in an experiment not considered part of the reactants or products?
Because they catalyze the reaction and are not participating or being created.
37
how can the cell can perform energy requiring/consuming reactions through energy coupling
The Transfer of energy from endergonic to exergonic processes or by Catabolism to anabolism
38
What is the role of phosphorylation/dephosphorylation in metabolism?
Add a Phosphate group to ADP to make ATP Remove a phosphate group from ADP or ATP to make AMP or ADP
39
What is the function of ATP in a cell?
ATP is the energy currency in the cell
40
What is ATP's Structure?
Adenosine and 3 Phosphate groups
41
Explain how ATP/ADP/AMP can gain or lose through phosphorylation and hydrolysis
Hydrolysis breaks off a phosphate group (AMP or ADP) and Phosphorylation adds a phosphate group (ADP or ATP)
42
Oxidation
A loss of electrons
43
Reduction
A gain of electrons
44
Describe the basic structure and functional role of NAD+ and contrast it with NADH
NAD+ is reduced, NADH is oxidized
45
Describe the basic structure and functional role of FAD and contrast it with FADH2
FAD is reduced, FADH2 is oxidized
46
Number of carbon atoms in glucose
6
47
Number of carbon atoms in pyruvate
3
48
Number of Carbon atoms in G3P
3
49
Number of Carbon atoms in Citric Acid
5
50
Where does the citric acid cycle occur in the cell?
Eukaryotic (Mitochondria) Cell Membrane (Prokaryotic)
51
How is a proton gradient created and how this gradient is used to synthesize ATP (by ATP synthase) by chemiosmosis
In the ETC, the proton gradient is used to oxidize and reduce each protein subunit to force an ADP and Phosphate group together at the ATP Synthase to generate ATP
52
What is the role of oxygen in Cellular respiration?
Oxygen allows substrate-level and oxidative phosphorylation to occur. Oxygen is also the final electron acceptor
53
Explain the difference between substrate-level and oxidative phosphorylation;
Substate Level- Citric Acid Cycle Oxidative- ETC/S
54
Explain the difference between substrate-level and oxidative phosphorylation;
Substate Level- Citric Acid Cycle Oxidative- ETC/S
55
Explain under what conditions it becomes necessary for a cell to switch to a fermentation pathway and the benefit of performing fermentation (as opposed to cellular respiration) under such conditions
Anaerobic conditions (No Oxygen) forces the cell into a fermentation pathway
56
Describe how other compounds (nitrates and carbonates) can be used as final electron acceptors in (anaerobic) respiration
Nitrates and carbonates all have oxygen in them and can suffice as final electron acceptors because of Oxygen's electron affinity.
57
Complementary Base Pairing
A-T G-C
58
Sense Strand
The strand with the coding sequence for a specific gene
59
Antisense strand
the strand with the complement of the coding sequence for a specific gene
60
Triplet Code
the standard version of the genetic code, in which a sequence of three nucleotides in a DNA or RNA molecule codes for a specific amino acid in protein synthesis
61
Antiparallel strands
each strand runs in 5' to 3' direction oppositely
62
Degenerate code
The genetic code is degenerate because there are many instances in which different codons specify the same amino acid
63
What is the structure of DNA
Features Deoxyribose Double-Stranded Contains Thymine in base pairs Sugar-Phosphate backbone
64
What is the difference between Ribose and Deoxyribose
Ribose contains oxygen Deoxyribose does not contain oxygen
65
What does 5' and 3' mean?
The directionality of nucleic acids
66
mRNA (Messenger RNA)
Translated from the sense strand of DNA
67
rRNA
Make up ribosomal subunits for translation
68
tRNA
Hold the anticodons and amino acids for polypeptide chain synthesis
69
Central Dogma of Biology
DNA-\> RNA-\> Protein
70
What is a genome?
All DNA in a cell
71
What is a Proteome?
All Proteins in a cell
72
What is a Metabolome?
All DNA, RNA, and Protein data in a cell
73
Transcriptome?
All RNA in a cell
74
Define Gene
the site on a chromosome that provides the information for a certain cell function
75
Define Chromosome
Tightly coiled bodies within the cell, composed of DNA, and are primary locations for genetic material
76
Define Chromatin
Genetic material in the nucleus (uncoiled)
77
What is the nature of the chromosomes in prokaryotes?
Single, Circular chromosome
78
What is the nature of chromosomes in eukaryotes?
Multiple, tightly coiled chromosomes in a nucleus
79
What is the structure of bacterial ribosomes
Large and Small subunits
80
What is the structure of bacterial ribosomes
Large and Small subunits
81
What are the different types of genomic DNA found in eukaryotes?
Nuclear Mitochondria Chloroplast
82
Define Codon
Triplet code that corresponds with an amino acid
83
Define Anticodon
Anticodons are located on tRNA molecules and are complementary of the codon and adds to the amino acid chain
84
What is the role of RNA Polymerase in transcription
RNA Polymerase copies DNA and transcribes it into mRNA
85
What is the role of transcription factors in transcription
a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence
86
Sense Strand of DNA
contains the coding information for a particular gene
87
Antisense strand of DNA
is a complement of the sense strand and holds noncoding information for that gene
88
Purines
Nitrogenous bases Adenine and Guanine
89
Pyrimidines
Nitrogenous Bases Cytosine Thymine Guanine
90
Purines | (Adenine, Guanine)
91
Pyrimidines
92
RNA
93
Sugar-Phosphate Backbone
94
DNA
95
Electron Transport Chain
96
Citric Acid Cycle
97
Glycolysis
98
Pyruvate Dehydrogenase Complex (Pyruvate/Pyruvic Acid converted into Acetyl CoA)
99
How many hydrogen bonds are between Adenine and Thymine?
2
100
How Many hydrogen bonds are beterrn Guanine and Cytosine?
3
101
Autorad (Autoradiography)
shows the sequences of nucleotides (each type located in a different lane) Gel electrophoresis
102
PCR
Polymerase Chain Reaction
103
Steps of PCR
Amplification, Specificity, and Sensitivity
104
Histones only occur in what type of cells?
Eukaryotic
105
Function of Insulator in Eukaryotic DNA
Prevents activity of a gene from influing its genetic neighbors
106
Repressor Function
Non-Coding segment slows down transcription
107
Promoter function
Binding site for RNA Polymerase
108
RNA Polymerase
DNA Copying Enzyme
109
Exon
a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence.
110
Intron
a segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.
111
SNRP
small nuclear ribonucleoproteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.
112
DHAP is converted into G3P by what enzyme?
Isomerase
113
Glycolysis results in how many ATP Molecules?
4 Total, 2 Net
114
How many NADH Molecules are produced in GLycolysis
2
115
116
ated in the Citric Acid Cycle

Microbiology 2125 (6 decks)

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