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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
Q

What is the significance of active sites with regard to enzyme function?

A

Active site binds to the substrate to catalyze a reaction

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26
Q

What is the significance of Allosteric sites with regard to enzyme function?

A

The altered activity of an enzyme due to the bonding of a molecule to a region other than the active site

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27
Q

what effect do factors such as pH, temperature, salt concentration and the presence of activators or inhibitors have on enzyme function?

A

They all have the ability to denature the protein and cause loss of function

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28
Q

What is Enzyme/Protein denaturation?

A

Alteration of native conformation and function by breaking bonds

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29
Q

Define Cofactor

A

An Enzyme accessory, usually a metallic Ion

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30
Q

Define a Coenzyme

A

Serves as transient carriers of specific atoms or functional groups during metabolic reactions. They operate in conjunction with an enzyme

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31
Q

What is the difference between competitive/noncompetitive enzyme inhibitors

A

Competetive enzyme inhibitors bind to the active site Noncompetitive enzyme inhibitors bond off the active site, but change conformation of the protein

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32
Q

What is a spontaneous reaction?

A

A reaction that does not require an enzyme to catalyze it

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33
Q

What is a nonspontaneous reaction?

A

A reaction that requires an enzyme and ATP to catalyze the reaction

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34
Q

What is an endergonic reaction

A

A reaction that absorbs surrounding energy

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35
Q

What is an Exergonic reaction

A

A reaction that releases energy into the surroundings

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36
Q

Why are enzymes in an experiment not considered part of the reactants or products?

A

Because they catalyze the reaction and are not participating or being created.

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37
Q

how can the cell can perform energy requiring/consuming reactions through energy coupling

A

The Transfer of energy from endergonic to exergonic processes or by Catabolism to anabolism

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38
Q

What is the role of phosphorylation/dephosphorylation in metabolism?

A

Add a Phosphate group to ADP to make ATP Remove a phosphate group from ADP or ATP to make AMP or ADP

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39
Q

What is the function of ATP in a cell?

A

ATP is the energy currency in the cell

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40
Q

What is ATP’s Structure?

A

Adenosine and 3 Phosphate groups

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41
Q

Explain how ATP/ADP/AMP can gain or lose through phosphorylation and hydrolysis

A

Hydrolysis breaks off a phosphate group (AMP or ADP) and Phosphorylation adds a phosphate group (ADP or ATP)

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42
Q

Oxidation

A

A loss of electrons

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43
Q

Reduction

A

A gain of electrons

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44
Q

Describe the basic structure and functional role of NAD+ and contrast it with NADH

A

NAD+ is reduced, NADH is oxidized

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45
Q

Describe the basic structure and functional role of FAD and contrast it with FADH2

A

FAD is reduced, FADH2 is oxidized

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46
Q

Number of carbon atoms in glucose

A

6

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47
Q

Number of carbon atoms in pyruvate

A

3

48
Q

Number of Carbon atoms in G3P

A

3

49
Q

Number of Carbon atoms in Citric Acid

A

5

50
Q

Where does the citric acid cycle occur in the cell?

A

Eukaryotic (Mitochondria) Cell Membrane (Prokaryotic)

51
Q

How is a proton gradient created and how this gradient is used to synthesize ATP (by ATP synthase) by chemiosmosis

A

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
Q

What is the role of oxygen in Cellular respiration?

A

Oxygen allows substrate-level and oxidative phosphorylation to occur. Oxygen is also the final electron acceptor

53
Q

Explain the difference between substrate-level and oxidative phosphorylation;

A

Substate Level- Citric Acid Cycle Oxidative- ETC/S

54
Q

Explain the difference between substrate-level and oxidative phosphorylation;

A

Substate Level- Citric Acid Cycle Oxidative- ETC/S

55
Q

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

A

Anaerobic conditions (No Oxygen) forces the cell into a fermentation pathway

56
Q

Describe how other compounds (nitrates and carbonates) can be used as final electron acceptors in (anaerobic) respiration

A

Nitrates and carbonates all have oxygen in them and can suffice as final electron acceptors because of Oxygen’s electron affinity.

57
Q

Complementary Base Pairing

A

A-T G-C

58
Q

Sense Strand

A

The strand with the coding sequence for a specific gene

59
Q

Antisense strand

A

the strand with the complement of the coding sequence for a specific gene

60
Q

Triplet Code

A

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
Q

Antiparallel strands

A

each strand runs in 5’ to 3’ direction oppositely

62
Q

Degenerate code

A

The genetic code is degenerate because there are many instances in which different codons specify the same amino acid

63
Q

What is the structure of DNA

A

Features Deoxyribose Double-Stranded Contains Thymine in base pairs Sugar-Phosphate backbone

64
Q

What is the difference between Ribose and Deoxyribose

A

Ribose contains oxygen Deoxyribose does not contain oxygen

65
Q

What does 5’ and 3’ mean?

A

The directionality of nucleic acids

66
Q

mRNA (Messenger RNA)

A

Translated from the sense strand of DNA

67
Q

rRNA

A

Make up ribosomal subunits for translation

68
Q

tRNA

A

Hold the anticodons and amino acids for polypeptide chain synthesis

69
Q

Central Dogma of Biology

A

DNA-> RNA-> Protein

70
Q

What is a genome?

A

All DNA in a cell

71
Q

What is a Proteome?

A

All Proteins in a cell

72
Q

What is a Metabolome?

A

All DNA, RNA, and Protein data in a cell

73
Q

Transcriptome?

A

All RNA in a cell

74
Q

Define Gene

A

the site on a chromosome that provides the information for a certain cell function

75
Q

Define Chromosome

A

Tightly coiled bodies within the cell, composed of DNA, and are primary locations for genetic material

76
Q

Define Chromatin

A

Genetic material in the nucleus (uncoiled)

77
Q

What is the nature of the chromosomes in prokaryotes?

A

Single, Circular chromosome

78
Q

What is the nature of chromosomes in eukaryotes?

A

Multiple, tightly coiled chromosomes in a nucleus

79
Q

What is the structure of bacterial ribosomes

A

Large and Small subunits

80
Q

What is the structure of bacterial ribosomes

A

Large and Small subunits

81
Q

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

A

Nuclear Mitochondria Chloroplast

82
Q

Define Codon

A

Triplet code that corresponds with an amino acid

83
Q

Define Anticodon

A

Anticodons are located on tRNA molecules and are complementary of the codon and adds to the amino acid chain

84
Q

What is the role of RNA Polymerase in transcription

A

RNA Polymerase copies DNA and transcribes it into mRNA

85
Q

What is the role of transcription factors in transcription

A

a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence

86
Q

Sense Strand of DNA

A

contains the coding information for a particular gene

87
Q

Antisense strand of DNA

A

is a complement of the sense strand and holds noncoding information for that gene

88
Q

Purines

A

Nitrogenous bases Adenine and Guanine

89
Q

Pyrimidines

A

Nitrogenous Bases Cytosine Thymine Guanine

90
Q
A

Purines

(Adenine, Guanine)

91
Q
A

Pyrimidines

92
Q
A

RNA

93
Q
A

Sugar-Phosphate Backbone

94
Q
A

DNA

95
Q
A

Electron Transport Chain

96
Q
A

Citric Acid Cycle

97
Q
A

Glycolysis

98
Q
A

Pyruvate Dehydrogenase Complex

(Pyruvate/Pyruvic Acid converted into Acetyl CoA)

99
Q

How many hydrogen bonds are between Adenine and Thymine?

A

2

100
Q

How Many hydrogen bonds are beterrn Guanine and Cytosine?

A

3

101
Q

Autorad (Autoradiography)

A

shows the sequences of nucleotides (each type located in a different lane) Gel electrophoresis

102
Q

PCR

A

Polymerase Chain Reaction

103
Q

Steps of PCR

A

Amplification, Specificity, and Sensitivity

104
Q

Histones only occur in what type of cells?

A

Eukaryotic

105
Q

Function of Insulator in Eukaryotic DNA

A

Prevents activity of a gene from influing its genetic neighbors

106
Q

Repressor Function

A

Non-Coding segment

slows down transcription

107
Q

Promoter function

A

Binding site for RNA Polymerase

108
Q

RNA Polymerase

A

DNA Copying Enzyme

109
Q

Exon

A

a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence.

110
Q

Intron

A

a segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.

111
Q

SNRP

A

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
Q

DHAP is converted into G3P by what enzyme?

A

Isomerase

113
Q

Glycolysis results in how many ATP Molecules?

A

4 Total, 2 Net

114
Q

How many NADH Molecules are produced in GLycolysis

A

2

115
Q
A
116
Q

ated in the Citric Acid Cycle

A

Microbiology 2125 (6 decks)

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