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Molecular Biology > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

Describe Deoxyribonucleic acid

A

-Repeating units
-nucleotides
-double-stranded
-the first step of the Central dogma
-DNA as chemical of heredity

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2
Q

How did Darwin contribute to the idea of DNA?

A

The theory of pangenesis

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3
Q

What is the theory of pangenesis?

A

Genetic traits are shaped by life experience and transferred by pangenes to
gamete cells via the blood enabling inheritance
Gemmules’ are shed by cells of the body, collected in the sex organs, and transmitted to the next generation

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4
Q

What did Mendel conclude about evolution?

A

Traits are inherited in a predictable manner of factors (genes) that exist in pairs. These split up when gamete cells are formed and reformed when the union of two gametes occurs during fertilization.

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5
Q

What did Sutton conclude in the 1900s about Mendel particles?

A

suggests for the first time in a concrete way that hereditary material (genes, after 1909) lay on the chromosomes that contain Mendel’s particles of heredity and that these chromosomes come in pairs

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6
Q

What did Miescher Isolate in 1869 and why was it important?

A

He would isolate a substance called nuclei from rupture membranes releasing acidic phospurus substances. With unique properties of nitrogen and phosphorus. The bases were known as A, G, C, T U

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7
Q

What is the structure of a nucleotide?

A

Phosphate group PO4, Five carbon sugars, Nitrogen-containing bases: Purine or pyrimidine

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8
Q

Name the Purines.

A

Adenine (A), Guanine ( G)

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9
Q

Name the Pyrimidines.

A

Thymine (T), cytosine (C), and RNA contain Uracil (U) not T

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10
Q

Where is chemical heredity located?

A

In the chromosome

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11
Q

In 1940 Which researchers found that Transformation of hereditary could be passed from dead to living and how?

A

1940-Griffith injected mice with various strains of one bacteria (based on a 1928 observation by Griffith who studied two strains of bacteria)
Virulent and Non-Virulent
Something transferred from the virulent (heat-killed strain) to the non-virulent
The non-virulent strain had become virulent

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12
Q

In 1944 which researcher proved that DNA was a possible hereditary material and how?

A

1944, Avery and coworkers
* Prepared mixture of the dead S strain (virulent)
and the live R strain
* Removed 99.9% of the protein from this mixture
* Transforming ability was not lost
* DNA digestion enzymes (DNase) completely removed the transforming ability
Determining the removal of DNA led to the loss of transformation leading to the conclusion that DNA was the hereditary material.

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13
Q

What are Chargaff’s rules?

A

1949
* Chargaff’s Analysis: DNA Is Not a Simple Repeating
Polymer
* Found base amounts differed, depending on the source
* Composition of nucleotides varied in complex ways
* Found proportions of certain nucleotides equal to others
* Proportion of adenine (A) equal to thymine (T)
* Proportion of guanine (G) equal to cytosine (C)

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14
Q

Who followed up the Avery experiment and how is it important?

A

1952-The Hershey-Chase Experiment: Some Viruses Direct Their Heredity with DNA; follow-up to Avery’s experiments
* Examined bacteriophage viruses that attack bacteria
* Bacteriophages possess either DNA or RNA, surrounded by a protein coat– In this case DNA
* Lytic virus injects viral genetic material into bacteria
* Causes production and release of more viruses when cell lyses

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15
Q

What atoms are found in protein and how are they marked?

A

Sulfur which can be labeled with radioactive material like S35

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16
Q

What atoms are found in DNA and how are they marked?

A

Phosphate which can be labeled with radioactive material like P32

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17
Q

What is the Lytic cycle?

A

The virus enters the cell where it will produce more phages and finally, causes lyses which leads to phages then going to attack other cells where the lytic cycle continues to take place or the lysogenic cycle can occur.

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18
Q

What is the Lysogenic cycle?

A

The phage integrates itself into the chromosome becoming a prophage. When cell replication occurs the prophage copies itself onto other daughter cells this can lead to either the production of many infected bacteria or the start of a lytic cycle.

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19
Q

Why is S35 used to target protein identification?

A

Proteins are made up of amino acids and it happens that the start codon also known as Methionine (met, AUG) is found In the majority of proteins it’s a good marker for proteins.

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20
Q

Why is P32 a good marker for DNA/RNA?

A

DNA is composed of a Phosphate backbone allows it to recognize it when exposed to P32.

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21
Q

Describe the procedure of the Hershey and Chase experiment. and what was learned in the process.

A

Step 1: Grow bacteria for 4 hours with S35 or P32; allow these isotopes to enter the cells
* Step II: Infect with bacteriophage and allow generation of new bacteriophage that are now labeled, then purify bacteriophage
* Step III: Infect fresh bacteria with newly labeled bacteriophage P32 or S35
* Step IV: Proceed with the identification of supernatant and pellet

-P32 labeled DNA was transferred into the CELL NOT Protein
-Progeny phage contained P32
- DNA is the hereditary material

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22
Q

Who proposed the idea of genes encoding for enzymes?

A

In 1940
Beadle and Tatum experiment with bread mold (Neurospora crassa), a haploid organism
* Proposed the one gene, one enzyme hypothesis
* We now know that some enzymes are composed of
multiple subunits encoded by different genes
* We now know that not all proteins are enzymes
* ONE GENE»>ONE POLYPEPTIDE (in this case we mean protein)

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23
Q

What are the exceptions to one gene->one polypeptide?

A

-some genes code for functional RNAs, not proteins
-some genes code for more than one polypeptide
-sometimes enzymes

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24
Q

Where is DNA located?

A

Nucleus

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25
Q

Where is protein synthesized?

A

Cytoplasm

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26
Q

who proposes the biological information flow? and what was it?

A

Crick
DNA-> RNA-> Protein
DNA acts as its template
with the existence of different RNAs

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27
Q

Name the main RNAs

A

rRNA
mRNA
tRNA

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28
Q

What is rRNA?

A

rRNA (ribosomal RNA discovered in the 1950s by Paul Zamecnik) 80% of all RNA in a cell

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29
Q

What is mRNA?

A

mRNA (Brenner, Monad 1960s) (made by transcription with RNA polymerase) also known as the messenger RNA

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30
Q

What is tRNA?

A

tRNA (1955 Crick hypothesized its existence): 3 bases in tRNA form base pairs with a triplet sequence in mRNA; amino acid is attached to tRNA

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31
Q

What does translation require?

A

Requires all 3 RNAs

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32
Q

Where do all RNAs come from?

A

All RNAs are transcribed from DNA genes

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33
Q

Explain what the human genome project found in 2003.

A

Most of our cells are diploid
* 46 chromosomes
* About 3 billion base pair
in 23 chromosomes
* About 37 trillion cells in the human body

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34
Q

What is life? what are the requirements for something to be considered life?

A

Life is a system capable of Darwinian evolution
-Raw materials
-Energy
-A barrier between the living and inanimate world
-catalysis ( enzymes)
-Biological information (DNA for long term storage)

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35
Q

What is a cell?

A
  • The cell is the smallest unit of organization that can perform all activities required for life
  • Every cell is enclosed by a membrane that regulates the passage of materials between the cell and its surroundings.
  • Every cell uses DNA as its genetic information.
  • Some viruses (parasitic infectious agents) use RNA BUT they are not
    considered cells
  • The cells of bacteria and archaea are prokaryotic, while all other forms of life are composed of eukaryotic cells
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36
Q

What are the three domains of life?

A

Archae, Bacteria, And eukarya

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37
Q

When did life appear on Earth?

A

3.6 billion years

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38
Q

What is the RNA or RNA-protein world hypothesis?

A

RNA hypothesis (proposed in the 1960s)
* RNA enzymes: replicate RNA
* Experiments using prebiotic conditions to prove this
* Discovery of Ribozymes/catalytic RNA (more than just splicing and ligation)
* In Ribosomes, it is the RNA that is the active part
* Recent discoveries that RNA can be self-replicating

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39
Q

What is LUCA?

A

The last universal common ancestor the root of the domain tree probably 3 billion years old

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40
Q

What genes are truly universal in all living systems?

A

All life uses DNA but…
* Only universal genes are those coding for the cellular machinery for protein synthesis and some parts of RNA transcription
* All organisms share the same genetic code (with very minor differences)
* The same code must have been present in LUCA

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41
Q

What is the building block for evolution?

A

Mutations are the building blocks of most of evolution they are the variation upon which natural selection can act, and they are the cause of much of the novelty we see occur in evolution

42
Q

The two tenets of natural selection are?

A

Genetic variation and competition

43
Q

What is Vertical Transmission?

A

DNA passed on from parent to offspring (reproduction)

44
Q

What is Horizontal Gene transfer (HGT)?

A

is the movement of genetic information between organisms, a process that includes the spread of antibiotic resistance genes among bacteria (except for those from parent to offspring), fueling pathogen evolution.

45
Q

Name the three types of HGT.

A

Transformation
Conjugation
Transduction

46
Q

What is Trasformation?

A

Bacteria take up DNA from the environment
ex. DNA that is released from a dead cell will make its way into a living cell

47
Q

What is Conjugation?

A

Bacteria directly transfer genes to another cell

48
Q

What is Transduction?

A

Bacteriophages(bacterial viruses) move genes from one cell to another

49
Q

E.coli

A

Common name - bacterium
Domain - Bacteria

50
Q

S.cerevisiae

A

Common name-Budding yeast
Domain- Eukaryote

51
Q

N. crassa

A

Common name- Bread mold
Domain- Eukaryote

52
Q

A.thaliana

A

Common name-mustard weed
Domain-eukaryote

53
Q

D. melanogaster

A

Common name- fruit fly
Domain-eukaryote

54
Q

M.musculus

A

Common name-House mouse
Domain-eukaryote

55
Q

Are mutations always harmful?

A

NO
* Harmful
* Hemophilia (X chromosome-linked)
* Huntington’s disease example (autosomal insertion)
* Cystic fibrosis is another example (autosomal deletion)
* Some added benefit
* CCR5 protection against HIV and smallpox infection
* Sickle-cell mutation provides some resistance to malaria

56
Q

Evolution relies on?

A

generally random changes in an organism’s genomic material—MUTATIONS

57
Q

What is a mutation?

A
  • Change in a single base pair
  • Substantial inversion, deletion, insertion of large segments
  • Some mutations affect genes directly, and some affect how DNA is used (for example transcribed)
  • Some changes matter, some don’t
  • ALL processes that are found in information transfer are highly- but not perfectly accurate and slow accumulation of mutations is inevitable
58
Q

What is a Covalent bond?

A

A bond between atoms where electrons are shared

59
Q

What is an ionic bond?

A

Uneven sharing of electrons between atoms

60
Q

What are van der Waals interactions?

A

When two atoms approach each other as they get closer, fluctuating charges cause weak non-specific attractive interactions.

61
Q

What leads to the stabilization of macromolecule structures by weak interactions?

A

The combined effects of multiple noncovalent forces, including hydrogen bonds, weak ionic bonds, hydrophobic effect, and van der Walls interactions allow the specific and stable association of molecules for example two proteins

62
Q

What are the 4 biomolecules that make up life?

A

Amino acids ( Proteins)
Sugars (Polysaccharides)
Fatty acids (Lipids; membranes )
Nucleotides (Nucleic acids)

These are all organized around Carbon

63
Q

What is the bond that unites amino acids?

A

Peptide bond

64
Q

What is the bond that unites nucleotides?

A

Phosphodiester bond

65
Q

What is the bond that unites Monosaccharides?

A

glycosidic bond

66
Q

What type of bonds do monomers form to make polymers?

A

Covalent bonds
-applies to polypeptides, nucleic acids, and polysaccharides

67
Q

What is a dehydration reaction and what does it lead to?

A

The loss of water in this case the net loss of H from a monomer and an OH from the other monomer to form polymers

68
Q

What is a hydrolysis reaction and what does it lead to?

A

The addition of water to break down a polymer so the direct opposite of the dehydration reaction.

69
Q

What is necessary for the assembly of phospholipids(bilayer)?

A

Noncovalent interactions

70
Q

What are the main functions of Nucleic acid?

A

Genetic information storage; protein synthesis

71
Q

What are the differences between Purines and Pyrimidines?

A

Purines are double-ringed structures that involve (A and G)
The bonding Nitrogen to the sugar lies on 9’
Pyrimidines are single-ringed structures that involve ( U, T, and C)
which has the bonding nitrogen to sugar lies on 1’

72
Q

What distinguishes RNA and DNA?

A

The main distinction lies in the 2’ Carbon that holds Hydrogen in DNA while the RNA has an OH group in the 2’ position.
Another notable key feature is that DNA has a nitrous base of thymine which has a methyl group in carbon 5’ while uracil holds a hydrogen atom in the 5’ position instead.

73
Q

What makes up a Nucleoside?

A

Base + Sugar

74
Q

What process must a nucleoside undergo to become a nucleotide?

A

phosphorylation
can have two or there phosphate groups.
ex. seen in adenosine nuecleoside (A)
mono -AMP
di -ADP
tri- ATP

75
Q

What is methylation of DNA? and Why is it significant?

A

-Addition of a CH3 group
-Happens in bases C, G,A
-Methylation is crucial for accurate DNA replication, protection from degradation in bacteria, and activating and silencing genes in eukaryotes.

76
Q

What is an observed RNA modification and what does it lead to?

A

-CH3 sees an addition in the ribose 2’OH or nucleotide base
-Loss of amino group on guanine which leads to a new base like inosine

77
Q

What makes RNA unique and different from DNA?

A

RNA folds in more interesting
ways upon itself since it is a single
stranded
RNA is much less stable than
DNA
* The 2’Hydroxyl group can
act as a chemically reactive
group
* This can contribute
to catalysis
Makes RNA labile, sensitive
especially in alkaline
solutions

78
Q

What makes Adenine different from Guanine?

A

Adenine has an amide group in the 6’ Carbon while Guanine has a Carbonly in the 6’ carbon

79
Q

What makes Uracil different from Thymine?

A

Uracil has Hydrogen in the 5’ carbon while Thymine has a methyl group in the 5’ carbon

80
Q

What makes Uracil different from Cytosine?

A

Uracil has a bond to a hydrogen atom while cytosine lacking that hydrogen has a double bond instead between 3’ and 4’

81
Q

What configurations can amino acids exist in but which is the one ribosomes use?

A

L amino acid and D amino acid
but L is what is used by all life

82
Q

What are the four components that make up amino acids?

A

Amino group ( NH3+)
R group ( varbriable)
Carboxly group ( COO-)
Hydrogen

with carbon at the center of it

83
Q

What are the names of the ends of an amino acid?

A

Amino Terminus (N-Terminus) , and Carboxyl Terminus (C-Terminus)

84
Q

What are the common modifications observed in amino acids?

A

Methylation, Acetylation, Phosphorylation, Glycosylation, and Hydroxylation.

85
Q

How do you distinguish the Nucleotide names of DNA and RNA?

A

The use of lowercase d in front of the nucleotide abbreviation
ex. DNA is represented by
dAMP, dGMP, dTMP, and dCMP
The d stands for deoxy which is a reference to the sugar that is seen in DNA
In comparison, RNA would show the abbreviation name of
AMP, GMP, UMP, CMP

86
Q

What does NTP stand for?

A

Nucleoside triphosphate

87
Q

What are all the dNTPs and NTPs

A

DNA
dATP, dGTP , dCTP , dTTP

RNA
ATP , GTP , CTP , UTP

88
Q

What is the role of ATP?

A

provides chemical energy via the transfer of phosphate to another molecule.

89
Q

What OTHER functions can ATP have?

A

ATP acts as a neurotransmitter in both peripheral and central nervous systems.

90
Q

What special roles can Nucleoside adenosine form part of?

A

Forms part of the structure of enzyme cofactors such as NAD+(cellular energy production) and NADP+ participating in photosynthesis and FAD ( activate form of vitamin B2)

91
Q

Regulatory molecules like cAMP and cGMP play a role in?

A

second messengers

92
Q

What type of bond is a phosphodiester bond?

A

covalent bond

93
Q

What is the name of the process that forms DNA and RNA polymers?

A

-DNA polymerase
-RNA polymerase

94
Q

How does the directionality of DNA synthesis occur and what is the directionality of the complementary strand?

A

5’ Phosphate to 3’ Hydroxyl direction

95
Q

Oligonucleotide?

A

Nucleic acid containing 50 or fewer nucleotides
such as primers

96
Q

Polynucleotide?

A

Longer nucleic acid than 50

97
Q

Why is DNA more stable than RNA?

A

DNA does not have the 2’ OH like RNA
DNA is also stable because of the hydrophobic stacking
RNA degrades more in its lifetime

98
Q

What does the idea of Tautomers relate to Nitrous bases?

A

Pyrimidine and Purine bases can exist as one of several isomers that differ in the placement of hydrogen atoms and double bond but the dominant tautomer is the one that can exist in physiological pH.

99
Q

Describe the DNA helix hydrogen bonding capabilities.

A

Antiparallel stands more energetically favored
backbone is hydrophilic
Nucleic acids are considered acidic
2 hydrogen bonds between AT and 3 hydrogen bonds between GC
( note that the H making the attracting bond is originally covalently bonded to a more electronegative atom like N and O)

100
Q

Describe the chemical properties of purines and pyrimides.

A

-Bases stack like coins
-the most energetically favored conformation is attained by reducing the exposure of the based surface to the aqueous environment, which is achieved by the bases moving closer together
-Hydrophobic stacking is caused by the fact that bases are hydrophobic and thus insoluble in water at the pH of cells
- in addition, van der Walls and electrostatic interaction play a role

Molecular Biology (5 decks)

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