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1
Q

What is the basic unit of life according to cell theory?

A

The cell

The cell theory states that the cell is the fundamental unit of structure and function in living organisms.

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2
Q

What are the two main types of cells?

A
  • Prokaryotes
  • Eukaryotes

Prokaryotes are single-celled organisms without a nucleus, while eukaryotes can be single-celled or multicellular and have a nucleus.

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3
Q

What are the characteristics of prokaryotes?

A
  • No nuclei
  • Single-celled
  • No membrane-bound organelles
  • Smaller than eukaryotes
  • Less DNA than eukaryotes

Examples include bacteria and archaea.

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4
Q

What are the characteristics of eukaryotes?

A
  • Has nuclei
  • Single-celled or multicellular
  • Has several membrane-bound organelles
  • Larger size & more complex
  • Has cell wall (plant cells)
  • Has microtubules

Examples include plants, fungi, animals, and humans.

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5
Q

What does the endosymbiotic theory explain?

A

The origins of mitochondria and chloroplasts

It suggests that these organelles originated from symbiotic relationships between early eukaryotic cells and engulfed prokaryotic cells.

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6
Q

What is the first step of the endosymbiotic theory regarding mitochondria?

A

An early anaerobic archaea engulfed an aerobic bacterial cell by phagocytosis

This initiated the process that led to the formation of mitochondria.

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7
Q

What is the central dogma of molecular biology?

A

Replication → Transcription → Translation

This describes the flow of genetic information within a biological system.

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8
Q

What is the role of mRNA in the information flow?

A

Transcribes DNA into a format that can be translated into proteins

mRNA serves as the template for protein synthesis.

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9
Q

What are the components of nucleic acids?

A
  • Pentose sugar
  • Nitrogenous base
  • Phosphate group

These are the fundamental building blocks of nucleotides.

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10
Q

What are purines and name two examples?

A
  • Adenine
  • Guanine

Purines are nitrogenous bases with a two-ring structure.

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11
Q

What are pyrimidines and name three examples?

A
  • Uracil
  • Thymine
  • Cytosine

Pyrimidines are nitrogenous bases with a single-ring structure.

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12
Q

What type of bonds are involved in the structure of DNA?

A
  • Hydrogen bonds
  • Hydrophobic interactions
  • Van der Waals attractions

These interactions contribute to the stability of the DNA double helix.

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13
Q

What is the primary structure of a protein?

A

Amino acid sequence

The primary structure determines the protein’s unique characteristics.

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14
Q

What are the four levels of protein structure?

A
  • Primary
  • Secondary
  • Tertiary
  • Quaternary

Each level of structure contributes to the overall shape and function of the protein.

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15
Q

What is the function of chaperone proteins?

A

Aid in protein folding

Chaperones help proteins achieve their proper three-dimensional structure.

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16
Q

What is the genetic code?

A

A system that correlates nucleotide sequences with amino acids

The genetic code is universal across most organisms.

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17
Q

What is a genome?

A

The entirety of an organism’s hereditary information

This includes all of its DNA or RNA.

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18
Q

What is the structure of nucleosomes?

A
  • Found in eukaryotes
  • Consist of DNA wrapped around histones
  • Histones are in an octamer/group of eight
  • Help to supercoil chromosomes
  • Regulate transcription/gene expression

Nucleosomes play a crucial role in DNA packaging and gene regulation.

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19
Q

What is the difference between introns and exons?

A
  • Exons are protein coding sequences
  • Introns are non-coding sequences

Introns are spliced out during RNA processing, while exons are expressed.

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20
Q

Fill in the blank: The human genome has approximately _____ base pairs.

A

3 billion

This is the total number of base pairs in the human genome.

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21
Q

What is the structure of nucleosomes?

A

Nucleosomes consist of DNA wrapped around proteins called histones, forming an octamer of eight histones.

Histones help to supercoil chromosomes and regulate transcription.

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22
Q

What are the functions of histones in nucleosomes?

A

Histones neutralize the negative charge of DNA, facilitate DNA packing, and regulate gene expression through modifications like methylation and acetylation.

Histones are rich in lysine and arginine, which contribute to their positive charge.

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23
Q

How do nucleosomes separate?

A

Nucleosomes separate when nucleases digest linker DNA and high salt concentration dissociates histones from DNA.

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24
Q

What proteins are involved in packaging nucleosomes in cells?

A

Sequence-specific clamp proteins and cohesins are involved in forming loops of interphase chromosomes; condensins replace cohesins in M phase to form double loops of chromatin.

This process is crucial for chromosome formation during cell division.

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25
What role do chromatin remodeling complexes play?
Chromatin remodeling complexes and histone modifying enzymes alter chromatin structure through processes like acetylation, methylation, and phosphorylation.
26
What is the difference between heterochromatin and euchromatin?
Heterochromatin is tightly packed and generally inactive, while euchromatin is loosely packed and active in transcription. ## Footnote The switching between these forms is controlled by histone modifying enzymes and chromatin remodeling complexes.
27
Describe the process of fluorescence in situ hybridization (FISH).
FISH involves denaturing DNA, mixing in fluorescent probe DNA, and allowing the probe to hybridize with complementary target sequences in chromosomes.
28
What occurs during DNA replication?
DNA replication occurs during the S phase of interphase, is semi-conservative, and involves helicase unwinding DNA, with each strand serving as a template for a new strand.
29
What is the role of DNA polymerase III in DNA replication?
DNA polymerase III adds nucleotides to the growing DNA strand in a 5' to 3' direction, starting from an RNA primer.
30
What are Okazaki fragments?
Okazaki fragments are short lengths of DNA synthesized on the lagging strand during DNA replication.
31
What is the purpose of ligase in DNA replication?
Ligase seals gaps between nucleotides and fragments, making sugar-phosphate bonds to complete the DNA strand.
32
What is the difference between conservative and semi-conservative DNA replication?
In conservative replication, the parental strand remains intact, while in semi-conservative replication, each daughter strand consists of one parental and one new strand.
33
How does the initiator protein function in DNA replication?
The initiator protein binds to the replication origin, destabilizes the DNA helix, and attracts helicases to begin replication.
34
What is the function of single-strand binding proteins during DNA replication?
Single-strand binding proteins keep DNA strands separated and prevent them from re-forming hydrogen bonds.
35
What types of DNA repair mechanisms exist?
DNA repair mechanisms include base excision repair, nucleotide excision repair, and repair of double-stranded breaks through non-homologous end joining and homologous recombination.
36
What is the role of telomerase in DNA replication?
Telomerase adds sequences to the ends of linear chromosomes to prevent the loss of genetic information during replication.
37
How is high fidelity maintained during DNA replication?
High fidelity is maintained through proofreading by exonucleases and strand-directed mismatch repair processes.
38
What defines a gene?
A gene is defined as the entire nucleic acid sequence necessary for the synthesis of a protein or RNA.
39
What is the transcription cycle in bacteria?
The transcription cycle in bacteria involves sigma factor binding to RNA polymerase, unwinding DNA, elongation of RNA, and termination.
40
What is the promoter sequence?
The promoter sequence tells RNA polymerase where to begin transcription, typically consisting of specific sequences upstream of the transcription start site.
41
What is the significance of RNA primers in DNA replication?
RNA primers are necessary for DNA polymerase to initiate DNA synthesis, as polymerase cannot start a new chain without them.
42
True or False: Both DNA strands can be transcribed.
True
43
What is the function of the promoter sequence?
Tells RNA polymerase and sigma factor where to begin transcription ## Footnote Promoter sequences are crucial for initiating transcription in both prokaryotic and eukaryotic cells.
44
What are the key components of the promoter sequence?
-35 nucleotides, -10 region, +1 start site ## Footnote These regions provide binding sites for RNA polymerase and transcription factors.
45
Which strand is transcribed during transcription?
Both strands can be transcribed, depending on the target gene ## Footnote The strands are complementary and antiparallel.
46
What is a terminator sequence?
A sequence that signals the end of transcription, often forming a hairpin structure ## Footnote This hairpin structure is formed when RNA base pairs with itself.
47
What is a hairpin structure in transcription?
A secondary structure formed when RNA begins to base pair with itself ## Footnote Hairpins typically form due to specific sequences like GGCGGC.
48
What are the main differences between eukaryotic and prokaryotic transcription?
- Eukaryotic is more complicated - Eukaryotic has more post-transcriptional modifications - Transcription and translation occur simultaneously in prokaryotes ## Footnote Eukaryotic mRNA undergoes extensive processing before translation.
49
How many RNA polymerases do eukaryotes require?
Multiple RNA polymerases ## Footnote Prokaryotes only require one RNA polymerase.
50
What is the TATA box?
A highly conserved sequence found ~30 bp upstream from the transcription start site ## Footnote The TATA box is crucial for the positioning of RNA polymerase II.
51
What is the role of TBP in transcription initiation?
TBP binds to the TATA box and distorts the DNA, attracting other transcription factors ## Footnote This process is essential for the correct assembly of the transcription machinery.
52
What are the steps in the initiation of transcription?
1. TBP binds to TATA box 2. Other transcription factors bind 3. RNAP II binds to the DNA 4. TFIIH unwinds DNA and phosphorylates RNAP II ## Footnote These steps are critical for the transition from initiation to elongation.
53
What is the function of the C-terminal domain (CTD) of RNA polymerase II?
The CTD is phosphorylated to facilitate the transition from initiation to elongation ## Footnote Phosphorylation of the CTD recruits various processing factors.
54
What is the process of mRNA capping?
A 5’ cap is added when mRNA is over 25 nucleotides long ## Footnote This modification protects mRNA from degradation by exonucleases.
55
What happens during splicing of pre-mRNA?
Introns are removed and exons are joined together ## Footnote This process is catalyzed by the spliceosome, composed of snRNPs.
56
What is the role of snRNPs in splicing?
They facilitate the recognition and removal of introns from pre-mRNA ## Footnote snRNPs are essential for the splicing process and consist of snRNA and proteins.
57
What is alternative RNA splicing?
The process that increases the number of gene products by producing different mRNA variants ## Footnote This mechanism allows for greater protein diversity from a single gene.
58
What is the significance of the genetic code?
It is universal and encodes all 20 amino acids ## Footnote The genetic code also exhibits redundancy, with multiple codons for the same amino acid.
59
What is the start codon and its role?
AUG (methionine) is the start codon that initiates translation ## Footnote The identification of the start codon is crucial for determining the reading frame.
60
What is the function of tRNA in translation?
tRNA carries amino acids to the ribosome and matches them to mRNA codons ## Footnote There are 61 possible tRNA anticodons that correspond to 64 mRNA codons.
61
How does translation ensure fidelity?
1. Aminoacyl-tRNA synthetases attach correct amino acids to tRNA 2. Only correctly base-paired tRNAs can add amino acids to the growing chain ## Footnote This two-step process minimizes errors in protein synthesis.
62
What are the three sites of the ribosome?
- A site (aminoacyl site) - P site (peptidyl site) - E site (exit site) ## Footnote These sites are essential for the stages of translation: initiation, elongation, and termination.
63
What happens during translation termination?
A release factor binds to the A site, triggering the release of the peptide chain ## Footnote This process concludes protein synthesis and leads to ribosomal dissociation.
64
What is the role of chaperones in protein folding?
Chaperones assist in the proper folding of proteins as they emerge from the ribosome ## Footnote They ensure that proteins achieve their functional three-dimensional structures.
65
What are some reasons for protein degradation?
- Improper folding - Wear and tear ## Footnote Proteins that are damaged or misfolded are typically targeted for degradation to maintain cellular function.
66
What is phosphorylation in the context of post-translational modification?
C-terminal domain of RNA polymerase is an example of phosphorylation ## Footnote Phosphorylation is the addition of a phosphate group to a molecule, often modulating the activity of proteins.
67
What is glycosylation?
Covalent addition of sugar in proteins, such as in cell membranes ## Footnote Glycosylation is crucial for protein stability, signaling, and recognition.
68
What role do cofactors play in proteins?
Cofactors like zinc and magnesium assist in the function of proteins, such as RNA polymerase ## Footnote Cofactors can be metal ions or organic molecules that are necessary for enzyme activity.
69
What is the purpose of covalent modifications in proteins?
They make proteins active and signal recruitment to correct membranes or organelles ## Footnote These modifications can include phosphorylation, acetylation, and methylation.
70
List two reasons for protein degradation.
* Does not fold properly * Wears out due to biochemical modification ## Footnote Proteins that are damaged or misfolded can be harmful to the cell and need to be degraded.
71
Describe the mechanism of protein degradation.
1. Ubiquitin molecules are covalently added to target protein 2. Directs protein to proteasome 3. Degraded by protease breaking peptide bonds 4. Amino acids are recycled in cells ## Footnote Ubiquitin tagging is a signal for the protein to be degraded, ensuring cellular homeostasis.
72
True or False: Proteins that do not fold properly are often targeted for degradation.
True ## Footnote Misfolded proteins can aggregate and disrupt cellular functions if not removed.
73
Fill in the blank: _______ are added to a target protein to signal its degradation.
[Ubiquitin] ## Footnote Ubiquitin is a small protein that tags other proteins for degradation via the proteasome.
74
What happens to amino acids after protein degradation?
They are recycled in cells for new proteins ## Footnote This recycling process is vital for maintaining the amino acid pool necessary for protein synthesis.

bio130 midterm (3 decks)

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