Bio exam 4

Genetic code and stuff

RNA Polymerase

An enzyme that catalyzes the formation of phosphodiester linkages between ribonucleotides, forming an RNA product that is complementary to the sequences of bases in a DNA template.

Template Strand

The strand in a DNA double helix that is “read” by RNA polymerase during transcription.

Non template strand (coding strand)

The strand in a DNA double helix that matches the sequence of bases in the RNA product of transcription, except that the DNA contains thymine (T) and the RNA contains uracil (U).

Promoter

The regulatory sequence in a gene or operon where RNA polymerase initiates transcription.

Anticodon

A sequence of three bases found at one end of a tRNA that binds to a codon in mRNA during translation via complementary base pairing.

Release Factor

A protein that fits into the A site of a ribosome, binds to a stop codon, and interacts with the ribosome to terminate translation.

Reading Frame

The sets of three-base codons in RNA or DNA that specify the primary sequence of amino acids in a protein; is set by the start codon, and identifies the subsequent sequence of codons.

Ribozyme

An RNA molecule that catalyzes a chemical reaction, analogous to enzymes, which are protein catalysts.

Genetic Code

The set of relationships between the 64 possible codons in mRNA and the amino acids that are added to a newly synthesized protein.

Codon

A group of three bases in an mRNA that codes for an amino acid.

Start Codon

The codon that signals where translation and thus protein synthesis begins. Usually AUG and also codes for the amino acid methionine (Met).

Stop Codon

A codon that signals where translation and thus protein synthesis ends. Usually UAA, UAG, and UGA.

Gene Expression

The entire set of processes that results in using the information stored in a gene

Positive control (over gene expression)

Mechanisms that increase the amount of active gene product available

Negative control (over gene expression)

Mechanisms that decrease the amount of active gene product available

Operon

A sequence of structural gene sequences whose products have related functions and that are under the control of the same promoter and other regulatory sequences, meaning that they are transcribed as a unit

Transcription factors

Proteins that regulate transcription, often by binding to regulatory sequences in DNA

Exons

In eukaryotic genes, sections of the coding sequence code for amino acids found in a protein product

Introns

In eukaryotic genes, sections of the coding sequence that are transcribed but later removed before an mRNA is translated into a protein product

Chromatin

The complex of DNA and histones that makes up a chromosome

Nucleosome

A group of four histone proteins that has DNA wrapped around it

Histone Proteins

Proteins that have an abundance of positively charged lysines and arginines in their primary structure, which interact with negative charges on the sugar-phosphate backbone of DNA to form nucleosomes

5’ cap

A modified form of the nucleotide guanine (G) that is added to the 5’ end of a pre-mRNA in eukaryotes, during RNA processing that occurs prior to export from the nucleus

Intron splicing

Removing introns from pre-mRNAs and rejoining exons into a continuous strand, during RNA processing that occurs prior to export from the nucleus

Protein phosphorylation

The addition of a phosphate group or ATP to a protein

Kinase

An enzyme that adds a phosphate group to other proteins

G₁ or first gap phase

The cell grows, meaning that organelles are replicated and the cell increases in volume. Transcription and translation occur at high rates during this phase. G₁ is also when the cell receives signals that tell it either to keep growing and dividing or to stop dividing. If the signals indicate that the cell should stop growth, the cell enters a long-term and non-dividing state called G₀ (pronounced gee-naught). For example, as a human embryo grows and eventually reaches adult size, more and more cells change structure, become specialized for their long-term function, and enter the G₀ phase. Your muscle cells and nerve cells are classic examples of cells that are in G₀ and do not divide.

S phase

If cells in G₁ receive signals for continued growth, the cycle continues. Specifically, they enter S phase and replicate their chromosomes, meaning that they synthesize DNA. (The S in S phase stands for "synthesis.")

G₂ phase

Once the chromosomes are replicated, the cell continues to grow during G₂, or "second gap" phase. A series of events in G₂ lay the groundwork for mitosis and cell division.

M phase

begins when the machinery that is required to condense chromosomes and begin moving them into position assembles. M phase ends when cell division results in two daughter cells. Both daughters then enter G₁.

G₁ checkpoint

Cells can only pass this checkpoint if (1) they receive social signals keeping them in a dividing state (versus exiting to G₀), (2) they are being supplied with adequate nutrients and have grown to adequate size to support division into two daughter cells, and most importantly, (3) their DNA is not damaged.

G₂ checkpoint

Regulatory proteins check to make sure that all chromosomes have been replicated properly and that the DNA is not damaged.

M checkpoint

As mitosis gets underway, regulatory proteins assess whether the microtubules that pull the sister chromatids apart are attached properly, and later that the chromatids have separated so that each daughter cell gets one and only one of each chromosome.

Proto-oncogenes

Genes whose products promote progression through the cell cycle

Oncogenes

When proto-oncogenes genes become mutated and overexpressed leading to cancerous phenotypes, they

Cancer

A family of diseases all characterized by uncontrolled cell division as the underlying cause.

Metastasis

The process of tumor cells breaking away from a tumor, traveling to new locations, and starting new tumors.

Cell Cycle

An orderly, highly regulated, and precisely controlled sequence of events that occurs as cells grow and divide.

Cell cycle checkpoints

Intervals in the cell cycle when regulatory proteins check specific aspects of the cell for damage, especially DNA, and allow or prevent continued progress through the cycle.

Tumor suppressors

Genes whose protein products function as regulatory molecules at cell cycle checkpoints, preventing uncontrolled division of damaged cells.

Which RNA strand would be produced from the template DNA shown below?

3′ ACGGTAGTTCAC 5′

5′ UGCCAUCAAGUG 3′

Imagine a gene has a promoter with a variation that causes RNA polymerase to bind more tightly than normal. How would this change most likely impact transcription?

More RNA will be transcribed from the gene

Which of the following sequence changes are most likely to disrupt the function of the protein product of this gene? Select all that apply.

• ACGGAA...CAGTGA

• ATGTGA...CAGTGA

Which of these mutations in a gene would likely result in no protein product being made at all? Select all that apply.

• a single-base mutation in the start codon

• a single-base mutation in the gene's promoter that prevents RNA polymerase from binding to the promoter

Mutations in the retinoblastoma gene (Rb) often lead to retina cancer in children. Cancerous alleles of Rb lead to no functional retinoblastoma protein (pRb) being made, which then results in cells dividing uncontrollably.

Based on this information, which conclusion about Rb is most accurate?

The normal Rb gene likely encodes a tumor suppressor protein.

A-site

Where amino acid-charged tRNAs enter the ribosome. If the anticodon of a tRNA binds to the exposed codon in the mRNA, tRNA and mRNA bind together

P-site

Where peptide bond formation takes place. The peptide bond forms between the amino acid held by the tRNA in this and the amino acid held by the tRNA in A-site.

E-site

Where tRNAs sit once the amino acid they were carrying has been added to the growing protein. The now uncharged tRNA exits the ribosome from this site.

Somatic mutation

Occurring elsewhere in the body, not passed down

germline mutation

occurs in sperm and eggs, passed to the next generation

induced mutations

Caused by a chemical, nitrous acid, base analogs, or physical (environment, sunlight, radiation)

Spontaneous mutation

Result of abnormality in DNA replication crossing over/anaphase

DNA Endonuclease

any mismatch is cut out, and reading starts over from the newly corrected base (middle of chain)

DNA exonuclease

Mismatch produce ‘bump’ in DNA

DNA polymerase detects this, backs up, and replaces it

Chops off end and restarts

cyclin dependent kinase (cdk)

kinase phosphorylates proteins, activating them

can only phosphorylate if enough cyclin is present must form complex to be activated

cyclins

proteins that vary concentration at various times of cell cycle

mutation

any change in the genetic information in DNA

Missense mutation

a change in a single base that alters the mRNA codon and changes the amino acid at that position in the protein product

nonsense mutation

a change in a single base that alters the mRNA codon to a new and premature stop codon in the mRNA, shortening the protein product

SIlent mutation

a change in a single base that alters the mRNA codon but doesn’t change the amino acid at that position in the protein product

frameshift mutation

a change in DNA that alters the reading frame of codons in an mRNA, resulting in altered codons in mRNA and altered amino acids in the protein product

Deleterious mutation

any mutation that decreases fitness; these mutations lead to early death and are terminal

cancer

a family of diseases all characterized by uncontrollable cell division as the underlying cause

Metastasis

the process of tumor cells breaking away from a tumor traveling to new locations and starting new tumors