CBG exam 2 flashcards

When does DNA replication happen?

Happens during the S phase of the cell cycle.

When does central dogma / transcription happen?

Anytime

Eukaryotes

An organism or cell that has a nucleus and membrane-bound organelles.

• Organisms that include animals, plants, fungi, and protist.

Prokaryotes

Single-celled organisms, such as bacteria.

How many cells do we start out as and end at?

• We start off as one cell; a zygote; after the sperm fertilizes the egg

• ~40 trillion cells are in a fully mature adult

  • Numerous cells must divide and differentiate to create a fully functioning organism

Central Dogma

Describes the process of DNA being transcribed to RNA and then translated to protein.

Transcription

The process of converting DNA to RNA.

Translation

The process of converting RNA to protein.

Reverse transcription

RNA to DNA

Protein synthesis takes place where?

In the cytoplasm and ribosomes of the cell

• (Protein synthesis is the process by which cells create proteins, the building blocks of all living organisms. It involves two main steps: transcription and translation)

mRNA

Messenger RNA that carries instructions from DNA to the ribosome to make protein.

rRNA

Ribosomal RNA, a structural component of ribosomes, needed to form peptide bonds.

tRNA

Transfer RNA, which aligns amino acids with proper codon.

snRNA

Small nuclear RNA required for splicing.

Promoter

• Required to recruit RNA initiation complex

• key component of transcription

• In eukaryotes the primary promoter is the TATA box (consensus sequence).

RNA initiation complex

Needed for RNA polymerase function, one member is a helicase.

TATA binding protein required to bind the promoter.

a key component of transcription

RNA Polymerase

Enzyme that recruits nucleotides to make RNA.

What is the primary promoter in eukaryotes?

The TATA box (consensus sequence)

• Promoter: DNA sequence to which RNA polymerase binds (initiation complex binds first). The region upstream of the transcription initiation site has 2 different consensus 6 base pair sequences. One at –10 and one at –35.

Transcription overview sequence

1. RNA initiation complex bind TATA box.

   • Specifically the first is TFIID (which contains TATA binding protein (TBP)).

2. Then RNA polymerase binds to complex.

3. Lastly remaining members of complex bind,

   • One member being a helicase.

Parts of Transcription sequence

• Initiation - After all members of complex are present RNA polymerase starts recruiting nucleotides

• Elongation - RNA polymerase moves 5’ to 3’ recruiting nucleotides.

• Termination - RNA polymerase reaches termination sequence and then detaches.

Elongation

RNA polymerase recruit's uracil instead of thymine. RNA polymerase lacks proofreading activity.

How can RNA polymerase afford to lack proofreading activity?

• Because RNA is typically synthesized quickly and is often not as critical as DNA, allowing for some errors without significant consequences.

RNA processing and turnover

• Transcriptional regulation is the major method to regulate gene expression, but RNA processing and turnover are also important

• Pre RNA’s are modified before transport to the cytoplasm. This includes modification of both ends and removal of introns

• 7-methylguanosine cap

• Polyadenylation of tail

• Splicing: introns are removed by splicing from exons

7-methylguanosine cap

a cap is placed on the 5’ end co-transcriptionally.

It stabilizes the RNA and facilitates binding of RNA to the ribosome

Polyadenylation of tail

the hexanucleotide AAUAAA signals polyadenylation. A nuclease cleaves the RNA and a polyA polymerase adds a 200 A tail.

This aids stability and translation into protein

Spliceosome

Complex of proteins and RNA that mediates the splicing reaction.

Ribozymes

RNA molecules that catalyze cleavage of RNAs at a specific recognition sequence.

Transfer RNAs (tRNAs)

needed for translation

adaptors to align the correct amino acid (AA) on the right codon. Codons are 3 bases that code 1 AA. tRNAs are 70 – 80 nucleotides long with a clover leaf structure

Two major sites in transfer RNA translation

an amino acid attachment site and an anticodon loop located at the opposite end to bind the right codon

Aminoacyl tRNA synthetases

Enzymes attaching specific amino acids to specific tRNAs.

Why are ribosomes needed for translation?

To catalyze protein synthesis.

Two subunits composed of protein and RNA.

Abundant (1x10⁶ in eukaryotic cells)

Ribosomal RNA deficiency disease

Treacher Collins Syndrome- Mutated TCO1 gene which is required for rRNA transcription.

Initiation , elongation , and termination

Initiation is complex in eukaryotes (>12 initiation factors) but simpler in prokaryotes.

• Starts when tRNA-methionine and mRNA bind to the small ribosomal subunit

The peptide chain elongates by subsequent addition of AAs as the ribosome moves down the mRNA. When a stop codon is reached (UAA), the reaction terminates, the protein is released and the ribosome dissociates from mRNA.

Initiation of translation

Methionine encoded by AUG, initiates translation in both prokaryotes and eukaryotes

• The 7- methyl guanosine cap of eukaryotic mRNA binds the ribosome and helps to align it for translation

Initiation, elongation and termination factors

The first step in prokaryotes is binding of 3 initiation factors to the ribosome. The mRNA and tRNA join, GTP is hydrolyzed and the 70S initiation complex is formed

• Initiation in eukaryotic cells is complex and requires at least 12 initiation factors. After initiation, elongation and termination factors are required for translation to be completed

Elongation of the peptide chain

1. Start with first amino acid, binding site, found in bacteria,

   first amino acid comes to the P site

   Everything else comes to the A

2. Peptide bond forms through dehydration reaction

3. Entire ribosome subunit shifts which pushed amino acid

4. First amino acid pops off and are then in the chain?

   To create long polypeptide chain

5. Continues until release factor binds to ?

Termination of translation

The release factor breaks the bond between the peptide chain and the tRNA

The nascent protein, tRNA, and ribosome all dissociate

Polysomes

Polysomes

mRNAs are translated by multiple ribosomes at one time and are spaced about 200 bases apart.

Two classes of mutations:

1. Point mutations

2. Frameshift mutations

Point mutations & its types

Substitution mutations where one base is replaced with another base.

Three types of point mutation:

1. Silent mutation

2. Missense mutation

3. Nonsense mutation

Silent mutation

A mutation that does not change the amino acid sequence of a protein

• example: UUA change to UUG

Missense mutation

A mutation that switches one amino acid for another.

Nonsense mutation

A mutation that results in an early stop codon in the protein.

Frameshift mutations

Mutations that alter the entire reading frame of a mRNA sequence.

(nucleotides are read three nucleotides at a time)

Two types of frameshifts:

1. Insertion mutation

   AUG-UCA-CUU-G

2. Deletion mutation

AUG-ACU-UG

Normal sequence:

AUG-CAC-UUG

Chaperones

Proteins that assist in the folding of other proteins.

• They work by assisting other proteins to self-assemble, possibly by stabilizing the unfolded intermediates

• example: proper folding might require both the carboxy and amino terminus. Chaperones maintain the protein until it is completely translated and ready to properly fold

Protein cleavage

Cleavage of the polypeptide chain is important for maturation.

contains signal sequence and signal peptidase

Signal sequence

20 amino acids at amino terminal that targets secreted proteins to the endoplasmic reticulum.

This sequence is hydrophobic and assists the protein through the membrane.

Signal peptidase

A sequence that allows a protein to enter the endoplasmic reticulum (ER).

The cell cycle

Organism

^

Cells ← 2 cells

^

Organelle

^

Macromolecules

^

Atom

How many humans would it take to stretch our DNA from the moon to the Earth?

In a single human, we have enough DNA to stretch from the surface of the earth to the moon

Chromosomes

• Offspring inherit chromosomes containing genetic material from parental generation.

• Chromosomes are made of two sister chromatids.

Sister chromatids

Made of chromatin

Chromatin

Made of histones and DNA

G1=

S =

• each half of the X =

G2 =

• G1= linear chromosome

• S = after it replicates,

  each half of the X = a sister chromatid but the whole X is a chromatid

• G2 = X

X shape means that the chromosome has already divided

Chromosome pairs

In humans, there are 22 pairs of autosomes and 1 pair of sex chromosomes.

• Y = male

• Don’t have a Y = female

Chromosomes in Species

• Chromosome number vary between species, the number of chromosomes within species remain consistent.

• Genes are carried on chromosomes, what are genes?

  • Coding regions in DNA

The phases of the cell cycle

• Interphase

• Mitosis (Diploid/somatic cells)

• Cytokinesis

Length and division of cell cycle

• The length of the cell cycle varies

• Most adult cells divide slowly (once every few days or weeks)

• Cancer cells and some normal cells (bone marrow, stomach) divide constantly.

• Embryo cells also divide fast during cleavage

Interphase

• G1 phase - Primary cell growth (cell organelles duplicated).

• S - DNA synthesis

• G2 - Secondary growth (centrosomes form)

• G0 - Cell leaves the cell cycle and enters cell cycle arrest.

Centrosomes

Organelles that organize microtubules during cell division.

• Contains 2 centrioles which are small cylinder-shaped organelles that help form mitotic spindle.

Mitosis

Process of cell division that includes stages:

1. prophase

2. prometaphase

3. metaphase

4. anaphase

5. telophase

Cytokinesis

Division of the cytoplasm following mitosis.

Prophase

Mitotic spindle forms, chromosomes condense, and nuclear envelope disappears.

Prometaphase

• Kinetochore forms at the centromere.

  • Centromere = Middle of the chromosome that connects the two arms of the chromosome

• Some kinetochores attach to centromere while others interact with opposite poles of cell

Metaphase

• Centrosomes go to opposite poles of the cell.

• Chromosomes line up along metaphase plate.

  • Sister chromatids are identical / no difference

Anaphase

Cohesion protein that holds sister chromatids together are degraded and sister chromatids are separated to opposite poles.

Telophase

• Nuclear envelope reappears, chromosomes become less condense and microtubules disassemble.

  • Start unwrapping

  • Centrosome breaks apart

Cytokinesis for animal vs. plant cells

Animal cell forms cleavage furrow (actin filaments).

Plant cell forms cell plate from cell wall (vesicles).

Mitosis diagram order