BSCI 170 - Midterm 3 Flashcards

• What is genetic material?

• Material used to store information necessary for a cell, an organelle, or a virus to carry out all physiological activities and to replicate itself.

• What should we expect from the cell’s genetics when one cell divides into two cells?

• The two cells should be genetically identical; ideally genetic information must be transferred unchanged to the next generation (limiting mutations)

• What organelle stores genetic material?

• The nucleus

• What is the Central Dogma of Biology?

• Information is stored in DNA

• DNA gets transcribed to RNA which is translated into proteins

• Transfer of information to proteins is irreversible

• What is reverse transcription?

• RNA can get transcribed back into DNA

• What are chromosomes?

• Linear stretches of DNA and protein that carry genetic information from cell to cell

• Composed of protein, DNA, and RNA!

• Genes are located on chromosomes

• What is the relationship between DNA, genes, and chromosomes?

• DNA is the basic building block of life (encodes all genetic information). Genes are specific segments of DNA that carry instructions for making proteins. Chromosomes are made up of DNA, and therefore carry genes as well.

• What is the Transforming Principle?

• refers to the idea where the genetic material from one organism can transfer traits to another, demonstrating that DNA is the substance responsible for heredity and gene expression.

• What are bacteriophages?

• “bacteria eaters”

• viruses that infect bacteria - take over cell metabolism to make more copies of themselves

• composed of DNA and proteins ONLY

• What are transferred during phage infection?

• Genes - DNA, not protein, is transferred during infection.

• What are Chargaff’s Rules?

• [A]=[T] and [G]=[C]

  • Ratio of A:T is always equal to 1 and Ratio of G:C is always equal to 1

  • The concentration of the nucleotides are different in different organisms

    • [A] = 24.7% in E. coli, but 30.4% in humans

  • The concentrations of the nucleotides are the same in different tissues in the same organism.

    • [A] = 30.4% in human liver and brain tissue

      • every cell has the exact same genes

• What does the shape of DNA look like?

• A helix with two strands

• What are the purines?

• Adenine and Guanine

  • Two rings in each

• What are pyrimidines?

• Cytosine and Thymine

• One ring each

• How are the bases arranged in the double-stranded DNA?

• Complementary pairs: Purine + Pyrimidine

• A-T, C-G (A-U in RNA)

  • Paired across the double helix, stabilizing hydrogen bonds form

• What is the basic replication model for DNA?

• The helix unwinds

• Both strands remain intact

  • Parental strands

• Each parent strand serves as a template for a new daughter strand

• The daughter strand is generated by Complementary Base Pairing to the parental strand

• How does DNA replicate?

• Semiconservatively: each new DNA molecule consists of one old strand and one newly synthesized strand, ensuring that genetic information is accurately passed on during cell division.

• What is semiconservative replication?

  • 

• Parent molecule

• Separation of strands

• Daughter DNA molecules, each consisting of one parental strand and one new strand

What are the three steps of DNA replication?

• Initiation

• Elongation

• Termination

What happens during initiation during DNA replication?

• Proteins bind to a specific location

  • Origin of Replication (ori)

• DNA helix unwinds and opens up

  • creates a replication bubble

    

• DNA replication extends from the origin on both strands and in both directions

How many origins of replication do bacterial chromosomes have?

• a single origin of replication that allows the entire circular DNA molecule to be copied efficiently during cell division.

• What is helicase?

• Unwinds the helix at the replication fork

• Necessary to generate the template strands (parental strands)

• What is the single-strand binding protein (SSBP)?

• Binds to and stabilizes the single-stranded templates

• Prevents the helix from rewinding

• What is topoisomerase?

• Causes single-stranded breaks in the DNA that allows the DNA to unwind and relieve the supercoil strain

• Makes it so the strands don’t become tangled

• The breaks are reattached before replication

• What is DNA Polymerase?

• Several different DNA polymerases (I,II,III)

• Building new DNA molecules from parent strands

• Different enzymes do different things:

  • Regular synthesis

  • Proofreading

  • Repair synthesis

• What are DNA polymerases’s functional restrictions?

• Copy DNA that is single stranded only (why we need to unwind DNA)

• Add only onto an existing free end

  • Cannot initiate a polymer from scratch

• Adds nucleotides ONLY onto -OH group of a 3’ end; never the 5’ end

  • Adds nucleotides so that the polymer extends only in the 5’ → 3’ direction

• What is a primer?

• The primer is a short (5-10 nucleotides) stretch of RNA with an available 3’ end for DNA polymerase to attack to and start adding more nucleotides to

  • A separate enzyme later removes (digests) the primer and replaces the RNA with DNA

• A primer is needed to initiate all new strands

• What is a primase?

• A primer is synthesized by the enzyme primase (catalyzes the reaction to generate the primer)

• Primase does not need a free 3’ end to start

• Is DNA parallel or antiparallel?

• Antiparallel

• What is the leading strand of the DNA?

• The leading strand is the DNA strand that is synthesized continuously in the 5’ to 3’ direction (against the 3’ to 5’ direction) following the replication fork as it unwinds.

• synthesized as one continuous strand

• Where is the direction of synthesis?

• Always toward the fork and away from the origin

• Where can DNA polymerase never add nucleotides?

• Onto a free 5’ end and elongate in 5’ direction

• Can only add nucleotides and elongate in 3’ direction

• How is DNA synthesized along the 5’ → 3’ strand?

• DNA is synthesized discontinuously as a series of short oppositely oriented fragments

• Direction of synthesis is toward to origin, not toward the fork as with the other strand

• What are okazaki fragments?

• Short discontinuous fragments synthesized on the lagging strand during DNA replication

• Each fragment needs a separate RNA primer

• The primer is eventually removed, and new DNA fills the space.

• What happens to the DNA polymerase when the okazaki fragment contacts the end of the neighboring okazaki fragment?

• It falls off

What is the lagging strand?

• The DNA strand synthesized discontinuously

What is DNA ligase?

• the enzyme responsible for joining Okazaki fragments together to create a continuous DNA strand

• How many DNA Polymerases are needed in DNA replication in the lagging strand?

• 2 DNA polymerases and 1 DNA ligase

• How many DNA Polymerases are needed in DNA replication in the leading strand?

• 1 DNA polymerase

What are mutations?

Errors in DNA replication

• What is the Genetic Code Problem?

• “How can information from the 4-letter code be converted in the 20-letter code?”

• What is The Triplet Code?

• Nucleotide triplets are the smallest possible unit to cover all 20 amino acids.

• What is each triplet of nucleotides called?

• A codon

• What are point mutations?

• Changes in a single base pair   

• What is the insertion point mutation?

• Addition of an extra base

• What is the deletion point mutation?

• Removal of a base

• What is the substitution point mutation?

• Replacement of one base with another

• What are spontaneous mutations?

• Error in DNA Replication

• Errors in DNA Repair

• Errors in Recombination (meiosis)

• What are wild-type mutations?

• Normal DNA strands that gets transcribed

• What are silent mutations?

• Mutations where a base pair is changed, but it doesn’t affect the amino acid being made

• What are missense mutation?

• A different amino acid is made due to a change in the codon

• What is a nonsense mutation?

• A specific change in the nucleotide sequence where a stop codon is mutated, high likelihood that that protein doesn’t work anymore

• What is a loss of stop substitution?

• a mutation that replaces a stop codon with one that codes for an amino acid, resulting in a longer mRNA chain

• What is a frameshift mutation?

• When you take out or put in a nucleotide, changes the reading frame

  • Insertion/Deletion

• What is transcription?

• Converting genetic information stored in DNA into RNA

• Synthesis of RNA under the direction of a DNA template

  • A “faithful” transcript of the DNA

• Similarities between RNA and DNA:

• Both are nucleic acids

• Both are linear, unbranches, asymmetric polymers

• Both use A,G,C bases

• Differences between RNA and DNA:

• RNA uses ribose, DNA uses deoxyribose

• RNA contains uracil (U) instead of thymine (T), which is found in DNA.

• RNA is usually single stranded, DNA is double stranded

• Transcription in prokaryotes vs eukaryotes:

• basic mechanism is the same: DNA to RNA

• What are the three stages of transcription?

• Initiation, elongation, and termination

• What is RNA polymerase?

• An enzyme that catalyzes the addition of complementary ribonucleotides (adds U,G,C,As) to growing RNA chain

• Eukaryotes have 3 RNA polymerases

• Where does RNA polymerase work off of?

• A single stranded DNA template (same as DNA polymerase)

• Which direction does RNA polymerase add nucleotides?

• Only in a 5’ to 3’ direction (like DNA polymerase), moves in the 3’ to 5’ direction along the template strand.

• How is DNA polymerase and RNA polymerase different?

• Unlike DNA polymerase, RNA polymerase does not need a free -OH at the 3’ end to begin working (does not need primase/primer)

• Also RNA polymerase does not need helicase like DNA polymerase does, it can melt the DNA double helix (creates its own transcription bubble)

• What is a promoter?

• Specific DNA sequence at 5’ end of gene where RNA polymerase binds

• Several dozen nucleotides long

  • The promoter includes the start side for transcription

  • The binding site for DNA polymerase

  • Determines which DNA strand is transcribed

• What is the transcription unit?

• DNA sequence that is actually transcribed

• What is downstream?

• The direction of transcription away from promoter regions toward the coding region of the gene.

• What is upstream?

• Upstream refers to the direction toward the promoter regions, indicating the area of the gene prior to transcription starting.

• What are transcription factors?

• help stabilize RNA polymerase binding to the promoter and transcribing

• regulate transcription initiation and rate

• What is the transcription initiation complex?

• formed when RNA polymerase and associated transcription factors bind to promoter

• What is a template strand?

• DNA strand that is copied

• What is the coding strand?

• complementary RNA to template strand that is synthesized during transcription

• What is the polyadenylation signal sequence?

• a specific sequence of nucleotides found in pre-mRNA that signals the end of transcription

• What is RNA Processing

• Eukaryotic RNA must be processed (cleaned up) in the nucleus before being used by ribosomes to make proteins

• What is the Primary Transcript/Pre-RNA?

• the initial RNA molecule synthesized from the DNA template during transcription.

• What are the three separate steps of eukaryotic RNA processing?

• 1) modify the 5’ end of the RNA (addition of a protective cap (modified G residue) that protects this transcript as this RNA moves out of the nucleus

• 2) modify the 3’ end of the RNA (adds 50-250 adenines for protection - is not part of the coding)

• 3) removal of internal noncoding RNA sequences (introns) and splicing together of expressed sequences (exons)

• What are introns/exons?

• Introns are noncoding sequences of RNA that are transcribed from DNA but are removed during the RNA processing stage, specifically in the splicing process, allowing only the coding sequences (exons) to remain in the final messenger RNA (mRNA) that will be translated into proteins.

• What is the function of the modified 5’ and 3’ ends from RNA processing?

• Modified 5’ and 3’ ends stabilize RNA by protecting it from degradation

• Modified 5’ and 3’ ends facilitate RNA transport from nucleus to cytoplasm

• Modified 5’ and 3’ ends help RNA get recognized by the protein synthesizing machinery (ribosomes)

• What is mRNA?

• mRNA, or messenger RNA, is a type of RNA that carries genetic information from DNA to the ribosome (only exons, no introns)

Introns

Sequences found in pre-mRNA that may regulate gene expression.They can be spliced out during RNA processing, distinguishing between noncoding and coding regions.

Alternative RNA splicing

The process where some genes encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing.

Modular architecture consisting of domains

Discrete regions that proteins often have, with different exons coding for the different domains of a protein.

Exon shuffling

A process that may result in the evolution of new proteins. This mechanism allows for the rearrangement of exons to create different protein combinations, potentially leading to new functional proteins.

Translation

The conversion of coded information (after transcription and processing) into a sequence of amino acids.

protein synthesis/translation

The synthesis of a polypeptide under the direction of mRNA.

Adaptors

Connect amino acids to mRNA.

Complimentary base pairing

Copying or transferring information from nucleic acid to nucleic acid.

Genetic Code Problem

Both DNA and RNA use 4 'letters' each, while proteins have 20 'letters'.

Nucleotide triplets

The smallest possible unit to cover all 20 amino acids, each triplet is called a codon.

Degenerate code

Each amino acid is represented by multiple codons.

Reading the Code

Each 3 nucleotides represents an amino acid and the code is nonoverlapping.

Extracting correct information requires the correct start site and Reading Frame.

Extraordinary conservation of the genetic code

Indication of commonality in all living organisms

Attachment of Amino Acid to tRNA.

Uses tRNA Synthetase enzyme

tRNA

Transfer RNA, which carries amino acids to the ribosome for protein synthesis.

Ribosomes

Very large macromolecular machines that contain both RNA and protein (RNPs).

Translation is divided into three stages.

Initiation, Elongation (and Translocation), Termination

Forming the Initiation Complex - Translation

Sets the reading frame.

Translocation - translation

Ribosome moves in 3' direction.

Elongation and Translocation Repeat - translation

Protein built in N-term to C-term Direction Continues until Stop Codon. The polypeptide chain is elongated as amino acids are added sequentially during translation.

Making Lots of Protein from a Single Gene

A gene can be transcribed repeatedly resulting in many copies of the mRNA.

Polyribosome

One mRNA can be simultaneously translated by many ribosomes.