Bio 241 Exam 2 Flashcards

Ch 15, 17, 18, 19

What is a double helix?

the secondary structure of DNA, consisting of two antiparallel DNA strands wound around each other. Some RNAs may also form a double helix in stem-and-loop secondary structures.

What is complementary base pairing?

the association between specific nitrogenous bases of nucleic acids stabilized by hydrogen bonding. Adenine pairs with thymine (DNA) or uracil (RNA), and guanine pairs with cytosine

What are parental strands?

A strand of preexisting DNA. The parental strand is used as a template during DNA synthesis and is also known as the template strand.

What is a daughter strand?

the strand of DNA that is newly replicated from a template. or parental, strand of DNA.

What is semiconservative replication?

the way DNA replicates, with each strand of an existing DNA molecule serving as a template to create a new complementary DNA strand.

What is a genome?

all the hereditary material (DNA in cells, DNA or RNA viruses) in a virus, cell, or organism, including but not confined to genes.

What is DNA polymerase?

any enzyme that catalyzes synthesis of DNA.

What is deoxyribonucleoside triphosphate?

the monomer used by DNA polymerase to polymerize DNA. Consists of the sugar deoxyribose, a base (A, T, G, or C) and three phosphate groups

What is the origin of replication?

the site on a chromosome where DNA replication begins

What is DNA helicase?

an enzyme that breaks hydrogen bonds between nucleotides of DNA< “unzipping” a double-stranded DNA molecule

What are Single-strand DNA-binding proteins (SSBPs)?

a protein that attaches to separated strands of DNA during replication, preventing them from re-forming a double helix.

what is topoisomerase?

an enzyme that prevents the twisting of DNA ahead of the advancing replication fork by cutting the DNA, allowing it to unwind, and rejoining it.

what is a primer?

a short, single-stranded RNA molecule that base-pairs with a DNA template strand and is used as a starting point for DNA synthesis by DNA polymerase

what is primase?

an enzyme that synthesizes a short stretch of RNA to use as a primer during DNA replication

What is RNA polymerase?

an enzyme that catalyzes the synthesis of RNA from ribonucleotides using a template usually consisting of DNA

What is a leading strand?

In DNA replication, the new strand of DNA that is synthesized in one continuous piece in a direction that follows the replication fork.

What is the lagging strand?

In DNA replication, the new strand of DNA that is synthesized discontinuously (as a series of short pieces that are later joined) in a direction moving away from the replication fork.

What are okazaki fragments?

short segment of DNA produced during replication of the lagging-strand template. These are eventually linked together to produce the lagging strand in newly synthesized DNA.

What is DNA ligase?

an enzyme that joins piece of DNA by catalyzing the formation of a phosphodiester linkage between the pieces

What is a replisome and what does it contain?

the macromolecular machine that copies DNA; includes DNA polymerase, helicase, primase, and other enzymes

What is a telomere?

the end of a linear chromosome that contains a short repeated sequence of DNA.

What is telomerase?

an enzyme that adds DNA to the ends of chromosomes to prevent their shortening by standard DNA synthesis; catalyzes DNA synthesis by guided by an RNA template that is part of the enzyme.

What are somatic cells?

any type of cell in a multicellular organism except eggs, sperm, and their precursor cells. (body cell)

What is proofreading?

mechanism for error correction during DNA synthesis in which dna polyermase recognized and removes a wrong deoxyribonucleotide added during DNA replication adn then continues synthesis

What is a mismatch repair?

a type of dna repair used to correct mismatched base pairs in DNA that result from mistakes in DNA synthesis

How do genes encode for proteins?

Genes encode for proteins through the production of messenger RNA (mRNA), which is used as a template for the translation proteins.

What other RNA products do genes encode for that isnt proteins

Ribosomal RNA (rRNA). transfer RNA (tRNA), and other RNA molecules such as microRNA (miRNA)

Central Dogma

1) Replication: DNA makes exact copies of iteselt so that genetic information can pass to new cells during division

2) Transcription: Cells copy a specific segment of DNA into a temporary messenger called mRNA. This happens inside the nucleus in eukaryotes.

3) Translation: Ribosomes read the mRNA code (in codons) to link amino acids together and build a functional protein.

What are the two exceptions to the Central Dogma.

1) Reverse transcription: Genetic information flows backward from RNA to DNA

2) Prions: Misfolded variant of a host cellular protein. When the abnormal prion contacts norma proteins, it forces them to refold into the infectious shape.

What is reverse transcriptase and where is it found

An enzyme that uses an RNA template to build a complementary DNA strand.

What is the importance of reverse transcriptase in RNA viruses.

This is an essential viral enzyme that converts single-stranded RNA into double-stranded DNA. This allows retroviruses to integrate their genetic material into the host cell’s genome.

What is the genetic code

The set of rules used by living cells to translate information stored in DNA or RNA into proteins. (nucleotide bases, codons, amino acids)

What is meant by the genetic code being redundant but not unambiguous?

More than one codon specifies the exact same amino acid. A single, specific codon never codes for more than one amino acid.

What is a codon and how is it related to the genetic code?

A codon is a sequence of three consecutive nucleotides in DNA/RNA molecule that acts as a single word in the genetic instructions for making proteins.

Why is maintaining the correct reading frame important?

It determines the exact sequence of amino acids that make up a protein.

What is a mutation?

a permanent change in the DNA sequence of an organism or virus.

What is a point mutation?

a mutation that results in a change or an instertion or deletion of a single base pair in DNA.

What is a chromosome-level mutation?

Any change in chromsome number, or the change in the composition of individual chromosomes as a result of inversions, deletions, or duplications during cell division.

What is a missense mutation?

a point mutation that changes one amino acid for another within a protein.

What is a nonsense mutation?

a point mutation that converts an amino-acid-specifying codon into a stop codon.

What is a silent mutation?

a point mutation that changes the sequence of a codon without changing the amino acid that is specified.

What is a frameshit mutation?

the addition or deletion of one or a few base pairs in a coding sequence that shifts the reading frame of the mRNA.

loss-of-function allele

a mutant allele that does not produce a functional gene product.

metabolic pathway

a linked series of biochemical reactions that sequentially changes an initial substrate to form a final product; the product of one reaction is the substrate of the next reaction.

messenger RNA

an RNA molecule transcribed from DNA that carries information (in codons) that specifies the amino acid sequence of a polypeptide.

Transcription

process of using a DNA template to make an RNA molecule that has a base sequence complementary to the DNA. DNA is transcribed to RNA by RNA polymerase

Translation

process of using the information in the base sequence of mRNA to synthesize proteins. Information in the mRNA is translated into proteins by ribosomes

reading frame

a series of adjacent non-overlapping, three-base-long sequences in DNA or RNA that specify a sequence of amino acids in a polypeptide. Set by the start codon.

start codon

the AUG triplet in mRNA where protein synthesis begins; methionine

stop codons

(UAG, UGA, UAA) that cause termination of protein synthesis

translocation

A type of mutation in which a piece of chromosomes moves to another chromosomes or during translation, the movement of a ribosome down a messenger RNA.

karyotype

the distinctive appearance of all the metaphase or pro-metaphase chromosomes in an individual, including the number of chromosomes, their length, and their banding patterns.

Understand the levels of DNA structure, from individual nucleotides making up chromosomes to the entire complement of the genetic material in an organism (genome).

1) Nucelotides

• each nucleotide has a 5-carbon sugar (deoxyribose), a phosphate group, and a nitrogenous base

• Contains adenine, thymine, cytosine, and guanine

• Sugar and phosphate groups link together via covalent bonds to form outer framework

2) DNA Strands

• Nucleotides bind together through phosphodiester bonds

• 5’ end and 3’ end

3) Double Helix

4) Chromosomes

5) Genes

6) Genomes

Describe the importance of covalent bonds and hydrogen bonds to the structure of a DNA molecule.

Covalent bonds: gives DNA its strong, stable, and flexible structure and they link the sugar and phosphate groups together to form the strong sugar-phosphate backbone on the outside of each DNA strand.

Hydrogen Bonds: weak electrical attractions between a hydrogen atom in one molecule and an electronegative atom. They connect the nitrogenous bases across the center of the double helix.

Describe the relationship between the structure of a DNA molecule and how it is replicated.

The two complementary strands can seperate and act as precise templates for building new partner strands

What are replication bubbles

where the strands of dna have been separated so that replication can begin

What are deoxyribonucleoside triphosphates (dNTPs)

the monomer used by DNA polymerase to polymerize DNA

When will DNA be replicated? Where does it occur?

DNA is replicated during the synthesis phase just before the cell divides.

How does replication differ on the leading and the lagging strand?

Leading: synthesized continuously in the same direction that the replication fork opens

Lagging: synthesized discontinuously in short pieces moving away from the fork.

Why is replicating telomeres on the lagging strand a problem?

DNA polymerase cannot copy the very last segment of the chromosome after the final RNA primer is removed.

What is nucleotide excision repair (NER)?

type of DNA repair that removes a damaged region in one strand of DNA and replaces it with the correct sequence using the underdamaged strand as a template

How does DNA damage increase the likelihood of cancers?

disrupts the normal instruction that control how cells grow, divide, and repair themselves.

What is meant by proofreading by DNA polymerase?

an error-correcting function that detects and removes incorrect, mismatched nucleotides immediately as new DNA strand is synthesized.

Understand thymine dimers

these are abnormal covalent links formed between adjacent thymine bases on the same DNA strand when exposed to UV radiation.

what is origin of replications

the site on a chromosome where DNA replication begins

what are replication forks

site where a double-stranded molecule of DNA is seperated into two single strands for replication and on which DNA synthesis occurs.

what is the template strand?

a strand of DNA or RNA used to make a new, complementary strand via complementary base-pairing. the stran

what is non-template strand/coding strand?

the strand of DNA that is not transcribed during synthesis of RNA. With the exception of T’s instead of U’s, its base sequence corresponds to that of the RNA produced from the other strand.

what is the core enzyme?

a general term for the enzyme within a multipart holoenzyme that is responsible for catalysis.

what are promoters?

what is sigma?

a bacterial protein that associates with the core RNA polymerase to allow recognition of promoters

what is downstream in reference to transcription?

the direction in which RNA polymerase moves along a DNA strand.

what is upstream in reference to transcription?

opposite to the direction in which RNA polymerase moves along a DNA strand.

what is elongation?

1) the process by which RNA lengthens during transcription

2) the process by which a polypeptide chain lengthens during translation

what is termination?

The release of the polypeptide and dissociation of a ribosome from mRNA when the ribosome reaches a stop codon.

what is the TATA box?

a short DNA sequence in many eukaryotic promoters that is important for assembling general transcription factors and RNA polymerase at the core promoter

What are general transcription factors?

general term for a protein that binds to a DNA regulatory sequence to influence transcription.

what is a poly(A) signal?

In eukaryotes, a short sequence of nucleotides near the 3’ end of the future mRNA that signals cleavage of the pre-RNA and addition of the poly(A) tail.

what are primary transcripts?

(eukaryotes) a newly transcribed RNA molecule that has not yet been processed to a mature RNA.

what is pre-mRNA?

Primary transcript of protein-coding genes, processed to form mRNA

what is RNA processing?

the changes that a primary RNA transcript undergoes to become a mature RNA molecule.

what are introns?

a region of a gene that is transcribed into RNA but is later removed

what are exons?

a transcribed region of a gene of a primary transcript that is retained in the mature RNA. mRNA exons code for amino acids.

what is splicing?

the process by which introns are removed from primary RNA transcripts and the remaining exons are connected together.

what are small nuclear ribonucleoproteins (snRNPs)

small RNAs associated with proteins and found in the nucleus of eukaryotic cells, where they form the spliceosome and catalyze splicing.

what is a spliceosome?

a large, complex assembly of snRNPs and many proteins that catalyzes removal of introns from primary RNA transcripts.

what is a poly(A) tail?

a sequence of about 100-250 adenine nucleotides added to the 3’ end of newly transcribed messenger RNA molecules

what is aminoacyl-tRNA synthetases?

an enzyme that catalyzes the addition of a particilar amino acid to its corresponding tRNA molecule

what is wobble pairing?

Nonstandard base-pairing between the nucleotide in the third position of a codon and the corresponding nucleotide in the anticodon of a tRNA. Wobble pairing allows one anticodon to read more than one codon, which in turn allows roughly 40 different tRNAs to read all 61 amino-acid-specifying codons.

Where in the cell does transcription take for prokaryotes?

cytoplasm

Where in the cell does transcription take for eukaryotes?

nucleus

Describe the flow of information from the genetic material to a functional protein molecule starting with DNA.

1) Transcription: DNA to RNA

2) Translation: RNA to Protein

3) Protein Folding and Post-Translational Modification

List the sequence of events during transcription of a gene.

1) Initiation: Promoter Recognition (transcription factors bind and RNA polymerase identify and bind to a specific region on the DNA upstream called the promoter and unwinding.

2) Elongation: Template reading (RNA polymerase reads the exposed DNA template strand in the 3’ to 5’ direction. RNA synthesis (RNA polyermase synthesizes a complementary single-stranded RNA molecule in the 5’ to 3’ direction).

3) Termination: Signal Recognition (RNA polymerase reaches a specific terminator sequence at the end of the gene). Release (the newly synthesized RNA transcript, RNA polymerase, and DNA template separate from one another).

What is the template strand of DNA?

• Direction of Reading: RNA Polymerase reads the template strand in the 3’ to 5’ direction

• Direction of Synthesis: Antiparallel , the complementary RNA transcript is built in the 5’ to 3’ direction

• Base complementary

How is sigma used in prokaryote transcription?

• Sigma promoter binding: when a sigma factor vinds to the core enzyme, it forms the RNA polyermaze, enabling the complex to bind specifically to promoter elements

• DNA unwinding: opens the double-stranded DNA at the promoter region to form the open complex.

What are transcriptions factors in eukaryotes?

• DNA-Binding Domain: Interacts directly with specific base sequences in DNA

• Activation/Repression Domain: interacts with RNA polymerase 2

• Signal-sensing: responds to external signal

Explain what happens to a pre-mRNA molecule (or primary mRNA transcript) during the process of RNA splicing

A single pre-mRNA molecule can have its exons joined in different combinations, allowing a single gene to produce multiple distinct protein isoforms.

Describe the importance of the 5’ and 3’ end modifications to eukaryotic mRNA molecules

5' capping and 3' polyadenylation are crucial for mRNA stability, export from the nucleus, and translation efficiency. These modifications protect the mRNA from degradation and assist in ribosome binding during translation.

Describe the structure of a ribosome, including the functional regions, and explain how they contribute to the process of translation

Ribosomes consist of a large and a small subunit, each made of rRNA and proteins. The functional regions include the A site (aminoacyl), P site (peptidyl), and E site (exit), which respectively facilitate tRNA binding, peptide bond formation, and the release of uncharged tRNAs.

Explain the interaction between mRNA, tRNA, and rRNA during translation

During translation, mRNA provides the template for the sequence of amino acids, while tRNA carries specific amino acids to the ribosome by matching its anticodon with the mRNA codons. rRNA forms the core of the ribosome's structure and catalyzes the peptide bond formation between amino acids.