BIO 271 Exam 2

What are nucleic acids made of?

nucleotides

What is a base sequence?

the nucleotides of a nucleic acid that appear in a certain order within the strand

What is the base sequence of DNA responsible for?

carrying and retaining the hereditary information in a cell

What is polymerization?

2 or more monomers combine to form larger molecules

What is the pH of a nucleotide?

7\.3

Why is it important for a nucleotide to have a basically neutral pH?

acidic or basic nucleotide would cause DNA and RNA to denature

What are the nucleotides that compose DNA called?

deoxyribonucleotides

What are the 3 components of a DNA nucleotide?

pentose sugar called deoxyribose

phosphate group

nitrogenous base

What is a nitrogenous base?

nitrogen-containing ring structure that is responsible for complementary base pairing between nucleic acid strands

What is a nucleoside?

the five-carbon sugar and nitrogenous base

What are the purines?

Adenine and Guanine

What are the pyrimidines?

Cytosine, Thymine, and Uracil

What is the difference between purines and pyrmidines?

Purines have a double ring while pyrimidines have a single ring q

What controls the specificity of genes?

Pyrophosphate

What is pyrophosphate used for in the cell?

energy

establishment of specificity

to stop the accumulation of any nucleotide in the cell

How are the nucleotides linked together?

phosphodiester bond

What is a phosphodiester bond?

linkage where the phosphate group attached to the 5’ carbon of the sugar of one nucleotide bonds to the hydroxyl group of the 3’ carbon of the sugar of the next nucleotide

What does phosphodiester bonding between nucleotides form?

sugar-phosphate backbone

What are deoxynucleotide triphosphates (dNTPs)?

nucleoside triphosphates containing deoxyribose

How is the sugar backbone of DNA formed?

linking deoxyribose sugars and phosphate groups

What is released as a pyrophosphate from the dNTP?

2 terminal unused phosphates

What happens to the pyrophosphate from the dNTPs?

it is hydrolyzed and the energy released is used to drive nucleotide polymerization

What is at the 3’ end of a nucleic acid strand?

carbon atom with a free hydroxyl

What is at the 5’ end of a nucleic acid strand?

carbon atom with a phosphate attached

What are Chargaff’s Rules?

a set of two observations made by Austrian biochemist Erwin Chargaff in the 1940s about the composition of DNA

What do Chargaff’s Rules state?

The amount of guanine in DNA is equal to the amount of cytosine. The amount of adenine in DNA is equal to the amount of thymine.

What do Chargaff’s Rules provide evidence for?

the complementary base pairing of DNA which is essential for the stability and structure of DNA

How do you denature DNA?

By exposing it to extreme heat or chemicals

Which nucleotide base pairs are easy to break and why?

Adenine and thymine because they have 2 hydrogen bonds between them rather than the 3 guanine and cytosine have

What is the structure of RNA?

single stranded and made of ribonucleotides linked by phosphodiester bonds

What does a ribonucleotide in an RNA chain contain?

ribose (pentose sugar)

one of the 4 nitrogenous bases (AUCG)

phosphate group

What do the structural differences between DNA and RNA do?

Make DNA more suited to carry genetic information and allow RNA to still perform its more short term functions

How does RNA stabilize itself?

folding on itself with self complementary regions

What is the difference between deoxyribose and ribose?

deoxyribose: 2’ carbon has a hydrogen and 3’ carbon has a hydroxyl

ribose: 2’ and 3’ carbons have a hydroxyl

What are the 3 main types of RNA present in protein synthesis?

messenger RNA (mRNA)

ribosomal RNA (rRNA)

transfer RNA (tRNA)

How does mRNA play an important role in protein synthesis?

it carries genetic information from DNA to the ribosome

What is important about the nucleotide sequence of mRNA?

it is complementary to the sequence of nucleotides in the DNA it was transcribed from

What is a codon?

sequence of 3 nucleotides

What does a codon in mRNA code for?

a specific amino acid

What are ribosomes?

the cellular organelles that make proteins

What are ribosomes made out of?

a large and small subunit

What does the large subunit contain?

most of the rRNA

What does the small subunit contain?

some rRNA and other proteins

What roles does rRNA play in protein synthesis?

Binding to mRNA and bringing it to the ribosome

Catalyzing the formation of peptide bonds between amino acids

How long are tRNA molecules?

70-90 nucleotides

What does tRNA do?

carries amino acids to the ribosome

What is an anticodon?

a sequence of 3 nucleotides that is complementary to a codon in mRNA

What does the base pairing between mRNA and tRNA do?

Allow for the correct amino acid to be inserted in the polypeptide chain being synthesized

What happens when an mRNA codon binds to the anticodon of a tRNA?

the amino acid carried by the tRNA molecule is added to the growing polypeptide chain at the ribosome

What triggers mRNA synthesis?

the mRNA carries the message from the DNA which controls all cellular activity in the cell. when a cell requires a certain protein to be synthesized, the gene for that protein is turned on and the mRNA is synthesized through transcription

Where is rRNA synthesized in prokaryotes?

cytoplasm

What synthesizes rRNA in prokaryotes?

RNA Polymerase 1

How are rRNA genes in prokaryotes organized?

into operons

What are operons?

clusters of genes transcribed together

What is the 1st step in tRNA synthesis in prokaryotes?

transcription in which the tRNA gene is transcribed by RNA polymerase

What is the 2nd step of tRNA synthesis?

processing in which different enzymes remove introns and add nucleotides to the ends of the transcript

What is the processed transcript called?

Precursor tRNA

What is the 3rd step of tRNA synthesis?

the addition of the CCA (cytosine-cytosine-adenine) tail to the 3’ end of the precursor tRNA

Why is the CCA tail important in tRNA synthesis?

it is how the ribosome recognizes the incoming tRNA

What is the final step of tRNA synthesis?

folding in which the tRNA folds into its mature form which is a cloverleaf structure with an anticodon loop and an amino acid attachment site

What is the ribosomal cycle?

process by which ribosomes are assembled, used to synthesize proteins, and then disassembled

What is a genome?

an organism’s genetic material

What is a genotype?

the full collection of genes that a cell contains within its genome

What is a phenotype?

The set of genes being expressed at any given point determines the cell’s activities and its observable characteristics

What are constitutive genes?

genes that are always expressed

What are housekeeping genes?

some constitutive genes that are necessary for the basic function of the cell

How is the vast majority of an organism’s genome organized?

in chromosomes

What are chromosomes?

discrete DNA structures within cells that control cellular activity

What are the characteristics of eukaryotic chromosomes?

linear, contain multiple distinct chromosomes

How many copies of each chromosome do eukaryotic cells carry?

2, they are diploid

What are the characteristics of prokaryotic chromosomes?

circular, usually only one in the nucleoid

How many copies of each chromosome do prokaryotic cells carry?

1, they are haploid

How is DNA packaged in prokaryotic cells?

found in nucleoid as a single circular chromosome and is supercoiled

What is supercoiling?

the process of twisting the DNA molecule around itself, which causes it to become more compact

What is DNA gyrase?

a type of topoisomerase found in bacteria that helps prevent the overwinding of DNA

What enzyme controls supercoiling?

topoisomerase

What is positive supercoiling?

twists in the same direction as the DNA helix; makes DNA more compact

What is negative supercoiling?

twists in the opposite direction of the DNA helix; makes DNA less compact

What is noncoding DNA?

DNA that does not encode proteins or stable RNA products and usually found in areas prior to the start of coding sequences of genes and DNA sequences located between genes (intergenic regions)

What is the function of noncoding DNA?

regulation of transcription or translation through the production of small noncoding RNA molecules

DNA packaging

chromosomal stability

What is extrachromosomal DNA?

additional molecules of DNA present outside of the chromosomes

How is extrachromosomal DNA usually maintained?

as plasmids

What is central dogma thoery?

DNA transcribed to RNA which is then translated to protein

the flow of genetic information from DNA to RNA to protein

What happens during transcirption?

a gene composed of DNA is read to produce an RNA molecule

What happens during the process of translation?

mRNA provides information for the ribosome to catalyze protein synthesis

What is gene expression?

the processes of transcription and translation

synthesis of specific protein with a sequence of amino acids that is encoded in the gene

What is rolling circle replication?

a type of replication used by plasmids

What is the 1st step of rolling circle replication?

RepA binds to the double stranded DNA at the origin of replication

What is the 2nd step of rolling circle replication?

RepA nicks one strand of the DNA and holds to the 5’ end

What is the 3rd step of rolling circle replication?

DNA Polymerase III binds to the 3’ of the nicked strand and begins to unidirectionally replicate the DNA using the un-nicked strand as a template and displacing the nicked strand

What is the 4th step of rolling circle replication?

RepA recruits helicase to unwind the DNA

What is the 5th step of rolling circle replication?

completion of replication at the site of the original nick results in full displacement of the nicked strand which may then recircularize into a single stranded DNA molecule

What is the 6th step of rolling circle replication?

RNA primase synthesizes a primer to initiate DNA replication at the single stranded origin site of the single stranded DNA resulting in a double stranded DNA identical to the other circular DNA molecule

What are the 3 steps in RNA transcription?

initiation, elongation, termination

Where are the recognition sites located on the DNA?

upstream in the promoter region at -35 nucleotides and -10 nucleotides

Where does the initiation of transcription begin?

at the promoter region

What is the promoter?

a DNA sequence onto which the transcription machinery binds and initiates transcription

What is the -10 nucleotide sequence called?

TATA box, TATAAT

What binds to the -35 sequence on DNA?

the sigma σ factor of RNA polymerase

How does the elongation part of transcription begin?

when the sigma subunit dissociates from the polymerase allowing the core enzyme to synthesize RNA