Biochemistry Chapter 4

What is DNA?

the genetic material in cells

What is RNA?

transcribes and translates DNA information into proteins

What is the most soluble out of bases, nucleosides, and nucleotides? Why?

nucleotides because of the phosphate group

Why are nucleosides more water soluble than bases?

because of the three OH groups on the sugar that allow for hydrogen bonds

What difference does the 2’-OH group vs the 2’-H affect?

secondary structure and stability

What links nucleotides together to form polynucleotide chains? What enzyme forms these?

3’-5’ phosphodiester bridges formed by RNA polymerase

What causes cyclic nucleotides? Which ones are important regulators of cell metabolism?

two ester bonds to the phosphoric acid, cAMP, cGMP

Where is the energy stored within ATP?

phosphoric anyhdride linkages

Why is ATP high energy?

electrostatic repulsion, stabilization of product, entropy increase

How many A per helical repeat in double helices?

34

How many base pairs per repeat in double helices?

10 base pairs

How many hydrogen bonds stabilize G-C pairs?

three

How many hydrogen bonds stabilize A-T pairs?

two

Where is the genetic information that DNA carries?

within the unique base sequence

How many base pairs in humans?

3 billion, close to one meter genome

What is negatively charged and can interact with metal ions?

phosphate

What hydrogen bonds with the polar sugar-phosphate backbone?

water

What electrostatic interactions stabilize the structure of double DNA helix?

between positive ions and phosphate groups

What interactions allow for base stacking?

hydrophobic reactions

What is the increase in UV absorbance with temperature called which also reflects the unwinding of the DNA double helix?

hyperchromism or hyperchromic shift

What is a melting curve?

graph of relative absorbance and temperature that shows where dsDNAs are separated

What factors affect melting temperature?

percent of GC and length

In what direction is exonuclease activity?

3’-5’

What is required for enzymatic activity in RNA polymerase?

Mg²⁺

What happens in RNA synthesis when oxygen lone pair attacks phosphate?

two phosphates will be removed and oxygen and phosphate become covalently linked

What are viruses?

supramolecular complexes of nucleic acid encapsulated in a protein coat

What does the complete virus life cycle include?

virus and host recognition, entry, replication, integration, transcription and translation, assembly, and release

What protein on virus cell interacts with CD4 receptor?

gp120

What does gp41 interact with to allow RNA to enter the cell?

CCR5

What are ribosomes? What is the ratio?

complexes of RNAs and proteins, 2:1

What is the function of rRNA?

scaffolding for ribosomal proteins

What is the function of the 5’ cap of m⁷-GTP in eukaryotic mRNAs?

protects RNA degradation from RNase

What enzyme removes one phosphate?

phosphohydrolase

What enzyme is step 2 done by?

guanylyltransferase

What enzyme is step 3 done by?

guanylate base methyltransferase

What enzyme is step 4 done by?

ribose methyltransferase

What complex is required to cleave the sequence where the Poly-A site will be inserted?

CPSF-CstF-CFI-CFII

What adds the poly A tail?

poly A polymerase

What does intron splicing require?

snRNA working with proteins

Where does splicing take place?

spliceosome complexes of 45 proteins and 5RNAs (snRNA)

What are the 5 RNAs in snRNA?

U1, U2, U4, U5, U6

What is the purpose of U3?

guiding site-specific cleavage of rRNA in nucleus

Where does spliceosome assembly occur?

pyrimidine tract

What are the first two and last two nucleotides in an intron?

GU and AG

Where does translation start?

ribosomal binding site

What is responsible for specific initiation of transcription?

sigma factor, recognizes promoter sequences

What is required in eukaryotes for formation of transcription complex?

transcription factors

What is the promoter?

the binding site of RNA polymerase

What features do prokaryotic promoters have? How many nucleotides does each have?

-10 feature, -35 feature, each have six nucleotides

What features do Eukaryotic promoters have?

TATA box (-25 feature) and CAAT box (-75 feature)

What methods can lead to transcription termination in prokaryotic cells?

hairpins and Rho

What binds to RNA polymerase in Rho-dependent termination?

NusA

What is the ribosome binding site in prokaryotic cells?

shine-dalgarno sequence

What is the start codon?

AUG

What are the stop codons?

UAA, UAG, and UGA

What is the genetic code?

the sequence of nucleotides coded in triplets in mRNA, that determines the sequence of amino acids in protein synthesis