Biochemistry Chapter 8 & 9 Flashcards

Questions and Answers

Give an example of a nucleoside, nucleotide, nucleic acid, pyrimidine, and purine.

Nucleoside: Adenosine; Nucleotide: ATP; Nucleic Acid: DNA; Pyrimidine: Cytosine; Purine: Adenine.

Classify nitrogenous bases as pyrimidines or purines.

Pyrimidines: Cytosine, Thymine, Uracil; Purines: Adenine, Guanine.

Distinguish between ribonucleotides and deoxyribonucleotides.

Ribonucleotides contain an OH group at the 2' carbon, while deoxyribonucleotides have an H.

Describe how nucleotides are linked together to form nucleic acids.

A phosphodiester linkage occurs between the phosphate of one nucleotide and the 3' hydroxyl of another. Signup and view all the answers

Describe the differences between DNA and RNA in terms of structure and function.

DNA is double-stranded, stores genetic information, and has thymine; RNA is single-stranded, transfers genetic information, has uracil, and includes mRNA, tRNA, and rRNA. Signup and view all the answers

Give the key features of the DNA double helix model.

The double helix is antiparallel, has complementary base pairing, and contains major and minor grooves. Signup and view all the answers

Explain how denaturation and renaturation can be followed spectrophotometrically.

Denaturation increases UV light absorption (hyperchromic effect), while renaturation decreases it (hypochromic effect). Signup and view all the answers

Explain how the %G-C base pairs and ionic strength influence the melting point of nucleic acids.

More G-C pairs raise melting points due to 3 hydrogen bonds; decreased ionic strength lowers melting points. Signup and view all the answers

Describe the polymerase chain reaction and its importance.

PCR amplifies DNA by separating strands, adding primers and polymerase, and repeating the process to exponentially increase DNA copies. Signup and view all the answers

Explain how DNA is sequenced by the Sanger method.

Dideoxynucleic acids (ddNTPs) halt polymerization; fragments are produced, then separated by electrophoresis. Signup and view all the answers

Describe the general procedures followed in cloning DNA.

Cloning involves cleaving a vector, ligating a DNA fragment, introducing it to a host cell, and propagating the recombinant DNA. Signup and view all the answers

Describe the characteristics of the restriction endonucleases most useful in recombinant DNA technologies.

They cleave DNA at specific sites and can leave sticky or blunt ends, facilitating DNA cloning. Signup and view all the answers

Discuss the different types of cloning vectors.

E. coli plasmid pBR322 has selectable markers and multiple cloning sites; BACs are used for large DNA fragments. Signup and view all the answers

Explain how cells are identified that contain the recombinant sequences.

Cells are identified using negative selection; those that survive antibiotic treatment likely contain recombinant DNA. Signup and view all the answers

Study Notes

Nucleosides, Nucleotides, and Nucleic Acids

Nucleoside is a nucleotide without a phosphate group.
Nucleotide contains a nitrogenous base, a pentose (ribose or deoxyribose), and a phosphate group.
Nucleic acids include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Pyrimidines include cytosine (C), thymine (T) in DNA, and uracil (U) in RNA.
Purines consist of adenine (A) and guanine (G).

Nitrogenous Base Classification

Nitrogenous bases are classified into pyrimidines and purines.
Common structures depicted in relevant figures (Figure 8-2).

Ribose vs. Deoxyribose

Ribonucleotides contain an OH group at the 2' carbon.
Deoxyribonucleotides have an H at the 2' carbon.

Nucleic Acid Structure Formation

Nucleotides link via a phosphodiester bond between the 5' phosphate of one and the 3' hydroxyl of the next.
This results in a phosphate-group bridge.

DNA vs. RNA

DNA has a helical structure with 10.5 base pairs per turn; A=T and C≡G pairing.
DNA is antiparallel, allows formation of hairpins, and primarily functions in genetic information storage and replication.
RNA includes mRNA (transfers genetic info), tRNA (adapters for amino acids during protein synthesis), and rRNA (ribosome components).
RNA is single-stranded with base pairs A-U and G-C, folding into various structures including hairpins and loops.

DNA Double Helix Model

Key features include antiparallel strands and complementary base pairing.
Experimental evidence from X-ray diffraction and Chargaff's rules supported the helical structure proposed by Watson & Crick.

Denaturation and Renaturation

Denaturation involves the unwinding of double strands, increasing UV absorption due to the hyperchromic effect.
Renaturation occurs as single strands anneal back into double-stranded form, decreasing UV absorption (hypochromic effect).

Melting Point Influences

G-C base pairs require more heat to dissociate than A-T pairs due to three hydrogen bonds.
Increasing G-C content raises melting points, while decreased ionic strength lowers melting points.

Polymerase Chain Reaction (PCR)

Involves heating DNA to separate strands, adding primers, and using taq polymerase for DNA synthesis.
Cycle repetition can amplify the target sequence exponentially.

Sanger Sequencing Method

Uses dideoxynucleotides (ddNTPs) to terminate DNA synthesis, creating fragments of varying lengths.
Electrophoresis allows analysis of these fragments from 3' to 5'.

General Procedures for DNA Cloning

Involves cleaving a cloning vector and DNA of interest with the same restriction enzyme, then ligating fragments together.
The recombinant DNA is introduced to a host cell for propagation.

Restriction Endonucleases and Cloning Vectors

Restriction endonucleases cut DNA at specific sites, leaving sticky or blunt ends.
Common cloning vectors include E. Coli plasmid pBR322 and bacterial artificial chromosomes (BAC), each with distinct features for cloning efficiency.

Selection of Recombinant Sequences

Negative selection via antibiotics (like ampicillin) identifies unsuccessful clones.
With BACs, colonies that aren't blue (due to disrupted lacZ gene) indicate successful recombinant DNA incorporation.

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Test your knowledge with these flashcards covering essential concepts from Biochemistry Chapters 8 and 9. Topics include nucleosides, nucleotides, nucleic acids, and types of bases in DNA and RNA. Assess your understanding and reinforce your learning for exams!