BIOL 200 Midterm Review
Study online at https://quizlet.com/_hw30zh
1. Central Dogma: DNA > RNA > Protein
2. Nucleotides: base, sugar, phosphate
3. Glycosidic Bond: Base and sugar bond
4. Nucleotide monomers: phosphates = acidic characteristics, covalently bonded to suger (phosphodiester
bond)
Hydrogenous base = covalently bond to sugar
Sugar
5. Purines: 2 ring base, Adenine, Guanine
6. Pyramidines: 1 ring base, RNA = uracil, cytosine, DNA = thymine, cytosine
7. Nucleoside: base, sugar
8. Amino Acid: building blocks of polypeptides, determines the shape of the polypeptide, 20 types
9. Protein functions: catlysis, transport, signalling, structure, motor, regulatory (control protein activity/gene
function)
10. Amino Acid Structure: Amino end (N-terminus), Carboxyl end (C-terminus), R groups
11. Special a.a.: Cysteine, glycine, proline
12. Cysteine: special a.a with sulfhydryl group, form disulfide bonds
13. Glycine: special a.a. with H symmetrical, intra/inter cross linking
14. Proline: special a.a. rigid ring structure
15. DNA shape: 5' end: free phosphate group attached to sugar phosphodiester bond: links nucleotides
3' end: free hydroxyl group on terminal end sugar
16. DNA "backbone": repeating phosphate-pentose units, holds no info
outside of dbl bond
within DNA structure
17. 3D structure of DNA: watson and crick, 2 polynucleotide strands wound together to form dbl helix (anti
//), bases stacked
18. Base pairing: complementary base
T dbl bonds to A, C triple bonds to G (stronger = more H bonds)
19. Right-handed Helix DNA: most DNA in cells
20. B DNA: major and minor groove, important for DNA-protein interactions, ex: TBP
R-H helix
21. A DNA: low humidity or high [salt], B DNA turns into A DNA
RNA-DNA, RNA-RNA exist in this form
, BIOL 200 Midterm Review
Study online at https://quizlet.com/_hw30zh
R-H helix
- smaller, wider
22. Z DNA: short DNA molecule of alternating purines and pyramidines
formed after transcription, tag for transcribed genes
L-H helix
- taller, longer
23. DNA denaturation and renaturation: important for DNA replication/transcription
unzipping and re-annealing of DNA
24. RNA secondary structures: hairpin, stem-loop
25. RNA tertiary structure: pseudoknot
26. Primary structure of protein: a.a. sequence
amino end, amide groups, r groups, carboxyl ends
27. Peptide Bond: linkange of one a.a. to another, on C terminus linking to next N terminus
28. Residue: amino acid
29. Secondary structure of protein: local folding
alpha-helix: stabilized by H bonds
beta sheet: 5-8 residues, r groups away/toward you, laterally packed beta strands, // or anti //
Beta turn: most common, 3-4 residues, glycine/proline twists and turns
30. Tertiary structure of protein: long range folding
stabilized by hydrophobic interactions b/w non-polar side chains
H bonds b/w polar side chains
Disulfide bonds b/w cysteine residues (covalent bond)
31. Quaternary structure of protein: multi-meric structure
pores (4 proteins) = potassium ion channel protein
32. Supramolecule structure of protein: large-scale assembly
10-100 polypeptides chains
general transcription factors: RNA polymerase, mediator complex, promotor, pre-initiation transcription complex
33. Motifs: combos of secondary structure proteins
34. Coil-Coil Motif: hydrophobic interactions
fibrous proteins
ex: collagen
, BIOL 200 Midterm Review
Study online at https://quizlet.com/_hw30zh
35. Helix-loop-helix Motif: ionic bonds involving Ca2+
ex: Ca2+ binding proteins
36. Zinc-finger Motif: contains Zn2+
ex: RNA, DNA, binding proteins
37. Domains: need these for certain proteins to function
ex: pyruvate kinase needs 3 domains
38. Reshuffling of motifs and domains: new proteins made
39. Ingredients for transcription in bacteria: DNA template, ribonucleotides (monomers for RNA
polymerization), RNA polymerase (catalyze synthesis of RNA
40. Ist step of transcription: Initiation
- polymerase binds to promoter (upstream of gene) in duplex DNA
forms "closed complex"
- polymerase melts duplex DNA
forms "open complex"
- polymerase catalyzes phosphodiester linkage of two initial rNTPs
41. rNTP: ribonucleotide tri-phosphate, building blocks of RNA synthesis
N = G, C, A, U
42. 2nd step of transcription: Elongation
- polymerase goes from 3' to 5'
- continues to melt DNA
- adds rNTPS to growing RNA
- formation of phosphodiester bonds b/w 3' OH and alpha phosphate group of incoming rNTP
43. 3rd step of transcription: Termination
- at stop site, polymerase releases completed RNA and dissociates from DNA
44. Holoenzyme: subunit of RNA polymerase
consists of core enzyme + sigma factor
alpha: loading entire onto transcript
beta: helps with phosphodiester linkage
45. Sigma factor: subunit of RNA polymerase
scans DNA until encounters promoter to bind with and form "closed complex"/to start transcription
46. How does sigma factor recognize promoter region?: RNA polymerase subunit
binds to specific sequence motifs (-10, -35 regions = start, stop site)
Study online at https://quizlet.com/_hw30zh
1. Central Dogma: DNA > RNA > Protein
2. Nucleotides: base, sugar, phosphate
3. Glycosidic Bond: Base and sugar bond
4. Nucleotide monomers: phosphates = acidic characteristics, covalently bonded to suger (phosphodiester
bond)
Hydrogenous base = covalently bond to sugar
Sugar
5. Purines: 2 ring base, Adenine, Guanine
6. Pyramidines: 1 ring base, RNA = uracil, cytosine, DNA = thymine, cytosine
7. Nucleoside: base, sugar
8. Amino Acid: building blocks of polypeptides, determines the shape of the polypeptide, 20 types
9. Protein functions: catlysis, transport, signalling, structure, motor, regulatory (control protein activity/gene
function)
10. Amino Acid Structure: Amino end (N-terminus), Carboxyl end (C-terminus), R groups
11. Special a.a.: Cysteine, glycine, proline
12. Cysteine: special a.a with sulfhydryl group, form disulfide bonds
13. Glycine: special a.a. with H symmetrical, intra/inter cross linking
14. Proline: special a.a. rigid ring structure
15. DNA shape: 5' end: free phosphate group attached to sugar phosphodiester bond: links nucleotides
3' end: free hydroxyl group on terminal end sugar
16. DNA "backbone": repeating phosphate-pentose units, holds no info
outside of dbl bond
within DNA structure
17. 3D structure of DNA: watson and crick, 2 polynucleotide strands wound together to form dbl helix (anti
//), bases stacked
18. Base pairing: complementary base
T dbl bonds to A, C triple bonds to G (stronger = more H bonds)
19. Right-handed Helix DNA: most DNA in cells
20. B DNA: major and minor groove, important for DNA-protein interactions, ex: TBP
R-H helix
21. A DNA: low humidity or high [salt], B DNA turns into A DNA
RNA-DNA, RNA-RNA exist in this form
, BIOL 200 Midterm Review
Study online at https://quizlet.com/_hw30zh
R-H helix
- smaller, wider
22. Z DNA: short DNA molecule of alternating purines and pyramidines
formed after transcription, tag for transcribed genes
L-H helix
- taller, longer
23. DNA denaturation and renaturation: important for DNA replication/transcription
unzipping and re-annealing of DNA
24. RNA secondary structures: hairpin, stem-loop
25. RNA tertiary structure: pseudoknot
26. Primary structure of protein: a.a. sequence
amino end, amide groups, r groups, carboxyl ends
27. Peptide Bond: linkange of one a.a. to another, on C terminus linking to next N terminus
28. Residue: amino acid
29. Secondary structure of protein: local folding
alpha-helix: stabilized by H bonds
beta sheet: 5-8 residues, r groups away/toward you, laterally packed beta strands, // or anti //
Beta turn: most common, 3-4 residues, glycine/proline twists and turns
30. Tertiary structure of protein: long range folding
stabilized by hydrophobic interactions b/w non-polar side chains
H bonds b/w polar side chains
Disulfide bonds b/w cysteine residues (covalent bond)
31. Quaternary structure of protein: multi-meric structure
pores (4 proteins) = potassium ion channel protein
32. Supramolecule structure of protein: large-scale assembly
10-100 polypeptides chains
general transcription factors: RNA polymerase, mediator complex, promotor, pre-initiation transcription complex
33. Motifs: combos of secondary structure proteins
34. Coil-Coil Motif: hydrophobic interactions
fibrous proteins
ex: collagen
, BIOL 200 Midterm Review
Study online at https://quizlet.com/_hw30zh
35. Helix-loop-helix Motif: ionic bonds involving Ca2+
ex: Ca2+ binding proteins
36. Zinc-finger Motif: contains Zn2+
ex: RNA, DNA, binding proteins
37. Domains: need these for certain proteins to function
ex: pyruvate kinase needs 3 domains
38. Reshuffling of motifs and domains: new proteins made
39. Ingredients for transcription in bacteria: DNA template, ribonucleotides (monomers for RNA
polymerization), RNA polymerase (catalyze synthesis of RNA
40. Ist step of transcription: Initiation
- polymerase binds to promoter (upstream of gene) in duplex DNA
forms "closed complex"
- polymerase melts duplex DNA
forms "open complex"
- polymerase catalyzes phosphodiester linkage of two initial rNTPs
41. rNTP: ribonucleotide tri-phosphate, building blocks of RNA synthesis
N = G, C, A, U
42. 2nd step of transcription: Elongation
- polymerase goes from 3' to 5'
- continues to melt DNA
- adds rNTPS to growing RNA
- formation of phosphodiester bonds b/w 3' OH and alpha phosphate group of incoming rNTP
43. 3rd step of transcription: Termination
- at stop site, polymerase releases completed RNA and dissociates from DNA
44. Holoenzyme: subunit of RNA polymerase
consists of core enzyme + sigma factor
alpha: loading entire onto transcript
beta: helps with phosphodiester linkage
45. Sigma factor: subunit of RNA polymerase
scans DNA until encounters promoter to bind with and form "closed complex"/to start transcription
46. How does sigma factor recognize promoter region?: RNA polymerase subunit
binds to specific sequence motifs (-10, -35 regions = start, stop site)
