CMB self-study Flashcards Preview

CMB > CMB self-study > Flashcards

Flashcards in CMB self-study Deck (133):
1

Prokaryotes vs Eukaryotes

Prokaryotes: no membrane enclosed organelles, chromatin in nucleoid Eukaryotes: membrane bound organelles and vesicles, nuclear membrane

2

Purines

Adenine (A) Guanine (G)

3

Pyrimidines

Cytosine (C) Thymine (T) in DNA only Uracil in RNA only

4

Nucleotide bonding

A bonds with T or U (2 bonds) and C bonds with G (3 bonds)

5

Nucleosides

Purines and pyrimidine bases + pentose (deoxyribose or ribose)

6

Nucleotides

Phosphorylated nucleosides (5' -OH of ribose or deoxyribose is phosphorylated)

7

Oglionucleotides

Short polymers of nucleotides (up to 30)

8

Role of Mg2+ and other cations

Shield phosphate groups from electrostatic intrastrand repulsion (balance the negative charges)

9

Why is circular DNA an advantage?

May provide protection from degredation by exonucleases

10

Active site

Includes substrate-binding site and catalytic site

11

Substrate-binding site

Determines specificity

12

Catalytic site

Contains catalytic residues which act on the substrate

13

-ase usually means

enzyme

14

B-DNA

Conformation primarily found in cells

15

A-DNA

Form taken by DNA-RNA hybrid during transcription

16

Z-DNA

Occurs within DNA sequences that control gene transcription

17

Causes of denaturation

Extreme pH, extreme ionic strength, high temp

18

Type I isomerases

Break only one DNA strand and allow it to rotate about the other to relieve supercoil. Also reseal (ligate) break

19

Type II isomerases

Act as ATPases-Using ATP, break both DNA strands, relax supercoil, reseal DNA

20

What are gyrases?

Topoisomerases which relieve supercoiling from unwinding of DNA. Prevent supercoiling that would be induced by unwinding DNA in DNA synthesis

21

Nalidixic acid

Antibiotic used for antibotic resistant UTIs. Inhibit gyrases and interferes with breaking and rejoining of DNA

22

Novobiocin

Antibiotic which blocks the binding of ATP (which blocks type II isomerases)

23

Cruciforms

Regions of DNA which interchain hydrogen bonds are broken and intrachain bonds form. Function in the control of replication and transcription

24

Triplex DNA functions and bonding

Triple stranded DNA. Usually in regions with string of purine bases. Functions in transcription control, initiation and termination of replication by enhancing stability of chromosome ends called telomeres. Forms hydrogen bonds with major groove of B-DNA with Hoogsteen pairing.

25

What is triple-stranded DNA associated with?

Hereditary persistance of fetal hemoglobin. Mutation prevents the triple stranded DNA from forming and fetal hemoglobin to continues to be transcribed

26

Hoogsteen pairing

Occurs on different faces of DNA than Watson and Crick pairing

27

Quadruplex DNA

Forms in immunoglobin genes that undergo recombination. Responsible for antibody diversity. Also present at the telomeres.

28

Histones (types, function)

Eight proteins (2 each of H2A, H2B, H3, H4) combine to form a histone disk octamer around which DNA supercoils. Interact with highly acidic phosphate residues of DNA in minor groove. H1 is not part of the octamer and functions to stabilize the DNA around the octamer. Histone genes have NO INTRONS.

29

Nucleosomes

1 _ turns of DNA with the histone disk but no H1

30

Chromatosomes

2 full turns of DNA with the histone disk + H1

31

Linker DNA

Between nucleosomes

32

Nucleofilament

Linear arrays of nucleosomes and chromatosomes

33

Heterochromatin vs Euchromatin

Heterochromatin is tightly packed and euchromatin is loose-more accessible and transcriptionally active

34

What do prokaryotes have instead of histones?

HU proteins

35

Prokaryote chromasome structure

One circular double stranded supercoil chromasome

36

Nucleoids

Bacterial chromosomes are compacted into ________ by interaction with HU proteins, cations, polyamines, RNA, and other nonhistone proteins

37

Palindrome

Each DNA strand is self-complimentary within the inverted region that contains the symmetry elements

38

Mirror repeat

Identical base pairs equidistant from center of symmetry within DNA segments

39

Direct repeat

Particular sequence repeated

40

Size of human genome

3.5x109 bp

41

Function of primer

Provides free -OH group to which nucleotides can be added

42

What is released as nucleotides are added to growing DNA strand?

Pyrophosphate (PPi) is released whenever phosphodiester bonds are formed

43

Which end of the strand are nucleotides added to?

3' end

44

How are primers removed?

Exonuclease activity removes primer nucleotides in 5' to 3' direction

45

Helicases

Unwind the DNA strands to allow them to separate

46

Single-stranded binding proteins (SSB)

Bind to DNA to keep the two strands from annealing

47

Types of prokaryotic DNA polymerases and functions

3 types: Pol I, Pol II, Pol III. All have 3'-->5' exonuclease proofreading activity. Pol I (intermediate processivity) synthesizes lagging strand and only one capable of primer removal (5'-->3' exonuclease activity). Pol II (low processivity) involved in DNA repair. Pol III (high processivity) synthesizes leading strand.

48

Sliding clamp

Donut shaped protein complex which encircles DNA strands. Prevents Pol III from detaching from the template until replication complete. Reason why Pol III has high processivity.

49

Processivity

Ability of the enzyme to remain on its substrate during synthesis

50

Replisome complex

Includes primosome, SSB proteins, Pol I and Pol III, other molecules needed for DNA replication

51

Primosome

Primases, ligases, helicases, and other proteins that bind to the origin of replication and are necessary for synthesizing the primer

52

Replicons

DNA segments between the origins of replication

53

Differences between prokaryote and eukaryote DNA synthesis

Eukaryotic DNA is much larger, packed into chromatin, and have lower rates of replication fork movement than in prokaryotes

54

Cell cycle order and events

M, G1, S, G2. Mitosis is where cell division occurs. In G1 cell increases in size and makes extra proteins, organelles--G1 checkpoint makes sure cell ready for S phase. In S DNA replication occurs. In G2 rapid cell growth and protein synthesis--G2 checkpoint makes sure cell ready to divide. Also can leave G1 and go into G0 resting phase when the cell has stopped dividing.

55

Cyclin-dependent kinases (CDK)

Controls the cell cycle by initiating cell division and DNA replication

56

Cyclins

Protein substrates of CDKs and activate them

57

Types of eukaryotic DNA polymerases and functions

2 types: _ and _. Polymerase _ (low processivity) synthesizes lagging strand, functions as a primase, and disassembles nucleosome prior to DNA replication. Polymerase _ (high processivity) synthesizes the leading strand, serves as 3'-->5' exonuclease proofreader.

58

Proliferating cell nuclear antigen (PCNA)

Serves as a clamp to kee the polymerase _ enzyme from dissociating. ::homologous to the sliding clamp in prokaryotes::

59

Replication protein A (RPA)

Bind to DNA to keep the two strands from annealing ::homologous to the SSB proteins in prokaryotes::

60

When does synthesis of histones occur?

During S phase, simultaneous to DNA replication

61

Reverse transcriptases

Enzymes that use RNA as a template for DNA synthesis (RNA dependent DNA polymerase)

62

Telomerase (definition, structure, and function)

Reverse transcriptase that replicates the telomeres. Contains RNA as part of its structure so functions as a template and an enzyme during replication. No proofreading so most error-prone of the DNA polymerases.

63

Retroviruses

Genomes are RNA. During viral infection RNA is copied into DNA and transcribed to produce more viruses.

64

AZT

Inhibits reverse transcriptases. Structural analog of dT, converted to triphosphate and incorporated into viral genome in place of dTTP (AZT competes and has a higher binding affinity than dTTP). Once incorporated into viral DNA, AZT causes premature termination of viral DNA synthesis because it lacks the 3' -OH site needed for the addition of nucleotides.

65

3 types of recombination

1. Homologous: occurs between homologous DNA on the same chromosome during prophase of meiosis. 2: Conservative site-specific recombination: insertion of bacteriophage DNA into bacterial genome. Homology is not required. Double stranded DNA is inserted at specific sites. 3: Transposition: Jumping genes which move from one site to another within a chromosome. May activate or inactivate gene if inserted into coding sequence. This can make bacteria antibiotic resistant by carrying transposons on plasmids (which can replicate independent of organism's DNA).

66

Types of RNA modified bases:

1. pseudouridine 2. dihydrouridine 3. methylated bases: methylguanosine, dimethylguanosine, methylinosine 4. ribothymidine

67

Hairpins

Single stranded RNA makes these by base pairing with itself

68

mRNA in prokaryotes

Polycistronic: can code for more than one protein

69

Cistron

Segment of DNA that contains all of the information for production of a single polypeptide

70

mRNA in eukaryotes

Mostly monocistronic: can only code for one polypeptide

71

mRNA half-life

Shortest of the RNAs (mins to several hours). Exceptions: mRNA in unfertilized eggs (dormant until fertilization) and mRNA that codes for hemoglobin in reticulocytes (very stable).

72

Post-translational modifications to mRNA

1. Inverted methylated base 5' cap: inverted from 5' phosphate to 5' phosphate linkage with 1st nucleotide (often methylated purine) instead of usual 3',5' phosphodiester bond. 2. Poly A tail: 20-200 adenine nucleotides, length of tail determines stability. Histone mRNA lacks poly A tail.

73

Shine-Dalgarno sequence

Untranslated leader sequence following the 5' cap in prokaryotic mRNA. There is also a nontranslated sequence following the stop codon.

74

Kozak sequence

Untranslated leader sequence following the 5' cap in eukaryotic mRNA. There is also a nontranslated sequence following the stop codon.

75

Stop codons

UAA, UAG, UGA

76

Start codon

AUG

77

Amounts of each type of RNA in cells

80% rRNA, 15% tRNA, 1% mRNA, the rest is other RNA

78

tRNA structure

Cloverleaf with 2 active sites: 1. Acceptor stem 3' -OH terminal CCA where amino acids attach 2. Anticodon loop which recognizes codons on the mRNA.

79

tRNA activation and functions

Needs to be activated (aminoacylated) by aminoacyl-tRNA synthetase. Has 2 functions: 1. Activate the amino acids for protein synthesis which occurs on the ribosome by binding to the acceptor stem 2. Recognize codons to ensure correct amino acid incorporated into the polypeptide chain using the anticodon loop

80

rRNA structure

Two components: large and small particles which are named according to sedimentation coefficient during centrifugation calculated in Svedberg units.

81

Small nuclear RNA (snRNA)

Recognizes introns on mRNA participating in splicing

82

Small cytoplasmic RNA (scRNA)

Involved in selection of proteins for export where it serves as signal recognition particle

83

Mitochondrial RNA (mtRNA)

Include mRNA, tRNA, and rRNA transcribed from mitochondrial DNA. Only one tRNA for each amino acid.

84

Ribonucleoprotein particles (RNP)

Small RNA/protein molecules which function in RNA processing, splicing, transport, control of translation, and protein recognition particles that target proteins for export. The RNA component of the RNP is a ribozyme.

85

Ribozymes

RNA enzymes

86

Ribonuclease P (RNase P)

True enzyme which cleaves pre-tRNA to generate mature 5' terminus of tRNA

87

RNAi

Control cell's phenotype by shutting down developmental genes or altering levels of expression. Control cellular differentiation.

88

In what direction is DNA read? What direction are DNA and RNA transcribed?

DNA is read in the 3'-->5' direction. DNA and RNA are transcribed in the 5'-->3' direction

89

Pribnow box

Found at the -10 region with the sequence TATAAT. Recognized by the RNA polymerase which attaches before the beginning of transcription.

90

Differences between DNA and RNA polymerases

RNA polymerases requires DNA template but no primers. RNA polymerases have no proofreading ability.

91

Structure of RNA polymerase

Holozyme consists of all 6 subunits: two _, _, _', _ (omega), _ (sigma). Without _ called the core enzyme.

92

RNA polymerase _ subunit function

Recognizes the promoter and then is released as the RNA polymerase begins to synthesize the RNA

93

Types of RNA polymerases and inhibitor sensitivity

3 nuclear (I,II,III) and 1 mitochondrial type. Distinguished by sensitivity to amanitin (mushroom poison)/rifampicin (antibiotic).

94

RNA polymerase I

Produces rRNA, insensitive to _-amanitin. Synthesizes a single transcript of the rRNA subunits at the same time to form pre-RNA (this ensures equal molar amounts of each subunit).

95

RNA polymerase II

Produces mRNA, very sensitive to _-amanitin. Present in the nucleus.

96

RNA polymerase III

Produces tRNA, sensitive to _-amanitin. Present in the nucleus.

97

Mitochondrial RNA polymerase

Produces all kinds of RNA, insensitive to _-amanitin but sensitive to rifampicin

98

Rifampicin as a drug

Treats Mycobacterium tuberculosis by inhibiting prokaryotic RNA polymerase by binding to the _ subunit.

99

rRNA gene location

Nucleolar organizer region of the nucleolus. Several hundred copies of each rRNA gene separated by spacer sequences.

100

3 general modifications of the RNA primary transcript

1. Removal of external (terminal sequences) and internal (spacer sequence) nucleotides by ribonucleases 2. Base modification 3. Addition of nucleotides

101

Post-translational modifications to tRNA

1. 5' end removed by ribonuclease P (ribozyme) 2. 3' end removed and terminal CCA is synthesized 3. Nucleotide bases modified (tRNAs contain the most modified bases of all nucleic acids)

102

Splicing (proteins involved, details, important sequences)

Small nuclear ribonucleoproteins called snRNPs (snurps) remove introns from pre-RNA. Break RNA at the 5' end of intron and join exons. All introns begin with GU (donor site) and end with AG (acceptor site) but not all GU or AG sequences are splice sites. U1RNA, U2RNA, and snurps discriminate the splice sites.

103

tRNA half-life

about 5 days

104

What makes the genetic code degenerate?

Amino acids have more than one codon except for Met and Trp

105

Which amino acids have only one codon

Met (methionine) and Trp (tryptophan)

106

Why no wobble effect with G at 3' position?

Makes sure there is no ambiguity coding for the stop codon, Trp, or Met

107

Aminoacyl-tRNA synthetase functions

Catalyze two reactions and has proofreading ability 1. Activation of amino acid with ATP forming the aminoacyl group 2. Transfer of the aminoacyl group to the tRNA

108

Methionyl-tRNAs in prokaryotes

1. Initiator tRNA: fMet-tRNA has formylated Met group and initiates protein synthesis 2. Carries Met for other positions in the protein (not formylated)

109

Methionyl-tRNAs in eukaryotes

No formylation of Met so all methionyl tRNAs are identical

110

Steps of protein synthesis

1. Initiating fMet-tRNA (prokaryotes) moved to P (peptidyl) site of ribosome small subunit 2. Large ribosome subunit joins complex 3. Peptidyltransferase transfers the initiating fMet-tRNA (prokaryotes) to E (exit) site and 2nd amino acid in sequence placed in the A (aminoacyl) site on ribosome 4. Peptide bond forms between amino acids 5. Elongation occurs until stop codon reaches the A site (no aminoacyl-tRNA binds with these codons).

111

Attachments on an amino acid

Carboxylic group (-COOH), Amino group (-NH2), Hydrogen (-H), specific side chain (-R)

112

What isomer of amino acids are in humans?

L amino acids (usually rotate polarized light to the left but not always)

113

Characteristics of peptide bond

Characteristics of a double bond so no rotation about the C-N, but _ carbons can rotate

114

Peptides vs proteins

Peptides are < 50 amino acids, proteins are > 50 amino acids

115

Disulfide bond role

Stabilize protein structure and involved in oxido-reductive reactions

116

Glutathione

Most important agent that fights reactive oxygen species. Composed of Glu-Cys-Gly. When membrane proteins get oxidized, glutathione reduces them.

117

Henderson-Hasselbalch equation

pH=pK + log (A-/HA) In bicarbonate buffer system equation is pH=pK + log (HCO3-/H2CO3) Increase in HCO3- causes pH to rise.

118

Primary protein structure

Order of amino acid residues

119

Secondary protein structure

Local 3D folding of the chain

120

Tertiary protein structure

3D structure of the protein which folds into domains. Hydrophobic side chains are inside away from water and hydrophilic side chains are on the outside and interact with water. Structure stabilized by noncovalent electrostatic, hydrophobic, hydrogen, and disulfide bonds.

121

Quarternary protein structure

non-covalent association of discrete polypeptide subunits into a multi-subunit protein. Subunits are noncovalently attached. ::not all proteins have a quarternary structure::

122

Protein secondary structure types

_-helix, _-pleated sheet, _-turn, random coil. Side chains do not participate in formation of secondary structures.

123

_-helix

L-amino acids form right handed _-helices. Kept together by H-bonds between carbonyl (C=O) groups and imino (N-H) groups directly above or below each other (~every 4th amino acid)

124

_-pleated sheet

Two polypeptide chains are aligned paralell or antiparalell. H-bonds between carbonyl (C=O) groups and imino (N-H) groups between adjacent chains.

125

_-turn

Reverse the direction of the polypeptide chain allowing the chain to form compact globular proteins

126

random coil

Anything that doesn't fit in the other secondary structure categories. Less ordered structure. Functional and found in binding sites or active centers of proteins.

127

Advantages of quarternary structure

Stability, genetically economical (in homomultimers only one gene needed to code for a complex protein), efficiency (active sites brought in close proximity and substrate channeled from one subunit to the other without diffusion and/or transport), cooperativity

128

Native structure

Final conformation of the protein which is the most stable (disulfide bonds form to help stabilize)

129

Chaperones

Belong to Heat Shock Protein family. Synthesis increases at high temps. Required for refolding proteins as they cross membranes, assembling proteins with multiple polypeptide chains (quarternary structure), and facilitating protein transport into the mitochondria and endoplasmic reticulum

130

4 types of bonds that stabilize proteins

1. Disulfide bonds: covalent linkages between -SH groups in cysteines to produce cystine (called a sulfide bridge) 2. Hydrophobic interactions: hydrophobic groups on inside of protein 3. Hydrogen bonds: between amino acid side chains and stabilize tertiary structure 4. Ionic (electrostatic interactions): salt bridges and can be repulsive or attractive--formed between positively and negatively charged side chains

131

Denaturation

Disrupts all but the primary structure. Occurs due to strong acids, strong bases, heating above 60 degrees C, or by adding denaturants like urea or detergents like SDS or guanidine. In cell leads to enzymatic removal of protein.

132

Alzheimers

Proteins fold in abnormal way and form aggregate long, fibrillar protein assemblies called amyloids

133

Creutzfeldt-Jakob disease

Nervous system dysfunction including ataxia, dementia, and paralysis and almost always fatal. Fibrous amyloid plaques develop in brain and cause degeneration caused by misfolding in the prion protein from soluble to insoluble conformation. Normal protein has 3 alpha helical and 2 small beta strand segments--change results in conversion of 2 alpha helices to beta strand conformations which polymerize.