Bio Ch 3/4 Flashcards
(107 cards)
1
Q
Which groups are located on an AA?
A
Variable R group, alpha-carboxyl group, alpha-amino group, tetrahedral alpha-carbon
2
Q
Another name for peptide bond? How is it broken in the body?
A
Amide bond. Proteolysis (proteolytic cleavage) by a protease (proteolytic enzyme)
3
Q
Which types of bonds are prevalent in primary structure vs secondary vs tertiary/quaternary?
A
Primary - Covalent (peptide) bonds
Secondary - H-bonding between backbone Carboxyl and Amino groups
Tert/Quat - non-covalent, van der Waals, H-bonds, disulfide bonds (cysteines), and electrostatic interactions
4
Q
Common disaccharides?
A
Sucrose, lactose, maltose, cellobiose
5
Q
Where are lipids found and what are there roles?
A
Adipose cells - triglycerides store energy
Membranes - Phospholipid bilayers
Cholesterol - Building block for steroid hormones
6
Q
What is a synonym for hydrophilic?
A
Lipophobic
7
Q
How is membrane fluidity changed?
A
Saturation level of phospholipids, length of fatty acid tails, temperature
8
Q
Chemical formula for isoprene?
A
(C5H8)n
9
Q
Terpene structure? Terpenoid Structure?
A
Linked isoprene units. Terpenoids are terpenes with functional group (like O)
10
Q
Structure of steroids
A
Three six carbon rings liked to a five carbon ring
11
Q
Structure of ATP?
A
Triphosphate, ribose, adenine
12
Q
Why does pyrophosphate contain a large amount of free energy in its anhydride bonds?
A
- Negative charges of phoshpates repel each other
- Orthophosphates have more resonance forms (PO4,PO4-,PO42-,PO3-) thus lower free energy
- Orthophosphate has more favorable interactions with water than linked phosphates
13
Q
Examples of purines? Structure?
A
Guanine and Adenine. Dicyclic aromatic
14
Q
What are the pyrimidines? Structure?
A
Cytosine, thymine, uracil. Monocyclic aromatic
15
Q
Which direction are polypeptides made/read?
A
Alpha-amino to alpha-carboxyl
16
Q
Which direction are polynucleotides made/read?
A
5’ to 3’
17
Q
How are nucleotides bounds?
A
Phosphodiester bond
18
Q
What is the secondary structure of DNA?
A
Right-handed double helix. Two strands are antiparallel orientation. 5’ A’s bound to 3’ T’s and 5’ C’s bound to 3’ G’s.
19
Q
How many H-bonds per nucleotide in two annealed/hybridized strands?
A
A-T -> Two
C-G -> Three
20
Q
How is double-helix stabilized?
A
Van der waals
21
Q
How is DNA packaged in prokaryotes and eukaryotes?
A
Supercoiled circular DNA in prokaryotes by DNA gyrase. Packed into chromatin by wrapping around octameric histones
22
Q
What is DNA wrapped around histones called? What is DNA between histones called?
A
Nucleosomes, linker DNA
23
Q
What are key differences between heterochromatic and euchromatin?
A
Heterochromatin- Densely packed, less transcription
Euchromatin- Lightly packed, more gene activity
24
Q
Structure of centromeres?
A
Heterochromatin, repetitive DNA sequences, spindle fibers, kinetochore, other multiprotein complexes
25
Structure of telomeres?
Repeated units (6-8 BP's, G rich) 50 to hundreds of BP's long, single and double stranded DNA, telomere-associated proteins, telomere cap proteins
26
Telomere repeat in humans?
5'-TTAGGG-3'
27
What is the start codon?
AUG
28
What are all the synonyms for stop (nonsense) codons?
UAA, UGA, UAG
29
Which enzymes are involved in generating and maintaining the open complex?
Helicase, topoisomerase, SSBPs
30
Which enzymes generate primers for replication?
Primosome/primase
31
What kind of reaction forms the growing strand of DNA?
3' hydroxyl group of the daughter strand nucleophilic attack to displace 5' pyrophosphate from the dNTP added
32
What are Okazaki fragments? How are they joined?
Small chunks of DNA comprising the lagging strand. DNA ligase
33
Describe prokaryotic DNA Pol III
Elongates the leading strand, high processivity, 3' to 5' exonuclease activity (proofreading function), no repair function
34
Describe prokaryotic DNA Pol I
Starts adding at the primer, low processivity, DNA Pol II takes over after about 400 BP's down from ORI, 3' to 5' exonuclease activity, removes primer via 5' to 3' exonuclease activity and adds DNA there, excision repair
35
What are the DNA Pols in prokaryotes?
DNA Pol I, II, III, IV, V
36
What is the Hayflick limit?
Number of times human cell type can divide until telomere length stops cell division.
37
What is telomerase?
Ribonucleoprotein complex containing a conserved RNA primer and a reverse transcriptase enzyme. Used to elongate telomeres, one primer length at a time. Only expressed in germline, embryonic stem cells, some white blood cells, and cancer cells.
38
What happens if telomeres get too short?
Cell enters senescent state, cells can activate DNA repair pathways, or active apoptosis.
39
What are examples of physical mutagens?
Ionizing radiation (Xrays), reactive chemicals (intercalators like ethidium bromide), biological agents (lysogenic viruses)
40
What are the types of mutations?
Missense, nonsense, silent, insertion, deletion, inversion, amplification, translocation and rearrangements, and loss of heterozygosity
41
What are frameshift mutations?
Mutations that cause a shift in the reading frame of the chromosome
42
What are the different types of transposons?
IS Element, Complex Transposon, Composite Transposon
43
What is the function of transposase?
Cut or copy the transposon and paste it in another genetic location (donor to acceptor)
44
What kind of mutations can transposons cause?
inversions, deletions and rearrangements
45
What is a loss of heterozygosity?
When a diploid organism loses the only normal copy of a gene, leaving the locus hemizygous
46
What is haploinsufficiency?
Loss of one allele and the remaining gene copy is not enough to support a normal state. Gene dose is insufficient.
47
What are inborn errors of metabolism?
Genetic diseases caused by single mutation in a single gene that codes for metabolic enzyme resulting in either inability to metabolize a toxic compound or inability to synthesize an essential molecule.
48
What is cancer driven by?
Accumulation of mutations either inherited or caused by carcinogen exposure
49
Where do mutations in a cancerous cell usually occur?
Oncogenes (mutation increases expression and promotes cancer) or tumor suppressor (suppresses cancer, decreased expression promotes cancer)
50
Examples of direct repair mechanisms?
Repair of UV-induced pyrimidine photodimers using visible light - photoreactivation. Used in bacteria and plants.
51
What are homology-dependent repair mechanisms?
Repair mechanisms that depend on the complementary strand
52
Examples of homology dependent repair?
Excision repair, mismatch repair (MMR)
53
How does an organism recognize the error strand in post-replication repair?
Bacteria - Methylation
| Humans - Free 3' terminus on leading strand, Okazaki fragments on lagging strand
54
Steps of homologous recombination?
1. Double strand break (DSB)
2. Nuclease and helicase generate single stranded DNA on broken DNA strands
3. Find complementary sister chromatid
4. Joint molecule (cross-linking)
5. DNA polymerase and ligase use sister chromatid to build new DNA
55
What is non-homologous end joining?
Repair used when there is no sister chromatid to use to fix DSB's. No specificity, ends are processed and joined. Often results in loss of base pairs or linking in abnormal way
56
How is RNA different from DNA?
1. Single stranded, except in some viruses
2. Contains uracil instead of thymine
3. Pentose is ribose
57
Regions of mRNA?
5' UTR containing regions for initiation and regulation, ORF (coding for the protein, contains start and stop codons), 3' end contains regulatory sequences that influence post-transcriptional gene expression
58
Monocistronic vs polycistronic?
Monocistronic - one gene one protein
| Polycistronic - one gene, multiple proteins
59
What is hnRNA?
Hetergenous nuclear RNA only in eukaryotes- needs to be processed via splicing, addition of cap and tail to become mature mRNA
60
What are two major types of ncRNA (non-coding RNA)?
tRNA - Used to carry AA to ribosome during translation
rRNA - Ribosomal RNA used as a major structural component of the ribosome, one of them is a ribozyme providing catalytic activity
61
What are snRNA?
Associate with proteins to form snRNP complexes in spliceosome
62
What is miRNA and siRNA?
Function in RNAi - form post-transcriptional regulation of gene expression. Bind to mRNA to increase or decrease translation.
63
What is piRNA?
PIWI-interacting RNA - work with PIWI proteins to prevent transposon mobilization
64
What is long ncRNA?
Help control basal transcription level in a cell by regulating initiation complex assembly on promoters. Contribute to many types of post-trancriptional regulation by controlling splicing and translation, imprinting and x-chromosome inactivation.
65
What chemical reaction drives DNA replication and transcription?
Hydrolysis of pyrophosphate from each nucleotide via nucleophilic attack by the growing strand
66
Where does transcription start vs replication?
Start site vs origin
67
What is upstream and downstream in transcription?
Upstream - towards 5' end of coding (sense)strand and transcript
Downstream - towards 3' endof coding strand (towards 5' end of template (antisense) strand
68
What are the components of RNA polymerase in prokaryotes?
alpha-beta-beta'-omega subunit for reapid elongation and a sigma factor to form the holoenzyme
69
What does typical bacterial promoter region encode?
Pribnow box at -10 and -35 sequence
70
What roles does the sigma factor of RNA pol in prokaryotes play?
Increase ability to recognize promoters and decrease nonspecific affinity of holoenzyme for DNA. Once open complex is formed along with several phosphodiester bonds, sigma factor drops off
71
Role of rho in prokaryotic transcription?
In some cases, help transmit termination signal
72
What is primary transcript in eukaryotic transcription by RNAP II?
hnRNA
73
How does hnRNA turn into mRNA?
Splicing, 5' cap and 3' poly A tail
74
What is splicing? Which enzyme performs it?
Removal of introns and joining of exons. Spliceosome
75
What are snRNP's in the spliceosome made of
Proteins and snRNA
76
What sequences do snRNPs bind to during assembly of sliceosome?
GU at 5' end, AG at 3' end and an adenine 15-45 bases upstream of the 3' splice site
77
Role of 5' cap and 3' poly A tail?
Protect mRNA from exonuclease digestions
78
What kinds of RNAP are there in eukaryotes and function?
RNAP I - Transcribes most rRNA
RNAP II - Transcribes hnRNA (mRNA), most snRNA and some miRNA
RNAP III - Transcribes tRNA, long ncRNA, siRNA, some miRNA, subset of rRNA
79
Where does AA bind to tRNA?
Amino acid receptor site
80
What is the Wobble Hypothesis of basepairing?
First two bases obey normal pairing rules, third base is more flexible
81
Which bases wobble base pair and with which codon bases?
1. G (anticodon) to U (codon)
2. U (anticodon) to G (wobble)
3. I (anticodon) to A, U or C (wobble)
82
How is tRNA loading/amino acid activation accomplished energetically?
Reaction coupling to the hydrolysis of two phosphate bonds on ATP
83
What is an ATP equivalent?
Unit of measure in relation to ATP hydrolysis - one ATP equivalent = one phosphate bond
84
How are AAs bonded to their tRNAs?
Aminoacyl-tRNA synthetase that is specific to each AA
85
What is the structure of the prokaryotic ribosome?
70S - made of 50S and 30S subunits
86
What is small subunit of prokaryotic ribosome?
16S rRNA and 21 peptides
87
What is the large subunit of prokaryotic ribosome?
23S and 5S rRNA and 31 peptides
88
What is the structure of the eukaryotic ribosome?
80S - 60 S and 40 S subunits
89
What is the small subunit of eukaryotic ribosome?
33 peptides and 1 rRNA (18S)
90
What is the large subunit of eukaryotic ribosome?
3 rRNA (5S, 5.8S and 28S) and 46 peptides
91
Which subunits of ribosomes (prokaryotic and eukaryotic ) have ribozyme activity?
23S(pro) and 28S(eu)
92
Three binding sites in both pro and eu ribosomes?
Aminoacyl-tRNA, peptidyl-tRNA, and exit-tRNA (APE)
93
What is the polyribosome?
Multiple ribosomes assembled on the mRNA translating it
94
Where does ribosome bind to on ORF of prokaryotic mRNA?
Ribosome binding site or Shine-Dalgarno sequence (-10)
95
What is the initiator tRNA in prokaryotes and where does it bind?
fMet-tRNA. P site of 70S ribosome bound to start codon
96
How do prokaryotic ribosomes catalyze bonding of two AA's in the elongation step?
Peptidyl transferase activity of 23S rRNA of large subunit
97
What is the initiator sequence on eukaryotic mRNA?
5' UTR sequence such as Kozak sequence
98
What is cap-independent translation?
Translation in eukaryotes that starts not at the 5' end but somewhere in the middle of the mRNA. mRNA has an IRES sequence that allows ribosomes to enter. Genes usually encode for dealing with stress or help activate apoptosis
99
How does DNA methylation inhibit transcription?
Physically blocks proteins from accessing DNA and methylated CpG groups recruit chromatin remodeling proteins
100
What are ways at the DNA level to regulate gene expression?
DNA Methylation, chromatin remodeling (histones), gene dose (CNV), genomic imprinting, x chromosome inactivation
101
What are two important to know examples of mechanisms used to control gene expression at transcription level in prokaryotes?
LAC operon - inducible
| TRP operon - repressible
102
What are UCE in eukaryotic RNA composed of ?
-50 core promoter containing binding sites for basal transcription complex and RNAP II, and a -25 TATA box
103
What is the TATA box used for?
TBP binding and initiation of transcription complex binding at promoter
104
How is transcription regulated in eukaryotes?
Activator protein binding to enhancer sequences, UCE's, gene repressor protein/transcription factor binding to promoter or other regulatory sequences, RNA translocation, mRNA surveillance, RNA interference
105
How is gene expression regulated at the protein/translation level?
Protein folding (chaperone mediated), covalent modification (acetylated, formylated, etc.), processing
106
What function does covalent modification serve in translational regulation of genes?
Use to change protein subcellular localization, target for degradation, change interactions, activate or inhibit or change enzyme affinity for substrates
107
What is processing in translational gene regulation?
Cleavage to produce mature or functional enzyme from an immature zymogen or proenzyme
