Molecular Genetics Flashcards
1
Q
Purines
A
Adenine
Guanine
2
Q
Pyrimidines
A
Cytosine
Thymine
Uracil
3
Q
Bond that links nucleotides
A
Phosphodiester
Connect 5’ C of one nucleotide with 3’C of the next
4
Q
Euchromatin
A
Chromatin less condensed
Polymerases can be recruited to facilitate transcription
5
Q
Heterochromatin
A
DNA highly condensed
Inaccessible to polymerases, transcriptionally inactive
6
Q
Methylation of DNA
A
represses gene expression
GATC- mismatch repair at A
CpG islands- silencing
7
Q
Acetylation of dna
A
Decondenses and opens chromatin
Decreases overall positive charge of histones allowing dna to loosely coil
8
Q
Histone methylation
A
Gene expression may be increased or decreased depending on level
Reversible repress transcription
9
Q
Metaphase chromosome
A
Highly condensed DNA structures that result from supercoiling chromatin
10
Q
Telomeres
A
Consist of 2500 repetitions of TTAGGG
prevent degradation of portions of chromosomes that contain coding sequences (genes)
Mainly expressed in germ cells
11
Q
Semiconservative
A
Dna replication follows this model
Strand of original helix serves as template for synthesis of new complementary strand
Each new daughter chromosome will contain one of the original “parent” strands and a newly synthesized “daughter” strand
12
Q
Initiation of DNA synthesis
A
Initiator proteins facilitate duplex opening at origins of replication and recruit helices: this established a replication bubble where replication enzymes can associate with each parent strand
13
Q
Single stranded binding proteins (SBBs)
A
Bind with newly separated parents strands, providing a physical barrier on each strand that prevents exposed nucleotides from interacting with free nucleotide or single strand polynucleotides
DNA polymerase and primate are able to easily displace SSBs, so presence doesn’t interfere with polymerization
14
Q
Polymerization
A
Synthesis of new dna strands accomplished by consecutively attaching free nucleotides according to the template
Harness stored energy in a free nucleotides triphosphate tail, polymerases create new phosphodiester bond
15
Q
Direction of DNA polymerase
A
Synthesizes new strand that is 5’-3’ by reading template strand that is 3’-5’
16
Q
Leading strand
A
Parent strand whose bases are being continuously exposed in 3’-5’ direction
17
Q
Lagging strand
A
Nucleotides are exposed in a 5’-3’ direction
18
Q
Okazaki fragment
A
Polynucleotide on the lagging strand
Each new stretch of DNA polymerase activity continues until the previous rna primer is encountered, creating this
19
Q
Processivity
A
Describes how likely a DNA polymerase is to remain bound to template strand.
DNA pol 3 has high processivity because it associates with a sliding clamp that anchors it to the template strand
20
Q
Okazaki fragments in prokaryotes
A
DNA polymerase replaces the rna primer with dna nucleotides and ligaments established phosphodiester bonds between fragments
21
Q
High fidelity
A
Property of DNA polymerase
Very accurate in pairing the appropriate nucleotides to the template strand
22
Q
Primers in eukaryotes
A
One of the subunits of DNA polymerase alpha has rna primase activity, allowing it to initiate polymerization
23
Q
DNA pol 1
A
Has both 3’-5’ and 5’-3’ exonuclease activity
24
Q
Nucleoside
A
Sugar plus nucleic acid (no phosphate)
25
Nucleosome
Two turns of dna wound around proteins
Also called histones
26
Histone acetylation
Reflexes dna coiling allows for transcription
27
DNA methylase
Repairs mismatch by adding methyl groups
28
DNA gyrase
Prokaryotes
Circular chromosome
Relaxes supercoil dna to allow replication
Ex: nalidixic acid/ ciprofloxacin
29
3 pol
Alpha (iDNA), epsilon (leading), delta (lagging)
30
Growth phase 1- cell cycle
G1
Cell prepares for dna replication by sending nutrition status and dna damage, number of organelles roughly double, cell grows in size
31
DNA synthesis phase- cell cycle
S phase
Cell replicated dna so each chromosome has two copies
Copied attached to each other by cohesin proteins in a centromere (called sister chromatids, or one chromosome)
At end of phase, cell ends up with 46 chromosomes, and double amount of histones
32
Growth phase 2- cell cycle
Cell continues to grow and prepares for division by reorganizing organelles and cytoskeleton
33
Mitotic phase - cell cycle
M phase
DNA condenses to form visible pairs of sister chromatic that are separated and moved to opposite poles of cell
Cell splits into two daughter cells (cytokinesis)
34
Resting phase - cell cycle
G0 phase
Cell exists cell cycle and becomes quiescent until receives external stimuli (growth factors) to replicate again, and it will enter at G1
Amount of time spent here depends on cell type (mature neurons spend most lifespan here, intestinal lining cells spend no time here )
35
Restriction point - cell cycle
Check on the cell cycle to make sure environment is still appropriate for cellular division before entering S
Regulated by growth factors
36
Cyclin D
First cyclin of cell cycle
Necessary for cell to start transition from G1 to S
Stimulated by growth factors and starts to associate with cyclin D-specific CDK4 (which phosphorylates proteins necessary for transition) and CDK6
37
Cyclin E
After cyclin D
Gets expressed at cyclin D/CDK4 levels increase
Promotes expression of proteins necessary to finish G1 to S transition as well as S phase proteins (including next cyclin A)
CDK 2
38
Cyclin A
Production of S and G2 proteins and cyclin B
CDK 1 and CDK 2
39
Cyclin B
Stimulated from cyclin A
Stimulates production of M phase proteins
CDK 1
40
Checkpoints of cell cycle
1: between G1 and S phase. Assures no damage to dna prior to replication
2: prior to M phase. Ensures all dna is replicated and decreases the risk of daughter cells missing chromosomes
3: halfway through M phase. Assures the homologous pairs of sister chromatids and centromeres are appropriately attached to mitotic spindle prior to separation
41
First checkpoint of cell cycle- retinoblastoma
G1/S, starts with expression of S phase-specific proteins controlled by transcription factor E2F (normally inhibited by retinoblastoma Rb protein, tumor suppressor)
Rb main target of CDK4 (cyclin D/CDK4 complex phosphorylation Rb, reducing its affinity for E2F)
42
First checkpoint of cell cycle- p53
Gets broken down in normal cells, stabilizes in cells with dna damage
Allows it to bind to its target on dna and initiate expression of cyclin-kinase inhibitor p21 (binds and inhibits cyclin E/CDK2…prevents transition from G1 to S)
If stabilized for too long, p53 activates apoptosis
43
First checkpoint of cell cycle - p16
CKI
Expressed in response to cellular stress and damages and acts by inhibiting CDK4
Inhibits cyclin D/ CDK4 complex from phosphorylating Rb, thus not allowing E2F to be released from Rb
44
Mitosis
Prophase- dna condenses into 46 pairs of sister chromatic linked by centromere
Metaphase- sister chromatic is align at center and prepare for separation
Anaphase- sister chromatic start separating and moving to opposite poles
Telophase- cell starts dividing in two, usually marked by formation of a cleft in cell membrane (cytokinesis)
45
Meiosis
Prophase 1- dna condensing into chromosomes, homologous chromosomes get linked by centrameres to make chromatid tetramers. Then exchange genetic info through formation of chiasmata and crossing over. Independent assortment, nondisjunction
Metaphase 1- tetramers line up in middle of cell
Anaphase 1-homologous chromosomes separate and move toward opposite poles
Telophase 1- cell splits in two, each new cell has 23 chromosomes, 1N
In part 2, each of the 23 pairs of sister chromatids split evenly between the resultant four 1N, 1C haploid cells
46
Genomic instability
Increased propensity for mutations including DNA base changes and structural alterations in the genomic DNA
47
Exogenous sources of genomic instability
Involve influences from our physical environment (UV light , ionizing radiation, carcinogens)
48
Endogenous sources of genomic instability
Involve unintended consequences of metabolic processes (errors in dna replication, oxidation, nitrosylation, hydrolysis of dna strands)
49
UV light on DNA
Pyrimidine bases absorb UV light to form abnormal covalent bonds called pyrimidine dimers
Interfere with nuclear processes such as transcription and replication
50
Somatic mutations
Occur in a single cell, which divides to produce clones with the same mutation
Ex: mccune- albright syndrome affects bone, skin, and endocrine tissues. Pt had mutation early in development that causes widespread expression of phenotype
51
Germline mutation
Occur in germ line, designed to produced sex cells
Passed to offspring and can result in diseases known as genetically inherited diseases
52
Point mutation
Alteration in single nucleotide
53
Silent mutation
Point mutation that has no effect on proteins structure
54
Missense mutation
Mutated codon encodes a different amino acid
55
Nonsense mutation
Introduced a stop codon and terminates translation prematurely
56
Frameshift mutations
Single nucleotide or any non triplet dna segment is deleted or inserted within the coding region of a gene
57
Direct repair of dna
Attempts to correct damaged nucleotides without severing the polynucleotides phosphodiester backbone
58
Base excision repair
Used if dna lesions affect only a single nucleotide
Includes introduction of uracil, deamination (alteration to base), depurination (loss of base), AP sites, ss breaks
DNA glycosylase (cuts glycosidic bond between wrong base as sugar)—> AP endonuclease—> pol 1 (beta)
Alkyladenine dna glycosylase over expression in UC
59
Nucleotide excision repair
For dna lesions that involve more than one nucleotide, UvrABCD (UvrAB recognizes distortion, C joins and A leaves, C cuts 5’ side and B cuts 3’ side, d unwinds Dna)
Relies on special ending leases to sever the phosphodiester backbone upstream and downstream of the lesion
Primarily occurs in G1 phase, important for UV light induced damage
Defects can cause xeroderma pigmentosum
60
Mismatch repair
Corrects errors in dna replication
MutSHL system (S binds to mismatch, H and L joint S, one of H subunits binds to methyl groups and makes dna loop)
Similar to NER, recognize hemimethylated dna
Primarily during G2/S phase
Defects can cause lynch syndrome (hereditary nonpolyposis colorectal cancer)
61
Homologous recombination
Uses homologous chromosomes as template to process severed strands, attempts to reconnect the complementary strands without loss of any nucleotide sequences
Ds breaks
Occurs mainly in S and G2
Ex: breast or ovarian cancer, BRCA1 mutation
62
Non homologous end joining (NHEJ)
Mechanisms that uses a special ligase complex to directly fuse the ends of two dna fragments. When homologous recombination isn’t possible due to degree of damage, cell will use this to reconnect severed strands
Not preferred over HR, this connects any two strands it can find. Error prone and can result in mutation
Immune system: generates Ig, TCR diversity
Ex: ataxia telangiectasia
63
Spontaneous mutations
DNA poly
Base tautomerization
Deamination (C—>U)
AP sites (ROS)
64
Induced mutations
Chemicals (alkylating agents, base analogues (bromouracil), intercalating agents (acridine orange), cross linking agents (cisplatin)
Radiation: ionizing vs UV
heat
65
Inversion mutation
Sequence gets flipped
66
Translocation
Sequence of dna moves from one spot to another
67
Duplication mutation
Same sequence duplicates over and over
Can occur from dna poly
68
Null mutation
Gene no longer makes protein
69
Translesional synthesis
Not repair, bypass lesions during dna replication S phase
Avoid replication arrest and apoptosis
Error prone: switching on alternative dna poly (that replicate past lesions with low fidelity)
Mutations —> SCID, pol eta in autosomal recessive XP variant
70
Female meiosis
Oogenesis completed before birth
Oocytes suspended at prophase 1 at birth
Meiosis continues during ovulation
Meiosis 2 beings after fertilization
1 large egg + 3 Polar bodies
71
Male meiosis
Starts at puberty
Constantly occurring
4 sperms
72
Transcription steps
Initiation:machinery that conducts transcription identifies genes and attaches to dna
Elongation : machinery moved along dna helix, elongating rna transcript as it goes
Termination: rna transcript complete, machinery disengages and releases rna (rho dependent or independent )(rna secondary structure hairpin loop, rna poly stops, rho comes in and dissociates complex for rho dependent)
(Rho independent hairpin loop occurs but has series of uracil, 2 hydrogen bonds in a row causes instability, everything falls apart, more common)
73
Eukaryotic promoters
CAAT (70-80 nucleotides upstream), TATA (25-30 nucleotides upstream) boxes
Poly 2 binds to promoter
First transcribed nucleotide of a gene is +1 site or start site (all after are +N, all before are upstream and -N)
Proximal regulatory sequences
74
Distal regulatory sequences
Enhancers (all pol 2 dependent genes also require these for efficient initiation and elongation) , recruite activating transcription factors that promote recruitment of rna poly 2, upregulating expression of target gene
silencers recruit repress or factors that inhibit transcription
75
Rna polymerase 2 transcription
Coding strand makes SENSE: aka the SENSE strand, the coding strand has the same sequence at the RNA
Antisense strand is template to make the rna
76
Rna processing of pre-mRNA to mRNA
7 methylguanosine cap to 5’ end (through 5’ to 5’ triphosphate bridge): facilitates export of mRNA to cytoplasm, protect mRNA from degradation by 5’ exonucleases
Addition of 3’ poly A tail: helps stabilize mRNA. Poly (A) binding proteins associate with the tail to shield RNA from exonucleases
Intron splicing : by spliceosome (composed of small nuclear ribonucleoprotein particles). Severs donor site 5’ phosphodiester bond and establishes new 5’-2’ bond creating a lariat shaped intermediate (loop), then forms bond between exons 3’ end (lariat released) and exons downstream 5’ end.
77
Three types of RNA used in translation
mRNA- gene transcript to be translated
Ribsosomal rna - forms ribosome that conducts translation
Transfer rna- carry amino acid into ribosome, using anticodon to ensure each amino acid is incorporated in the correct order into growing peptide chain
78
Translation initiation
60S and 40S ribosomal subunits, initiator tRNA picks up Met initiator amino acid (30S and 50S to make 70S for bacteria)
Initiation factors elF1 and elF3 bind to 40S, GTP an elF2 bind to tRNA
40S separates from 60S, attaches to anticodon of tRNA
Initiation complex binds to mRNA, scans for start codon AUG
After it finds start codon, 60S joins complex and initiation factors are released
79
Translation elongation
A site- entry point for new tRNA transporting amino acid
P site- contains tRNA containing growing peptide (initial Met-tRNA is positioned)
E site- exit point for tRNA after it has delivered amino acid
New tRNA carrying peptide enters A site, incorrect peptide gets rejected and new tRNA enters and is checked
Amino acid on tRNA in p site moves to tRNA on A site, growing peptide moved from P to A site
Ribosome moves a codon forward
Empty tRNA now in E site moves away, cycle restarts
Ends once stop codon is reached (UAA, UGA, UAG)
ATP provides energy during tRNA Activation
GTP provides energy during Gripping and Going (translocation)
80
Translation termination
One of the three stop codons is positioned in A site
Stop codon recognized by release factor protein
Catalyzes cleavage of tRNA at P site and growing polypeptide
Polypeptide released from ribosome and ribosome is dissociates into two subunits and is ready for new cycle
81
Alpha amanitin
Death cap mushroom
Binds to rna pol 2
Hepatotoxicity
82
Actinomycin D
Brand cosmegen
Intercalating agent
Rna Pol in prokaryotes and eukaryotes
83
Constitutive/ housekeeping genes
Always on no matter what
84
Regulatory proteins
Activator
Repressor
85
Lac operon- lactose
Cap site- promotes rna pol binding when cap binds
Promoter- when rna pol binds
Operator- blocks rna poly when repressor binds
LacZ- beta colactosidase
LacY-permase
LacA- lactose acetylase
Operator turned on when lactose is present. Lactose binds to lac I and changes it’s confirmation, no longer functional and can no longer bind to gene. Transcription takes place
Absence of lactose, it’s off. Lac I repressor will bind to operator prevents rna poly from transcribing gene
86
Lac operon- glucose
Glucose high…atp high…amp low…cAMP low. Lactose unavailable
Glucose low… atp low… amp high…cAMP high (cap-cAMP complex binds to cap site of operon, rna polymerase properly bound at promoter) lactose available
When cAMP and repressor protein bound, no glucose and no lactose
Cal binding site, promoter, and operator, high glucose and lactose
87
Alternative splicing
Splicing different introns at different times, for variety
88
Amino glycosides
Streptomycin
Tobramycin
Gentamicin
Binds 30S misread mRNA
89
Tetracyclines
Bind 30S block tRNA
90
Macro slides
Erythromycin
Azithromycin
Bind to 50S prevent peptide bonds
91
Chloramphenicol
Bind 50S prevent peptide bonds
