Mutations & Endo Flashcards
1
Q
Genes in Genome
A
- Have complete or nearly complete sequences of many species (sequence and align smaller fragments)
- Try to to predict mRNA and protein by looking for sequences matching (promoter and terminator, splice donors/acceptors, start/stop codons, open reading frame)
2
Q
Transcriptome
A
Sequence all the RNAs that a cell makes, map back to genome
Tell where DNA is transcribed
3
Q
Very Little of Human Genome Makes Exons
A
Mostly remnants of transposable elements
parasitic DNA that splices itself in and out of genomic DNA
4
Q
Genome
A
All genetic information in an organism
5
Q
Sources of Mutations
A
- DNA replication (DNA polymerase can insert wrong nucleotides. Proofreads by excising mismatched bases (exonuclease activity), not always successful)
- Transposable elements and some viruses (splice in and out of DNA, cause damage, move genomic DNA)
- Chemical damage (to bases, breaks in one or both DNA strands)
6
Q
Point Mutations
A
Change or loss of single base pair
Synonymous –> codes for same amino acid
Missense –> wrong amino acid
Nonsense –> stop codon
7
Q
Frameshift
A
Deletion of insertion of anything other than 3^n nucleotides (3x)
8
Q
DNA Repair
A
Fix base errors using template on other strand
Repair missing double-stranded DNA using similar DNA from other chromosome as template
Get mistakes during repairs –> deletions, duplications, inversions
9
Q
Genomes Protect Themselves Against Selfish Nucleic Acids
A
DNA that reproduces better can win out over cell’s DNA- the “selfish gene”
Mechanisms evolved that recognize and degrade “foreign” DNA
10
Q
Bacterial Restriction Enzymes
A
- Recognize short, specific, often “palindromic” (same forwards and backwards) DNA sequences, get double strand cleavage
- In some cases for attacking viral DNA. Cell’s own DNA modified so enzymes can’t attach it.
- Some create overhangs, great for cutting and splicing together DNA fragments
11
Q
CRISPR
A
- Bacteria steals bit of viral DNA, splices them into its chromosome
- Transcribe into guide RNA that helps enzyme and bind to/cleave virus DNA
12
Q
DNA Nucleotides Control
A
- Where to 5’cap and polyadenylate eukaryotic primary RNA signal (bind enzymes for each)
- Where to splice eukaryotic primary RNA (bind snRNA of spliceosomes)
- How to encode templates for rRNA, tRNA, snRNA, etc.
- Whether RNA polymerase transcribes DNA template, and how well it works!
- How stable mRNA is and how it is translated.
13
Q
Gene Expression
A
Not all cells make functional proteins from all the DNA
14
Q
Eukaryotic Gene Expression
A
- Controlled at many steps
- More complex
15
Q
Transcription Factor Proteins
A
- Bind to specific nucleotide sequences
- Alter transcription of nearby genes
- Affect binding or activity of RNA polymerase
16
Q
Prokaryotic Transcripton Factor
A
- Repressor binds to Operator DNA next to promoter
- Blocks RNA polymerase from transcribing
- Ex Lac Operon
17
Q
Regulation of Eukaryotic Transcription
A
- Complex
- Multiple transcription factors per gene
- Some stimulate transcription by binding enhancer DNA
- Others repress transcription by binding silencer DNA
18
Q
Change if a transcription factor is active
A
- Bind to or modify transcription factor protein
- Change expression of gene that codes for it
19
Q
Chromatin Remodeling
A
- Change wrapping of DNA by histone proteins
- Histones wrap DNA into nucleosomes (harder to transcribe)
- Transcription factors modify histones and make DNA more accessible
( Addition of acetyl groups)
20
Q
DNA Methylation
A
Add methyl groups to bases
- Temporary
- Doesn’t change base-pairing/replication
- Reduces transcription of nearby genes
21
Q
Epigenetic Changes
A
- Do not alter nucleotide sequence
- Can still last many cell generations
- Transcription factors can rebind after
DNA replication, network of interactions
can be self-reinforcing - Histone modifications, DNA methylation
can act as local trigger for modification of
new histones and methylation of
replicated DNA - But not as permanent as GENETIC
change = changing nucleotide sequence
22
Q
DNA Mutations & Epigenetics
A
Change whether and where to bind transcription factor in DNA
Alter transcription and histones
Change whether and where to methylate DNA
23
Q
DNA Translocations
A
Put regulatory region for 1 gene next to coding region for another and change 2nd gene’s expression
24
Q
Chromatin
A
Strands of chromosomes, DNA, histones, transcription factors
25
Nucleolus
Site of rRNA synthesis, assembly of large and small ribosomal subunits
26
Nuclear Envelope
2 Lipid Bilayers
27
How to Proteins know where to go
Have a signal sequence of amino acids that bind to specific structure
28
Protein Import into Nucleus
Proteins have import signal
Binds importin
Importin shuttles back and forth in nuclear pore imports
29
RNA Export from Nucleus
RNA binds export adaptor proteins with nuclear export signal sequences
30
Endoplasmic Reticulum
Network of membrane-enclosed tubes, discs,
Continuous w/ outer nuclear envelope
31
Rough ER
Has ribosomes along cytoplasmic side
Proteins that get inside ER, Golgi, vesicles made by ribosomes outside rough ER
Secretion signal sequence --> allows insertion of growing proteins though signal sequence receptor in RER
Where transmembrane proteins are inserted into membrane (signal anchor sequences)
32
All Secreted Proteins
Have secretion signal sequence
Made at and inserted into RER
Transported into vesicles
Sent to Golgi
Packaged into secretory vesicles
Secreted by exocytosis
33
Smooth ER
Inside has enzymes for synthesis of membrane lipids/steroids/carbs
Store things and release via pores (muscle contraction)
34
Golgi Apparatus
Stack of flattened membrane-bound discs or layers
Molecules transported from innermost to outermost layers (cis-trans)
35
Processing in Golgi
Proteins;
Cleaved to make smaller polypeptides
Covalently linked to other proteins
Covalently linked to other molecules (glycosylation)
36
Lysosomes
Digestive enzymes
Kept acidic w/ proton pumps
Membrane has transport proteins to export digested molecules to cytoplasm
37
Cytoskeleton
Intracellular rods and fibers that support cell
| Moved by motor proteins
38
Microtubules
Thickest diameter
Helical polymer made of dimers of tubulin proteins
Stable girders or move things
39
How do microtubules move things?
Lengthening or shortening
Using motor proteins (kinesin or dynein)
Slide past each other via motor proteins
40
Cilia & Flagella
Fine, bendable projections from a cell enclosed by a membrane
Microtubules in the ring (9+2), connected by dynein
Cilia = many, short
Flagella = few, long
41
Microfilaments
Smallest diameter
Made of actin
Move things by: lengthening or shortening, using motor proteins to move past each other or along microfilaments (mysoins)
Muscle contraction, rapid cell shape changes, intracellular movement (cell division), cytoplasmic streaming
42
Intermediate Filaments
Intermediate diameter
Mostly structural (meshwork inside membranes, shape cell or organelles)
Many different types
43
Coat Proteins
makes crosslinked fibers
Shape membranes, make vesicles
44
Fission
Prokaryotic cell divsion
DNA in circular chromosome
Replicate DNA
Attach each chromosome to membrane, separated by cell elongation
Make new membrane and cell wall (organized by tubulin like protein)
45
Eukaryotic DNA
Linear DNA
Set number per species
Different chromosomes --> different proteins and genes
1 copy of each chromosome per cell
46
Mitosis
Daughter cells have the same amount of chromosomes
1. Chromosomes duplicate and move to opposite ends to make the spindle
2. Microtubules attach to chromosomes
3. Chromosomes align in the center of the cell
4. Sister chromatids separate and move to opposite poles
5. Nuclear envelope reforms and chromosomes condense
6. Cytoplasm divides
47
Mitotic Spindle
Some microtubules attached to centrosomes
Others extend from one pole to the other
Kinetochore = shortens and slides to control movement
48
Cytokinesis Plants vs Animals
Animals:
Cleave furrow needs contractile ring of microfilaments/myosin
Animals
Cell plate made of fused vesicles in center of cell
49
Cell Cycle
G1 --> Gap 1
S Phase -- > Synthesis
G2 --> Gap 2
M --> Mitotic
50
Cell Cycle Checkpoints
G1 --> cell large enough, nutrients, signals
G2 --> happy, all DNA replicated
M --> all chromosomes attached to spindle
51
How is the cell cycle regulated?
Cyclin
Levels increase until reach the checkpoint, then activate CDK and degrade
Different cyclin for each checkpoint
52
Diploid
2n
pairs of homologous chromosomes
Somatic Cells
53
Haploid
n
Cells have 1 of each homologue
Gametes
54
Homologues
Not copies of each other
Inherited from gametes
Same genes in same regions but have different versions/alleles of genes with different DNA sequences
55
Non animal life cycles
Haploid cells divide to produce multicellular haploid stage before making gametes
56
Meiosis 1
Meiotic spindle lines up homologous chromosomes next to each other
Separates homologous chromosomes
Sister chromatids stay together
Pair of replicated homologues into tetrad
Crossing over recombines parts of chromosomes
57
Meiosis 2
No DNA replication
Sister chromatids separate
58
Why have sexual reproduction?
Increases diversity of traits
Helps species survive changing environment
Spreads adaptive mutations
Intermixes mutant alleles of genes
59
Transformation
Specialized channels take up DNA from outside, gets incorporated into chromosome
60
Conjugation of Bacteria
Long extension of membrane (pili)
Pili don't pass entire chromosomes, but fragments from chromosomes or plasmids
61
Why did Mendel cross pea plants?
1. He could control which ones mated with which
2. Peas have easily visible and inheritable traits
3. Mendel could get lots of seeds and plants from 1 mating
62
Phenotype
Physical trait
63
Genotype
What genetic information the individual passes on to offspring
64
Dominant Alleles
Control phenotype if present
65
Recessive Alleles
Control phenotype only with no dominant alleles present
66
Homozygous
Alleles of a gene on both homologues = identical
67
Heterozygous
One of the alleles of that gene is different
Will have dominant phenotype but can pass recessive trait to offspring
68
Mendel's Law of Segregation
The 2 alleles in the parent segregate from each other during formation of gametes
Pp parents produce gametes that are P or p with equal probability
69
Independent Assortment
How one gene's alleles segregate does not change how another gene's alleles segregate (Rr vs Yy)
RrYy x RrYy --> 9 : 3 : 3 : 1 ratio
70
Gamete rule
2^N
N = number of heterozygous pairs
71
Complications with Mendelian Inheritance
1) What if a gene is on a sex chromosome (sex-linked)?
2) What if two genes are “linked” on the same chromosome?
3) What if an allele is not really dominant or recessive, more than two alleles, causes multiple phenotypes?
4) What if one phenotype is influenced by more than one gene?
72
Autosomes
Non-sex chromosomes
73
Sex chromosomes
One sex has 2 different sex chromosomes
74
SRY Gene
On Y chromosome
Directs development of testes
75
Sex Linked
Genes on sex chromsome
76
XY Hemizygous
Half diploid for allele of X linked gene and allele of Y linked gene
77
Dosage Compensation
Mammals inactivate transcription from one of the two X chromosomes
Random chromosome inactivation blocks most transcription --> epigenetic mosaic
Female mammals are a mosaic of cells that act hemizygous for 1 X
78
Barr Bodies
Condensed X chromosomes tightly wrapped by histones
Makes it easier to adjust for sex chromosome monosomy/trisomy
79
Nondisjunction
Failure of chromosomes or chromatids to separate during meiosis
Leads to chromosome dosage problems after fertilization
80
Aneuploidies
Trisomy --> 3 of a homologue
Monosomy --> single homologue
