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Bio 151 > Mutations & Endo > Flashcards

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)
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2
Q

Transcriptome

A

Sequence all the RNAs that a cell makes, map back to genome

Tell where DNA is transcribed

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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

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4
Q

Genome

A

All genetic information in an organism

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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)
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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

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7
Q

Frameshift

A

Deletion of insertion of anything other than 3^n nucleotides (3x)

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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

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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

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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
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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
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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.
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13
Q

Gene Expression

A

Not all cells make functional proteins from all the DNA

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14
Q

Eukaryotic Gene Expression

A
  • Controlled at many steps

- More complex

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15
Q

Transcription Factor Proteins

A
  • Bind to specific nucleotide sequences
  • Alter transcription of nearby genes
  • Affect binding or activity of RNA polymerase
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16
Q

Prokaryotic Transcripton Factor

A
  • Repressor binds to Operator DNA next to promoter
  • Blocks RNA polymerase from transcribing
  • Ex Lac Operon
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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
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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

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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)
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20
Q

DNA Methylation

A

Add methyl groups to bases

  • Temporary
  • Doesn’t change base-pairing/replication
  • Reduces transcription of nearby genes
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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
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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

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23
Q

DNA Translocations

A

Put regulatory region for 1 gene next to coding region for another and change 2nd gene’s expression

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24
Q

Chromatin

A

Strands of chromosomes, DNA, histones, transcription factors

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25
Q

Nucleolus

A

Site of rRNA synthesis, assembly of large and small ribosomal subunits

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26
Q

Nuclear Envelope

A

2 Lipid Bilayers

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27
Q

How to Proteins know where to go

A

Have a signal sequence of amino acids that bind to specific structure

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28
Q

Protein Import into Nucleus

A

Proteins have import signal
Binds importin
Importin shuttles back and forth in nuclear pore imports

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29
Q

RNA Export from Nucleus

A

RNA binds export adaptor proteins with nuclear export signal sequences

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30
Q

Endoplasmic Reticulum

A

Network of membrane-enclosed tubes, discs,

Continuous w/ outer nuclear envelope

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31
Q

Rough ER

A

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)

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32
Q

All Secreted Proteins

A

Have secretion signal sequence

Made at and inserted into RER

Transported into vesicles

Sent to Golgi

Packaged into secretory vesicles

Secreted by exocytosis

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33
Q

Smooth ER

A

Inside has enzymes for synthesis of membrane lipids/steroids/carbs

Store things and release via pores (muscle contraction)

34
Q

Golgi Apparatus

A

Stack of flattened membrane-bound discs or layers

Molecules transported from innermost to outermost layers (cis-trans)

35
Q

Processing in Golgi

A

Proteins;

Cleaved to make smaller polypeptides

Covalently linked to other proteins

Covalently linked to other molecules (glycosylation)

36
Q

Lysosomes

A

Digestive enzymes

Kept acidic w/ proton pumps

Membrane has transport proteins to export digested molecules to cytoplasm

37
Q

Cytoskeleton

A

Intracellular rods and fibers that support cell

Moved by motor proteins

38
Q

Microtubules

A

Thickest diameter

Helical polymer made of dimers of tubulin proteins

Stable girders or move things

39
Q

How do microtubules move things?

A

Lengthening or shortening

Using motor proteins (kinesin or dynein)

Slide past each other via motor proteins

40
Q

Cilia & Flagella

A

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
Q

Microfilaments

A

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
Q

Intermediate Filaments

A

Intermediate diameter

Mostly structural (meshwork inside membranes, shape cell or organelles)

Many different types

43
Q

Coat Proteins

A

makes crosslinked fibers

Shape membranes, make vesicles

44
Q

Fission

A

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
Q

Eukaryotic DNA

A

Linear DNA

Set number per species

Different chromosomes –> different proteins and genes

1 copy of each chromosome per cell

46
Q

Mitosis

A

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
Q

Mitotic Spindle

A

Some microtubules attached to centrosomes

Others extend from one pole to the other

Kinetochore = shortens and slides to control movement

48
Q

Cytokinesis Plants vs Animals

A

Animals:

Cleave furrow needs contractile ring of microfilaments/myosin

Animals

Cell plate made of fused vesicles in center of cell

49
Q

Cell Cycle

A

G1 –> Gap 1
S Phase – > Synthesis
G2 –> Gap 2
M –> Mitotic

50
Q

Cell Cycle Checkpoints

A

G1 –> cell large enough, nutrients, signals

G2 –> happy, all DNA replicated

M –> all chromosomes attached to spindle

51
Q

How is the cell cycle regulated?

A

Cyclin

Levels increase until reach the checkpoint, then activate CDK and degrade

Different cyclin for each checkpoint

52
Q

Diploid

A

2n

pairs of homologous chromosomes

Somatic Cells

53
Q

Haploid

A

n

Cells have 1 of each homologue

Gametes

54
Q

Homologues

A

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
Q

Non animal life cycles

A

Haploid cells divide to produce multicellular haploid stage before making gametes

56
Q

Meiosis 1

A

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
Q

Meiosis 2

A

No DNA replication

Sister chromatids separate

58
Q

Why have sexual reproduction?

A

Increases diversity of traits

Helps species survive changing environment

Spreads adaptive mutations

Intermixes mutant alleles of genes

59
Q

Transformation

A

Specialized channels take up DNA from outside, gets incorporated into chromosome

60
Q

Conjugation of Bacteria

A

Long extension of membrane (pili)

Pili don’t pass entire chromosomes, but fragments from chromosomes or plasmids

61
Q

Why did Mendel cross pea plants?

A
  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
Q

Phenotype

A

Physical trait

63
Q

Genotype

A

What genetic information the individual passes on to offspring

64
Q

Dominant Alleles

A

Control phenotype if present

65
Q

Recessive Alleles

A

Control phenotype only with no dominant alleles present

66
Q

Homozygous

A

Alleles of a gene on both homologues = identical

67
Q

Heterozygous

A

One of the alleles of that gene is different

Will have dominant phenotype but can pass recessive trait to offspring

68
Q

Mendel’s Law of Segregation

A

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
Q

Independent Assortment

A

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
Q

Gamete rule

A

2^N

N = number of heterozygous pairs

71
Q

Complications with Mendelian Inheritance

A

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
Q

Autosomes

A

Non-sex chromosomes

73
Q

Sex chromosomes

A

One sex has 2 different sex chromosomes

74
Q

SRY Gene

A

On Y chromosome

Directs development of testes

75
Q

Sex Linked

A

Genes on sex chromsome

76
Q

XY Hemizygous

A

Half diploid for allele of X linked gene and allele of Y linked gene

77
Q

Dosage Compensation

A

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
Q

Barr Bodies

A

Condensed X chromosomes tightly wrapped by histones

Makes it easier to adjust for sex chromosome monosomy/trisomy

79
Q

Nondisjunction

A

Failure of chromosomes or chromatids to separate during meiosis

Leads to chromosome dosage problems after fertilization

80
Q

Aneuploidies

A

Trisomy –> 3 of a homologue

Monosomy –> single homologue

Bio 151 (4 decks)

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