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Molec and Genetic Processes > Midterm > Flashcards

Midterm Flashcards

1
Q

Central Dogma

A

DNA to RNA to PROTEIN

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2
Q

Laws of Inheritance

A
  • each individual has 2 copies of each gene, 1 copy from each parent
  • dominant and recessive alleles
  • for a particular gene, individuals can be homozygous or heterozygous
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3
Q

Law of Segregation

A
  • an individuals maternal and paternal chromosomes segregate from one another during gamete formation (meiosis)
  • one gamete carries one allele for each gene
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4
Q

Law of Independent Assortment

A

segregation of a pair of alleles for one trait (gene) has no effect on the segregation of alleles for another trait
ie. alleles do not influence each other when it comes to sorting into gametes

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5
Q

Transcription

A

copying of one strand of DNA into a complementary RNA sequence by enzyme RNA polymerase

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6
Q

RNA S value

A
  • Svedberg unit
  • measure of the sedimentation rate during centrifugation
    – affected by both mass and shape
  • larger the molecule, the larger the S value, the faster the sedimentation
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7
Q

Why are there many repetitive copies of rRNA genes in the genome?

A

rRNA is not translated so there is no RNA to protein amplification step to create the many copies the cell needs

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8
Q

function of snoRNA

A
  • form snoRNPs by binding to core proteins
  • stablize rRNA through chemical modifications
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9
Q

function of tRNA

A

have anti-codon sequences that base-pair with codon sequence in mRNA to select correct sequence of A.As to incorporate into polypeptide

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10
Q

transcription of snoRNA

A

transcribed in introns by RNA polymerase 2

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11
Q

transcription of tRNA

A
  • encoded by DNA sequences located in small clusters of repeats scattered around the genome
  • transcribed by RNA pol 3
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12
Q

What happens to RNA left behind in nucleus?

A

default fate of RNA in nucleus is degradation in RNA exosome by RNA exonucleases

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13
Q

How is mRNA selected for export from nucleus?

A
  • proteins can bind to it and signal it is ready for function/export
  • nuclear transport receptors help guide completed RNA to pas through channels in nuclear membrane created by nuclear pore complex proteins
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14
Q

overlapping code

A

ribosome would move one nucleotide at a time when reading genetic code

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15
Q

non-overlapping code

A

ribosome would move 3 nucleotides at a time when reading genetic code
- codons are non-overlapping

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16
Q

structure of tRNA

A
  • contains complementary nucleotide sequences that base-pair to form short double-helical regions
  • cloverleaf structure
  • contains unusual bases that have been post-transcriptionally modified by enzymes
  • loop regions create binding sites for specific proteins
  • triplet CCA at 3’ end is the A.A. acceptor arm
  • anti codon loop at other end
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17
Q

silent mutation

A

alters the nucleotide sequence, but still encodes the same amino acid

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18
Q

nonsense mutation

A

leads to a stop/termination codon

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19
Q

frameshift mutation

A

deletion or insertion of nucleotide bases that shifts the way the sequence is read

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20
Q

missense mutation

A

base pair substitution that produces an amino acid different from the usual amino acid at that position

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21
Q

Aminoacyl-tRNA synthetase

A
  • catalyzes charging a tRNA with an
    amino acid
  • interacts with tRNA to bind and recognize both the anticodon loop and then amino acid acceptor arm
  • adds the amino acid to AMP (“activation”) and then transfers it to the tRNA
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22
Q

editing site of aminoacyl-tRNA synthetase

A
  • used for proofreading
  • Only incorrect amino acids will fit in the editing site and will be cleaved by hydrolysis
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23
Q

structure of ribosomes

A
  • composed of small and large subunit
  • mRNA threaded through small subunit and the polypeptide exists via tunnel through large subunit
    small subunit: decodes mRNA by interacting with anticodon end of tRNA
    large subunit: helps peptide synthesis by interacting with animoacyl-tRNA and catalyzing peptide bond formation
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24
Q

ribozyme

A

RNA that has catalytic function

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25
Q

consequences of errors in splicing

A
  • RNA degradation
  • frameshift mutations
  • missense mutation
  • impaired mRNA transport
  • accumulation of unspliced intermediates
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26
Q

messenger RNA (mRNA)

A

intermediate between DNA and protein – used as a template for protein synthesis by ribosomes in cytoplasm
- pre-mRNA is synthesized by DNA polymerase 2

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27
Q

transfer RNA (tRNA)

A

Required for translation of mRNA information into polypeptide sequence i.e. convert the language of nucleotides to the language of amino acids.
- synthesized by RNA polymerase 3

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28
Q

5’ cap functions

A
  • Prevents 5’ end from being digested by exonucleases
  • Plays a role is transport out of nucleus and initiation of mRNA translation to protein
  • Helps cells to distinguish mRNA from other types of RNA molecules.
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29
Q

Addition of 5’ cap

A
  1. RNA Triphosphatase removes the terminal phosphate group, leaving a disphosphate
  2. Guanyl transferase adds a GMP in an inverted orientation (5’ end of guanosine faces 5’ end of RNA), which forms 5’-5’ triphosphate bridge
  3. Position 7 of the guanine base is
    then methylated by RNA methyltransferase.
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30
Q

functions of 3’ poly (A) tail

A
  • acts as a recognition site for assembly of protein complex that carries out polyadenylation
  • Protects from digestion by exonucleases
  • Can be used to isolate mRNA from total RNA using oligo dT column (significant tool in molecular biology)
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31
Q

Addition of poly (A) tail

A
  1. CstF & CPSF are processing proteins that initiate cleavage to create a new 3’ end
  2. poly (A) polymerase (PAP) then adds an adenosine to the new 3’ end
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32
Q

alternative splicing and cell function

A
  • allows 1 gene to be used for the production of multiple different sequences of proteins (splice isoforms)
33
Q

ribsomal RNA (rRNA)

A

Doesn’t serve informational purpose like mRNA but instead provide structural support and catalyze the chemical reaction in which amino acids are covalently linked to each other
- synthesized by either RNA polymerase 1 or 3

34
Q

TFIID (general transcription factor)

A

recognizes TATA box and other DNA sequences near transcription start point

35
Q

TFIIH (general transcription factor)

A
  • unwinds DNA at the transcription start point
  • phosphorylates Ser 5 of the RNA polymerase C terminal domain (CTD)
  • releaseds RNA polymerase from promoter
36
Q

TATA Box

A
  • located about 25-35 base pairs before transcription start site
  • promoter element
  • site of assembly of preinitiation complex (PIC)
  • binds transcription factors (TFIID)
37
Q

Transcription elongation factors

A
  • Spt4, Spt5, and Elf1
  • help polymerase transcribe through nucleosomes
  • form a wedge to pry DNA away from histone core
  • directly destabilize histone-DNA interactions
38
Q

Chromatin remodelling factors

A
  • modify chromatin packaging to allow transcription factors access to the genes
39
Q

RNA polymerase 2

A

transcribes the DNA into RNA

40
Q

Types of Highly Repetitive DNA

A
  • satellite DNA: generally found at centromeres and telomeres
  • minisatellite DNA: highly variable (differ between individuals), basis for DNA fingerprinting in criminal and paternity tests
  • microsatellite DNA: highly variable, can be used to compare closely related populations
41
Q

Types of Moderately Repetitive DNA

A
  • genes: many copies of rRNAs and histones genes
  • non-coding
42
Q

Changes in Repetitive DNA sequences

A
  • they are unstable
  • can be expanded or destroyed by
    slippage events which causes misalignment
43
Q

regions of syteny

A

blocks that carry genes in a conserved order but are now located in different positions

44
Q

2 main mechanisms through which transposons move

A
  1. Cut and paste (DNA transposons)
    - catalyzed by transposase enzyme
  2. Copy and Paste (LINEs and SINEs)
    - involves RNA intermediate
45
Q

How do transposons cause genetic change?

A
  • transposition can cause mutation or disruption
  • can also result in the addition or removal of gene coding or regulatory sequences, results in exon shuffling which is important for evolution of genes
46
Q

exon shuffling

A

molecular mechanism for the formation of new genes, where two or more exons from different genes are recombined between introns, yielding rearranged genes with altered functions

47
Q

How does unequal crossing over cause genetic change?

A

example: Genes 1 & 2 misalign during meiosis
- one gamete loses part of DNA (deletion) and will be missing gene 2
- other gains an extra piece of DNA (duplication) and will have extra gene 2

48
Q

How can new genes be generated from pre-existing genes?

A
  • substitutions, insertions, and deletions can create different variants of a genes
  • gene duplication can give rise to multi-gene families
  • translocations can create new genes by exon shuffling
  • horizontal gene transfer (non-sexual movement of genetic info between genomes)
49
Q

pseudogens

A

“Genes” that have a similar sequence to the gene family but have accumulated so many mutations that they are now non-functional

50
Q

orthologs

A

genes separated by speciation

51
Q

paralogs

A

genes separated by duplication events

52
Q

Single Nucleotide Polymorphisms (SNPs)

A
  • Most common variability among humans is single nucleotide differences
  • SNPs in protein-coding regions contribute to the phenotypic differences in humans (alleles)
53
Q

Relationship between SNPs and Alleles

A

Some SNPs / sets of alleles can be inherited together (linked)

54
Q

haplotypes

A

a particular combination of alleles on a chromosome that are inherited together

55
Q

Proofreading function of DNA polymerase

A
  • DNA polymerase has a separate catalytic sites for polymerization and for editing
  • DNA is pushed into the editing site when a mismatch is detected
56
Q

Strand-directed mismatch repair

A
  1. Recognition of mismatch (by MutS protein)
  2. Identification of newly synthesized strand
  3. Removal of incorrect nucleotides from new
    strand
  4. Resynthesis of excised segment (using other
    strand as template)
  5. Ligation to seal DNA backbone
57
Q

How does structure of DNA make replication possible?

A
  • Open up DNA (make it single stranded) so that each individual strand can serve as template for synthesis of complimentary new strand
  • Complimentary base-pairing allows the selection of the correct nucleotides to properly replicate the sequence
  • Hydrogen bonds between bases allow DNA strands to be separated.
  • Ability to reversibly make single-stranded DNA (and use it as a template) is critical for DNA replication
58
Q

Why is DNA replication 5’ to 3’

A
  • Incoming nucleoside triphosphate base pairs with the template strand and is then covalently attached
    to the 3’ OH
  • The hydrolysis of the bond between phosphates provides the energy to create this new bond (Could
    NOT work if trying to extend the 5’ phosphate)
59
Q

What affects DNA melting (Tm)?

A
  • since there is a higher # of hydrogen bonds holding G/C bonds together, the higher the GC content, the higher the Tm
60
Q

What is Tm?

A

the temperature at which 50% of the double-stranded DNA is changed to single-stranded DNA

61
Q

C0t value

A
  • the curve provides an index about the amount of renaturation of DNA
  • combination of DNA concentration and incubation time
62
Q

Somatic vs Germline Mutation

A

Somatic: arise during individual’s lifetime in tissues other than germ cells, not passed on
Germline: changes to DNA that you inherit from the egg and sperm cells during contraception, can be passed on

63
Q

Mitosis

A
  • one cell divides once to form two identical diploid cells
  • required for growth, repair and asexual reproduction
  • DNA is replicated once
64
Q

Meiosis

A
  • single cell divides twice to produce 4 daughter cells
  • four daughter cells contain half the amount of genetic material and known as our sex cells (gametes)
  • four daughter cells are haploid (consist of half the number of chromosomes of the parent cell)
  • DNA is replicated once
65
Q

mitotic spindle

A
  • forms during prophase
  • pulls duplicated chromosomes apart
66
Q

microtubules

A

form the mitotic spindles

67
Q

kinetochores

A
  • on the sides of the centromeres
  • provides site of attachment for spindle fibers
68
Q

cohesin

A
  • protein complex that mediates cohesion between replicated sister chromatids
69
Q

centromere

A
  • links a pair of sister chromatids together during cell division
  • helps cell divide up its DNA during division
70
Q

Crossing over

A
  • allows alleles on DNA molecules to change positions from one homologous chromosome segment to another
  • occurs in prophase 1
71
Q

nucleosomes

A
  • fundamental structural unit of chromatin
  • beadlike structure, short length of DNA wrapped around octametric core of histone proteins
72
Q

chromatin

A
  • material that makes up chromosomes
  • complex of DNA, histones, and non histone proteins found in nucleus
73
Q

histones

A
  • DNA binding protein
  • form nucleosome cores which DNA is wrapped around in chromosomes
74
Q

epigenetic inheritance

A
  • inheritance of phenotypic changes in a cell or organism that does not result from changes in nucleotide sequence of DNA
  • can be due to positive feedback loops of transcription regulators or heritable modifications in chromatin
75
Q

heterochromatin

A

highly condensed, generally transcriptionally inactive

76
Q

euchromatin

A
  • less compacted and functionally active
  • accessible for binding and transcription
77
Q

Consequences of covalent modifications of histones

A
  • loosens chromatin structure
  • ability to recruit specific proteins to modified stretch of chromatin
  • recruited proteins act with modified histones to determine how and when genes will be expressed
78
Q
A

Molec and Genetic Processes (2 decks)

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