Structure of nucleic acids and genome organization

Question 1

replication of DNA is catalyzed by which enzyme.

requires

DNA strand grows in which direction?

Answer 1

DNA polymerases

1. requires
   
   1. template
      
      1. ssDNA
   2. substrates
      
      1. dATP, dGTP, dCTP and dTTP
2. growth in the 5’->3’ direction

Question 2

differentiate from prokaryote and eukaryote origin of replication

Answer 2

1. similar
   
   1. _melting -seperating of the DNA_
   2. BIDIRECTIONAL synthesis
2. differences
   
   1. euk
      
      1. multiple OriC’s
      2. RNA primers are removed by RNAse H,

Question 3

what enzymes are involved in folowing, for prokaryotes

1. melting the DNA
2. keeping the two strands apart?
3. unwinding the double helix

Answer 3

1. DnaA
   
   1. protein binds and melts dsDNA
2. DNA helicase
   
   1. unwinds double helix
3. ssDNA-binding
   
   1. proteins bind to ssDNA
   2. keep strands separated
   3. they protect ssDNA from nucleases

Question 4

What is the generation/solution to a supercoil?

Answer 4

1. generation
   
   1. unwinding of the DNA forms positive supercoilds ahead of replication fork.
   2. These can interfere with helicase function
2. solution
   
   1. topoisomerase removes the supercoil, by nicking one side, rotating the DNA and ligating

Question 5

DNA

1. DNA polymerase read DNA in the ______ direction
2. DNA polymerase synthesizes DNA in the ______ direction
3. what is the consequence of this action
   
   1. describe the two
   2. direction and type of synthesis

Answer 5

1. DNA polymerase
   
   1. reads in the 3’->5’ direction
   2. synthesizes in the 5’->3’ direction
2. two types of strands form b/c the DNApol can only perform the above directions
   
   1. leading strand
      
      1. being copied i nthe direction of replication fork
      2. continuously synthesized
   2. lagging strand
      
      1. being copied in the direction away from the replication fork
      2. okazaki fragments:small fragments of DNA
      3. discontinuously synthesized

Question 6

describe enzymes involved in initiation and elongation of DNA

Answer 6

1. DnaA- melts DNA
2. SSB-keep from reanealing
3. helicase - unzips DNA
4. leding strand
   
   1. continuous polymerization by DNApol3
5. lagging strand
   
   1. primase establishes RNA primers
   2. DNApol3 - starts at the RNA primer and continues until it reaches the next RNA fragment
   3. DNA pol1 - locates the space between DNA and RNA, replaces the RNA primer with DNA
   4. Ligase forms P bond between 3’ and 5’ end

Question 7

what are the functions of DNA ligase?

Answer 7

1. Form bond in the okazaki fragments, between 3’ and 5’ phosphates.
2. DNA repair and recombination
3. recombinant DNA etchniques

Question 8

explain each phase of cell replication

Answer 8

1. G0
   
   1. non replicative
2. G1
   
   1. period preceding replication
3. S
   
   1. replication occurs during
4. mitosis
   
   1. seperationg of the cells
5. G2
   
   1. chromosomes are formed

Question 9

When the RNA primer is removed from extreme 5’ end of the chromosome, what the consequence of this? solution?

Answer 9

shortening of tthe new strand can result in loss of genetic information and is associated with aging

1. soluution
   
   1. telomeres
      
      1. region of highly repetitive DNA at tthe end of chromosomes
      2. 300-600 base pairs in yeast
      3. function
         
         1. buffer consumed during cell division
         2. protect the ends from nucleases
         3. limit** cells to a fixed **number of divisions, in most somatic cells
      4. replaced by telomerase
         
         1. this enzyme is active in cancer cells, germ and stem cells

Question 10

describe the mechanism of telomerase

Answer 10

1. telomerase - ribonucleoprotein complex composed of proteins and RNA
   
   1. RNA-dependent DNA pol
   2. contains a telomerase RNA component
      
      1. which is complementary to a repetitive sequence in telomere
   3. mechanism
      
      1. uses hte 3’ end of DNA as a primer and TERC asa template to extend 3’ end of DNA
      2. once a single-stranded portion of telomere end is extended an RNA primer is produced to fill a single-stranded portion of chromosome

Question 11

describe the affect of shorter telomeres

Answer 11

shorter telomeres affect hematopoiesis.

decreases the stem cell supplies

Question 12

Describe 3 disease associated with TERC

Answer 12

1. telomerase RNA component
   
   1. Aplastic anemia
   2. autosomal dominant dyskeratosis congenita
   3. familial MDS-AML

Question 13

Tm depends on

Answer 13

Tm = melting point of DNA, temperature at which 50% of the dsDNA is separated

GC content

1. higher GC= higher Tm

Question 14

describe nucleases

1. function
2. types

Answer 14

nucleases

1. phosphodiester bonds are recognized and cleaved
2. types
   
   1. specific
      
      1. can recognize and bind a specfic sequence of nucleotides
   2. nonspecific
      
      1. can cleave nucleic acids at random positions

Question 15

describe the following test

1. FISH
2. sounthern blot
3. northern blot
4. PCR

Answer 15

1. FISH
   
   1. fluorescent in situ hybridization, used to detet specific sequences in genome
2. southern blot
   
   1. DNA detection specific sequences after separation in the gel
3. Northern blot
   
   1. RNA detection specific sequences after separation in the gel
4. PCR
   
   1. is used to ampligy specific DNA sequences

Question 16

describe the organization of geneomes in the following

1. viruses
2. prokaryotes

Answer 16

1. Viruses
   
   1. lack complete systems for replication, transcripttion, and translation. hijack hosts system for their reprodcution
2. prokaryotes
   
   1. circular c’some
   2. DNA-protein complex is located in nucleoid
      
      1. ​these organism lack a defined nucleus
   3. plasmid
      
      1. small circular DNA molecules
      2. replicate autonomously, outside host genome
      3. used for genetic engineering and lateral gene transfer

Question 17

describe the DNA associated with histones to form chromatin- 2 types

Answer 17

1. Diffuse euchromatin
   
   1. transcriptionally active
2. condense-hetterochromatin
   
   1. transcriptionally silent

Question 18

before mitosis DNA is replicated and forms two _____ ______.

What is the name of the region that microtubules attach to?

What about mtDNA?

Answer 18

DNA is replicated and form two sitster chromatids

centromer is the region of chromosome to which the microtubules of the spindle attach during cell division

mtDNA is independent of host cell division, must tkeep up and move on its own, nherited maternally

Question 19

explain the CFTR gene: 7q31.2

Answer 19

• 7=chromosome number
• q=long arm
• 31= region, band
• 2=sub band

Question 20

what is the basic unit of heredity in all living organisms?

what is the name of a specific spot on that unit?

alternative version of a this unit are called?

Answer 20

gene = the basic unit of heredity in all living organisms

genetic locus is a position of a gene on a c’some

alleles= alternative versions of agene.

homologous chromosome-each gene has a matching gene on a complimentary c’some (one from mom and one from dad)

Question 21

how many c’somes do the following have ?

1. haploid cell
2. diploid cell

Answer 21

1. haploid
   
   1. 23 c’somes
2. diploid
   
   1. 46 c’somes
      
      1. 22autsomal pairs
         
         1. each composed of two homolous c’somes
      2. 2 sex chromosomes

Question 22

explain the structure used to compact DNA.

what are the superstructures?

Answer 22

histones

1. RNA protein core allowing supercoiing of DNA
   
   1. DNA + core = nucleoid
2. basic proteins (+ charge)
3. five major classes
   
   1. H2A,H2B,H3,H4, and H1

Question 23

what makes up the nucleosome core?

describe the structures and super structures.

Answer 23

• wrapping -140 bp of DNA around nucleosome clore
  
  • nucleosome core= 2 of tthe following (H2A,H2B,H3, and H4)

many nucleosome cores coiled up generate a solenoid (aka 30nm fiber)

function= controlling transcription

Question 24

list the composition and organization levels involved with DNA

Answer 24

1. DNA-double helix
2. chromatin
3. 30nm=solenoid
4. chromosome

Question 25

describe the organization of DNA and c’somes while in a non dividing cell

Answer 25

each chromosome occupies distinct territory

these locations of specific c’some can change over time and can be different in different cell types

Question 26

what test is useful for spotting large chromosomal/sex abnormalities

Answer 26

karyotyping

• colchicum autumnale binds to tubulin and inhibits mitosis. allowing for the karyotype study
  
  • also used to treat gout

Question 27

discuss and categorize the chromosome abnormalities

Answer 27

1. structural abnormalities-structure is altered
   
   1. deletion
   2. duplication
   3. inversion
   4. substitution
   5. translocation
2. numerical abnormalities
   
   1. monosomy
      
      1. missing one csome
   2. trisomy
      
      1. more than two csomes

Question 28

a patient has progressive deterioration of motor skills. Karyotyping showed the following.

What is the genetic condition of this disease?

Answer 28

Ataxia

1. aberrant chromosome 4
   
   1. portion of c’some 12 was deleted and replaced with a portion of c’some 4

Question 29

Give three examples of numerical chromosome abnormalities

Answer 29

1. klinefelter syndrom
   
   1. most common male chromosomal disease
   2. males are infertile, gynecomastia
   3. higgh incidence of germ cell tumor and male breast cancer
2. edwards syndrome
   
   1. caused by trisomy of c’some 18
   2. kidney malformation
   3. heart defects
   4. developmental delays, intrauterine growth retardation
   5. low birth weight
3. patau syndrom
   
   1. is caused by trisomy of c’some 13
   2. can result in microencephaly
   3. heart/kidney defects
   4. abnormal genitalia

Question 30

comprises 5% of the RNA in the cell

1. function
2. modifications

Answer 30

mRNA

1. carries genetic information from nucleus to the site of protein synthesis
2. modifications
   
   1. cap on the 5’ end is REQUIRED for initiation of translation
      
      1. added during transcription
   2. coding region
      
      1. portion to be translated
   3. polyAtail
      
      1. 3’ end to stabilize mRNA
      2. added after translation

Question 31

70% of RNAs

Answer 31

1. rRNA
2. synthesis of rRNA and assembly of ribosomes occur in the nucleolus
3. mitochondrial ribosome is similar to bacterial ribosome
4. prokaryotes
   
   1. 3 types of rRNA + proteins
5. eukaryotes
   
   1. 4 types of rRNA + protieins

Question 32

Jimmy has a mutation where Cystiene is not being added to his proteins. What RNA is affected?

1. types?
2. functions?
3. structure

Answer 32

tRNA

1. 20 different tRNAs
   
   1. one tRNA for each amino acid
2. carries amino acid, on 3’ end, to ribosomes. Reads codon with anticodon.
   
   1. acts as proofreading mechanism during translation
3. small molecule. 80 nucleotides . primary structure differs, but all develop into a cloverleaf shape. formed through antiparallell base paring.
   
   1. posttranscriptional modification

Question 33

list the types of RNA

1. involved in maturation of RNAs precursors - splicing
2. repress protein biosynthesis.
   
   1. derived from?
   2. prevent
   3. size
3. Xist RNA example
   
   1. define Xist RNA
   2. involed in
   3. length
4. HOTAIR is an example
   
   1. length

Answer 33

1. snRNA
   
   1. a component of small nuclear ribonuclearproteins (snRNPs)
2. miRNA
   
   1. derived from endogenous genes
   2. repress protein biosynthesis, usually by preventing the ribosome binding to mRNA or promotes mRNA degradation
   3. 20-24 nucleotides in length
3. lncRNA long noncoding RNA
   
   1. Xist RNA= x inactivation specific transcript, inactivating one ofthe two x c’somes
   2. involved in epigenetic modification
   3. 200bp and longer
4. linRNAs-large intergenic non coding RNA
   
   1. over 200bp
   2. hotair= overexpressed in breast tumors
      
      1. found to increase the expression of specific proto-oncogenes that participate/result in breast tumor

Question 34

Jay has a mutation in a protein that cleaves pre-miRNA.

Define and describe this?

Answer 34

Drosha and Dicer are proteins that cleave pre-miRNA.

AGO froms binds single stranded miRNA and form RISK complex

RISCs are a nucleoprotein complexes that regulate targeted genes expression

risc function

1. translational repression
2. translational activation
3. mRNA cleavage