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KCUMB Molecular Biology > EXAM I Ferguson > Flashcards

EXAM I Ferguson Flashcards

1
Q

What two bonds are important in the formation of DNA?

A

Glycosidic - links sugar to base

Phosphodiester - links bases

10bp/turn

symmetric

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2
Q

How many nts are distributed over how many chromosomes?

A

3.2x10^9 nts over 24 different chromosomes

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3
Q

What are banding patterns, karyotyping, and whole chromosome painting used for?

A

The identification and detection of chromosome numbers

Banding pattern - staining & light microscopy

Karyotyping - detect abnormalities, determine loss or gain of chromosomes

Whole Chrom. Painting

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4
Q

3 requirements to pass genetic information to daughter cells

A

OriR

Centromere - kinetochore attachment

Telomere

(ENTIRE genome is replicated; DNA serves as its own template)

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5
Q

What are the common interactions between DNA and histone proteins?

A

H.H.S. - hungry, hungry, salty!

Hydrophobic interactions

H-bonds

Salt linkages - Arginine & Lysine

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6
Q

What are the roles of arginine and lysine during the packing of DNA with histones?

A

They are (+) charges which neutralizes the (-) charge of the DNA backbone, allowing the interactions (hydrophobic, H-bonds, salt linkages) to occur

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7
Q

What does chromatin remodeling allow for? What enzyme is used? And does this process require energy?

A

Looser arrangment of histones around DNA to allow greater access for proteins

Helicase requires ATP - cuts linker DNA into fragments

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8
Q

Define epigenetics and provide some examples

A

The study of changes in organisms caused by gene expression modifications RATHER than alteration of the genetic code itself

i.e. DNA methylation, Maternal Imprinting, Histone modifications, chromatin structures

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9
Q

Evidence that histones are more than just structural (they’re also functional; 3 ways)

A

Highly conserved

DNA contains equal amounts of histone and nonhistone protein

Heterochromatin is used for gene silencing & passed on to daughter cells = Drosophila experiment (zone of inactivation) = position effect

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10
Q

Which amino acid(s) are important in histone modification? What enzymes add and remove it?

A

Lysine

Methylation of lysine via methyl transferase, removed by methyl demethylase

Acetylation of lysine via histone acetyl transferase (HATs), removed by histone deacetylase complexes (HDACs)

Serine = phosphorylated

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11
Q

What is the function of the code-reader complex for histone codes? List its components, what are some examples of the consequences of the histone codes? Function of code reader enzymes?

A

Binds histone codes on the N-terminus histone tail via covalent modifications which determines DNA packaging in nucelosomes

Components: protein modules (that bind specific histone modifications on nucleosomes), scaffold protein

Displays catalytic activity

Ex: gene silencing, gene expression, etc.

Code reader enzymes spread the marker over chromosome for continued modification

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12
Q

Function of barrier proteins during nucleosome/chromatin modification; example is HS4 region

T/F - remodeling is dependent upon ATP

A

Barrier sequences (i.e. proteins or enzymes) halt the spread of chromatin modification

HS4 region protect beta-globin locus from silencing, containing a cluster of histone acetylase binding sites

True - ATP-dependent chromatin remodeling protein - assists with condensation/decondensation

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13
Q

Explain the role of centromeric heterochromatin (H3) in chromatin modifications

Which set of histones are always passed on to daughter cells in forming the centromere?

A
  • H3 histone = CENP-A that forms kinetochore (required for the attachment of mitotic spindle)

Centromere sequences contain non-required alpha satellite DNA, also found at non-centromeric positions

New centromeres can spontaneously form on fragmented DNA

  • H3-H4 tetramer directly inherited
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14
Q

What type of chromatin is rich in gene expression? Where are heterochromatin located during gene expression?

A

Euchromatin

Heterochromatin = towards or inside the nucleus

Active chromatin form loops

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15
Q

What is the role of condensins? T/F ATP required?

A

Used during condensation (disentangelment of sister chromatids to allow separation for cell division), which aids the compaction via ATP hydrolysis to coil DNA into chromatids

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16
Q

How do genomic changes occur (genome evolution)

A

Via mistakes during DNA replication: (rare)

I (goto) DownTown, SD

Inversions, Translocations, Deletions, Substitutions, Duplication

Base pair substitutions

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17
Q

How are phylogenetic trees used for comparative genomics?

A

Able to compare genomes of contemporary organisms; they show differences between humans and apes

Able to determine sequence conservation

One reason for sequence conservation could be that eliminating mutations could interfere with important genetic functions = purifying selection

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18
Q

What is the purpose of sequence comparisons in genome evolution?

A

Helps to provide inside into purpose or function

5% human genome conserved, but 1.5% codes for proteins

Therefore, the human genome is highly conserved

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19
Q

Describe the importance of gene duplication in regards to the globin chain

A

Duplication and Divergence

Started with a single-chain globin that binds 1 oxygen molecule, evolution allowed for a 2nd globin chain by gene duplication followed by mutation, resulting in 4 globin chains binding 4 oxygens

Mutation gave rise beta and alpha genes; translocation = moved alpha to separate chrom.; further duplication & mutation = more specialized beta molecules (fetal, adult)

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20
Q

Why do germ cells and somatic cells have a high fidelity rate?

A

Germ-cells = to maintain the species

Somatic cells = to avoid uncontrolled proliferation/cancer

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21
Q

What are the key players in DNA replication?

A

DNA Polymerase

DNA Primase

Helicase

OriR (A-T rich)

ssDNA Binding Protein

Topoisomerase

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22
Q

What is the function of mismatch repair during DNA replication? What players are involved?

A

Corrects the errors that DNA proofreading (via 3’-5’ exonuclease) does not fix

MutS - sticks and binds to mismatch

MutL - looks for errors and triggers degradation of nicked strand

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23
Q

What are the proteins at the replication fork in DNA replication? ATP required?

A
  • Sliding Clamp + Clamp loader - keeps DNA polymerase on DNA when moving and is removed once it encounters a double strand
  • Assembled via ATP hydrolysis
  • Stays on continuously in leading strand, new clamps are assembled on lagging strand at each Okazaki fragment
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24
Q

At what rate does helicase unwind DNA?

A

1000 nt pairs/sec

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25
What is the role of helicase loading proteins (Cdc6 and Cdt1) and Cdks during DNA replication regulation?
Helicase loading proteins **bind to ORC** ## Footnote **Cdks removed helicase loading proteins, activating helicase and unwinding DNA and loading DNA polymerase** **= S phase**
26
How are histones disassembled (broken up into) during replication and how are they reassembled afterwards?
Disassembled = destablized into **H3-H4 tetramer distributed randomly to daughter duplexes and 2 H2A-H2B dimers** (1/2 old; 1/2 new) **with the help of histone chaperones (chromatin assembly factors) directed by _sliding clamp PCNA_** Daughter strands contain a hybrid of parental and new histones = epigenetic inheritance
27
Explain the role of telomerase in replicating chromosome ends; what is the special sequence? Define T-loops
On the lagging strand, there is not enough space for primase to place ~10nts at the end, **telomerase** replenishes by elongating parental strand in 5'-3' direction using an RNA template and DNA polymerase continues replicating lagging strand **Ensures that 3' end is longer leaving a protruding SS end that loops back and tucks into repeat = _T-loops_ protects ends** _Shelterin_ - protective cap
28
What is caused by dyskeratosis congenita in telomeres?
**Mutant telomerase RNA gene** Prematurely shortened telomeres; chromosome ends aren't stablized and secured (T-loops)
29
What are the two types of DNA damage and what are the results if not repaired?
**Depurination -** Removing a purine (A/G) base via hydrolyzing glycosyl linkages leaving a free OH group = can result in **_deletion_** **Deamination -** switching out bases resulting in **_base-pair substitutions_**; i.e. UV radiation makes covalent bonds b/w adjacent pyrimidines (T-T, C-T) = **pyrimidine dimers**
30
What are the 4 types of DNA repair pathways?
**B**oys **N**ever **T**ake (you on) **D**ates Base excision repair Nucleotide excision repair Trancription-coupled repair Double-stranded break repair (homologous vs. non)
31
Describe the mechanism of base excision repair; what are the key players
**DNA glycosylases** (unique for each base; i.e. uracil specific) scans and **cleaves glycosyl bond connecting base w/ sugar** ## Footnote **AP endonuclease and phosphodiesterase cut phosphodiester backbone removing the base** **AP endonuclease directly repairs depurinations**
32
Describe the mechanism of Nt excision repair; what makes it different from base excision repair?
The way damage is removed is different; **phosphodiester bond is cleaved on both sides** Bulky lesions are removed i.e. chemically-induced, thymine dimers **_Multienzyme complex scans double helix;_** Gap is repaired by **DNA polymerase and ligase**
33
What is the mechanism of transcription-coupled repair? What disease is associated with this?
Active RNA polymerase is linked with DNA repair = occurs simultaneously = urgent repair systems RNA stays along, waits, and continues transcription by fixing the repair first **Cockayne's Syndrome** - defect in the coupled-repair **RNA polymerase is permanently stalled at sites of damage**
34
Why are methylated cytosines problematic (DNA repair)
Deamination of methyl-C produces T mismatched with G which is recognized by **a DNA glycosylase** which is relatively ineffective Occurs at some **CpG sequences** and is associated with inactive genes
35
Which DNA repair mechanism is most prominent in humans?
**Non-homologous double strand break repair** Broken ends are joined and sealed via DNA ligation with a few nts being lost
36
Define the ATM protein that's involved in DNA repair
Kinase that generates **intracellular signals** that alert the cell to DNA damage and **upregulates expression of DNA repair genes** Mutation = AT; Ataxia telengiectasia - neurodegeneration, predisposition to cancer, etc.
37
List two ways in which double stranded breaks can occur
Homologous recombination Nonhomologous end joining - Broken ends are joined and sealed via DNA ligation with a few nts being lost
38
List the steps in repairing ds stranded breaks via homologous recombination (HR) (can also repair broken or stalled replication forks)
1. 5' ends are degraded by **5' exonuclease**, leaving a 3' overhang 2. 3' end invades homologous ds template and primes repair DNA synthesis = **strand invasion** 3. Back home; The newly synthesized 3' end of invading strand anneals w/ original damaged DNA via complementary base pairing 4. gaps filled and ligated
39
Importance of RecA protein in single strand DNA pairing?
RecA **directs the invading single strand to search for homologous sequence to invade and form a _heteroduplex DNA_ = synapsis reaction**
40
List the major differences between homologous recombination and non-homologous end joining ds break repair processes
**Homologous Recombination:** * Template = daughter DNA duplex * No loss or alteration of DNA * Can repair other types of DNA damage, conserved **Non-Homologous End-Joining** * No template required * Mutation created at repair site (due to overhang; flush ends being chewed by exonuclease) * Translocations can occur
41
What two events occur that cause homolognous recombination?
**Crossing over** **Gene conversion** Occurs after meiosis and duplication on the diploid cell
42
When does meiotic recombination occur and what does it begin with? List the basic steps
**Maternal and paternal homologous chromosomes are paired** **Begins with a double stranded break** **Strand invasion** **Double Holliday junction** **Resolution**
43
Define Holliday Junction
**DNA intermediate with 4 DNA strands from two different helices** Transient structures Cleaved by **Endonuclease (RuvC); 2 outcomes:** **Crossing Over = rare** **Gene Conversion = common**
44
What occurs in each scenario of the Holliday Junction?
Left - cut at BOTH HJ (both crosses); strands separate with **minimal exchange of sequences** Right - cut in opposite directions; **each chromosome are swapped = crossover event**
45
What occurs during branch migration? Does this mechanism require energy? What type of DNA does a recombination event create?
Strand invasion occurs and one strand creates a branch point and moves along the heteroduplex Requires ATP **Recombination results in heteroduplex DNA**
46
What _rare_ event doesn't allow for equal exchange of genetic material between maternal and paternal genes? When does this occur
**Gene Conversion** Occurs during homologous recombination during DNA synthesis Due to mismatch repair in heteroduplex DNA regions
47
What are the 3 types of transpositional recombination? List the type of Conservative site-specific recombination?
**DNA-only transposons** **Retroviral-like Retrotransposons** **Nonretrovial Retrotransposons** Bacteriophage lambda
48
Define transposon; what enzyme does it encode?
Specialized DNA segments that move from one position in the genome to another Can provide antibiotic resistance in bacteria Encodes **Transposase** that allows insertion into a target DNA site
49
What can occur from meiotic errors?
**Nondisjunction** - homologs fail to separate; common during egg development at Meiosis I (most common abnormality) **Aneuploid -** abnormal chromosome number **Euploid -** normal chromosomes!!! :))
50
Define **conservative site specific recombination**; what are the three outcomes and what causes them to occur; how does this differ from transposition? Which microbe uses this?
Mediates rearrangements of other types of mobile DNA elements (other than transposons); **Bacteriophage lambda; can be used to turn genes on/off = *Cre-lox recombination*** **DNA integration, DNA excision, DNA inversion** EACH DNA contains special recognition sites for recombinase, no intermediates **Sites are same oritentation = _integrated or excised_** **Inverted sites = _DNA inversion_**
51
Define cohesin used in meiosis I, when do chromosomes replicate?
Cohesin - holds two sister chromatids together during S phase Replication uccurs during **S phase** Plays important role in segregating homologs during meiosis I, in meiosis II, sister chromatids are separted and cohesin breaks down
52
# Define 3 terms that occur during Prophase I Bivalent Chiasma Synaptonemal complex
**Bivalent -** 4 chromatin structure containing replicated maternal and replicated paternal chromosomes (2 chromosomes, 4 chromatids) **Chiasma -** crossing over **Synaptonemal complex -** where homologs are joined via small region of homology = **pseudoautosomal region**
53
What are the 5 phases of prophase? What occurs at each step
**L**ittle **Z**ebras **P**ack **D**ancing **D**icks **Leptotene -** homologs begin to condense/pair **Zygotene -** *_synaptonemal complex forms_* *via **transverse filaments*** **Pachytene -** *_crossing-over_* **Diplotene -** breaking down of synaptonemal complex **Diakinesis -** max condensation, homologs separate, transition into metaphase
54
55
Where in the body is the sex chromosome determined during primordial germ cell development? What gene is important for testis development?
**Genital ridge** * PGCs proliferate via mitosis then meiosis to differentiate into mature haploid gametes * **SRY gene -** cells diff into Sertoli cells, Sox9 gene. Sertoli cells secrete anti-Mullerian hormone and induce Leydig cel diff.
56
Where does spermatogenesis occur?
**Seminiferous tubules -** maturation moves them closer to the lumen
57
What are the requirements of fertilization?
**Albumin -** helps extract cholesterol from membrane, increasing ability to fuse w/ acrosome membrane **Ca2+, HCO3- -** initiation of capacitation-associated changes
58
List the basic steps of fertilization
1. Sperm binds to zona pellucida 2. Acrosomal rxn 3. Penetration thru ZP 4. Fusion of plasma membranes 5. Sperm contents enter egg cytoplasm; cortical rxn occurs & meiosis resumes **(high [Ca2+])**
59
Describe the cortical rxn
The release of enzymes via cortical granules from the egg to change ZP to block **polyspermy** **Inactivation of ZP3** so it doesn't bind to sperm or induce acrosome rxn
60

KCUMB Molecular Biology (6 decks)

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