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Molecular Genetics > Topic 1 > Flashcards

Topic 1 Flashcards

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1
Q

What is the primary concern for molecular genetics?

A

DNA–> Transcription–> RNA–> Translation–> Proteins

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2
Q

What are the building blocks for DNA nucleic acids?

A

DNA nucleotide monomers that form polymers

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3
Q

What are the building blocks of RNA nucleic acids?

A

RNA nucleotide monomers

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4
Q

What bonds link nucleotides?

A

Phosphodiester bond

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5
Q

Describe phosphodiester bonds.

A

Covalent bond that is strong and difficult to break. Requires restriction enzymes, rather than heat to break the bonds.

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6
Q

What are the 3 major parts for nucleotides?

A

Sugar + Base + Phosphate

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7
Q

What is base + sugar?

A

Nucleoside

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8
Q

What are the purines?

A

Adenine and Guanine

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9
Q

What are the pyrimidines?

A

Cytosine, Thymine, & Uracil

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10
Q

How are purine nucleosides named?

A

Adenosine & Guanosine

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11
Q

How are pyrimidine nucleosides named?

A

Cytidine, Thymidine, & Uridine

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12
Q

How are all the base nucleotides named?

A

Adenylate, Guanylate, Cytidylate, Thymidylate, Uridylate

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13
Q

What kinds of sugars to ATP, CTP, UTP, TTP, & GTP have?

A

Ribose

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14
Q

How do they look if they are deoxyribose?

A

No sugar on C-2. dATP, dGTP, dCTP, dTTP, & dUTP.

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15
Q

Draw the 5 bases and how they bond.

A

Now-recognize which base is given on the exam. *Will be on there.

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16
Q

How do you get from Cytosine to Uracil?

A

Deamination-Deaminase removes amino group to form C=O to become uracil in RNA.

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17
Q

How do you name a phosphodiester bond?

A

By where the oxygens are attached. 3’-5’ phosphodiester bond.

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18
Q

Why do DNA & RNA molecules have 5’ & 3’ ends?

A

Free ends that aren’t involved in a phosphodiester bond. 3’ free hydroxyl and 5’ phosphate.

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19
Q

How many bonds between G-C & A-T

A

G-C–> 3 H-bonds: A-T–> H-bonds

20
Q

Which base pairing group has a higher Tm?

A

G-C because more H-bonds. PCR depends on this.

21
Q

What is the 5’ and 3’ end in reference to?

A

The individual bases, not the entire strand.

22
Q

Describe DNA structure.

A

Runs anti-parallel; forms double helix; Contains major and minor grooves (alternate);

23
Q

What are important proteins associated with DNA?

A

Histone proteins important for packing DNA tightly, especially during cell division; Scaffolding proteins are also important to further pack DNA. Gene transcription-contains transcription factor proteins to recruit RNA Polymerase. DNA replication-Topoisomerase, Helicase, DNA Polymerase, Ligase, etc.

24
Q

What forces DNA to stay helical?

A

Hydrophobic stacking of bases and Watson-Crick base pairing

25
Q

What kind of DNA replication does DNA use?

A

Semi-conservative-Half conserved because 1 strand is original and the new strand is newly synthesized.

26
Q

What is the biological significance of the A-form of DNA?

A

Typical for A-form to form DNA-RNA hybrids. This happens during transcription when DNA is used as a template to transcribe RNA.

27
Q

What is the significance of the B-form of DNA?

A

The promoter sequence, which is the TATA box, is usually B-form DNA.

28
Q

What is the significance of the Z-form of DNA?

A

Methylated CpG (p=phosphodiester bond) island. It is an epigenetic mechanism used by cells to control gene expression. CpG islands typically occur at or near transcription sites. Cytosine is present followed by a guanosine. The cytosine can be methylated which inhibits gene expression.

29
Q

Compare A, B, and Z form of DNA.

A

A-form: Right handed, purine stretches, 11 base pairs/turn, and low degree of hydration.
B-form: Right handed, mixed sequences, 10 base pairs/turn, and high degree of hydration.
Z-form: Left handed, alternating purine and pyrimidines, 12 base pairs/turn, and high degree of hydration.

30
Q

What does it mean if there are lots of GpC islands?

A

There is a functional gene downstream. Use this to determine how many functional genes in the human genome.

31
Q

What is the central dogma?

A

DNA–>DNA=Replication
DNA–>RNA=Transcription
RNA–>DNA=Reverse Transcription (retroviruses attacking host cell)
RNA–>Protein=Translation

32
Q

Where does transcription occur? Translation?

A

Transcription=Nucleus, Translation=Cytoplasm

33
Q

What is the exception to the location of transcription and translation?

A

The mitochondria-It can do transcription and translation as well as chloroplast in a plant cell.

34
Q

What level is gene transcription mainly controlled at?

A

Transcription level-Making or not making RNA says whether or not to make proteins. AKA the rate limiting step in gene expression is transcription.

35
Q

Describe RNA transcription.

A

Transcription factors bind to promoter sequence and help to recruit RNA Polymerase-doesn’t require as many cofactors as DNA Polymerase. It can unwind the DNA strand on its own. Uses DNA template to make RNA strand. There is a template strand of DNA, a coding strand of DNA (one that looks identical to RNA except for U/T0. You deposit this strand to GeneBank because you give a single strand to them. (Sense strand=Coding strand)

36
Q

What are Cis-elements?

A

Refer to promoter sequence or DNA sequence in promoter region.

37
Q

What are the main Cis elements?

A

GC B=box, TATA box, CAAT box-These are very close to intron and exon sequences.

38
Q

What are some other Cis elements that are also found in some genes?

A

TRE=TPA response element
CRE=cAMP response element-important second messenger

Genes expression can be controlled/regulated by these two things

39
Q

What are the transcription factors for the 3 main promoter sequences?

A

GC box=Spl
TATA box=TFIID & TATA box binding protein
CAAT box=many different ones-C/EBP, CTF/NF1

40
Q

What does +1 side mean on a gene?

A

That is the start sequence where transcription begins. Transcription start/initiation site

41
Q

Is anything before +1 transcribed? Is +1?

A

Anything negative is not transcribed and the promoter site is usually not transcribed.

42
Q

What main two domains do transcription factors have?

A

DNA binding domain-Helps TF bind to promoter sequence.

Activation Domain-Allows other proteins to interact and begin transcription.

43
Q

What are the 3 major processes that happen after transcription in eukaryotic cells?

A

5’ (methylated) guanosine cap & 3’ Poly A tail added by RNA polymerase II. Then splicing occurs in the primary RNA transcript.

44
Q

Describe splicing details.

A

Happening in the splicosome/nucleosome. Most introns begin with GU/T and end with AG. GU=splicing donor site (5’ end) and AG=splicing acceptor site (3’ end). Branch site has very conservative A sequence. These 3 sites are recognized by small nuclear ribonucleo proteins (SnRNP).

45
Q

Describe mechanism 1 of RNA splicing.

A

SnRNP recognizes splicing donor site and cleaves it at the 5’ end. A nucleophilic attack occurs from -OH on branching site at the GU sequence, resulting in the formation of a lariat. Then cleavage at the 3’ end occurs and ligation of the exons occurs.

46
Q

Describe mechanism 2 of RNA splicing.

A

U1 SnRNP recognizes and binds to splice donor site. U2 SnRNP recognize and bind to branch site. It is cut and U4, U5, and U6 bind to the donor and acceptor sites and finish splicing process.

Molecular Genetics (7 decks)

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