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Flashcards in Molecular Genetics Deck (80):
1

Nucleotides: consists of what? Give 2 examples

Nucleotides consists of 3 parts - nitrogen base, a sugar, and a phosphate.

DNA and RNA are polymers of nucleotides.

2

DNA replication:

Involves in separating(unzipping) the DNA molecule into two strands, each of which serves as a template to a new, complementary strand.

3

Semiconservative replication:

One stand of the two is old, the other is new.

4

DNA replication:

Helicase:

An enzyme that unwinds the DNA helix, forming a Y-shaped replication fork.

5

DNA replication:

Single-strand binding proteins:

Prevent single strands of DNA from recombining.

6

DNA replication:

Topoisomerases:

Break and rejoin the double helix, allowing the twists to unravel and preventing the formation of knots.

7

DNA replication:

DNA Polymerase: Describe and state which direction

Catalyzes the antiparallel elongation of new DNA strands.

Moves in the 3'---->5' direction along each template strand.
Attaches to the RNA primers and begins ELONGATION, the adding of DNA nucleotides to the complement strand.

8

DNA replication:
Antiparallel

Moves in the 5'--->3' direction.

9

DNA replication:
Leading Strand:

Works continuously as more DNA unzips
5' ------> 3'

10

DNA replication:
Lagging Strand:

Forms in the direction away from the replication fork in a series of fragments called Okazaki fragments.

11

DNA replication:

DNA Ligase:

Connects okazaki fragments.

12

Primase

Initiates DNA replication at special nucleotide sequences(called ORGINS OF REPLICATION) with short segments of RNA nucleotides called RNA PRIMERS.

Primase is an enzyme that synthesizes short RNA sequences called primers. These primers serve as a starting point for DNA synthesis. Since primase produces RNA molecules, the enzyme is a type of RNA polymerase.

13

Telomeres

Each time the DNA replicates, some nucleotides from the ends of the chromosomes are lost. To protect against the possible loss of genes at the ends of the chromosomes, eukaryotes have special nonsense nucleotide sequence. Telomeres are the caps at the end of each strand of DNA that protect our chromosomes, like the plastic tips at the end of shoelaces.

Telomeres are an essential part of human cells that affect how our cells age.

14

Replication of Telomere:

2 problems can occur when replication reaches the end of the DNA strand.

1. Not enough template strand where primase can attach.

2. Last primase is removed=> in order to change RNA to DNA, there must be another DNA strand in front of the RNA primer-----> DNA poly. cannot build after removing RNA primer ---> ultimately that RNA is destroyed by enzymes that degrade RNA left on the DNA

15

Telomerase:

Telomeres are created and maintained by the enyme Telomerase.

Enzyme that attaches to the end of template strand and extends the template strand by adding short sequence DNA over and over, allowing elongation of lagging strand to continue.

16

Gene or genotype

Used to represent the genetic information for a particular trait.

17

One-gene-one-enzyme hypothesis

A gene that is defined as a DNA segment that codes for a particular polypeptide.

18

3 Kinds of RNA molecules produced during transcription

Step 1: mRNA

mRNA is basically instructions for the creation of a protein. (the m stands for messenger...) ...proteins are made in the ribosomes and they are made from 'amino acids' and basically these mRNA's tell the amino acids how to align to make a specific protein...

19

Protein Synthesis
Step 1: If the DNA triplets to be transcribed is:

Then the strand of mRNA codons that forms are:

5' --AAA TAA CCG GAC--3'

3'--UUU AUU GGC CUG--5'

20

3 Kinds of RNA molecules produced during transcription

Step 2: tRNA

Consists of about 80 nucleotides. It is a short RNA molecule that is used for transporting amino acids to their proper place on the mRNA template. It contains an ANTICODON.

21

3 Kinds of RNA molecules produced during transcription

Step 2: tRNA: What is in the anticodon?

AAA UAA CCG GAC

This is a short RNA molecule that is used for transporting amino acids to their proper place on the mRNA template.

During translation, the anticodon of the tRNA base pairs with the codon of the mRNA.

22

3 Kinds of RNA molecules produced during transcription

Step 3: rRNA

Describe and state its 3 binding sites.

Nucleolus is an assemblage of DNA actively being transcribed into rRNA.

As ribosome, has 3 binding sites:
1.)One for mRNA
2.) one for tRNA that carries a growing polypeptide chain (P site)
3.)One for 2nd tRNA that delivers the next aa(A site).

Termination sequences include UAA, UGA, UAG. Together w/ proteins, rRNA forms ribosomes. Ribosome is assembled in nucleolus but large and small subunits exported separately to cytoplasm.

23

Transcription:

The process by which the information in a DNA sequence is copied(transcribed) into a complementary RNA sequence.

24

Transcription: INITIATION (1st step)

Also defy a "promotor region"

TATA box?

Begins when an enzyme, RNA polymerase, recognizes and binds to DNA at the PROMOTOR REGION. The promotor "tells" RNA polymerase where to begin transcription and which of the two strands to transcribe.

The TATA box meditates the binding of RNA polymerase to the DNA.

25

Transcription: ELONGATION (2nd step)

RNA polymerase unzips DNA and assembles RNA nucleotides using one strand of DNA as template; only one DNA strand is transcribed.
This occurs in the 5'-----3' direction.

26

Transcription: TERMINATION (3rd step)

Occurs when the RNA poly. reaches a special sequence of nucleotides that serve as a termination point. At this point, mRNA is cut free from the DNA template.
In eukaryotes, the termination region often contains the DNA sequence AAAAAA.

27

mRNA Processing:
1. 5' cap (-P-P-P-G-5')

A 5' cap consisting of a modified guanine nucleotide is added to the 5' end. This cap helps the RNA strand bind to the ribosome in the cytoplasm during translation.

28

mRNA Processing:
2. A poly- A tail (-A-A-A.....A-A-3')

This sequence is attached to the 3' end of the mRNA; Tail consists of 200A; provide stability and control movement of mRNA across the nuclear envelope.

29

mRNA Processing:
3. RNA splicing

Removes nucleotide segments from mRNA; before mRNA moves into cytoplasm.

Basically the Introns are removed, but the Exons stay!

30

mRNA Processing:

Alternative Splicing

Allows different mRNA's to be generated from the same RNA transcript; selectively removing differences of an RNA transcript into different combinations => each coding for a different protein product.

31

Translation:

After transcription, the mRNA, tRNA, and ribosomal units are transported across the nuclear envelope and into the cytoplasm.

Translation is the process by which the codons of an mRNA sequence are changed into an amino acid sequence.

32

Translation: Aminoacyl- tRNA

in cytoplasm, This amino acid attaches to tRNA at 3' end, require 1 ATP.
This forms an tRNA with an amino acid.

tRNA is made of nucleo tides, not amino acids.

33

Translation: 1st step Initiation

Begins when mRNA becomes attached to a subunit of the ribosome. This first codon is always AUG.

34

Translation: (2nd) Elongation:

What does it bind to?
What is translocation?

next tRNA binds to A site, peptide bond formation, tRNA without methionine is released, the tRNA currently in A site moves to P site(TRANSLOCATION) and the next tRNA comes into A site and repeat process.

35

Translation: (3rd) Termination:

Occurs when the ribosome encounters one of the 3 stop codons. UAG, UAA, UGA.

A release factor breaks the bond between the tRNA and the last amino acid of the polypeptide chain.

36

Translation: Post-translation

Translation begins on a free floating ribosome signal peptide at the beginning of the translated polypeptide may direct the ribosome to attach to the ER, in which case the polypeptide is injected into the ER lumen.

If injected, polpyeptide may be secreted from the cell with Golgi.

37

Mutation:

Also describe a point mutation. What does this include?

Also, what is a frameshift?

Any sequence of nucleotides in a DNA molecule that does not exactly match the original DNA molecule from which it was copied.

A POINT MUTATION is a single nucleotide error. This includes substitution, deletion, insertion, frameshift.

A frameshift mutation occurs as a result of a nucleotide deletion or insertion.

38

Mutation: Silent Mutation

New codon still codes for the same amino acid.

39

Mutation: Nonsense Mutation:

Also called missense mutation. This happens when point mutations or frameshifts changes a codon within a gene into a stop codon.

40

Mutation: Nuetral mutation:

no change in protein fxn

41

Repair Replication Mechanisms:
1. Proofreading
2. Mismatch repair
3. Excision repair

Proofreading: DNA polymerase checks base pairs

Mismatch repair: enzymes repair things DNA polymerase missed

Excision repair: enzymes remove nucleotides damaged by mutagens(chemicals that cause mutations)

42

DNA Organization:
Chormaton
Nucleosome
Histone

In eukaryotes, DNA is package with proteins to form a matrix called CHROMATIN. The DNA is coiled around bundles of 8 or 9 HISTONE proteins to form DNA-histone complexes called NUCLEOSOMES.

43

DNA Organization:

Euchromatin and Heterochromatin

1. Euchromatin: loosely bound to nucleosomes, actively being transcribed.
2: Heterochromatin= represents areas where the nucleosomes are more tightly packed and where DNA is inactive. Because of its condensed arrangement, heterochromatin stains darker than euchromatin.

44

DNA Organization: Transposons ( or jumping genes)

DNA segments that can move to new location on same/different chromosome;

Some transposons consist only of DNA that codes for an enzyme that enables it to be transported. Other transposons contain genes that invoke replication of the transposon. After replication, the transposon is transported to a new location.

45

What does a virus consist of?

-Nucleic Acid
-Capsid
Capsomeres
-Envelope

Virus is a nucleic acid( RNA/DNA may be double/single stranded) but not both!

Capsomeres - assemble to form the capsid.
Capsid(protein coat)- encloses the nucleic acid.
Envelope - surrounds the capsid of some viruses.

46

What type of viruses only attack bacteria?

Bacteriophages, or phages.

47

Replication of viruses: Lytic Cycle:

The phage enters a host cell, takes control of the cell machinery, replicates itself, and then causes the cell to burst, releasing a new generation of infectious phage virus. These new viruses infect and kill thousands of cells in the same manner.

48

Lytic Cycle: DNA virus

DNA is replicated and form new viral DNA => transcribed to produce viral proteins (DNA + viral proteins assemble to form new viruses)

49

Lytic Cycle: RNA virus

RNA serves as mRNA = translated into protein(protein + RNA => new virus)

50

Lytic Cycle: Retroviruses

e.g. A family of RNA viruses containing a reverse transcriptase enzyme which allows the viruses' genetic information to become part of the genetic information of the host cell upon replication.

51

Lysogenic cycle:

Define
What is a provirus?

Viral DNA is temporarily incorporated into the DNA of the host cell/

A virus in this dormant state called a PROVIRUS( or if a bacteriophage, a prophage) The virus remains inactive until some trigger is active. When triggered, lytic cycle begins.

52

Prions:

Not viruses or cells. Misfolded version of proteins in brain that cause normal version to misfold too. Fatal.

53

Teichoic Acids

They are on a cell wall of bacterium are used as recognition + binding sites by bacterial viruses that cause infections; also provide cell wall rigidity: only found on gram-positive bacteria!

54

Molecular Genetics of Bacteria:

Bacteria are prokaryotes with no nucleus or organelles, single circular DNA molecule(tightly condensed and called a nucleoid), no histones or other assoc. proteins. Replicate DNA in bother directions from single point of origin

55

Molecular Genetics of Bacteria: Binary Fission

Bacteria reproduces by binary fission( chromosomes replicates, cell divides into 2 cells ; each one bearing one chromosome. Lacks nucleus => lack microtubles, spindle, centrioles.

56

Molecular Genetics of Bacteria: Plasmids

What are EPISOMES?

Short, circular DNA outside chromosome (carry genes that are beneficial but not essential for survival) Replicate independently.

EPISOMES are plasmid that can incorporate into bacterial chromosome.

57

Genetic Variations:

Conjugation

Know F plasmid and R plasmid.

The process of DNA exchange between bacteria. A donor bacterium produces a tube, or PILUS to the recipient.

F Plasmid = contains the genes that enable a bacterium to produce pili.

R Plasmids = provide bacteria with resistance against antibiotics

58

Transduction

The process by which DNA is transferred from one bacterium to another by a virus. It also refers to the process whereby foreign DNA is introduced into another cell via a viral vector.

59

Transformation:

Occurs when bacteria absorb DNA from their surroundings and incorporate it into their genome.

60

Regulation of Prokaryotic Gene Expression: Operon

What does it do and describe the following componenets

1. Promotor
2. Operator
3. Structural Genes
4. Regulatory Gene

Control gene transcription

1. Promotor: Sequence of DNA where RNA polymerase attaches to being transcription.
2. Operator: Region that can block action of RNA polymerase if occupied by regressor protein.
3. Structural genes: DNA sequences that code for related enzymes.
4. Regulatory genes: Located outside of operon region, produces REGRESSOR PROTEINS. Other produce ACTIVATOR PROTEINS that assist the attachment of RNA polymerase to promotor region.

61

Lac Operon (E.Coli)

Controls breakdown of lactose. Regulatory genes produces active repressor(bind operator) and block RNA pol. When lactose is available, lactose binds repressor and inactivates it ==> RNA poly can now transcribe. Lactose indudes the operon. The enzymes that the operon produces are said to be INDUCIBLE ENZYMES.

62

Trp Operon(E. Coli)

Produces enzyme for tryptophan synthesis; regulatory genes produce an inactive repressor ==> RNA pol produces enzymes. When tryptophan is available, no longer need to synthesize it internally: it binds to inactive repressor and activates repressor ==> able binds operator and block RNA poly. Tryptophan is COREPRESSOR.

63

Trp Operon : Repressible enzymes

When structural genes stop producing enzymes only in presence of an active repressor. Unlike repressible enzymes, some genes are CONSTITUTIVE(constantly expressed) either naturally or due to mutation.

64

Regulation of Eukaryotic Gene Expression:

Regulatory Proteins

Repressors and activators, influence RNA pol's attachment to promoter region.

65

Nucleosome Packing:

What is methylation and acetylation?

Influences whether a section of DNA will be transcribed.
METHYLATION of histones ( tighter packing = preventing transcription_

ACETYLATION of histones = uncoiling and transcriptions proceeds

66

RNA Interference:

short interfering RNAs(siRNAs) block mRNA transcription or translation, or translation degrade existing mRNA.

67

Human Genome:

98% of human DNA does not code for protein productl noncoding DNA: regulatory sequences- control gene expression , introns- interrupt genes, repetitive sequences-can't do transcription. Causes multiple diseases like Huntingtons disease.

68

Recombinant DNA:

Contains DNA segments or genes from different sources. The transfer of these DNA segments can come from viral transduction, bacterial conjugation, transposons.

69

Recombinant DNA technology:

uses RESTRICTION ENZYMES to cut up DNA and left it with a sticky end(unpaired).

70

Recombinant DNA: Vector

Such as plasmid because DNA molecule used as a vehicle to transfer foreign genetic material into another cell.
- To introduce foreign DNA into plasmid, the plasmid is treated with the same restriction enzyme so the same sticky end to bind. DNA stabilize the attachments.

71

Recombinant DNA: Gel Electrophoresis

Restriction fragments can be separated by this. In this process, DNA fragments of different lengths are separated as they diffuse through a gelatinous material under the influence of an electric field.

72

Restriction fragment length polymorphism (RFLPs)

Restriction graments between individuals are compared, fragments in length are observed because of POLYMORPHISM(different length in DNA sequences).

73

DNA Finger printing

RFLPs at crime scene compared to RFLPs of suspects.

74

Short Tandem Repeat (STF)

Repeat of 2-5 nucleotides and different between all individuals except identical twins.

75

Reverse Transcriptase:

Introns often prevent transcriptions; this enzyme makes DNA molecule directly form mRNA, DNA obtained from this manner is COMPLEMENTARY DNA (cDNA) which lacks introns that suppress transcriptions.

76

Polymerase chain reaction PCR

uses synthetic primers(may be DNA or RNA) to clone DNA.

77

Nucleotides

DNA is a polymer consisting of repeating units of nucleotides.

78

Nucleosomes

The double helix of DNA wraps twice around a core of histones, forming NUCLEOSOMES which look like beads on a string.

79

In RNA, uracil(U) replaces....

Thymine.

80

Which codons are the "stop codons"

UAA, UGA, and UAG are stop codons and terminate all sequences.