Molecular Genetics

Flashcard 1

Front: What is DNA replication?

Back:
DNA replication is the process of creating an identical copy of DNA before cell division.

Key features:

• Begins at the origin of replication

• DNA strands separate and serve as templates

• New strands are synthesized using complementary base pairing

• DNA synthesis occurs only in the 5' → 3' direction

Flashcard 2

Front: Where does DNA replication begin?

Back:
Replication begins at a specific DNA sequence called the origin of replication.

At the origin:

• DNA unwinds

• Replication forks form

• DNA synthesis proceeds outward

Flashcard 3

Front: What is a replication fork?

Back:
A replication fork is the Y-shaped region formed when DNA is unwound and separated into two single strands during replication.

It is the active site of DNA synthesis.

Flashcard 4

Front: What is the function of helicase?

Back:
Helicase unwinds and separates the DNA double helix by breaking hydrogen bonds between complementary bases.

Result:

• Produces two single DNA strands

• Creates replication forks

DAT Tip: Helicase = "unzips" DNA.

Flashcard 5

Front: What is the function of topoisomerase?

Back:
Topoisomerase relieves torsional strain created ahead of the replication fork.

Mechanism:

1. Breaks DNA strands

2. Relieves supercoiling

3. Rejoins DNA strands

Without topoisomerase, DNA would become excessively twisted.

Flashcard 6

Front: What are single-stranded binding proteins (SSBs)?

Back:
Proteins that bind separated DNA strands near the replication fork.

Functions:

• Prevent strands from reannealing

• Stabilize exposed single-stranded DNA

• Keep strands available for replication

Flashcard 7

Front: Why is an RNA primer necessary?

Back:
DNA polymerase cannot begin synthesis from scratch.

It requires:

• A free 3'-OH group

• Existing nucleotides

Primase creates an RNA primer that provides this starting point.

Flashcard 8

Front: What is primase?

Back:
Primase is the enzyme that synthesizes short RNA primers during DNA replication.

Function:

• Creates starting points for DNA polymerase

Flashcard 9

Front: What is the function of DNA Polymerase III?

Back:
DNA Polymerase III:

• Synthesizes new DNA strands

• Adds nucleotides to the 3' end

• Works only in the 5' → 3' direction

Major replication enzyme in prokaryotes.

Flashcard 10

Front: In which direction is DNA synthesized?

Back:
DNA is always synthesized:

5' → 3'

Meaning:

• New nucleotides are added only to the 3' end.

DAT Favorite Question

Flashcard 11

Front: What is the leading strand?

Back:
The leading strand:

• Is synthesized continuously

• Grows toward the replication fork

• Requires only one RNA primer

Flashcard 12

Front: What is the lagging strand?

Back:
The lagging strand:

• Is synthesized discontinuously

• Grows away from the replication fork

• Requires many RNA primers

• Produces Okazaki fragments

Flashcard 13

Front: Why is the lagging strand synthesized discontinuously?

Back:
Because DNA polymerase only synthesizes DNA in the 5' → 3' direction.

As DNA unwinds:

• The lagging strand must be built in short segments

Flashcard 14

Front: What are Okazaki fragments?

Back:
Short DNA fragments synthesized on the lagging strand.

Characteristics:

• Each fragment starts with an RNA primer

• Later joined together by DNA ligase

Flashcard 15

Front: What is the function of DNA Polymerase I?

Back:
DNA Polymerase I:

1. Removes RNA primers

2. Replaces RNA with DNA nucleotides

Flashcard 16

Front: What is the function of DNA ligase?

Back:
DNA ligase seals gaps between Okazaki fragments.

Specifically:

• Forms phosphodiester bonds

• Creates a continuous DNA strand

Flashcard 17

Front: What are telomeres?

Back:
Telomeres are repetitive DNA sequences at chromosome ends.

Functions:

• Protect chromosome ends

• Prevent loss of important genes during replication

Flashcard 18

Front: Why do chromosomes shorten after replication?

Back:
DNA at chromosome ends cannot be completely copied.

Result:

• Chromosomes shorten slightly with each replication cycle

Telomeres buffer this loss.

Flashcard 19

Front: What is telomerase?

Back:
Telomerase is the enzyme that synthesizes and extends telomeres.

Function:

• Maintains chromosome length

• Helps prevent genomic information loss

TRANSCRIPTION Flashcard 20

Front: What is transcription?

Back:
Transcription is the synthesis of RNA from a DNA template.

Key point:

• Only a specific gene is transcribed

• Entire genome is NOT copied

Flashcard 21

Front: What is the difference between replication and transcription?

Back:

Replication	Transcription
Copies entire genome	Copies one gene
Produces DNA	Produces RNA
Occurs before cell division	Occurs for gene expression

Flashcard 22

Front: What is a promoter?

Back:
A promoter is a DNA sequence where RNA polymerase binds to initiate transcription.

Characteristics:

• Located upstream of the gene

• Essential for transcription

Flashcard 23

Front: What happens if the promoter region is deleted?

Back:
Gene expression is greatly reduced or completely prevented because RNA polymerase cannot bind.

Most effective way to stop expression of a gene.

Flashcard 24

Front: What are transcription factors?

Back:
Proteins that bind promoter and regulatory regions to control transcription.

Functions:

• Increase or decrease transcription

• Help recruit RNA polymerase

Flashcard 25

Front: Why are transcription factors important in eukaryotes?

Back:
Eukaryotic RNA polymerase requires transcription factors to initiate transcription efficiently.

Flashcard 26

Front: Describe transcription initiation.

Back:
Steps:

1. RNA polymerase binds promoter

2. DNA unwinds

3. Transcription begins

Flashcard 27

Front: Describe transcription elongation.

Back:
RNA polymerase:

• Reads DNA template strand

• Synthesizes complementary RNA nucleotides

• Continues until termination sequence reached

Flashcard 28

Front: Describe transcription termination.

Back:
Steps:

1. RNA polymerase reaches termination sequence

2. RNA transcript released

3. RNA polymerase detaches

Flashcard 29

Front: What post-transcriptional modifications occur in eukaryotes?

Back:

1. Addition of 5' cap

2. Addition of poly-A tail

3. RNA splicing

Flashcard 30

Front: What is the purpose of the 5' cap?

Back:
Functions:

• Protects mRNA from degradation

• Helps ribosome recognize mRNA

• Increases stability

Flashcard 31

Front: What is the purpose of the poly-A tail?

Back:
Functions:

• Protects mRNA

• Increases stability

• Facilitates export from nucleus

Flashcard 32

Front: What is RNA splicing?

Back:
Process of removing introns and joining exons together to create mature mRNA.

Flashcard 33

Front: What are exons?

Back:
Exons are protein-coding regions retained in mature mRNA.

Flashcard 34

Front: What are introns?

Back:
Non-coding regions removed during RNA splicing.

They do not encode functional protein sequences.

Flashcard 35

Front: What is alternative splicing?

Back:
Process where different combinations of exons are joined.

Result:

• Multiple proteins can be produced from one gene

Flashcard 36

Front: What is translation?

Back:
Translation is the synthesis of proteins using mRNA information.

Occurs at ribosomes.

Back:
Translation is the synthesis of proteins using mRNA information.

Occurs at ribosomes.

Flashcard 37

Front: What is the start codon?

Back:
AUG

Codes for:

• Methionine (Met)

Signals translation initiation.

Flashcard 38

Front: Describe translation initiation.

Back:
Steps:

1. Small ribosomal subunit binds mRNA

2. Methionine-tRNA binds AUG

3. Large ribosomal subunit joins

Flashcard 39

Front: What are the ribosomal A, P, and E sites?

Back:

A Site

• Incoming aminoacyl-tRNA enters

P Site

• Holds growing polypeptide chain

E Site

• Exit site for empty tRNA

Flashcard 40

Front: Describe translation elongation.

Back:
Steps:

1. tRNA enters A site

2. Peptide bond forms

3. Ribosome shifts

4. tRNA moves A → P → E

Protein grows one amino acid at a time.

Flashcard 41

Front: What are the stop codons?

Back:

• UAA

• UAG

• UGA

These do NOT code for amino acids.

Flashcard 42

Front: Describe translation termination.

Back:
When a stop codon enters the ribosome:

• Release factors bind

• Polypeptide released

• Ribosome disassembles

Flashcard 43

Front: What is a point mutation?

Back:
A mutation involving a single nucleotide.

Can be:

• Substitution

• Insertion

• Deletion

Flashcard 44

Front: What is a substitution mutation?

Back:
One nucleotide is replaced by another nucleotide.

May produce:

• Silent

• Missense

• Nonsense mutations

Flashcard 45

Front: What is a silent mutation?

Back:
Codon changes but amino acid remains unchanged.

Reason:

• Genetic code is redundant

Protein function typically unaffected.

Flashcard 46

Front: What is a missense mutation?

Back:
Mutation changes one amino acid to another.

Protein function may change.

Flashcard 47

Front: What is a nonsense mutation?

Back:
Mutation converts an amino acid codon into a stop codon.

Results:

• Premature termination

• Truncated protein

• Usually nonfunctional

Flashcard 48

Front: What is an insertion mutation?

Back:
Addition of one or more nucleotides into DNA sequence.

Flashcard 49

Front: What is a deletion mutation?

Back:
Removal of one or more nucleotides from DNA sequence.

Flashcard 50

Front: What is a frameshift mutation?

Back:
Mutation that shifts the reading frame.

Usually caused by:

• Insertions

• Deletions

Effects:

• Alters all downstream codons

• Produces severely altered proteins

Flashcard 51

Front: What is a forward mutation?

Back:
Changes a wild-type allele into a mutant allele.

Flashcard 52

Front: What is a backward mutation?

Back:
Reverts a mutant allele back to the wild-type allele.

Flashcard 53

Front: How does bacterial DNA replication occur?

Back:
Replication:

• Begins at one origin

• Proceeds bidirectionally

• Continues until chromosome completely copied

Flashcard 54

Front: What is binary fission?

Back:
Asexual reproduction in bacteria.

Steps:

1. DNA replicates

2. Cell elongates

3. Cell divides into two daughter cells

Flashcard 55

Front: How does bacterial cell division differ from mitosis?

Back:

Bacteria:

• No mitotic spindle

• Replication and segregation occur simultaneously

Eukaryotes:

• Use mitotic spindle

• Undergo mitosis

Flashcard 56

Front: What are plasmids?

Back:
Small circular double-stranded DNA molecules separate from bacterial chromosome.

Flashcard 57

Front: Why are plasmids important?

Back:
They often carry beneficial genes such as:

• Antibiotic resistance

• Metabolic functions

• Virulence factors

Flashcard 58

Front: Do plasmids replicate independently?

Back:
Yes.

Plasmids replicate independently of the bacterial chromosome.

Flashcard 59

Front: What is an operon?

Back:
A cluster of genes regulated together in prokaryotes.

Contains:

• Promoter

• Operator

• Structural genes

Flashcard 60

Front: What is the promoter in an operon?

Back:
DNA sequence where RNA polymerase binds.

Flashcard 61

Front: What is the operator?

Back:
DNA region that controls access of RNA polymerase.

Can bind:

• Repressors

• Activators

Flashcard 62

Front: What are structural genes?

Back:
Genes that encode proteins needed by the cell.

Flashcard 63

Front: What are regulatory genes?

Back:
Genes that encode proteins controlling expression of other genes.

Flashcard 64

Front: What is a repressor?

Back:
Protein that binds operator and decreases transcription.

Flashcard 65

Front: What is an activator?

Back:
Protein that increases transcription by helping RNA polymerase bind the promoter.

Flashcard 66

Front: What is the Lac Operon?

Back:
An inducible operon responsible for lactose metabolism.

Key idea:

• Lactose present → operon ON

• Lactose absent → operon OFF

Flashcard 67

Front: What does the Lac Operon produce?

Back:
Enzymes necessary to metabolize and break down lactose.

Flashcard 68

Front: What is the Trp Operon?

Back:
A repressible operon involved in tryptophan synthesis.

Purpose:

• Produces enzymes required to make tryptophan

BACTERIAL GENE TRANSFER Flashcard 69

Front: What is conjugation?

Back:
Transfer of DNA between living bacteria through direct contact.

Requires:

• Donor cell

• Recipient cell

• Pilus

Flashcard 70

Front: What is an F plasmid?

Back:
A fertility plasmid containing genes needed to form a pilus during conjugation.

Flashcard 71

Front: What is transformation?

Back:
A bacterium takes up free DNA from its environment.

Requires:

• Competent recipient cell

Flashcard 72

Front: What is transduction?

Back:
Transfer of bacterial DNA by a bacteriophage (virus).

Flashcard 73

Front: Which bacterial gene transfer method uses a virus?

Back:
Transduction

Virus involved:

• Bacteriophage

Flashcard 74

Front: Which bacterial gene transfer method uses direct contact?

Back:
Conjugation

Uses:

• Pilus

• Cell-to-cell contact

Flashcard 75

Front: Which bacterial gene transfer method uses environmental DNA?

Back:
Transformation

Flashcard 76

Front: What is the genome?

Back:
The complete genetic information of an organism.

DAT fact:

• Most of the human genome is non-coding DNA.

Flashcard 77

Front: What is the transcriptome?

Back:
The complete set of RNA molecules produced by a cell.

Includes:

• mRNA

• rRNA

• tRNA

• other RNAs

Flashcard 78

Front: What is the proteome?

Back:
The complete set of proteins produced by an organism or cell.

Flashcard 79

Front: Which enzyme unwinds DNA?

Back: Helicase

Flashcard 80

Front: Which enzyme relieves supercoiling?

Back: Topoisomerase

Flashcard 81

Front: Which enzyme synthesizes RNA primers?

Back: Primase

Flashcard 82

Front: Which enzyme adds DNA nucleotides?

Back: DNA Polymerase III

Flashcard 83

Front: Which enzyme removes RNA primers?

Back: DNA Polymerase I

Flashcard 84

Front: Which enzyme seals Okazaki fragments?

Back: Ligase

Flashcard 85

Front: DNA synthesis direction?

Back: 5' → 3'

Flashcard 86

Front: Start codon?

Back: AUG (Methionine)

Flashcard 87

Front: Stop codons?

Back: UAA, UAG, UGA

Flashcard 88

Front: Leading strand synthesis?

Back: Continuous

Flashcard 89

Front: Lagging strand synthesis?

Back: Discontinuous

Flashcard 90

Front: What produces multiple proteins from one gene?

Back: Alternative splicing

Flashcard 91

Front: Lactose present → Lac operon?

Back: ON

Flashcard 92

Front: Virus-mediated bacterial gene transfer?

Back: Transduction

Flashcard 93

Front: Direct-contact bacterial gene transfer?

Back: Conjugation

Flashcard 94

Front: Environmental DNA uptake?

Back: Transformation

Flashcard 95

Front: Most effective way to stop gene expression?

Back: Delete the promoter region