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Cell Cycle Regulation Study Guide

A comprehensive guide to the cell cycle, covering its regulation by CDKs and cyclins, checkpoints, and the molecular machinery that ensures accurate cell division. Suitable for students of biology and molecular genetics.

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Cell Cycle Regulation and Signal Transduction Pathways

Regulation of the Eukaryotic Cell Cycle

The eukaryotic cell cycle is precisely regulated by Cyclin-Dependent Kinases (CDKs) and cyclins, involving checkpoints and surveillance mechanisms to ensure accurate division.

  • Cyclins
  • Cell cycle checkpoints
  • Interphase
  • G1, S, and G2 phases
  • Cell cycle synchronization
  • DNA content analysis

Regulation of Cyclin-CDK Activity and Cell Cycle

  • CDK activity regulation
  • Cyclins
  • CDK Inhibitors
  • SCF (Skp1-Cullin-Fbox Complex)
  • E2 ubiquitin-conjugating enzyme
  • G1/S transition
  • Metaphase/Anaphase transition
  • Mitotic exit

G Protein-Coupled Receptor Signaling Mechanisms

G protein-coupled receptors respond to extracellular signals to activate G proteins that function as on-off switches for intracellular signaling pathways.

  • G protein-coupled receptors
  • G proteins
  • Signal transduction
  • Effector enzymes
  • Ion channels
  • Second messenger molecules
  • cAMP

The Ras/MAP Kinase Signaling Pathway

RTKs and cytokine receptors activate the Ras GTPase switch protein to initiate a Raf-MEK-MAPK kinase cascade that phosphorylates transcription factors.

  • Ras/MAP kinase pathway
  • GTPase switch protein Ras
  • Guanine nucleotide exchange factors (GEFs)
  • GTPase-activating proteins (GAPs)
  • MAP kinase cascade
  • Phosphorylation of transcription factors
  • Gene expression regulation

Regulation of Transcription Factor Activity

Lipid-soluble hormones bind to lipid-hormone receptors to regulate gene expression through specific response elements.

  • Transcription factor activity
  • Lipid-soluble hormones
  • Lipid-Hormone Receptors
  • Transcriptional Activators
  • Response elements
  • Nuclear-receptor superfamily

Signal Transduction and G Protein-Coupled Receptors

Extracellular signals from hormones and signaling peptides activate plasma membrane or cytosolic receptors to initiate signal transduction pathways involving G-protein switches, second messengers, and protein phosphorylation.

  • Signal transduction
  • G-protein coupled receptors (GPCRs)
  • GTPase switch proteins
  • Second messengers
  • Protein kinases
  • Protein phosphatases
  • Heterotrimeric G proteins

Regulation of CDK Activity and Cell Cycle

The regulation of CDK activity through activating and inhibitory phosphorylation controls transitions between the stages of the cell cycle.

  • CDK activity regulation
  • Restriction point
  • Activating phosphorylation
  • Inhibitory phosphorylation
  • CDK-Activating Kinase (CAK)
  • Cdc25 phosphatase
  • Mitotic entry

Molecular Mechanisms of Cell Cycle Regulation

Molecular mechanisms governing the initiation of DNA replication, G1–S phase transition, and surveillance mechanisms in cell cycle regulation.

  • G1–S phase transition
  • Rb protein
  • E2F transcriptional activator
  • Cyclin D/CDK4
  • Cyclin D/CDK6
  • Cyclin E-CDK2
  • S-phase initiation
  • Proteolysis of inhibitor proteins
  • Replication Origins
  • Pre-replication complex (pre-RC)
  • S-phase cyclins
  • Mitosis protein degradation
  • Cell cycle checkpoints
  • DNA damage response system
  • ATM and ATR kinases
  • DNA-PK

Mechanisms of Transcription and Gene Expression Analysis

Techniques for Analysis of Gene Expression

This lecture discusses several techniques used in the analysis of gene expression including PCR, DNA sequencing, RNA sequencing, and RT-PCR.

  • Polymerase Chain Reaction (PCR)
  • Taq polymerase
  • DNA sequencing
  • Massive parallel DNA sequencing
  • RNA sequencing
  • Reverse Transcription PCR (RT-PCR)
  • Quantitative analysis of gene expression
  • RNA-Dependent-DNA Polymerase
  • Transcription

Prokaryotic and Eukaryotic Transcription and Gene Expression Regulation

A comparison of prokaryotic and eukaryotic transcription processes involving RNA polymerases, promoter elements, and regulatory mechanisms such as activators, repressors, and the lac operon.

  • Prokaryotic transcription
  • Eukaryotic transcription
  • RNA polymerase
  • Sigma factors
  • General Transcription Factors
  • Promoter elements
  • Pre-initiation complex
  • Transcriptional activators
  • Transcriptional repressors
  • Enhancers
  • Silencers
  • Chromatin structure

Eukaryotic RNA Polymerase Structure and Function

Eukaryotic RNA polymerases consist of multiple polypeptides that transcribe various RNA types including mRNA, rRNA, tRNA, and snRNA.

  • RNA polymerase I
  • RNA polymerase II
  • RNA polymerase III
  • RPB1 polypeptide
  • Clamp domain
  • Bridge
  • Catalytic center
  • Carboxy-terminal domain (CTD)
  • RNA splicing
  • Transcription initiation
  • Transcription elongation
  • mRNA processing

RNA Polymerase II Promoters and Transcription Factors

RNA polymerase II genes are regulated by conserved basal promoter elements, promoter-proximal binding sites, distal enhancers or repressors, and chromatin structure through the assembly of general transcription factors.

  • RNA Polymerase II Promoters
  • General Transcription Factors
  • Core Promoter Sequences
  • TATA box
  • Initiator
  • TFIIB (TFIIB Recognition Element)
  • Preinitiation complex
  • TBP
  • TFIIB
  • TFIID
  • TFIIF
  • DNA helicases
  • Protein kinases
  • Elongation factors

Mechanisms of Eukaryotic Gene Control and Regulation

Epigenetics and Chromatin Structure Inheritance

Epigenetic memory of transcription is achieved through the reconstitution of chromatin structure and epigenetic marks like DNA methylation and histone modifications after the passage of the replication fork.

  • Epigenetic memory of transcription
  • DNA methylation
  • Histone methylation
  • Histone acetylation
  • Histone deacetylation
  • Heterochromatin
  • Euchromatin
  • Post-transcriptional gene regulation
  • Reconstitution of chromatin structure
  • De novo Methyltransferase
  • Histone post-translational modifications

Post-transcriptional Gene Control and Alternative Splicing

Post-transcriptional gene control involves pre-mRNA being capped, spliced, and polyadenylated before being exported to the cytoplasm through alternative splicing mechanisms.

  • Post-transcriptional Gene Control
  • Splicing
  • Spliceosome complex
  • Exons
  • Introns
  • SR proteins
  • snRNPs
  • Alternative Splicing
  • Alternative cleavage
  • Poly(A) sites

Antibody Production and Applications

Antibodies are natural immunoglobulins produced by B-lymphocytes to combat invading exogenous proteins called antigens.

  • Antibodies
  • Immunoglobulins
  • B-lymphocytes
  • Antigen
  • Monoclonal antibody
  • Polyclonal antibodies
  • Immuno-fluorescence
  • Immuno-precipitation
  • Chromatin Immunoprecipitation
  • ChIP-seq
  • RNA polymerase II

Chromatin Mechanisms of Transcriptional Repression and Activation

Molecular mechanisms of transcriptional repression and activation involve position-dependent and position-independent gene silencing through histone acetylation, deacetylation, and chromatin remodeling.

  • Heterochromatin and euchromatin
  • Histone de-acetylation
  • Lysine acetylation
  • S. cerevisiae telomere repression
  • Rap1 and Sir proteins
  • Promoter-dependent regulation
  • Chromatin-remodeling complexes
  • Mediator complex
  • Transcription activators and repressors
  • Bromo-domains

Regulatory Sequences in Protein-Coding Genes

Expression of eukaryotic genes is regulated through multiple control regions within DNA including promoter-proximal elements and enhancers.

  • Regulatory sequences
  • Transcriptional activators
  • Transcriptional repressors
  • Promoter-proximal elements
  • Enhancers
  • TATA/Initiator promoters
  • CpG island promoter
  • DNA-binding domain
  • Activation domains
  • Repression domains
  • Mediator
  • Histone Modifiers
  • Chromatin Remodelers
  • Deletion analysis

Motifs in DNA-Binding Domains

This topic discusses motifs in DNA-binding domains including zinc fingers, leucine zippers, and helix-loop-helix motifs used in combinatorial dimerization and transcriptional control.

  • Zinc Fingers
  • Leucine Zippers
  • Helix-loop-helix motif
  • Combinatorial dimerization
  • Transcription factors
  • DNA-binding domains
  • Transcriptional activators
  • Transcriptional repressors

Molecular Mechanisms of Chromatin and Transcription

Eukaryotic activators and repressors modulate gene expression by recruiting co-activator or co-repressor complexes that affect chromatin structure and the histone code.

  • Eukaryotic activators and repressors
  • Chromatin remodeling
  • Transcriptional activation and repression
  • Pioneer Transcription Factors
  • Nucleosome structure
  • Histones
  • Post-translational modifications
  • Histone code
  • Acetylation
  • Phosphorylation
  • Ubiquitination
  • Methylation

Overview of Eukaryotic Gene Control

Eukaryotic gene control involves epigenetic regulation and transcriptional control through chromatin-mediated mechanisms to execute precise developmental and tissue-specific programs.

  • Eukaryotic gene control
  • Epigenetic regulation
  • Chromatin-mediated regulation
  • Euchromatin
  • Heterochromatin
  • Transcriptional regulation
  • Transcriptional control

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