BB2704 – Molecular and Cellular Biology

Flashcards from Molecular and Cellular Biology Lecture

What is DNA synthesis?

The molecular events that allow the assembly of new DNA strands.

What is DNA replication?

The synthesis of a semi-conservative DNA or the copying of double-stranded DNA, necessary for cell reproduction before cell division.

What are the phases of cell division?

G1 (growth phase-1), G0 (growth arrest), S (synthesis phase, DNA replication), G2 (growth phase-2), and M (Mitosis, cell division).

Describe the semi-conservative replication model.

Two parental strands separate and make a copy of itself, resulting in two daughter molecules, each with one old and one new strand after one round of replication.

What was the key finding of the Meselson-Stahl experiment in 1958?

DNA replication is semi-conservative.

What is the Origin of Replication (ORI)?

A unique DNA sequence of a replicon at which DNA replication is initiated and proceeds typically in a bidirectional fashion.

What is a Replication Fork?

The point at which replication occurs, and the site of the progressive unwinding of the double-stranded DNA and duplication of the template DNA.

Describe the structure of OriC in E.coli.

245bp in length with an AT-rich region (3 copies of 13bp repeats), DnaA boxes (5 copies of 9bp), and GATC methylation sites.

What are ARS1 and ARS307 in Saccharomyces cerevisiae?

Autonomously replicating sequences that allow plasmids to replicate autonomously, about 200bp in length with repeat elements.

What is the Origin Recognition Complex (ORC)?

A yeast protein isolated by Bell and Stillman in 1992 that binds to autonomously replicating sequences.

What are leading and lagging strands?

One strand is synthesized as a continuous molecule (leading), but the other is made in short sections or pieces (lagging).

What are Okazaki fragments?

Short, separated segments of DNA synthesized on the lagging strand, which are joined by DNA ligase.

What are ter sites in E.coli?

Termination sequences that serve as binding sites for the Tus terminator protein.

What does Tus protein do?

Blocks the progression of replication forks in specific directions.

Name the Proteins and Enzymes of DNA Replication?

DNA Polymerase, Helicase, Single-strand binding proteins, Topoisomerases/gyrases, and Ligase

What is the function of DNA Polymerase?

Catalyzes the formation of poly-nucleotide chains through the addition of nucleotides to the leading strand.

What is the function of Helicase?

Unwinds the DNA to allow polymerase access

What is the function of Single-strand binding proteins (SSB)?

Prevent the strands of parental DNA from re-forming a double helix.

What is the function of Topoisomerases/gyrases?

altering DNA conformation and relaxing tension in the DNA strands

What is the function of Ligase?

Joining up DNA ends after synthesis

In what direction does the new strand grow?

5' to 3' direction.

Name the Prokaryotic DNA polymerases?

DNA Polymerase I, DNA Polymerase II, DNA Polymerase III, DNA Polymerase IV, DNA Polymerase V

Name the Eukaryotic DNA polymerases?

DNA polymerase alpha(α), delta(𝝳), Epsilon(ε), beta(β), gamma(γ)

What is 3′-5’ exonuclease activity?

Acts as a proofreading mechanism, correcting polymerase mistakes by removing incorrectly matched bases.

What is the Klenow fragment?

A fragment of DNA polymerase I from E. coli comprising the polymerase unit and a domain with 3′ → 5′ exonuclease activity.

Why are Toposiomerases important?

Enzymes that alter the topological conformation of DNA, type I cut one strand and type II/ gyrases cut both strands.

Name the list of enzymes with their function?

Gyrase (relieves torsional strain), Helicase (unwinds DNA), Single Strand Binding Proteins (keep DNA single stranded), Primase (provides RNA primer), DNA Polymerase (Matches and joins nucleotides), and Ligase (joins adjacent DNA strands)

What is transcription?

The synthesis of single-strand (ss)RNA from a double-strand (ds)DNA template, occurring in the 5' to 3' direction.

Name the different types of RNA

tRNA, rRNA, snRNA, mRNA

List the key steps in transcription

Initiation, Elongation, Termination

Describe promoters

Sequences in the DNA just upstream of the RNA synthesis initiation site, containing conserved sequences required for specific binding of RNA polymerase.

List the two 6 bp elements are found around 10 and 35 bases before the start site of transcription?

-35 Sequence: TTGACA enhances binding of the σ factor of RNA polymerase and -10 Pribnow box: TATAAT important for DNA unwinding

Describe the core enzyme of the E.coli RNA polymerase

Core enzyme (2α, β, β’, ω) will begin transcription just about anywhere & Sigma factor (σ) provides specificity, is primarily responsible for promoter recognition.

Name the key steps in transcription

Initiation, Elongation, Termination

Name the types of termination events in E.coli

Rho independent (Intrinsic termination) & Rho-dependent

Describe Eukaryotic transcription

Whereas all genes are transcribed by a single RNA polymerase in bacteria, eukaryotic cells contain 3 different RNA polymerase that transcribe distinct classes of genes

Name 5 general transcription factor

5 different general transcription factor & Additional regulatory elements (enhancers, chromatin modifiers, silencers

List the 3 RNA polymerase in Eukarytoes

mRNA: RNA polymerase II, tRNA: RNA polymerase III, 5.8S, 18S, 28S: RNA Polymerase I, 5S: RNA polymerase III, scRNA + snRNA: RNA polymerase II + III

Describe Post-transcriptional Processing

5' capping, Splicing, and Polyadenylation

Name transcription termination models:

Anti-terminator model (allosteric model) & Torpedo model

What is Translation?

The mechanism of protein synthesis, turning mRNA into a peptide.

Name the nonpolar amino acids?

Glycine, Alanine, Saline, Leucine, Isoleucine, Methionine, Tryptophan, Phenylalanine + Proline

Name the polar amino acids?

Serine, Threonine, Cysteine, Tyrosine, Asparagine + Glutamine

Name the Electrically charged amino acids?

Aspartame acid, Glutamic acid, Lysine, Arginine + Histidine

How are peptides bonds formed?

Formed through condensation reaction between amine + carboxylic acid group, Meaning a molecule of H2O is released

What is the function of Ribosomes?

Translaction occurs at the ribosome & Ribosomes are composed of approximately 60% rRNA + 40% protein

Name the 3 processes of ribosomes in translation?

tRNA carries the amino acids & The tRNA molecule attaches at the aminoacyl (A) site, then is transferred into the peptidyl (P) site and then leaves by the exit (E) site

Describe Activation/Charging of tRNA?

Aminoacylation – the process of adding an aminoacyl group to a compound & Produces tRNA molecules with their CCA 3' ends covalently linked to an amino acid

List the 3steps how translation occurs?

Initiation, Elongation, Termination

Describe N-formyl-methionyl-tRNA (fMet-tRNA)

The initiator tRNA gains its modified amino acid in a 2 stage reaction & Stage 1: it is charged with the amino acid to generate Met-tRNAf

Describe initiation in bacteria

Requires:An mRNA, A ribosome, A specific initiator tRNA, & 3 initiation factors (IFs)

Describe Shine Dalgarno

Is a consensus sequence in the mRNA. It contains: The AUG initiation codon, A purine rich sequence at -10 on the mRNA pairs with the 16S rRNA of the 30S ribosome subunit

What's the different roles of Elongation Factors?

EF-Tu (EF-1A) – G protein that binds aminoacyl-tRNA and delivers it to the A site, EF-Ts (EF-1B) – Guanine-nucleotide exchange factor (GEF), & EF-G (EF-2) – G protein that promotes translocation of mRNA

Describe termination steps in translation

Peptide bond formation/translocation occurs until the stop (UGA) codon on the mRNA is reached. & Once release factors occupy the A site, peptidyl transferase catalyze transfer of the polypeptide to H2O.

State the eukaryotic factors in the transaltion termination

Eukaryotic release factor 1 (eRF1) recognizes the stop codon in the A site & eRF3 releases eRF1 from the ribosome, and several initiation factor, together with ABCE1-directed nucleotide hydrolysis, dismantle the complex, thus recycling ribosome subunits

Describe Gene expression regulation

Some poteins are required continuosly - the genes encoding them are expressed constitutively & Many other proteins are required for specific purposes – the genes are inducible under particular conditions

What is The Operon?

enzyme genes for the metabolic pathway, which are clustered together in functional complex under coordinate control, in bacteria

What are the components of the Lac operon?

The lac operon includes 3 structural genes (lacZ, lacY + lacA) that are transcribed in unison & The lacl gene regulates the operon by producing the lac repressor protein

Describe +ve control of Lac operon

+ve control is mediated by a substance that senses glucose levels inside the cell Cyclic AMP (cAMP) & +ve regulator protein called the catabolite activator protein (CAP), which is active only in the presence of cAMP

What are the potential control points in gene expression in Eukaryotes?

Genome (Chromatin remodelling), Transcriptional control (Turning on and off of mRNA formation), Post- Transcriptional control (Regulation of the processing of a pre-mRNA into a mature mRNA), Translational control (Regulation of the rate of initiation), Post-Translational control (protein activaity control)

What are euchromatin and heterochromatin?

Euchromatin is associated with an open chromatin conformation and Heterochromatin is more compact and refactory to factors that need to gain acess to DNA

Describe Cis-Acting elements

Core Promoter – where the general transcription factors and RNA polymerase assemble for the initiation of transcription; has sequence that is common to most genes Control elements – regions upstream of a gene that regulate transcription by binding certain proteins; have sequences that is unique to a particular gene

Name Trancriptional Factors interacting with cis-acting elements?

General TFs - bind at core promoter sites in association with RNA polymerase & Regulatory TFs - bind to various regulatory sites of particular genes; they either stimulate (transcriptional activators) or inhibit (transcriptional repressors) transcription of adjacent genes

Describe the Mechanism of Post-Transcriptional Regulation

At the level of RNA (RNA processing and stability) & At the level of translation (use of RNA-binding proteins, use of non-coding RNAs

Describe Regulatory RNAs

Noncoding RNAs (dsRNAs) can prevent the expression of specific genes through complementary base pairing & Small-interfering RNAs (siRNA), Micro-RNAs (miRNAs

What is the effect of inflammation on the body?

A controlled inflammatory response is benefical (provides protection against infection), but it can be determental if de-regulated (causes septic shock)

Describ Acute and Chronic Inflammation

Acute Inflammation - is a short-term response to injury, infections and irritation that usually results in healing & Chronic Inflammation - is a long-term response to more factors including viral infections stress, poor nutrition and processes related to aging.

Describe Transcription Factors

Transcription factors are proteins involved in the regulation of gene expression that bind to the regulatory regions upstream of genes and either facilitate or inhibit transcription

List the important mechanism in Programmed Cell Death (PCD)

Important mechanism in both development and homeostasis in adult tissue for removal of either superfluous, infected, transformed or damaged cells by activation of an intrinsic suicide program

Name the purpose of Cells division

Cells divide to reproduce and create identical copies of themselves & Cells divide to repair damaged or dead cells in multicellular organism

List the types of Cell division?

Binary Fission, Meiosis, Mitosis

What is the 2 main phases og the cell cycle?

Interphase (G1 + S + G2) + M phase (mitosis + cytokinesis)

List the 3 checkpoints in the cell cycle?

G1/S checkpoint: restriction point, G2/M checkpoint, M checkpoint: spindle checkpoint

What does G0 do in the cell cycle?

G0 (quiescent) - non-proliferative cells (neurons and heart muscles cells)

List the phases found in M phase of the cell cycle

Prophase, Metaphase, Anaphase, Telophase

List the Cell signalling processes:

Reception: Extracellular signal molecule Receptor protein & Transduction: Intracellular signaling protein - Effector proteins & Response: Activation of cellular response

Name direct types of extracellular signals

Via cell-cell contact, Gap junction signalling (cells communicate directly with their immediate neighbour through gap junctions), Contract-dependent signalling (involves contact between 2 cells, in which a ligand on 1 cell surface binds to a receptor on the other cell

Name In Direct types of extracellular signals

Paracrine signalling (water-soluble signalling molecules (cytokines or grow factors), Autocrine signalling (water-soluble signalling molecules), Electrical signalling (signals molecules (neurotransmitters), Endocrine signalling (hormones) signalling molecules

Name 3 major classes of receptors

G-protein-coupled receptor (GPCRs), Enzyme-linked receptors (ELRs), & Channel-linked receptors

What is the Extra cellular matrix

Non-cellular 3d structural network that support the cellular components to form tissue + organs

Describe the Components of ECM

Fibroblasts (Connective tissue), Collagens (Resist tension + stretchable), Elastin (Elastic protein), Fibronectin (Links components of the matrix to one another + to cells) , Glycosaminoglycans & Proteoglycans

List the 3 cell-cell junctions

Adherens junctions, Desmosomes, & Tight junctions

List the types Selectins?

L-selectins, E-selectins + P-selectins

What type of Intergins are bind to cell-adhesion molecules?

αL:β2, αM:β2, αX:β2 & α5:β1

What is the Extravasation

Integrin Beta-1 signaling, Secretion of MMPs + pro-angiogenic factors Migration, Force generation, Optimal tumour cell stiffness

What is the Cell migration

Requires matrix metalloprotease (MMPs) to remodel + degrade the ECM & Requires adhesion (integrins)

List the Function of Cytoskeleton cell skeleton?

Is a structural framework for the cell, Gives shape to the cells, Anchors organelles + attaches cell to surface, Is a contractile machinery to transport vesicles, organelles + chromosomes divide cytoplasm

Name 3 type cytoskeletons?

Actin (7nm diameter), Intermediate filament (10nm diameter), Microtubule (25nm diameter)

What type cellular architecture and membrane functions is there?

Cytoplasmic membrane, Nuclear envelope, Mitochondria, chloroplasts, peroxisomes , Endoplasmic reticulum (ER), Golgi apparatus & Vesicles

List the major membrane lipids?

Phosphoglyceride, Sphingolipids, Sterols (Cholesterol)

List the function of the different proteins transmembrane adhesion?

Junctions (cell connection), Enzymes (metabolic pathways), Transport (facilitated diffusion, active transport), Recognition (cell markers), Anchorage (cytoskeleton attachment), Signal transduction (hormone receptors)

Describe the 3 transmembrane segments in the transmembrane?

Pumps, Carriers, Channels

Describe transport carrier

Integral membrane proteins that transport substrates across membranes. Transport relies on existing solute gradients and is reversible. Types of carriers: Uniporters, Antiporters, Symporters

Describe Membrane physiology in action

Glucose transport (intestine), Sodium-chloride transport (kidney tubule) , Salt/water transport (respiratory tract)

Describe the mitochondria structe?

Outer membrane (surrounds intermembrane space) & Inner membrane (surrounds the matrix; site of electron transport chain and ATP synthase)

Name the Energy Generation Pathways

Glycolysis, Fatty Acid Oxidation, Citric Acid Cycle Krebs, Oxidative Phosphorylation

What are the main factors in cell communication

Through survival signlas, and through chemokines

Describe the role played by the nuclear import receptors

Recognize the nuclear localization signals