cell bio memorise

name and briefly describe 2 non-covalent and 2 covalent interactions of protein

Non-covalent interactions

• Hydrogen bonds: Weak attractions between polar groups (e.g., between N–H and C=O groups) that help stabilize protein secondary and tertiary structure.

• Hydrophobic interactions: Nonpolar amino acid side chains cluster together in the protein interior, minimizing contact with water and stabilizing folding.

Covalent interactions

• Disulfide bonds: Strong covalent bonds formed between two cysteine residues, stabilizing protein structure, especially extracellular proteins.

• Peptide bonds: Covalent bonds between amino acids that form the primary structure of proteins by linking the amino group of one amino acid to the carboxyl group of another.

list all the functions of the lipids in the cells and give an example of each

membrane lipids: phospholipids

energy storage: triglycerides

signaling molecules: steroid hormones

membrane signaling and recognition: glycolipids

precursors: cholesterol

define the terms: homologous chromosomes, sister chromatids, telomere, nucleosome

• Homologous chromosomes: A pair of chromosomes that have the same genes in the same positions but may carry different alleles.

• Sister chromatids: Two identical copies of a single replicated chromosome, held together at the centromere after DNA replication.

• Telomere: Repetitive DNA sequences at the ends of chromosomes that protect them from degradation and prevent loss of genetic information during replication.

• Nucleosome: The basic unit of chromatin, consisting of DNA wrapped around a core of histone proteins.

describe briefly the double stranded breakage repair systems of DNA

• Non-homologous end joining (NHEJ)

  • The broken DNA ends are directly rejoined without a template.

• Homologous recombination (HR)

  • Uses a sister chromatid as a template to accurately repair the break.

compare nuclear and mitochondrial genomes

Feature	Nuclear genome	Mitochondrial genome
Location	Nucleus	Mitochondria
Structure	Linear chromosomes	Circular DNA
Size	Large	Small
Replication	Occurs in S phase, cell cycle–controlled	Independent of cell cycle, continuous replication
Function	Encodes most cellular proteins	Encodes genes mainly for oxidative phosphorylation and mitochondrial translation machinery

describe briefly the translation elongation in eukaryotes (components, steps, etc.)

components

• Ribosome (80S): composed of 40S and 60S

• mRNA

• tRNAs

• Elongation factors

• A, P, E sites on the ribosome

• GTP

Steps of elongation

1. Codon recognition (A-site entry)

2. Peptide bond formation

3. Translocation

4. Exit of empty tRNA

define promoter, how is it recognized in eukaryotes and in prokaryotes?

definition: a specific DNA sequence located upstream of a gene that serves as the binding site for RNA polymerase and transcription factors, initiating transcription.

Recognition in prokaryotes: RNA polymerase binds directly to the promoter with the help of a sigma (σ) factor.

Recognition in eukaryotes: RNA polymerase cannot bind directly to the promoter; requires multiple general transcription factors (GTFs)

describe the process of eukaryotic ribosome biogenesis

1. rRNA transcription: preRNA

2. Processing of rRNA

   • The pre-rRNA is chemically modified and cleaved into mature rRNA species with the help of small nucleolar RNAs (snoRNAs) and proteins.

3. Ribosomal protein synthesis in the cytoplasm and import to the nucleus

4. Assembly of ribosomal subunits

   • rRNAs combine with ribosomal proteins to form the small (40S) and large (60S) ribosomal subunits in the nucleolus.

5. Export to cytoplasm

   • The pre-40S and pre-60S subunits are exported through nuclear pore complexes to the cytoplasm.

6. Final maturation

list the macromolecules of the cells and their building blocks

proteins: amino acids; nucleic acids: nucleotides; carbohydrates: monosaccharides; lipids: fatty acids + glycerol

list the four major targets of antibiotics

cell wall synthesis; cell membrane; protein synthesis; nucleic acid synthesis

explain the essence of eukaryotic gene expression regulation, and list all the ways of it

definition: eukaryotic gene expression is tightly controlled to ensure that specific genes are expressed only in the right cells, at the right time, and in the right amount.

levels: transcriptional, post-transcriptional, translational, post-translational

list the steps of eukaryotic mRNA maturation and describe one of them in details

1. 5′ capping: A modified guanine nucleotide is added to the 5′ end of the pre-mRNA via a 5′–5′ triphosphate linkage. This cap protects the mRNA from degradation, helps in nuclear export, and is essential for recognition by the ribosome during translation initiation.

2. Splicing

3. addition of poly-A tail

list all the components of intrinsic apoptosis

cell stress signal, Bcl-2 family proteins, mitochondria, cytochrome c, APAF-1, ATP, caspase 9, executioner caspase

describe the steps of southern blotting (say how you can visualize it as well)

1. DNA extraction + restriction digestion: DNA is cut into fragments using restriction enzymes.

2. Gel electrophoresis: Fragments are separated by size in a gel.

3. Denaturation: DNA is made single-stranded.

4. Blotting (transfer): DNA is transferred onto a membrane.

5. Hybridization: A labeled complementary DNA probe binds to the target sequence.

6. Washing: Unbound probe is removed.

7. Detection (visualization): Signal from the probe is detected (radioactive, fluorescent, or chemiluminescent), showing specific DNA bands.

name the 2 ways of protein degradation using cell cycle regulation

1. Ubiquitin–proteasome system

   • Intracellular proteins are tagged with ubiquitin molecules and then recognized and broken down by the proteasome, a large protein complex that degrades them into small peptides.

   • Mainly degrades short-lived, misfolded, or regulatory proteins in the cytosol and nucleus.

2. Lysosomal degradation

   • Proteins are delivered to the lysosome, where they are broken down by acidic hydrolase enzymes.

   • Occurs via endocytosis, autophagy, or vesicular transport and mainly degrades long-lived proteins, organelles, and extracellular material.

name 2 effectors and 2 secondary messenger molecules of mammalian primary G proteins

effectors: adenylyl cyclase, phospholipase C

secondary messengers: cAMP, IP₃

Compare the main types of protein transport

Type of protein transport	Main destination	Mechanism	Co-translational or Post-translational
Gated transport	Nucleus ↔ cytoplasm	Transport through nuclear pore complexes (NPCs)	Post-translational
Transmembrane transport into ER	Endoplasmic reticulum	Passage through ER translocon (Sec61)	Co-translational
Transmembrane transport into mitochondria	Mitochondria	TOM/TIM translocators	Post-translational
Vesicular transport	ER ↔ Golgi ↔ lysosome/plasma membrane	Membrane-bound vesicles	Post-translational
Protein export from nucleus	Nucleus → cytoplasm	Export through nuclear pore complexes	Post-translational

describe the components of the regulation of the lac operon

1. Structural genes

• lacZ

• lacY

• lacA

2. Regulatory elements

• Promoter (P)

• Operator (O)

• lacI gene

3. Regulatory proteins and signals

• Lac repressor

• Allolactose

• CAP

• cAMP

what are the components and the functions of the cytoskeleton

Components of the cytoskeleton

1. Microfilaments (actin filaments)

2. Intermediate filaments

3. Microtubules

Functions of the cytoskeleton

• Cell shape and structural support

• Cell movement

• Intracellular transport

• Anchoring of organelles

• Cell adhesion and tissue organization

describe the main characteristics of gel electrophoresis and list the types of them

characteristics:

• Separates DNA, RNA, or proteins based on size or charge

• Molecules move through a gel matrix under an electric field.

• Negatively charged molecules migrate toward the positive electrode.

• Smaller molecules move faster and farther than larger ones.

• Produces a band pattern that allows comparison and analysis of samples.

Types:

• Agarose gel electrophoresis.

• Polyacrylamide gel electrophoresis (PAGE)

• SDS-PAGE

• Native PAGE

• Capillary electrophoresis

give 4 common features of tumor cells and describe one of them in detail

• Uncontrolled proliferation: they continue to divide even in the absence of growth signals and can bypass checkpoints → continuous and excessive cell division, forming a growing tumor mass.

• Resistance to apoptosis

• Genomic instability

• Ability to invade and metastasize

compare the functions and effects of siRNA and miRNA

Feature	siRNA	miRNA
Function	Targets a specific mRNA for gene silencing	Fine-tunes expression of multiple genes
Effect	Causes complete degradation of target mRNA	Causes translation inhibition and/or partial mRNA degradation

what is amino acid activation? Why is it important?

definition: the process in which an amino acid is attached to its specific tRNA by an enzyme called aminoacyl-tRNA synthetase, forming an aminoacyl-tRNA

importance:

• Ensures correct matching of amino acids with their corresponding tRNAs, maintaining translation accuracy.

• Provides activated amino acids needed for peptide bond formation during protein synthesis.

• Is essential for efficient and faithful translation of the genetic code into proteins.

name 2 unicellular modern organisms. What are the advantages and disadvantages of them?

E.coli; amoeba

adv.: rapid reproduction, simple structures

disadv.: no structural complexity, no division of labour