SCT I

Question 1

Define endosymbiosis.

Answer 1

During evolution, a eukaryotic organism, already equipped with adequate cytoskeleton and internal membrane systems engulfed a prokaryotic organism and they started to live together for their mutual benefit.

Mitochondria came about when an aerobic prokaryote performing oxidative phosphorylation was internalized.

Question 2

Define the central dogma.

Answer 2

Flow of genetic information is unidirectional and follows the path:

DNA&raquo_space; RNA&raquo_space; Protein&raquo_space; Property (Phenotype)

Question 3

Define transcription.

Answer 3

The process in the nucleus by which the genetic information contained in a template strand of DNA is copied into an RNA of complementary base sequence.

Transcription is carried out by an enzyme called RNA polymerase.

This is the first step in gene expression.

Question 4

Define an exon.

Answer 4

Are sequences of genes that code part of/entire gene product.

In eukaryotes, the exons are separated by non-coding sequences called introns.

During transcription, the introns are also transcribed as mRNAs, but are then cut out from the transcript before translation.

Question 5

Define an intron.

Answer 5

A nucleotide sequence in a gene that does not participate in encoding the protein product.

Introns occurring in eukaryotes are transcribed in mRNA, but are then removed from the transcript before translation.

Question 6

Define RNA maturation.

Answer 6

Post-transcriptional modifications in eukaryotic cells by which primary transcript RNA is converted into mature RNA.

The process includes three major steps:

1. Addition of a 5’ end capping
2. Addition of a 3’ poly-a-tail
3. RNA splicing

Question 7

Define RNA splicing.

Answer 7

A post-transcriptional process by which introns are removed and exons are covalently joined to one another as part of generating the mature messenger RNA.

Alternative splicing allows a single gene to code for multiple proteins.

Question 8

Define 5’ end capping.

Answer 8

A post-transcriptional process by which a specially altered nucleotide (7-methylguanosine triphosphate) is added to the 5’ end of the primary RNA transcripts to protect the mRNA from degradation by RNases.

It is part of RNA maturation.

Question 9

Define poly (A) tailing.

Answer 9

A post-transcriptional process by which ~ 200 adenine bases are attached to the 3’ end of the primary RNA transcripts.

It is a part of the RNA maturation process.

Poly(A)Tail is important for nuclear export, translation, and stability of mRNA

Question 10

Define translation, genetic code.

Answer 10

Process in which the cytoplasm by which a polypeptide chain is synthesized from an mRNA molecule containing the genetic information.

In cytoplasm, the ribosome reads the sequence of themRNA bases as triplets.

Genetic code describes the relationship between the base triplets and the corresponding amino acids in the polypeptide.

Question 11

Define heterotroph.

Answer 11

An organism that synthesizes ATP by degradation of organic material produced by other organisms.

ATP is used to produce the organism’s own organic compounds and to carry out other cellular process.

All animals, protozoans, fungi, and most bacteria are heterotrophs.

Question 12

Define autrotroph.

Answer 12

An organism which uses the sunlight as energy sources or produces ATP molecules by simple oxidative processes.

The produced ATP molecules are used to create its own organic compounds by biosynthesis or to carry out other processes of the cells.

Plants and certain bacteria are autotrophs.

Question 13

Define prokaryote.

Answer 13

Cell in which there is no real cell nucleus.

Genetic material of the cell is found in the cell plasma, and there are no cell membrane-bound organelles or cytoskeleton.

Bacteria and cyanobacteria are prokaryotes.

Question 14

Define eukaryote.

Answer 14

Living organisms that have a nucleus separated by a membrane from the cell plasma, have a structured internal membrane system and cytoskeleton.

Most of the organisms belong to this group.

Question 15

Define primary biogenic elements.

Answer 15

Include Carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and phosphorus (P).

They constitute 98% of the cells, which is explained by the fact that these elements form the bulk of the organic matter of living organisms.

H and O also form water.

Question 16

Define secondary biogenic elements.

Answer 16

The proportion of secondary biogenic elements in cells is about 2%. This group includes, among others, sulfur (S), iron (Fe), chlorine (Cl), sodium (Na), potassium (K), and calcium (Ca)

Question 17

Define organic substances.

Answer 17

Compounds formed by joining several carbon atoms. Organic substances of high energy content formed through metabolism in living organisms include carbohydrates, fats, and proteins.

Question 18

Define amino acids.

Answer 18

Molecules containing amino and carboxyl groups. In α-amino acids,s the amino group is attached to the α-carbon of the carboxylic acid chain. The proteins of most living cells are built from different α-amino acids.

Question 19

Define deoxyribonucleic acid (DNA).

Answer 19

Hereditary material of cells in constructed of two polynucleotide chains, which form a double-helix structure. In the nucleotides constituting the DNA, the sugar is deoxyribose and the nitrogenous bases are adenine (A), cytosine (C), guanine (G), and thymine (T).

In the helix, the two chains are bound together by hydrogen formed between the complementary bases. The base order of one strand clearly defines the other. DNA molecules differ inthe base sequence of the polynucleotide chains.

The role of DNA is the storage of information and its transmission into the daughter cells, as well as the indirect control of protein synthesis.

Question 20

Define ribonucleic acid (RNA).

Answer 20

A polymer molecule composed of ribonucleotide units. In the nucleotides constituting RNA, the sugar is ribose and the nitrogenous bases are adenine (A), cytosine (C), guanine (G) and uracil (U).

The major types of RNA molecules are messenger RNA (mRNA) , transfer RNA (tRNA), ribosomal RNA (rRNA), and smaller nuclear RNA (snRNA).

mRNA: transmit genetic information from DNA to proteins. mRNAs are produced upon the process of transcription.

rRNA: together with ribosomal proteins build the ribosomes. tRNAs are involved in translation, transporting amino acids to the ribosomes and decoding the genetic information from mRNA to proteins.

snRNA: are involved in mRNA splicing.

Other RNA types such as small interfering RNA (siRNA), microRNA, are involved in the regulation of gene expression.

RNA viruses have genomes composed of RNA

Question 21

Define cytoplasm (cell plasma).

Answer 21

A gelatinous material that fills the cells where the cell’s metabolic processes take place. Characteristic of all cells.

Question 22

Define lipids.

Answer 22

Organic compounds formed in living organisms with varying composition and structure that have a common feature that they are well soluble in apolar solvents. Hydrolyzable lipids include neutral fats and phospholipids.

Neutral fats are built from glycerol and three fatty acid molecules, while phospholipids also contain a polar part formed by phosphoric acid and an alcohol molecule.

Steroids and poly-isoprenoids belong to the group of nonhydrolyzable lipids.

Question 23

Define amphipathic molecule.

Answer 23

Molecules containing apolar and polar moieties are called amphipathic substances.

Such molecules are phospholipids. Amphipathic molecules in water are turned towards each other by their apolar (hydrophobic) hydrocarbon chains forming a micelle.

Question 24

Define polar, apolar.

Answer 24

Molecules or parts of molecules with unequal charge distribution are polar. Polar particles interact readily with water (hydrophilic). A molecule or a part of a molecule that does not undergo charge separation is apolar. Therefore, it does not enter into significant interaction with water.

Question 25

Define **cell cortex**.

Answer 25

A 3D protein network on the intracellular side of the cell membrane. it is composed primarily of actin filaments and actin-binding proteins, but in many cells, spectrin dimers are also important components. The net-like structure is anchored to transmembrane proteins by membrane proteins, They play a role in maintaining plasma membrane integrity, determining cell shape, cell motility and regulating the function of various membrane proteins. Disruption of their structure can lead to pathological conditions.

Question 26

Define **glycocalyx**.

Answer 26

A viscous coating layer on the extracellular side of the cell membrane composed of carbohydrates, mainly associated with proteins and less frequently with lipids. It plays a role in cell surface protection, cell adhesion and signal transduction. The composition of the glycocalyx helps immune cells to differentiate between normal, self and abnormal or non-self cells. It may help in the cellular entry of various pathogens. Increased levels can play a role in the development of resistance to anticancer therapies.

Question 27

Define the **asymmetry of the lipid bilayer**.

Answer 27

The lipid composition of the outer and inner layers of the cell membrane is different, which is a consequence of active translocation by flippase and floppase enzymes. The different geometrical structure of the major lipids components in the two layers contributes to the spontaneous curvature of membranes, which is necessary for the shaping of cells and vesicles. Phosphatidylserine is found only in the inner layer of the plasma membrane in intact cells, but in apoptotic cells it also appears in the outer layer and acts as an ‘eat-me’ signal resulting in the clearance of the dying cell by phagocytes.

Question 28

Define **scramblase, flippase, floppase**.

Answer 28

Enzyme proteins involved in the vertical asymmetry of lipid bilayers that facilitate the otherwise extremely slow spontaneous translocation of phospholipids between the two layers of the membrane. Scramblases facilitate the random shuffling of lipids between the two layers without energy investment, and are non-specific. Flippases translocate lipids inwards. Floppases translocate lipids outwards, they are active transporters (hydrolyze ATP to function) and are specific for their substrate.

Question 29

Define **lipid rafts**.

Answer 29

Are 10-200 nm diameter, cholesterol-, glyco- and sphingolipid-rich domains in the cell membrane, held together mostly by lipid-lipid and protein-lipid interactions. They are characterized by lower fluidity, increased thickness, rigidity and packing density compared to other regions of the membrane. They are able to assemble or segregate various proteins, dynamically regulating the quality and quantity of molecules interacting in them, and thus the efficiency of signal transduction processes. They play a role in membrane trafficking, cell adhesion and migration, synaptic transmission, cytoskeletal organization and pathogen entry into the cell.

Question 30

Define **signalosome**.

Answer 30

Protein complex of various signaling elements, whose association and activities are primarily regulated by protein-protein interactions. The composition and assembly of the signalosome dynamically changes in space and time and thereby ensures the specific and speed of signal transduction. High concentration of membrane proteins provided by lipid platforms as well as scaffold proteins can serve to enhance the interaction with downstream signaling molecules. Synapses and immune synapses are prominent examples.

Question 31

Define **endoplasmic reticulum (ER)**.

Answer 31

An intracellular membrane system characteristic of eukaryotic cells located in the cytoplasm near the nucleus. The surface of the rough ER (RER) binds ribosomes, which synthesize proteins that need to be in the membrane or in the interior (lumen) of the RER, where their final structure is obtained and are further modified. Then they are packaged into vesicles and transported to the Golgi apparatus. The smooth ER (SER) lacks ribosomes, it is important for metabolic reactions, including the synthesis of phospholipids and fatty acids, and various detoxification processes.

Question 32

Define **golgi complex**.

Answer 32

An organelle usually located near the nucleus, which is composed of flattened membrane disks, the cisternae, stacked upon each other, it has a polarized organization with various compartments characterized by different enzymes, the cis-Golgi network, the cis-, medial-, and trans-cisternae, and the trans-Golgi network. Its function is the post-translational modification of proteins coming from the endoplasmic reticulum, sorting and shipping of proteins to their intended destinations.

Question 33

Define **lysosome**.

Answer 33

A membrane-bound organelle with a variable appearance. It is the most important place where degradation of materials inside the cells takes place. The material to be degraded can be of intracellular and extracellular origin. Lysosomes contain acid hydrolases which can only work at an acidic pH generated by H⁺-ATPases located in their membrane. A primary lysosome contains only the enzymes, but not the materials to be digested. Secondary lysosomes contain both the acid hydrolases and the materials to be degraded.

Question 34

Define **peroxisome**.

Answer 34

A membrane-bound organelle, which may have an endosymbiotic origin and it is present in large amount in liver and kidney cells. The enzymes of peroxisomes are used in oxidative decomposition process. Catalase, another characteristic peroxisomal enzyme, neutralizes hydrogen-peroxide generated as a by-product in peroxisomal oxidation by converting it to water.

Question 35

Define **storage disease**.

Answer 35

Diseases characterized by lysosomal dysfunction arising as a result of an inherited mutation of one of the lysosomal enzymes. The lack of enzyme activity results in accumulation of undigested substrates in the lysosomes.

Question 36

Define the **lipid-water partitioning coefficient and its significance in transport**.

Answer 36

A quotient used for characterization of the hydrophobic character. It is the ratio of equilibrium concentrations of a molecule measured in contiguous lipid- and water phases: R = C_L / C_W The access of lipid-soluble/more hydrophobic molecules into the cell across the membrane is faster and such molecules reach higher intracellular concentrations.