E1-1 blue words

Question 1

prokaryote

Answer 1

Major category of living cells distinguished by the absence
of a nucleus; includes the archaea and the eubacteria
(commonly called bacteria).

Question 2

eukaryote

Answer 2

An organism whose cells have a distinct nucleus and
cytoplasm.

Question 3

bacterium

Answer 3

Microscopic organism that is a member of one of the two
divisions of prokaryotes; some species cause disease.
The term is sometimes used to refer to any prokaryotic
microorganism, although the world of prokaryotes also
includes archaea, which are only distantly related to each
other. (See also archaeon.)

Question 4

plasma membrane

Answer 4

The protein-containing lipid bilayer that surrounds a living
cell.

Question 5

cytoplasm

Answer 5

Contents of a cell that are contained within its plasma membrane but, in the case of eukaryotic cells, outside the nucleus.

Question 6

cytosol

Answer 6

Contents of the main compartment of the cytoplasm,
excluding membrane-enclosed organelles such as
endoplasmic reticulum and mitochondria. The cell fraction
remaining after membranes, cytoskeletal components, and
other organelles have been removed.

Question 7

organelle

Answer 7

A discrete structure or subcompartment of a eukaryotic
cell that is specialized to carry out a particular function.
Examples include mitochondria and the Golgi apparatus.

Question 8

nucleus

Answer 8

In biology, refers to the prominent, rounded structure that
contains the DNA of a eukaryotic cell. In chemistry, refers to
the dense, positively charged center of an atom.

Question 9

nuclear envelope

Answer 9

Double membrane surrounding the nucleus. Consists of
outer and inner membranes, perforated by nuclear pores.

Question 10

nuclear pore

Answer 10

Channel through which selected large
molecules move between the nucleus
and the cytoplasm.

Question 11

chromosome

Answer 11

Long, threadlike structure composed of DNA and proteins
that carries the genetic information of an organism;
becomes visible as a distinct entity when a plant or animal
cell prepares to divide.

Question 12

endoplasmic reticulum

Answer 12

Labyrinthine membrane-enclosed
compartment in the cytoplasm of
eukaryotic cells where lipids and
proteins are made.

Question 13

lysosome

Answer 13

Membrane-enclosed organelle that breaks down worn-out
proteins and organelles and other waste materials, as well
as molecules taken up by endocytosis; contains digestive
enzymes that are typically most active at the acid pH found
inside these organelles.

Question 14

hydrolase

Answer 14

A general term for enzymes that catalyze a hydrolytic cleavage reaction. These enzymes break down molecules by adding water, which cleaves a covalent bond in the process​.

Question 15

mitochondrion

Answer 15

Membrane-enclosed organelle, about the size of a
bacterium, that carries out oxidative phosphorylation and
produces most of the ATP in eukaryotic cells.

Question 16

peptide bond

Answer 16

Covalent chemical bond between the
carbonyl group of one amino acid and the
amino group of a second amino acid.

Question 17

N-terminus

Answer 17

The end of a polypeptide chain that carries a free -amino
group.

Question 18

C-terminus

Answer 18

The end of a polypeptide chain that carries a free carboxyl
group (–COOH).

Question 19

polypeptide

Answer 19

A linear chain of amino acids linked together by peptide bonds. It is formed during the process of translation when amino acids are sequentially added to a growing chain. Polypeptides are the basic building blocks of proteins but are not necessarily functional molecules on their own.

Question 20

polypeptide backbone

Answer 20

Repeating sequence of the atoms (–N–C–C–) that form the core of a protein molecule and to which the amino acid side
chains are attached.

Question 21

disulfide bond

Answer 21

Covalent cross-link formed between the sulfhydryl groups
on two cysteine side chains; often used to reinforce a
secreted protein’s structure or to join two different proteins
together.

Question 22

hydrogen bond

Answer 22

A weak noncovalent interaction
between a positively charged
hydrogen atom in one molecule
and a negatively charged atom,
such as nitrogen or oxygen, in another; hydrogen bonds are
key to the structure and properties of water.

Question 23

ionic bond

Answer 23

Interaction formed when one atom donates electrons to
another; this transfer of electrons causes both atoms to
become electrically charged.

Question 24

Van der Waals forces

Answer 24

Weak noncovalent interaction, due to fluctuating electrical
charges, that comes into play between two atoms within a
short distance of each other.

Question 25

secondary structure

Answer 25

Regular local folding pattern of a polymeric molecule. In proteins, it refers to helices and sheets.

Question 26

tertiary structure

Answer 26

Complete three-dimensional structure of a fully folded protein.

Question 27

protein domain

Answer 27

Segment of a polypeptide chain that can fold into a compact, stable structure and that often carries out a specific function.

Question 28

enzyme

Answer 28

A protein that catalyzes a specific chemical reaction.

Question 29

active site

Answer 29

Region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation.

Question 30

induced fit model

Answer 30

This model proposes that when a substrate approaches an enzyme, the enzyme undergoes a conformational change to mold itself around the substrate. This adjustment ensures a tighter binding, which increases the specificity and catalytic efficiency of the enzyme. This dynamic interaction is different from the rigid "lock-and-key" model and emphasizes the enzyme's flexibility in facilitating chemical reactions​.

Question 31

conformational change

Answer 31

The specific three-dimensional shape or arrangement of atoms in a molecule, particularly in macromolecules like proteins and nucleic acids.

Question 32

kinase

Answer 32

An enzyme that catalyzes the transfer of a phosphate group from a high-energy molecule, such as ATP, to a specific substrate. This process, called phosphorylation, is a critical regulatory mechanism in cells, often altering the activity, function, or location of the substrate protein.

Question 33

phosphatase

Answer 33

An enzyme that catalyzes the removal of a phosphate group from a molecule, often from a protein. This process is called dephosphorylation. Protein phosphatases are highly specific enzymes that regulate various cellular functions by reversing the action of kinases and modifying the phosphorylation state of target proteins.

Question 34

phosphorylation

Answer 34

The biochemical process in which a phosphate group is covalently attached to a molecule, typically a protein, lipid, or sugar. This process is mediated by enzymes called kinases, using a high-energy phosphate donor such as ATP. Phosphorylation is reversible through the action of phosphatases, which remove phosphate groups, restoring the molecule to its unphosphorylated state.

Question 35

purines

Answer 35

A type of nitrogenous base characterized by a double-ring structure composed of a six-membered and a five-membered nitrogen-containing ring fused together. The two primary purines in biological systems are: Adenine (A) Guanine (G)

Question 36

pyrimidines

Answer 36

A type of nitrogenous base characterized by a single six-membered ring structure composed of carbon and nitrogen atoms. The three primary pyrimidines in biological systems are: Cytosine (C) – found in both DNA and RNA. Thymine (T) – found only in DNA. Uracil (U) – found only in RNA, replacing thymine.

Question 37

base

Answer 37

Molecule that accepts a proton when dissolved in water; also used to refer to the nitrogen-containing purines or pyrimidines in DNA and RNA.

Question 38

nucleotide

Answer 38

Basic building block of the nucleic acids, DNA and RNA; a nucleoside linked to a phosphate.

Question 39

dNTP

Answer 39

(deoxynucleoside triphosphate) is a molecule that serves as the building block for DNA synthesis. Each dNTP consists of three main components: Deoxyribose sugar: A five-carbon sugar lacking a hydroxyl group (-OH) at the 2' carbon, distinguishing it from ribose found in RNA. Nitrogenous base: Either a purine (adenine or guanine) or a pyrimidine (cytosine or thymine). Three phosphate groups: Connected in a chain, providing the energy needed for incorporation into the growing DNA strand.

Question 40

NTP

Answer 40

(nucleoside triphosphate) is a molecule that serves as the building block for RNA synthesis and plays various roles in cellular energy transfer and signaling. Each NTP consists of: Ribose sugar: A five-carbon sugar with a hydroxyl group (-OH) attached to the 2' carbon, distinguishing it from the deoxyribose in dNTPs. Nitrogenous base: Either a purine (adenine or guanine) or a pyrimidine (cytosine or uracil). Three phosphate groups: Connected in a chain, providing energy for biochemical reactions.

Question 41

phosphodiester bond

Answer 41

A chemical linkage between two molecules via a phosphate group. In biological contexts, it specifically refers to the bond that connects nucleotides in nucleic acids (DNA and RNA), forming the sugar-phosphate backbone. Structure of a Phosphodiester Bond: Components: A phosphate group (PO₄³⁻). The 3' hydroxyl group (-OH) of one nucleotide's sugar. The 5' hydroxyl group (-OH) of the adjacent nucleotide's sugar. Formation: During DNA or RNA synthesis, a condensation reaction occurs. The 5' phosphate group of a new nucleotide reacts with the 3' hydroxyl group of the last nucleotide in the chain, releasing a molecule of water (H₂O). This reaction is catalyzed by enzymes like DNA or RNA polymerases. Role in Nucleic Acids: Backbone structure: Phosphodiester bonds link the sugars of adjacent nucleotides, creating a repeating sugar-phosphate chain that forms the structural framework of DNA and RNA. Polarity: The bonds create a directionality, giving nucleic acids a 5' to 3' orientation, critical for replication and transcription. Phosphodiester bonds are stable under physiological conditions but can be hydrolyzed by specific enzymes, such as nucleases, to break down DNA or RNA.

Question 42

5'

Answer 42

(five-prime) refers to one end of a nucleic acid strand (DNA or RNA) and indicates the orientation of the sugar-phosphate backbone in the molecule. It is named after the fifth carbon of the sugar molecule in the nucleotide. Structure: In a nucleotide, the 5' carbon of the sugar (deoxyribose in DNA or ribose in RNA) is covalently attached to a phosphate group. The 5' end of a nucleic acid strand is the end where the phosphate group is free (not linked to another nucleotide). Significance in Nucleic Acids: Polarity: Nucleic acids have directionality, meaning one end is the 5' end, and the other is the 3' end (with a free hydroxyl group attached to the 3' carbon of the sugar). Replication and transcription: DNA and RNA synthesis occur in the 5' to 3' direction, meaning nucleotides are added to the free 3' end. Molecular biology applications: The 5' end often contains specific features, such as caps in eukaryotic mRNA, which protect the RNA from degradation and facilitate translation.

Question 43

3'

Answer 43

(three-prime) refers to one end of a nucleic acid strand (DNA or RNA) and indicates the orientation of the sugar-phosphate backbone in the molecule. It is named after the third carbon of the sugar molecule in the nucleotide. Structure: In a nucleotide, the 3' carbon of the sugar (deoxyribose in DNA or ribose in RNA) has a hydroxyl group (-OH) attached. The 3' end of a nucleic acid strand is the end where this hydroxyl group is free (not linked to another nucleotide via a phosphodiester bond). Significance in Nucleic Acids: Polarity: Nucleic acids have a 5' to 3' directionality, meaning the sequence and synthesis occur from the 5' end to the 3' end. DNA and RNA synthesis: During replication and transcription, new nucleotides are added to the free 3' hydroxyl group of the growing strand. Enzymatic function: Enzymes like DNA and RNA polymerases specifically require a free 3' hydroxyl group to catalyze the addition of nucleotides.

Question 44

PCR

Answer 44

Technique for amplifying selected regions of DNA by multiple cycles of DNA synthesis; can produce billions of copies of a given sequence in a matter of hours.

Question 45

primers

Answer 45

Short sequences of nucleotides (usually 18–30 bases long) that serve as the starting point for DNA or RNA synthesis. They are essential in various biological processes and laboratory techniques involving nucleic acid replication or amplification. Types and Features: DNA Primers: Typically used in laboratory techniques like polymerase chain reaction (PCR) or DNA sequencing. Synthesized as short, single-stranded oligonucleotides complementary to the target DNA sequence. RNA Primers: In natural DNA replication, RNA primers are synthesized by the enzyme primase to provide a free 3'-OH group for DNA polymerase to begin DNA synthesis. Functions: Provide a Starting Point: DNA and RNA polymerases cannot initiate synthesis de novo; they require a free 3' hydroxyl (-OH) group to add nucleotides. Specificity in PCR: DNA primers target specific sequences, ensuring amplification of the desired region of the DNA. Replication in Cells: RNA primers initiate the synthesis of Okazaki fragments during lagging-strand replication. Applications: PCR: Primers anneal to the template DNA, enabling exponential amplification of the target sequence. DNA Sequencing: Used to initiate the sequencing reaction. Gene Cloning: Primers with specific sequences can introduce mutations, restriction sites, or other modifications into the amplified product.

Question 46

taq polymerase

Answer 46

A heat-stable DNA polymerase enzyme derived from the bacterium Thermus aquaticus. It is widely used in PCR (polymerase chain reaction) to synthesize DNA at high temperatures during repeated cycles of denaturation, annealing, and extension.

Question 47

denaturation

Answer 47

The process in which a molecule loses its native structure, leading to the disruption of its functional state. This term is commonly used in the context of proteins and nucleic acids. In Proteins: Denaturation disrupts the secondary, tertiary, or quaternary structure of a protein, caused by external factors such as heat, pH changes, or chemical agents. The peptide bonds (primary structure) remain intact, but the protein loses its functional shape. In Nucleic Acids (e.g., DNA): Denaturation involves the separation of the two strands of a DNA double helix into single strands by breaking hydrogen bonds between complementary bases. This occurs during processes like PCR or under high-temperature conditions.

Question 48

annealing

Answer 48

The process in molecular biology where complementary single-stranded nucleic acids (e.g., DNA or RNA) bind together to form a double-stranded structure through base pairing. Contexts of Annealing: PCR (Polymerase Chain Reaction): Annealing occurs during the second step of PCR, where primers bind to their complementary sequences on the DNA template. This step is temperature-dependent, typically performed at 50–65°C, depending on the primer sequences. DNA/RNA Hybridization: Annealing describes the binding of complementary DNA or RNA strands, often used in techniques like Southern or Northern blotting. Key Features: Specificity: Annealing requires a high degree of sequence complementarity. Reversibility: If conditions (e.g., temperature or ionic strength) are changed, the strands may separate again (denature).

Question 49

extension

Answer 49

The process in molecular biology where a DNA polymerase enzyme synthesizes a complementary DNA strand by adding nucleotides to the 3' end of a primer. This step occurs after primer annealing and is essential for DNA replication and amplification. Context in PCR: Role: During the extension step of PCR, the polymerase extends the primer by incorporating deoxynucleoside triphosphates (dNTPs) complementary to the template strand. Temperature: Typically occurs at 72°C, the optimal temperature for Taq polymerase. Key Features: Extension proceeds in the 5' to 3' direction. The length of the newly synthesized strand depends on the duration of this step, which is proportional to the DNA fragment's size.

Question 50

gel electrophoresis

Answer 50

A laboratory technique used to separate molecules such as DNA, RNA, or proteins based on their size, charge, or shape. It relies on the movement of charged molecules through a gel matrix under the influence of an electric field. Key Steps: Preparation: A gel (commonly made of agarose for nucleic acids or polyacrylamide for proteins) is prepared and placed in an electrophoresis chamber filled with a buffer. Loading: Samples are mixed with a loading dye and added to wells in the gel. Separation: An electric current is applied. Negatively charged molecules (e.g., DNA) migrate toward the positive electrode (anode). Smaller molecules move faster and farther through the gel matrix compared to larger ones. Visualization: The separated molecules are stained (e.g., with ethidium bromide for DNA) and visualized under UV light or another detection method. Applications: DNA analysis: Verifying the size of PCR products or DNA fragments. Protein analysis: Identifying proteins by size using SDS-PAGE. RNA analysis: Assessing RNA integrity

Question 51

ladder

Answer 51

A solution containing a mixture of DNA, RNA, or protein molecules of known sizes or molecular weights. It is used as a reference or standard in gel electrophoresis to estimate the sizes of unknown samples. Key Features: Composition: DNA/RNA ladders consist of nucleic acid fragments of specific lengths (e.g., 100 bp, 500 bp, 1 kb). Protein ladders contain proteins with defined molecular weights (e.g., 10 kDa, 50 kDa). Purpose: The ladder is loaded into a designated lane on the gel alongside samples. After electrophoresis, the ladder provides a visual scale for determining the size or molecular weight of the molecules in the sample lanes. Visualization: DNA/RNA ladders are stained with dyes (e.g., ethidium bromide or SYBR Green). Protein ladders are pre-stained for direct visualization or stained after gel electrophoresis.

Question 52

conformational change

Answer 52

The alterations in the shape or structure of a molecule, often triggered by external factors such as binding to a ligand, changes in pH, temperature, or post-translational modifications.