350 Pre-req pre-test study guide F23

**Describe the evolutionary relationships between the 3 domains of life (*****Bacteria*****,** ***Archaea*****, and** ***Eukarya*****).**

The three main branches of life, which include Bacteria, Archaea, and Eukarya. These domains represent the major groups of organisms based on evolutionary relationships.

Endosymbiotic theory

A theory that states that the mitochondria and chloroplasts were once free-living bacteria that were engulfed by a proto-eukaryote host cell- becoming a true eukaryotic cell.

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Evidence:

* Mitochondria and chloroplasts have their own DNA
* Mitochondria and chloroplasts can replicate independently
* Mitochondria and chloroplasts have their own ribosomes
* Mitochondria and chloroplasts have double membranes
* Mitochondria and chloroplasts are similar in size to bacteria
* Mitochondria and chloroplasts have similar metabolic processes to bacteria

Describe the levels of organization (structural and taxonomic) among life and living things. (how do we  classify living organisms?)

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What is binomial nomenclature?

The system of naming organisms using two parts: the genus and the specific epithet. This system was developed by Carl Linnaeus and is used to provide a unique scientific name for each species.

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Remember: Genus is capitalized, while the specific epithet is not. All names should be italicized.

What is a **Phylogenetic Tree?**

A phylogenetic tree is a diagram that shows the possible evolutionary relationships between different organisms or species. It illustrates the branching patterns of common ancestors (using either structural traits or genomic trends (or both) and can be used to determine the relatedness and evolutionary history/branching of different groups.

Remember Acids and Bases?

Acids are substances that have a high concentration of hydrogen ions (H+) and a low pH (1-6). (This also corresponds with a low level of Hydroxide ions (OH-).

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Bases, on the other hand, have a low concentration of hydrogen ions and a high pH (7-14). These commonly have a higher concentration of Hydroxide ions.

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pH Scale: (-log H+)- The pH scale serves to measure the concentration of hydrogen ions (H+) within a solution and, thus, the acidity or basicity of a substance. Lower numbers are more acidic, and higher numbers are more basic.

What are hydrophilic and hydrophobic substances? What are the differences between the two?

Hydrophilic (“water-loving”) substances are molecules that can mix or dissolve in water, while hydrophobic (“fear water”) substances repel or do not mix with water.

Hydrophilic molecules are typically polar and can form hydrogen bonds with water, allowing them to easily surround themselves with water and dissolve into a solution.

Hydrophobic molecules are commonly nonpolar and do not form hydrogen bonds with water.

What is a monomer? What about a polymer? How are they related?

A monomer is a single unit or molecule that can join together with other monomers to form a larger, more complex molecule called a polymer.

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Polymers are made up of repeating units of monomers.

phylogenetic tree

A diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. This is used to track the possible evolutionary relationships between organisms. Remember: These are just educated guesses using the maximum amount of parsimony (least number of logical jumps)

binomial nomenclature

System of two-part scientific names for an organism, which includes genus and specific epithet; always written in Latin(ish) and italicized. Remember: First part (genus) is capitalized while the specific epithet is not

polar molecule

Molecules that possess regions of positive and negative charge within itself.

polar covalent bond

Type of covalent bond that forms as a result of unequal electron sharing, resulting in creating slightly positive and negative charged molecule regions.

nonpolar molecule

Molecules that do not have any electrical charges or partial charges.

Hydrophobic

Do not mix with water (nonpolar substance) "fear of water"

Hydrophilic

Mix with water (polar substance); "water-loving"

adenosine triphosphate (ATP)

The cell's main energy-carrying molecule that transfers energy for specific reactions within the cell. Composed of an adenine base, ribose sugar, and three phosphate groups.

dehydration (condensation) reaction

A reaction between two molecules, monomers, or macromolecules that form a bond together and creates a molecule of water. This is commonly called dehydration synthesis.

hydrolysis reaction

A reaction of 1 polymer that breaks its bond by using water to separate the molecules. Causing a negative net loss of water.

Carbohydrate

One of the four macromolecules that makeup a cell that used to store sugars t break down later for energy.

Monosaccharide

Simplest form of sugars which generally are glucose. Has 3-7 carbons with aldehyde group attached

Disaccharide

Multiple monosaccharides when they form a bond together through a dehydration (condensation) reaction

glycosidic bond

A covalent bond between two sugar molecules or sugar and something else.

N terminus

The start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. N Terminus\= New Terminus

C terminus

The end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). C terminus\= Closing Terminus

primary structure

Amino acids' unique sequence in a polypeptide chain at the lowest level of structure and organization of proteins.

secondary structure

The folding of polypeptide chains to form a secondary structure of α-helix and β-pleated sheet through hydrogen bonding

tertiary structure

The 3D structure of proteins when folding occurs further to create several side chains bonds like disulfide bonds, hydrogen bonds, ionic bonds, and hydrophobic bonds.

quaternary structure

Basically multiple tertiary structures that are intertwined together showing different structures usually coated in different colors in diagrams.

denature/denaturation

The process of breaking bonds to fix malfunctioning proteins or other molecules from its original state. (Allows unfolding of proteins)

alpha helix

Type of secondary protein structure formed by folding the polypeptide into a helix shape with hydrogen bonds stabilizing the structure

beta pleated sheet

Secondary structure in proteins in which hydrogen bonding forms "pleats" between atoms on the polypeptide chain's backbone

disulfide bond

A type of bond that allows folding of protein structure through two sulfide molecules interacting as a side chain.

nucleic acid

Biological macromolecule that carries the cell's genetic blueprint and carries instructions for the cell's functioning

Nucleotide

Monomer of nucleic acids; contains a pentose sugar, one or more phosphate groups, and a nitrogenous base

sugar phosphate backbone

DNA's backbone that holds all nucleotides together to form high-energy strands of nucleotides bonded together.

deoxyribonucleic acid (DNA)

Double-helical molecule that carries the cell's hereditary information missing a -OH group on its 2' carbon with a H instead

ribonucleic acid (RNA)

Single-stranded, often internally base-paired molecule that is involved in protein synthesis and has -OH group at its 2' carbon.

nitrogenous base

A, T, C, G, U, a component of a nucleotide which is glycosidic bonded to a sugar molecule.

deoxyribose sugar

A pentose sugar that lacks -OH group on its 2' carbon and acts as a component of a nucleotide.

ribose sugar

A pentose sugar that has -OH group on its 2' carbon and acts as a component of a nucleotide for RNA.

Phosphate

Component of a nucleotide that builds up the backbone of DNA or RNA strands which has energy in this group.

phosphodiester bond

Linkage covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking neighboring nucleotides' two pentose sugars.

fluid mosaic model

Describes the plasma membrane's structure as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to proteins or lipids, respectively), resulting in a fluid character (fluidity).

Phospholipid

A lipid containing a phosphate group within its structure. More specifically, two fatty acid chains connected to a glycerol backbone that is attached to a phosphate group and a polar head.

saturated fatty acid

A type of fatty acid that is saturated with high amounts of C-H bonds (ex: butter). These can be packed tightly together as they are all straight hydrocarbon bonds.

unsaturated fatty acid

A type of fatty acid that is unsaturated (less carbon to hydrogen bonds \= more carbon to carbon bonds) EX: Olive oil. These have "bent" arms, meaning they cannot be as tightly packed together and thus remain more fluid.

integral protein

Protein integrated into the membrane structure that interacts extensively with the membrane lipids' hydrocarbon chains and often spans the membrane.

peripheral protein

Protein at the plasma membrane's surface either on its exterior or interior side.

*lipid-linked protein

Lipid-anchored proteins are proteins located on the surface of the cell membrane that are covalently attached to lipids embedded within the cell membrane.

transport protein

Membrane protein that facilitates a substance's passage across a membrane by binding it.

transmembrane protein

Protein that goes completely through the plasma membrane to allow a channel of molecules to pass from extracellular to intracellular or vice versa.

membrane leaflet

Glycoprotein on top of the plasma membrane on the extracellular surface.

central dogma of biology

States that genes within DNA specify the sequence of mRNAs, which in turn specify the sequence of proteins. DNA → RNA → Protein

Transcription

Process through which messenger RNA forms from a template of DNA

Translation

Process through which a protein is formed from a template of mRNA

Protein

Biological macromolecule composed of one or more amino acid chains

RNA polymerase

RNA primase, synthesizes an RNA segment that is about five to ten nucleotides long and complementary to the template DNA.

transcription factor

Protein that binds to the DNA at the promoter or enhancer region and that influences transcription of a gene

messenger RNA (mRNA)

RNA that carries information from DNA to ribosomes during protein synthesis

ribosomal RNA (rRNA)

RNA that ensures the proper alignment of the mRNA and the ribosomes during protein synthesis and catalyzes forming the peptide linkage

transfer RNA (tRNA)

RNA that carries activated amino acids to the site of protein synthesis on the ribosome

Splicing

Process of removing introns and reconnecting exons in a pre-mRNA

poly-A tail

A series of adenine nucleotides that are attached to the 3' end of an mRNA to protect the end from degradation of mRNA.

5' cap (7-methylguanosine cap)

A stabilizing structure to allow for stability in an mRNA from degrading.

Introns

Genes that are not involved within the process of protein coding.

Exons

Genes that correspond to protein coding sequences

Ribosomes

Cellular structures associated with protein synthesis

peptide bond

Bond formed between two amino acids by a dehydration reaction

amino acid

A protein's monomer; has a central carbon or alpha carbon to which an amino group, a carboxyl group, a hydrogen, and an R group or side chain is attached; the R group is different for all 20 common amino acids

Codon

A group of three adjacent nucleotides in an mRNA molecule that specifies either one amino acid in a polypeptide chain or the termination of polypeptide synthesis

start codon

Codon in mRNA which has instructions to begin translation that signals tRNA to synthesis proteins

stop codon

One of three codons in mRNA for which no normal tRNA molecule exists and that signals the termination of polypeptide synthesis

Methionine

AUG codon used to start sequence of translation as seen in the Genetic code table

Anti-codon

A group of three adjacent nucleotides in a tRNA molecule that pairs with a codon in mRNA by complementary base pairing

DNA gel electrophoresis

A technique used to separate different bands of DNA length through splitting fragment by splicing them to observe genes of interest

*marker or ladder

A specific area of the genome detected to see if it can be manipulated or observed

DNA replication

Process done to produce more copies of DNA helices from a parental or template strand for the process of mitosis

replication bubble

The unwind and open region of the double helix that forms a bubble in the process of replicating another strand

origin of replication (ori)

The location where DNA replication begins in the center of the replication fork

replication fork

Y-shaped structure formed during the initiation of replication

DNA polymerase

Molecule used to add nucleotides in the 5' to 3' direction or remove the RNA primase on the lagging strand

Primer

Short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides

template strand

The DNA strand used to replicate another strand from by using it to encode another strand with complementary nitrogenous bases or the strand used for transcription

Pyrophosphate

Two phosphate groups linked by esterification. Released in many of the synthetic steps involving nucleotide triphosphates

*3' OH (3' hydroxyl)

The 3' end of the DNA strand which can terminate the extension of the strand

nucleoside triphosphate

A nucleoside containing a nitrogenous base bound to a 5-carbon sugar (either ribose or deoxyribose), with three phosphate groups bound to the sugar

helicase

Protein that unzips the double helix by breaking hydrogen bonds between nitrogenous bases

primase

Proteins that allow RNA synthesis to occur through RNA primers which can allow DNA polymerase to attach and extend off of

ligase

Protein that glues Okazaki fragments together to create one continuous strand

Topoisomerase

Enzyme that helps relieve the strain on DNA when unwinding by causing breaks and then resealing the DNA

sliding clamp

Protein that helps to hold the DNA polymerase in place when nucleotides are being added

single strand-binding proteins

Proteins that bind to single-stranded DNA to prevent DNA from rewinding back

leading strand

Strand of DNA that extends 5' to 3' from the replication fork which has continuous development since it only needs one primase

lagging strand

Strand of DNA that extends 3' to 5' from the replication fork which has Okazaki fragments and discontinuous replication and needs ligase to glue fragments together

continuous DNA replication

Replication of a new strand from a template strand in the direction 5' to 3' that is not interrupted by primases

Okazaki fragments

Fragments of DNA of the lagging strand that need to be ligated together since primase interrupts their replication

discontinuous DNA replication

3' to 5' strand that cannot be replicated in a constant manner that is interrupted by primase in its path

Operon

Proteins that are needed for a specific function, or that are involved in the same biochemical pathway, are encoded together in blocks (programs certain proteins to be produced trp and lac)

Gene

The basic unit of heredity represented by a specific DNA segment that codes for a functional molecule

Chromosome

Structure within the nucleus that comprises chromatin that contains DNA, the hereditary material