Biology Concept Map

Carbohydrates are a biomolecule that works as a fast source of energy for organisms and also serves as a building material. Carbohydrates are made up of Carbon, Hydrogen, and Oxygen molecules.

Monosaccharides are simple sugars. They can be Glucose, Galactose, or Fructose

Glucose is a simple sugar that contains 6 carbons. Glucose can either be a chain or ring structure.

The ring structure of Glucose has two forms, the Alpha (α) or beta (β) structure.

The beta ring has the OH group above the Carbon. 

The Alpha ring has the OH group below the Carbon.

Lipids, like fats, oils, butter, and cholesterol, are a form of long-term energy.

Triglycerol is a Lipid that is made up of a glycerol back bone and three fatty acids.

Fatty Acids can either be saturated or unsaturated. Saturated fats only consist of single-bonded carbons and are typically solid at room temperature. Unsaturated fats have two carbons double bonded to each other and are usually liquid at room temperature.

Phospholipids are amphipathic molecules which means they have both hydrophilic and hydrophobic parts. The head of a phospholipid is hydrophilic since it is polar like water. The tail is nonpolar, so it is hydrophobic.

Proteins hold many functions including Enzymes, Defense, Storage, Transport, hormones, Receptors, Contration and motor, or structure.

Polypeptides are chains of amino acids bonded together after dehydration/condensation to form peptide bonds. Polypeptides have two ends, the C-terminus and the N-terminus. The C-terminus is the end that has the Carboxyl group. The N-terminus is the end that has the Amino group.

The primary structure is a long chain of amino acids bonded together through peptide bonds.

The secondary structure can either be Alpha helices or beta-pleated sheets that are held together by hydrogen bonding between the double-bonded O in carboxyl and the H in amino.

The tertiary structure occurs when the polypeptides in the secondary structure fold due to interactions between the R-groups. The R-group interactions can either be hydrophobic interactions (between nonpolar groups), Hydrogen bonding (usually between polar groups), ionic bonding (between charged groups), or a covalent bond (only between two CH2SH groups that form disulfide bonds).

The quaternary structure is a result of multiple tertiary structures held together by interchain interactions.

Nucleic Acids are polymers made up of Nucleotides. Nucleic acids are formed through dehydration/condensation which results in phosphodiester bonds/linkages between Nucleotides. Nucleic Acid runs from 5'-3' (carbon number).

DNA, Deoxyribonucleic acid, provides directions for its own replication. DNA also directs the synthesis of mRNA, and with that, it controls protein synthesis (also known as gene expression).

Nitrogenous bases are either pyrimidines or purines. Pyrimidines are composed of just a single ring. Purines are composed of two rings. Nitrogenous bases in DNA hydrogen bond with their complementary base which allows DNA to hold the double-stranded helix shape. Adenine pairs with Thymine (or Uracil), and Guanine pairs with Cytosine.

Cells where most of the DNA is in the nucleus.

The nucleus is an organelle that is bounded by a double membrane. DNA is organized into discrete units called chromosomes inside the nucleus. Each chromosome is one long DNA molecule associated with proteins. The DNA and proteins of chromosomes together are called chromatin. Chromatin condenses to form discrete chromosomes as a cell prepares to divide.

The nuclear envelope is the double membrane that surrounds the nucleus. It is perforated by pores and is continuous with the endoplasmic reticulum.

Centrosomes are located near the nucleus and are referred to as the ‘microtubule organizing center’. There is a pair of centrioles within the centrosome.

Centrioles are what form the spindle fibers that help chromosome movement during cell division.

The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis. There is usually one or more of these in the nucleus.

The cytoskeleton extends throughout the cell. Its main functions are to help support the cell and maintain its shape and provide anchorage for many organelles and molecules. There are 3 different parts to the cytoskeleton. Microtubules are hollow tubes made of 13 columns of tubulin molecules. Its functions are maintenance of cell shape, cell motility, chromosome movements in cell division, and organelle movements. Microfilaments are two intertwined strands of actin. Its functions are maintenance of cell shape, changes in cell shape, muscle contraction, cytoplasmic streaming, cell motility, and cell division. Intermediate filaments are fibrous proteins of the keratin family supercoiled into thicker cables. Its main functions are the maintenance of cell shape, anchorage of the nucleus, and certain other organelles, and formation of the nuclear lamina. Intermediate filaments are more permanent. They don't assemble/disassemble as microtubules and microfilaments do.

Cilia are very similar to flagella, but they are only found in eukaryotic cells. The structure is the same. It consists of a group of microtubules sheathed by the plasma membrane, a basal body that anchors it to the cell, and a motor protein called dynein, which drives the bending movements. The only difference between the two is that cilia occur in large numbers on cell surfaces.

The golgi apparatus is made of different sacs. One side receives vesicles from the endoplasmic reticulum while the other side releases vesicles after making changes to them.

The smooth endoplasmic reticulum lacks ribosomes attached to it. Its functions are to synthesize lipids, metabolize carbs, detoxify drugs and poisons, and store calcium ions.

The surface of the rough endoplasmic reticulum is studded with ribosomes. Its functions are secreting glycoproteins and distributing transport vesicles, and it is considered to be a membrane factory for the cell.

Cytoplasm is the fluid inside a cell where most chemical reactions take place.

Chloroplasts are a type of plastid found in plant cells. It contains an inner and outer membrane as well as other membranous sacs called thylakoids. Thylakoids are stacked to form a granum. Stroma is the fluid inside the chloroplast that surrounds the granum.

The central vacuole serves as a repository for inorganic ions, including potassium and chloride. They are the largest component found in many mature plant cells. There is a solution inside called cell sap that stores the inorganic ions. They are important to cell growth because the cell grows as they absorb water.

The mitochondria are the site for several reactions involved in cellular respiration to make ATP. Their function is why they are known as the 'powerhouse of the cell'. They have a double membrane. An outer membrane and an inner membrane that folded into cristae. The space between the inner and outer membrane is called the intermembrane space and the space inside mitochondria is called the matrix. The matrix contains DNA and free ribosomes, and it is the location of the catalyzation of some of the metabolic steps of cellular respiration.

Peroxisomes are specialized metabolic compartments bounded by a single membrane and are packed with enzymes. The chemical reactions that occur in this organelle extract hydrogen atoms from certain molecules and add these to oxygen to form hydrogen peroxide which is then converted to water.

Lysosomes are packed with enzymes that promote the hydrolysis of biological molecules (enzymes needed to break covalent bonds). They are acid hydrolases, meaning they function in acid. Membrane proteins called H+ pumps pump H+ to help maintain a low pH inside lysosomes so the enzymes are functional. There are 2 ways lysosomes are able to get the food particles into the cell. One way is through phagocytosis: when the cell extends its membrane to engulf a foreign cell or food particle. A part of the membrane pinches off forming a food vacuole inside the cell. The vacuole fuses with the lysosome membrane so the enzyme can come in contact with molecules and digest them. Digestion products go into the cytosol to serve as nutrients for the cell. The second way is through autophagy: when lysosomes use hydrolysis enzymes to recycle the cell’s own organic material. An example of this would be when a damaged organelle becomes surrounded by a membrane so it is in a vesicle. Lysosome fuses with the outer membrane of the vesicle and enzymes digest the inner membrane and all the materials of the damaged organelles. The digested materials are then released into the cytosol for reuse.

Flagellum is present in both eukaryotic and prokaryotic cells. They are limited to one or a few per cell. It helps with the movement of the cells.

The cell wall is present in both prokaryotes and plant cells. The purpose of the cell wall is to provide strength and protection for the cell. Plant cell walls consist of the primary cell wall, which is relatively thin and flexible, the middle lamella, a thin layer between the primary walls of adjacent cells, and some may have a secondary cell wall, which is added between the plasma membrane and the primary cell wall.

Plasmodesmata are the channels present between plant cells. They go through cell walls to connect neighboring cells allowing water and other nutrients to travel from one cell to another.

Disaccharides are two monomers bonded together by dehydration/condensation, resulting in an alpha (α) 1-4 glycosidic bond. An example of a Disaccharide is Maltose which is made up of two glucose molecules bonded together.

Polysaccharides, also known as Glycans, are long chains of monosaccharides that are all bonded through alpha (α) 1-4 glycosidic bonds. Polysaccharides can also have branching which is formed by alpha (α) 1-6 glycosidic bonds. Glycans can serve two main functions: (energy) storage or structure.

Cis-unsaturated fats have hydrogen bonds on the same sides of the double-bonded carbons

Trans-unsaturated fats have hydrogen bonds on opposite sides of the double-bonded carbons.

Since phospholipids are amphipathic, the hydrophobic parts try to hide from the surface to avoid water. This results in three different formations: the micelle, liposome, or a phospholipid bilayer as seen in cell membranes.

Where the genetic material (DNA) is located.

Sticky layer made of polysaccharide or protein. This helps the bacteria stick to substrate or each other and protects against dehydration or from attacks by the host's immune system.

Fimbriae are short hair like projections that help the cell stick to substrate or to each other, while piliis are long projections that form a channel between two bacterial cells to transfer DNA from one to the other.

Original cells produce a copy of their chromosome and surrounds it with multiple layers of cell wall material to form this endospore. This protects against extreme and harsh conditions.

Both prokaryotes and eukaryotes have a plasma membrane. It is a selectively permeable barrier and the mechanical boundary of cells. It is the location of many metabolic processes, such as respiration and photosynthesis. Nutrient and waste transport and detection of environmental cues for chemotaxis occur here.

Ribosomes are complexes of ribosomal RNA and protein. Their function is to make proteins in 2 locations in cells - in the cytosol (free ribosomes) and on the outside of the endoplasmic reticulum (bound ribosomes). Most protein is made on free ribosomes. Bound ribosomes make proteins that are either inserted in the membrane or secreted out of the cell.

Presence of DNA that is separated from the main bacterial chromosome.

Allows for buoyancy for floating in aquatic environments.

Stores of carbon and phosphate. As well as other substances.

This space has hydrolytic enzymes and binding proteins to process nutrients.

Brings mRNA, tRNA with the first amino acid, and the two subunits of the ribosome together using GTP. Proteins needed to initiate translation are called initiation factors.

Protein is escorted to the ER by SRP and translation continues in the ER. The protein is then released in the ER lumen.

Transcription is the first of two steps of Gene Expression. Transcription is the process of making an mRNA strand out of a DNA template strand. Translation in prokaryotic cells occurs in the cytoplasm. However, in Eukaryotic cells, Translation occurs inside the nucleus.

The initiation phase is the process of starting the mRNA strand on a template DNA Strand.

Initiation of Translation is done by an enzyme named RNA Polymerase which is unique to prokaryotes. RNA Polymerase binds to the promoter. RNA Polymerase can only create an mRNA strand going from 5' to 3'. Because of this, RNA Polymerase picks the DNA strand that runs from 3' to 5'. After the RNA polymerase binds to DNA it unwinds the strands and the Polymerase begins the mRNA synthesis.

Elongation is the phase where the RNA strand is extended. RNA Polymerase (II) moves downstream, unwinding the DNA and adding nucleotides to the 3' end of the RNA strand.

Termination is the phase where the RNA strand is released from the polymerase and the DNA template strand.

After Transcription is completed in Prokaryotes, translation can begin since the RNA strand is already in the cytoplasm.

The AAUAAA sequence is a special sequence that signals to the cell to make a cut in the pre-mRNA strand and release it from the template DNA strand.

When pre-mRNA is released a modified G nucleotide is added to the 5' end of the strand. This special nucleotide is called the 5' cap. The cap protects the mRNA strand from being disturbed while it is transported out of the nucleus.

The pre-mRNA is still not ready for the translation since it contains both introns and exons. The introns need to be removed, leaving exon sequences in the RNA.

RNA splicing is the process of removing the introns from the pre-mRNA.

Spliceosomes are complexes of snRNA and proteins that remove introns from RNA. The spliceosome binds to the intron and pushes out of the RNA strand, leaving exons behind.

RNA is considered mature m-RNA when the introns have been removed.

When pre-mRNA is released poly-A polymerase adds a poly-A tail to the 3' end of the strand. The poly-A tail is a long sequence of A's. The poly-A tail helps stabilize the mRNA strand.

Termination is the phase where the RNA strand is released from the polymerase and the DNA template strand.

After Transcription is completed in Prokaryotes, translation can begin since the RNA strand is already in the cytoplasm.

The AAUAAA sequence is a special sequence that signals to the cell to make a cut in the pre-mRNA strand and release it from the template DNA strand.

When pre-mRNA is released a modified G nucleotide is added to the 5' end of the strand. This special nucleotide is called the 5' cap. The cap protects the mRNA strand from being disturbed while it is transported out of the nucleus.

The pre-mRNA is still not ready for the translation since it contains both introns and exons. The introns need to be removed, leaving exon sequences in the RNA.

RNA splicing is the process of removing the introns from the pre-mRNA.

Spliceosomes are complexes of snRNA and proteins that remove introns from RNA. The spliceosome binds to the intron and pushes out of the RNA strand, leaving exons behind.

RNA is considered mature m-RNA when the introns have been removed.

When pre-mRNA is released poly-A polymerase adds a poly-A tail to the 3' end of the strand. The poly-A tail is a long sequence of A's. The poly-A tail helps stabilize the mRNA strand.

Transcription starts on a nucleotide in DNA that is called the Transcription Start Point. It is also referred to as the +1 or the first nucleotide. The right side of the DNA template strand is numbered with positive numbers and is named the Downstream Region. The left side is numbered with negative numbers and is called the Upstream Region. The transcription process moves downstream.

The promoter is a sequence in the DNA that is located a little upstream of the starting site.

In Eukaryotes, a protein called Transcription Factor is required. The transcription factor binds to the Promoter before RNA Polymerase III can bind to the operator and the TATA box. Transcription factor indicates where RNA Polymerase needs to bind.

In Eukaryotes, the initiation of Translation is done by an enzyme named RNA Polymerase II. RNA Polymerase II binds to the promoter. RNA Polymerase II can only create an mRNA strand going from 5' to 3'. Because of this, RNA Polymerase II picks the DNA strand that runs from 3' to 5'. After the RNA polymerase binds to DNA it unwinds the strands and the Polymerase begins the mRNA synthesis.

DNA replication is the process of making replicas of the parent DNA strand.

DNA Replication starts at a sequence of nucleotides called the Origin of Replication (ORI).

The two strands of a double-stranded DNA separate at the ORI and form a Replication bubble with two forks at each end.

Prokaryotes have a small circular DNA called Plasmid DNA which only requires one Replication bubble to form for DNA replication to occur.

Since DNA in Eukaryotes is longer, multiple Replication Bubbles form. Eventually, the bubble will fuse and speed up the replication process.

Since Eukaryotic DNA is so long, it needs a protein called Topoisomerase that unwinds any wound-up sections of DNA.

For DNA replication to start, the two strands must be separated by a protein called Helicase. Helicase breaks the hydrogen bonds between the two strands, causing them to split apart.

An SSB (Single Stranded Binding) protein binds to both single-strand DNA to prevent the two strands from forming hydrogen bonds again.

Primase binds to a single-stranded DNA to make an RNA primer which is complementary to the parent strand's sequence.

Okazaki fragments are the small section of DNA that goes from 3' to 5' (according to the DNA template strand),

In the lagging strand, many RNA primers are placed by Primase.

Another polymerase called DNA Polymerase I removes all the RNA primers and replaces them with DNA nucleotides.

An enzyme called Ligase comes in to seal any gaps between the fragments by connecting the nucleotides with phosphodiester bonds through condensation.

A sliding clamp is a protein that works with DNA polymerase to prevent it from falling off the parent strand during replication.

Chromosomes are made of DNA and proteins.

They bind to distal control elements called enhancers and bring about increased levels or lower levels of transcription.

Enhancer sequences can be present close to or far from the gene they control. They can be present on either side of the gene they control.

Control elements are segments of noncoding DNA that serve as binding sites for transcription factors.

They bind to the promoter and regions near the promoter to bring about low levels of transcription (background/basal)

An operon comprises multiple genes which are involved in the same pathway in the cell. These genes are regulated together.

The fibrous double-stranded DNA with proteins attached to it is called chromatin.

The histones that are part of the nucleosome are H2A, H2B, H3, and H4. There are 2 of each of these histones in the histone core, so the total number of histones would be 8 (octamer).

Nucleosomes consist of a histone core with DNA wound around it twice.

Proteins bind to operators and turn on/off gene expression for multiple genes at the same time.

Positive regulation implies that the operon gene expression is on. Expression is at high levels when the activator is bound to the operator.

While in negative regulation, if the repressor protein is bound to the operator sequence then the gene expression is off.

The TATA box is a sequence that contains multiple T'a and A's in the promoter.

A single strand of RNA. The anticodon binds the codon, 5' to 3', in the mRNA and the amino acid is attached to the 3' end of the tRNA.

Made of RNA and proteins. Prokaryotes have 70S while eukaryotes have 80S ribosomes. Each ribosome has a small and large subunit that come together during translation.

Chlorophyll is the light-harvesting pigment found in chloroplasts. The structure consists of a porphyrin ring (light-absorbing head) and a hydrocarbon tail (interacts with hydrophobic regions of proteins in thylakoid membranes).

When pigments absorb light, an electron is elevated from a ground state to an unstable state.Electrons fall back down to the ground state, releasing photons that cause an afterglow called fluorescence.

cell growth, accumulates materials for DNA synthesis

DNA synthesis occurs, and DNA replication results in duplicated chromosomes

cell synthesizes proteins needed for cell division

Chromosomes condense, nucleoli begin to break down and disappear outside the nucleus, and the mitotic spindle begins to form. Centrosomes move apart toward opposite ends of the nucleus due to the lengthening of microtubules.

Degradation of the nuclear envelope occurs. Kinetochore forms at the centromere of each chromatid. Microtubules extend from each centrosome and attach to the kinetochore. Kinetochore of unattached sister chromatid associated with microtubules from opposite centrosome

Centrosomes are at opposite ends. Chromosomes align the center of the cell between poles at a 90° angle

Each sister chromatid is now an independent chromosome.

CO2 from the atmosphere is added to ribulose biphosphate using an enzyme called rubisco (ribulose biphosphate carboxylase). A 6-carbon unstable intermediate is formed and immediately splits to form two molecules with 3 carbons (3 phosphoglycerates).

6 molecules of ATP and 6 molecules of NADPH are used to form 6 molecules of glyceraldehyde 3 phosphates (G3P), of which 5 molecules continue on to make more ribulose biphosphate. 1 of the molecules of G3P leaves the cycle to form glucose and other sugars

This is the reaction-center chlorophyll a absorbs at 700 nm.

This is the reaction-center chlorophyll a absorbs at 680 nm.