master the garden

part two botany basics: internal plant parts
photo l. fowler

In this second installment of botany basics  – Cells: are the basic structural and physiological units of plants and of life in all organisms. They are eukaryotic cells, which have a true nucleus along with specialized structures called organelles that carry out different functions. Plant cells have special organelles called chloroplasts, which create sugars through photosynthesis. They have cell walls that provides structural support. Meristems, xylem and phloem (plant tissue) are large organized groups of similar cells that work together to perform similar functions. It may appear that I have ventured into the weeds with detail in this installment – but I believe that a more detailed overview is essential to understanding the structure and function of cells.

When I first approached the botany part of my horticultural studies, I admit I was a bit intimidated. It was a ‘new language’ for me, and armed with only a vague memory of high school biology courses and some basic overview of botany in Master Gardener education, I was less then enthusiastic. It was fortunate that I found myself in a class at Lake Washington Institute of Technology with a horticulture professor who deconstructed the science of botany and presented the information in a lively and holistic form – one that an accidental gardener could digest and comprehend.

I am still not a proficient – but I have found the science of botany less intimidating and I have acquired an enthusiasm and desire to continue my education through practical experience and study. If you find you are hesitant to open your copy of Botany in a Day, have faith! My advice is to break it down and deconstruct the information. Attend a class or two, if you can – there are also some great videos on line – and take a break from your (dry) text books… a novel or two…I can suggest The Triumph of Seeds, by Thor Hanson to wet your appetite for all things Botanical.

“Sometimes I wish I could photosynthesize so that just by being, just by shimmering at the meadow’s edge or floating lazily on a pond, I could be doing the work of the world while standing silent in the sun.”

Robin Wall Kimmer, Braiding Sweetgrass

cells deconstructed

With the organization of any biological system, and in this case – eukaryotic cells, the emphasis will be on the compartmentalization of cellular functions. As you visualize the cell, this compartmentalization allows varied ‘micro-environments’ to exist in close proximity, with membranes as boundaries for the organelles. As you read about each component below – imagine them as a compartment with different functions separated by membranes which are made up of primarily hydrophobic lipid elements (predominantly water) through which the cell can perform a wide variety of tasks allowing it to sense, judge, and respond to its environment.

cell wall

With very few exceptions, (viruses are considered organisms) all organisms have cells as their basic unit of life. Tiny clusters of genetic details and molecular machinery build everything from roots to petals. Cells range in shape and size and each plant, animal, bacteria, and fungi are unique in cellular features, however, all eukaryotic cells have organelles, a nucleus, and plasma membrane – only fungi and plant cells have cell walls, a porous, supportive, and protective shell that gives the cell structure. Compared to most animal cells, which are soft and require bones to provide structure, plants and fungi have cell walls for structure.

The cell wall is constructed by the the protoplast, the living part of a cell. In multicellular plants, these cell walls are held together by middle lamella in addition to tiny pores, plasmodesmata, that provide a living interconnection between protoplast.

The protoplast contains a number of organelles to which the cell membrane (plasmalemma) is a boundary from the outside environment. Unlike the cell wall, the cell membrane is not porous to substances, but mediates the movement of substances in-and-out of the protoplast by selective control.


The plasma membrane, cytoplasm , and the nucleus are major components of the protoplast. Almost all of the cellular metabolic activity occurs in the cytoplasm which consists of various organelles and the hyaloplasm in which they are suspended.


Plastids are membrane bound organelles that contain pigments or a combination of both pigments (photosynthesis) and stored food materials, and they are recognized by their internal structure and content which determines the cell color.


In plant cells the major cytoplasmic organelles are plastids, mitochondria, dictyosomes, vacuoles, vesicles and ribosomes.

Mitochondrion is a much smaller organelle compared to the plastid. It releases energy from food materials for use in cellular functions.

Dictyosomes, which are layers of flattened membrane-bound sacs, function in the formation and encapsulation of various materials (modify proteins, and polymerize sugars to polysaccharides) for delivery to destinations within the cell – like the cell wall, for secretion, or for storage.

Small, membrane-enclosed sac organelles, vesicles, store and transport substances within the cell parts and from cell to cell.

The waste treatment and recycling plant for cells! Usually only one large vacuole occupies the bulk in plant cells, and is bound by a single membrane (tonoplast). They contain an aqueous solution that many substances are dissolved in, while some are held in crystal form. They function as recycling reservoirs for some substances and a waste storage area for others.


Bound by a double membrane, nuclear envelope, consists of an outer and inner membrane that is pressed together – the nucleus is suspended in this clear fluid and is a large structure containing the genetic material that determines the cell structure and function of the mature cell as well as the form and function of the plant. Perforations, nuclear pores, are thin discs in the envelope that function in transport molecules of RNA, ribosomal proteins, and carbohydrates through the nuclear envelope.

Within the nucleus is the nucleolus. A small spherical structure that is the control center for the production of RNA (ribonucleic acid) and important mechanism for interpreting genetic information. The matrix material that the genetic material and nucleolus are suspended in is the nucleoplasm.

The outer layer of the nuclear envelope is in contact with the cytoplasm, and it is semipermeable allowing a selective trafficking of substances like proteins and RNA’s occurs between the nucleoplasm and the cytoplasm.

Ribosomes may be found free in the cytoplasm, individually or in clusters (polysomes). RNA produced within the nucleus is assembled into ribosomes and then transferred to the cytoplasm through nuclear pores.


Ribosomes are not bound by a membrane but are still considered organelles. Their function is structural protein and enzyme formation and can be found scattered in the cytoplasm or attached to various membranes. Most frequently attached to endoplasmic reticulum (ER – which functions in the production of proteins and other substances) a prevalent membrane system in the cytoplasm and also to the surface of the nucleus.

Additional reading:

The Molecular Biology of Plant Cells, H. Smith

Plant Cell Biology, William dashek, Marcia Harrison

Botany for beginners, maxwell Tyden Masters

cell types


Parenchyma are diverse cells – have many different shapes and be very specialized in their function. They have only a primary cell wall and retain the ability for future cell division. Parenchyma cells contain a nucleus and when they are first formed, they are densely cytoplasmic and have several small vacuoles.

The memory card (in our phone) would be the vacuole because it stores information in the phone like a vacuole does in a cell.

Based on their function specialized parenchyma cells can grouped as:

  • Ground tissue: food creation and storage – support during and after growth
  • Storage tissue: specifically modified for storage of energy (generally in the form of carbohydrates) or water
  • Chlorenchyma: thicken the cell walls with extra cellulose to help support the plant
  • Aerenchyma: spongy tissue that forms spaces or air channels in the leaves, stems and roots of some plants, which allows exchange of gases between the shoot and the root –see picture below…

There are several distinct storage tissues in plants. Three examples are:

  • Seed endosperm: designed to store food for the developing embryo and seedling. The endosperm is filled with lipid bodies, protein bodies and especially amyloplasts containing starch.
  • Storage parenchyma: specialized as large water storage tissue in many succulent and xerophytic plants with greatly expanded vacuole. The cells are chlorophyll-free and thin-walled.
  • Ray parenchyma: important storage tissue to store carbohydrates and proteins over the winter in stems and these stored materials are used to support new spring shoot and leaf growth. Ray parenchyma cells grow horizontal to the developing stem, sometimes deep within the non-living xylem cells.
let’s talk green…

Chloroplasts are like green solar cells. They are the dominant plastid type found in all plants that are green, but details of their structure can vary among different photosynthetic plant groups. In most land plants (photosynthetic vascular plants) they are numerous (algae, however can have as few as one).

Chloroplasts contain chlorophyll pigments, primarily xanthophylls, (yellows) and carotenoids (yellows, oranges and reds) are present in lesser amounts. The combination of different pigments produces the various shades of green. With the exception of autumn, when the chlorophyll degenerates resulting in fall color, chlorophyll can effectively mask these other pigments.

Like other plastids, chloroplasts are surrounded by an outer membrane and inner membrane. Through selective control these membranes mediate the movement of substances in and out of the chloroplast. The internal space enclosed by the chloroplast double membrane is filled with a colorless hydrophilic matrix or stroma, which contains DNA, ribosomes and some temporary products of photosynthesis.

The grana and stroma lamellae form a membrane system lying within the stroma of vascular plants. Numerous grana are present in each chloroplast, but some nonvascular plants have only one large granum.

Thylakoids, which are flattened, membrane bound sacs, are aggregated into a stacks of 2 to about 100 (kind of like pancakes) to form one granum. Granum are interconnected by membrane-bound stroma lamellae and all pigments in the chloroplast are held within the membranes.

Chloroplasts increase their number by a process of similar to cell division – they also contain their own genetic material and ribosomes. They produce large amounts of food material, but only a small amount is used as an energy source by the photosynthetic cell – excess food materials can be stored within the chloroplast as starch.

Chloroplast is essential to photosynthesis*; providing the primary means of capturing solar light energy into a stable, storable energy form and held in carbohydrates that provide the main energy resource for all living organisms.

*Photosynthesis will be covered in more detail in future installments

Collenchyma cells have primary walls that are usually thickened especially at corners or edges. They function for structural support.

They are characterized by having a thickened primary cell wall that is not lignified. Collenchyma cells and fibers both function to support the stem or leaf, but unlike fibers, collenchyma cells are usually living at maturity. Cross-section of English ivy (Hedera helix)

Sclerenchyma are strengthening tissue in a plant that have thickened lignified walls, which make them strong and waterproof. They are commonly classified into support types and conducting forms.

Support sclerenchyma is comprised of sclereids and fibers. This tissue reduces wilting, but it is energetically costly for the plant to create.

Conducting types of sclerenchyma are the tracheids and vessel elements of the xylem, the tracheary elements of plants.

Sclerenchyma tissue, when mature, is composed of dead cells that have heavily thickened walls containing lignin and a high cellulose content , and serves the function of providing structural support in plants.

plant hormones

There are five major types of plant hormones: auxin, gibberellin, cytokinin, ethylene, and abscisic acid. These hormones can work together or independently to influence plant growth and act as ‘chemical messengers’ produced in one part of the plant and carrying a message to another.

Auxin – Involved in tropisms, apical dominance and in cell growth and cell expansion (elongation). Produced primarily in parts of the plant that are actively growing, like the very tip of the stem, it travels in one direction in a plant – downward from the top to the bottom – from the stem tip to the roots. It is the only plant hormone known to do this. Therefore the concentration of auxin is highest at the top of the plant and decreases as you get closer to the roots, this controls the overall shape of the plant and helps keep the primary stem of a plant the leader.

Auxin maintains apical dominance and prevents additional lateral buds and branches from growing on the side of the stem. If the primary stem of a plant is pruned, the auxin source is removed, then no single stem is dominant – apical dominance is removed.

Auxin will move to the shadier side of the plant stem causing those cells to grow longer, while the cells on the light side of the plant stem remain the same size. Phototropism is the ability of a plant, or other photosynthesizing organism, to grow directionally in response to a light source.

Gibberellin – involved in breaking dormancy of seeds and buds; promotes growth and stem elongation between nodes on the stem, and effects several developmental stages in plants.

Gibberellin elongates the inter-nodes (node is a place on a stem where a leaf attaches) so it is easiest to see the absence of this hormone in dwarf and rosette plants where there is little space between nodes on a stem and the leaves are clustered toward the base of the plant.

Cytokinin – promote cell division and making of new plant organs; prevent senescence. Cytokinin is produced in the root apical meristems and travel upward with water through the stem in xylem. the movement of cytokinins is passive and does not require energy.

Cytokinins delay senescence or the natural aging process that leads to death in plants. In the cell cycle, cytokinins promote the movement from the G2 phase to the M phase (they encourage cells to divide.

Cytokinins are involved in repair – If a plant becomes wounded, it can repair itself with the help of cytokinins and auxin. These hormones work together and if the concentration is equal, then normal cell division will take place – If the concentration of auxin is greater than cytokinin then roots will form. If the concentration of auxin is less than cytokinin then shoots will form.

Etylene – involved in fruit ripining and rotting and abscision. Ethylene exsists as a gas and can be produced in almost any part of a plant, and can diffuse through the plant’s tissue, outside the plant, and travel through the air to affect a totally different plants.

The formation of ethylene requires oxygen, and the agricultural industry has used this information to control the partial pressure of oxygen and carbon dioxide in a truck carrying produce (specifically low O2 high CO2) to prevent ethylene synthesis and slow the ripening process. This is helpful when fruits and vegetables are grown in one region of the world and then shipped many miles away to be sold.

Abscisic acid – involved in closing the stomata; maintain dormancy. Abscisic acid is produced in drought leaves, drought roots, and developing seeds to alert the rest of the plant that it is water stressed. It can travel both up and down in a plant stem in the xylem or phloem.

Water molecules exit a plant through tiny pores in the leaves called stomata. Each stoma has two kidney bean shaped guards on either side of the pore, whose job it is to open and close the stoma. When the guard cells are full of water, or turgid, the stoma is open. When water leaves the guard cells, they become flaccid, and the stoma is closed. In the absence of water, abscisic acid travels to the guard cells with a message to close.

glossary of terms

Advantageous root – roots that arise from an organ other than the primary root—usually a stem, sometimes a leaf

Anther – The pollen sac on a male flower

Apex – The tip of a root or shoot

Apomixis – process of reproduction in which plants produce seeds without fertilization

Apical dominance – The tendency of an apical bud to produce hormones that suppress growth of buds below it on the stem

Axil – The location where leaf joins the stem

Bolting – plants produce a flowering stem in a natural attempt to produce seeds as a means of survival when under stress

Bulb – structurally a short stem with fleshy leaves or leaf bases that function as food storage organs during dormancy

Cambium – A layer of growing tissue that separates the xylem and phloem and continuously produces new xylem and phloem cells

Carotenoids – are plant pigments responsible for bright red, yellow and orange hues in many fruits and vegetables. Carotenoids are a class of phytonutrients (“plant chemicals”) and are found in the cells of a wide variety of plants, algae and bacteria. They help plants absorb light energy for use in photosynthesis

Chlorophyll – The green pigment in leaves that is responsible for trapping light energy from the sun

Chloroplast – A specialized component of certain cells; contains chlorophyll and is responsible for photosynthesis

Cell membrane(plasmalemma) also called the plasma membrane is found in all cells that separates the interior of the cell from the outside environment.  

Cell wall – a rigid layer of polysaccharides lying outside the plasma membrane of the cells of plants, fungi, and bacteria. In the algae and higher plants it consists mainly of cellulose.

Cold hardy – generally measured by the lowest temperature a plant can withstand

Corm – a rounded underground storage organ present in plants such as crocuses, gladioli, and cyclamens, consisting of a swollen stem base covered with scale leaves

Cortex – Cells that make up the primary tissue of the root and stem

Cotyledon – The first leaf that appears on a seedling. also called a seed leaf.

Cuticle – A relatively impermeable surface layer on the epidermis of leaves and fruit

Cytoplasm – protoplasm enclosed by the plasma membrane of cell, excluding the nucleus in eukaryotic cells and cellular DNA in prokaryotic cells

Dicot – having two seed leaves

Dictyosomes – are stacks of flat, membrane-bound cavities (cisternae) that together comprise the Golgi apparatus. Within the dictyosomes, proteins are stored, modified, sorted, and packed into vesicles

Herbaceous – vascular plants that have no persistent woody stems above ground

Hyaloplasm – clear fluid portion of cytoplasm as distinguished from the granular and net-like components

Hydrophilic – having a tendency to mix with, dissolve in, or be wetted by water

Epidermis – The outermost layer of plant cells

Eukaryota – domain comprised of eukaryotes or organisms whose cells contain a true nucleus

Fibrous roots – a network of feeding lateral roots found on most plants

Grana – Grana, the plural of granum, are stacks of structures called thylakoids which are little discs of membrane on which the light-dependent reactions of photosynthesis take place. Stacked into grana, the shape of the thylakoids allow for optimum surface area, maximizing the amount of photosynthesis that can happen

Guard cell – Epidermal cells that open and close to let water, oxygen and carbon dioxide pass through the stomata

Internode – the space between nodes on a stem

Lateral root – roots that branch from larger primary roots

Meristem – Specialized groups of cells that are a plant’s growing points.

Meristematic zone – located at the tip of a root and manufactures cells: it is an area of cell division and growth

Mesophyll – A leafs inner tissue, located between the upper and lower epidermis; contains chloroplasts and other specialized cellular parts (organelles)

Middle lamella – a layer which cements the cell walls of two adjoining plant cells together.

Mitochondria –  are small, organelles inside of cells, and they are the power center of the cell. They take raw material and transform it into a form of energy that the plant can easily use

Monocot – having one seed leaf

Mycorrhizae – symbiotic association between certain fungi and roots of a plant

Node – an area on a stem where a leaf, stem, or flower bud is located

Nucleus –  highly specialized organelle that serves as the information processing and administrative center of the cell

Nucleolus – a spherical body of the nucleus of most eukaryotes that becomes enlarged during protein synthesis and contains the DNA templates for ribosomal RNA

Nucleoplasm – similar to the cytoplasm of a cell, the nucleus contains nucleoplasm, also known as karyoplasm, or karyolymph or nucleus sap. The nucleoplasm is a type of protoplasm, and is enveloped by the nuclear envelope. The nucleoplasm includes the chromosomes and nucleolus

Ovary – The part of a female flower where the eggs are located

Petiole – The stalk that attached a leaf to the stem

Phloem – Photosynthate-conducting tissue

Pistil – The female flower part; consists of a stigma, style, and ovary

Plastids – is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. They often contain pigments used in photosynthesis, and the types of pigments in a plastid determine the cell’s color

Plasmodesmata – a narrow thread of cytoplasm that passes through the cell walls of adjacent plant cells and allows communication between them.

Primary root – originating at the lower end of a seedlings embryo and continues to elongate downward. It may or may not persist into plant maturity, and has limited branching – it is called a tap root

Protoplast – the protoplasm of a living plant or bacterial cell whose cell wall has been removed

Respiration – the process of converting sugars and starches to energy

Rhizomes – a continuously growing horizontal underground stem which puts out lateral shoots and adventitious roots at intervals

Ribonucleic acid (RNA) – is one of two forms of genetic information in the cell. RNA  works together with deoxyribonucleic acid (DNA)  to help express genes, but RNA has a distinct structure and set of functions within the cell 

Ribosomes – A sphere-shaped structure within the cytoplasm of a cell that is composed of RNA and protein and is the site of protein synthesis

Root cap – group of cells protecting the apical meristem at the root tip

Root hairs – delicate, elongated epidermal cells that occur in a zone behind the root’s growing tip with the function of increasing the roots surface area and absorptive capacity

Scaly bulb – as seen in true lilies, has naked storage leaves, unprotected by any papery covering, that make the bulb appear to consist of a series of angular scales. 

Senescence –  in plants is the process of aging.  Plants have both stress-induced and age-related developmental aging. Chlorophyll degradation during leaf senescence reveals the carotenoids, such as anthocyanin and xanthophylls and is the cause of autumn leaf color in deciduous trees

Stamen – The male flower part; consists of an anther and a supporting filament

Stigma – The top f a female flower part; collects pollen

Stolon – a creeping horizontal plant stem or runner that takes root at points along its length to form new plants

Stoma (pl. stomates, stomata) – tiny openings in the epidermis that allow water, oxygen, and carbon dioxide to pass into and out of a plant

Stroma lamellae – Granum and stroma lamellae. In higher plants thylakoids are organized into a granum-stroma membrane assembly. A granum (plural grana) is a stack of thylakoid discs. Chloroplasts can have from 10 to 100 grana. Grana are connected by stroma thylakoids, also called intergranal thylakoids or lamellae

Style – The part of a female flower that connects the stigma to the ovary. Pollen travels down the style to reach the ovary, where fertilization occurs

Tap root – see Primary root

Thylakoids – each of a number of flattened sacs inside a chloroplast, bounded by pigmented membranes on which the light reactions of photosynthesis take place, and arranged in stacks or grana

Totipotent cells – can form all the cell types in a body. In plants, almost all plant cells contain all the genetic information necessary to reproduce a complete plant.

Transpiration – the process of losing water (in the form of vapor) through stomata

Tropism – the turning of all or part of an organism in a particular direction in response to an external stimulus

Tuber – thickened underground part of a stem or rhizome, e.g. in the potato, serving as a food reserve and bearing buds from which new plants arise

Tunicate bulb –  has a paper-like covering or tunic that protects the scales from drying and from mechanical injury. Include: tulips, daffodils, hyacinths, grape hyacinths (muscari), and alliums

Turgor – Cellular water pressure; responsible for keeping cells firm

Vacuoles – a space or vesicle within the cytoplasm of a cell, enclosed by a membrane and typically containing fluid

Vascular tissue – Water, nutrient, and photsynthate-conducting tissue (xylem and phloem)

Vegetative structures – The vegetative (somatic) structures of vascular plants include two major organ systems: (1) a shoot system, composed of stems and leaves, and (2) a root system

Vesicles – small structure within a cell, consisting of fluid enclosed by a lipid bilayer. Vesicles form naturally during the processes of secretion (exocytosis), uptake (phagocytosis) and transport of materials within the cytoplasm

Xanthophylls – a yellow or brown carotenoid plant pigment which causes the autumn colors of leaves

Xerophytic – is a species of plant that has adaptations to survive in an environment with little liquid water, such as a desert or an ice- or snow-covered region in the Alps or the Arctic.

Xylem – Water and nutrient-conducting tissue

Zone of elongation – located behind the meristem. Cells in this area increase in size through food and water absorption. As they grow, they push the root through the soil

Zone of maturation – located directly beneath the stem. Cells in this zone become specific tissues such as epidermis, cortex, or vascular

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