There are several important concepts and theories in plant physiology and biochemistry that you should be familiar with for Paper II of UPSC Botany Optional Subject. These concepts and theories are fundamental to understanding the functioning and biochemical processes of plants. Here is a detailed explanation of some key topics:

1. Photosynthesis:
- Photosynthesis is the process by which plants convert sunlight, water, and carbon dioxide into glucose and oxygen.
- It involves two stages: light-dependent reactions and light-independent reactions (Calvin cycle).
- The light-dependent reactions occur in the thylakoid membranes of chloroplasts and involve the absorption of light energy to produce ATP and NADPH.
- The Calvin cycle takes place in the stroma of chloroplasts and uses ATP and NADPH to fix carbon dioxide and produce glucose.

2. Respiration:
- Respiration is the process by which plants break down glucose to release energy for cellular activities.
- It occurs in the mitochondria and involves the oxidation of glucose to produce ATP, carbon dioxide, and water.
- The process can be aerobic (with oxygen) or anaerobic (without oxygen).

3. Transpiration:
- Transpiration is the loss of water vapor from the aerial parts of plants, primarily through stomata.
- It helps in the absorption and transport of water and minerals from the roots to the leaves.
- Transpiration also plays a role in cooling the plant and maintaining turgor pressure.

4. Hormones:
- Plant hormones are chemical messengers that regulate various physiological processes.
- Some important hormones include auxins, gibberellins, cytokinins, abscisic acid, and ethylene.
- Auxins promote cell elongation, gibberellins regulate growth and development, cytokinins stimulate cell division, abscisic acid controls seed dormancy and drought responses, and ethylene is involved in fruit ripening.

5. Photoperiodism:
- Photoperiodism is the physiological response of plants to the duration of light and dark periods.
- It plays a crucial role in flowering, dormancy, and other developmental processes.
- Plants can be classified as short-day, long-day, or day-neutral based on their flowering responses to different photoperiods.

6. Nitrogen metabolism:
- Nitrogen is an essential nutrient for plants, and its metabolism involves several important processes.
- Nitrogen is absorbed as nitrate or ammonium ions and converted into amino acids, proteins, and other nitrogenous compounds.
- Nitrogen fixation by symbiotic bacteria, nitrate assimilation, and ammonium assimilation are key processes in nitrogen metabolism.

These are some of the important concepts and theories in plant physiology and biochemistry that you should be familiar with for Paper II of UPSC Botany Optional Subject. Understanding these topics will provide a strong foundation for studying plant biology and its applications.