AP Bio: Semester 1 Final Exam

Enzyme

* Type of protein
* Speeds up rate of reaction
* Is not consumed
* A catalyst
* Example: Sucrase

Substrate

* The reactant on which the enzyme works (very specific)
* When bound together = enzyme substrate complex
* Example: Sucrose

Active Site

- Region of enzyme where substrate binds

Induced fit

* Change in shape of active site to fit snugly around the substrate
* Occurs when substrate enters

Enzyme examples:

* Lactase: breaks lactose
* ATP synthase: makes ATP
* DNA Polymerase
* RuBisCO

activation energy (Ea)

* The amount of energy that reactants must absorb before a chemical reaction will start
* Sometimes called the free energy of activation
* Enzymes lower activation energy needed to start a reaction

Enzymes are picky

* about substrate
* about temperature
* about pH

Rate of reaction

How fast does the enzyme turn substrate into product?

Slope = rate of reaction

Compounds which help enzymes

Cofactors and coenzymes

Coenzymes

* Non-protein
* Non-protein, large, organic (contain carbon) molecules


* Bind near active site
* Examples: many vitamins
* NAD
* FAD
* Coenzyme A

Cofactors

* Non-protein, small, inorganic, compounds & ions
* Bound with enzyme molecule
* ex. Mg, K, Ca, Fe, Zn, Cu

Enzyme Inhibition

Inhibitors: Molecules that reduce enzyme activity

Type of enzyme inhibitors

* competitive inhibition
* non-competitive inhibition
* Allosteric regulation
* Irreversible inhibition
* Feedback inhibition

Competitive inhibitor

- Inhibitor and substrate "compete" for active site- Inhibitor fits in active site

Noncompetitive (allosteric inhibitor)

- Inhibitor binds to site other than active site- Allosteric inhibitor binds to allosteric site- Causes enzyme to change shape- Conformational (shape) change- active site no longer functional- ex. some anticancer drugs- Inhibit enzymes involved in DNA synthesis or cell division

Allosteric Regulation

- Type of Noncompetitive- Conformational changes by regulatory molecules- Enzyme gets "locked" in open or closed form- Inhibitors- Keep enzyme in inactive form- Activators- Keep enzyme in active form

Irreversible Inhibition

Inhibitor permanently binds to enzyme- Competitive or non-competitive- Permanently changes shape of enzyme- Ex. nerve gas

Feedback Inhibition

- To regulate metabolic pathways the cell switches on (activates) or off (inhibits) the genes that encode specific enzymes- The product of a metabolic pathway shuts down the pathway- Prevents a cell from wasting chemical resources- Product is used by next step of pathway- Final product is inhibitor of earlier step- Allosteric inhibitor of earlier enzyme- No unnecessary accumulation of product

Aerobic and Anaerobic

- Aerobic: with oxygen- Anaerobic: without oxygen- Cell respiration usually refers to aerobic- Use 1 glucose in equation- Body can consume fats

Respiration equation

glucose + oxygen --\> carbon dioxide + water + energyC6H12O6 + 6CO2 --\> 6CO2 + 6H2O + energy (ATP)- Reactions are catabolic: break larger things down into smaller things

Cycle of ATP and ADP

- Adenosine Triphosphate and Adenosine Diphosphate- Removing P from ATP releases energy- Phosphorylation: adding P back to ADP to make ATP

Mitochondria parts

outer membrane

Aerobic Cellular Respiration steps

- Glycolysis- Citric Acid Cycle/Krebs Cycle- Electron Transport Chain/Oxidative Phosphorylation

Glycolysis

- "sugar break down"- Occurs in cytoplasm- Oxygen not required- Breaks 6 carbon glucose into 2

OIL RIG

Oxidation is losing electrons

Citric Acid Cycle (Krebs Cycle)

- Pyruvate go into mitochondria- Undergo pyruvate oxidation

Electron Transport Chain (ETC)

- Also called oxidative phosphorylation- Protons (H+) pumped into inter-membrane space with energy from NADH and FADH2- Oxygen the final electron acceptor- H2O is a byproduct- Protons (H+) mover down concentration gradient through enzyme ATP synthase

Anaerobic Respiration

Fermentation + Glycolysis

Fermentation

- Regenerates NAD+ to be reused again in glycolysis- Two types- Lactic acid fermentation (animals and bacteria)- Alcoholic fermentation (plants and yeast)

Lactic acid fermentation

- Pyruvate changes to lactates/lactic acid- Electrons from NADH go to lactic acid- Now NAD+

Alchololic Fermentation

- Instead of lactic acids

Plants

- Eukaryotes- Autotrophs- Multicellular

Photosynthesis

A process that uses carbon dioxide

Photosynthesis equation

6CO2 + 6H2O + light energy \------\> C6H12O6 + 6O2

Leaves

Where photosynthesis occurs (specifically in mesophyll cells)

Stomata (stoma)

- pores in a plant through which gases are exchanged between the plant and the atmosphere- Where CO2 enters and O2 is released- Can close if H2O loss is too big

Chloroplast

An organelle found in plant and algae cells where photosynthesis occurs- Thylakoid (many granum)- Stroma (inside space)- Outer membrane- Inner membrane

Thylakoid parts

- Thylakoid membrane- Thylakoid space

Plant pigments

Plants absorb/harvest photons of some wavelengths of light- found in chloroplast- 2 major types- chlorophylls: absorb blue and red

reflect green- carotenoids: absorb green/blue

reflect red

orange and yellow

Location of chlorophyll

thylakoid membrane

chlorophyll structure

porphyrin ring and hydrocarbon tail

Wavelengths of light

Photosynthesis overview

2 parts1. Light reactions (light dependent reaction)- occurs in thylakoid membrane- uses light energy to make ATP and NADPH for calvin cycle2. Calvin cycle (dark reactions

Light reactions

1. Light hits photosystem II and electrons get excited (gain energy)2. Excited electrons leave photosystem II and travel down the proteins of the ETC3. Energy from electrons pump H+ from stroma into thylakoid space4. Water is split to replace electrons lost by photosystem

Calvin cycle

Overview: uses ATP and NADPH to convert CO2 into sugar3 parts: carbon fixation

Carbon fixation

- CO2 enters the cycle- Enzyme rubisco combines CO2 with RuBP to form intermediate- ATP are used to make this happen (now ADP)

Reduction

- intermediate is reduced to G3P a building block for glucose- electrons come from NADPH (NADP+)- some G3P leave cycle

regeneration

- Some G3P stay in cycle

Two types of cells

prokaryotes and eukaryotes

Prokaryote

- Unicellular- No membrane bound organelle- Domains Bacteria and Archaea

Eukaryotes

- Membrane bound organelles- Uni- or multi-cellular organelles- Domain Eukaryota- animals

Prokaryotic cells

- No membrane bound organelles-DNA in "Nucleoid" region- Unicellular- Small- Domains- Bacteria- Archaea

Eukaryotic cells

- Has membrane bound organelles- Nucleus contains DNA- Unicellular or Multicellular- Larger- 10x bigger than prokaryotes- Domain:- Eukarya

Nucleus

- Contains genetic information in the form of chromosomes or chromatin- Has a nucleus for ribosome production- Surrounded by a phospholipid nuclear membrane (envelope_- Only in eukaryotes

Cytoplasm

- "jelly goo" that is within the cell membrane- Has organelles/structures in it- Found in eukaryotes and prokaryotes

Ribosomes

- Structures that build proteins during protein synthesis- Free-floating or attached to the rough ER- Found in eukaryotes and prokaryotes

Rough Endoplasmic Reticulum

- Help with protein production and shipping- Have ribosomes attached- Eukaryotes only

Smooth Endoplasmic Reticulum

- Synthesis of lipids- Detoxifications- Storage of calcium ions- Eukaryotes only

Golgi apparatus (body)

"warehouse" for receiving

Vesicles

Small "containers" made from ER or golgi membrane that move products around the cell- Eukaryotes only

Vacuoles

- Large vesicles for storing products- Plant cells have a large central vacuole filled with water- Eukaryotes only

Lysosomes

- Digestive organelle where larger molecules are broken down- Contains hydrolytic enzymes- Eukaryotes only

Mitochondria (mitochondrion)

- Site of cell respiration- ATP is generated- Found in both plants and animals- Eukaryotes only

Chloroplasts

- Site of photosynthesis- Converts energy from sun into sugar molecules- Plants and Algae only- Eukaryotes only

Centrosomes

- Helps with cell division (mitosis) in animal cells- Contains centrioles- Eukaryotes only

Cytoskeleton

- Reinforces cell's shape- Helps with cell movement- Includes- Microfilaments

cell (plasma) membrane

- Discussed in detail last lecture- Found in plants

Cell Wall

- Protects

Cilia (cilium)

- Short appendages containing microtubules present of some eukaryotes- Used in locomotion

Flagella (flagellum)

- "Tail-like" appendage found on some eukaryotes- Used in locomotion

What determines a cells function

1. Size

Endosymbiotic Theory (Endosymbiosis)

- Mitochondria and chloroplasts were once free-living prokaryotes engulfed by an early ancestor of eukaryotic cells- The engulfed cell formed a relationship with the host cell- over the course of evolution

Evidence for endosymbiosis

Mitochondria and chloroplasts:- have their own circular DNA

Protein Production Steps

1.DNA in nucleus2. Specific segment/chunk of ATCG's = gene3. mRNA built from gene (transcription)4. mRNA comes out from nucleus via nuclear pore5. Ribosomes clamp onto mRNA

Why are cells small?

- Surface area to volume ration- surface are/volume- If cells are bigger

Osmosis

- Diffusion of water- Movement down its concentration gradient: from where there is more water (less solute) to less water (more solute)- "Water wants to even things out

Water balance in cells

- Hypotonic- Hypertonic- Isotonic- Tonicity

Hypotonic

- less solute

Hypertonic

- More solute

Isotonic

- Same amount of solute and water

Tonicity

- The measure- Tonicity is relative

Animal cells in solutions

Hypotonic: Lysed

Plant cells in solutions

Hypotonic: TurgidIsotonic: FlaccidHypertonic: Plasmolyzed

Water Potential

Solution potential + Pressure Potential- Water moves from regions of high water potential to regions of low water potential- Unit=bars

Solute Potential

Determined by solute concentration

Always negative

Pressure Potential

Pressure from membranes/walls

can be positive or negative

Solute potential equation

- -iCRT- i = ionization constant- NaCl=2

Components of cell (plasma) membrane

phospholipids

Phospholipid bilayer

- Hydrophobic tails- Hydrophilic heads- Amphipathic (hydrophilic and hydrophobic)

Proteins

- Peripheral proteins- Integral proteins

Peripheral proteins

bound to surface of membrane

Integral Proteins

Penetrate hydrophobic core- Transmembrane proteins: span entire membrane

Carbohydrates

- Glycoproteins- Glycolipid

Glycoprotein

- Oligosaccharides bonded to protein- Helps with cell to cell recognition

Glycolipid

- Oligosaccaride bonded to lipid- Helps with cell to cell recognition

Steroids

Cholesterol:- Regulates cell membrane fluidity- 4 carbon rings