Biology enzymes unit 1, Biology 3 Unit 1

Cilia

short microtubule hairs that move substances across the surface of eukaryotic cell

Enzymes

biological catalyst protein that speeds up the rate of chemical reactions in biological processes.

- chemical reactions must overcome energy barrier

- enzymes make that happen in real time

- provide a home for reaction, reactants bond ,and enzyme facilitates

- lowers the activation energy making it easier for chemical reactions to occur faster

- unchanged at the end of reaction

- names often end in "-ase"

EXAMPLE: Lactase

- enzyme in mammalian intestine

- lactase digests lactose into glucose and galactose

- lactase expression normally declines with age, so lactase builds up in intestine: "lactose intolerance."

- Some people have mutation: "lactose persistence"

Active site

The part of an enzyme where the chemical reaction occurs.

Substrate

reactant of an enzyme-catalyzed reaction

Enzymes are sensitive to changes in...

Temperature

PH

Activators and Inhibitors

Enzyme changes in temperature

- enzyme favorite temperature is body temperature

- if it gets colder enzymes won't work well because in lower temperature, molecules move slowly

- If it gets hotter, an enzyme denatures/unravels in boiling temperature and active site will be gone so the reaction cannot proceed

Enzyme changes in PH

- all enzymes have a preferred pH depending on where they work; in humans around 7, human stomachs that's lower

-if you raise or lower pH, that affects hydrogen bonding and denatures the enzyme and it won't work well

Enzyme activators

proteins or small molecules that bind to an enzyme and increase its activity

enzyme inhibitors

A chemical that interferes with an enzyme's activity and decreases it

Energy

the ability to do work

-potential

-kinetic

potential energy

stored energy due to location or chemical bonds

kinetic energy

energy of motion

Phototrophs

obtain energy from light; ex. plants

Chemotrophs

obtain energy from external chemical compounds.

Organic: carbs, triglycerides, protein

Inorganic: hydrogen sulfide, hydrogen, sulfur, iron, and ammonia

ATP

(adenosine triphosphate) main energy source that cells use for most of their work

- Structure: adenine + ribose + phosphate group with 3 phosphates

- chemical work, mechanical work, and transport work

- can be regenerated

ATP cycle

How a cell regenerates its ATP supply. ADP forms when ATP loses a phosphate group, then ATP forms as ADP gains a phosphate group.

- form of energy transfer

Laws of thermodynamics (energy transformations)

1. Energy cannot be created or destroyed in universe

2. Energy transfers are inefficient; even our own

Humans are about 40% efficient. You heat up.

Plasma membrane (cell transport)

- Phospholipid bilayer

- cholesterol for fluidity

- proteins embedded

- selectively permeable

selectively permeable

only small, lipid soluble molecules can pass directly through the membrane

- Large (too big), charged (hate non-polar fatty acid phospholipid tails), and polar (hate nonpolar phosphate head) cannot pass through membrane; except water

Transport Mechanisms

passive and active transport

passive transport

- No ATP

diffusion, facilitated diffusion, osmosis

high to low concentration

Simple diffusion

movement of permeable solute molecules across membrane from area of high to low concentration: "with/down the concentration gradient"

Facilitated diffusion

Diffusion of substances with/down their concentration gradient using protein carrier

- for charged particles

- for polar particles and down concentration gradient as well

- all particles that need assistance

Osmosis

diffusion of water from a less concentrated to a more concentrated solution, thus equalizing the concentrations

Concentration = solute per solvent

- Concentration inside and outside cell affects osmosis: Hypertonic solution, hypotonic solution, isotonic solution

Osmosis: Hypertonic Solution

Solute concentration is greater than that inside the cell; cell loses water

- cell shrivels

Osmosis: hypotonic solution

Solute concentration is less than that inside the cell; cell gains water

- cell inflates

Osmosis: isotonic solution

a solution whose solute concentration is equal to the solute concentration inside a cell

- happy cell

Active Transport

- uses ATP

Uses energy to transport substances up/against their concentration gradient using protein carriers

- Endocytosis

- Exocytosis

low to high concentration

Exocytosis

Process by which a cell releases large amounts of material

Domain Bacteria

simple cell, microscopic

The 4 kingdoms of domain eukarya are...

- kingdom protista: tend to be watery; can be single or multicellular organisms ex. kelp, algae

- kingdom fungi ex. mushrooms, yeast

- kingdom plantae ex. plants

- kingdom animalia: move and eat ex. us, animals

Electron Shells

First Electron Shell (inner shell) Capacity - 2 electrons

Second electron shell (outer shell) capacity - 8 electrons

Chemical bonds occur between atoms with incomplete outer shells.

Saturated fats

no double bonds, solid at room temperature, saturated with hydrogen, and riskier for health

structure: stiff/solid

unsaturated fats

double bonds, fluid at room temperature, not saturated, and healthier triglycerides

structure: bent/fluid which makes it healthier because its harder to get stuck during digestion

Denaturation

when proteins unravel due to breaking of hydrogen bonds

Protein structure sensitive to:

- high temperature

- high and low pH

- Prions: infectious proteins

Chromosome

structure made of DNA

- stored in nucleus of every cell

- humans have 23 pairs

Gene

region of chromosome that codes for a protein

- Humans have 20,000

- there are also regulatory regions upstream of them

light microscope

passes light through specimen, lenses magnify up to 1000 times

Fluorescence confocal microscopy

uses fluorescently tagged molecules to view intracellular structures

Eukaryotic Cells

- Contain nucleus

- Found in animals, plants, protists, fungi (kingdoms of domain eukarya)

- 2 billion years young

- evolved from prokaryotes by endosymbiosis and invagination

Peroxisome

membrane-bound organelle that detoxes harmful compounds by transferring hydrogen to water (generating hydrogen peroxide)

Endocytosis

process by which a cell takes material into the cell by using ATP to infold its membrane

- endocytosis of large particles is called phagocytosis

Biology

the study of life

The 3 domains that species of organisms are divided into...

Domain bacteria

domain archaea

domain eukarya

Domain Archaea

simple cell, microscopic, extremes

Domain Eukarya

complex cell, can be multicellular ex. humans

Has 4 kingdoms

The Scientific Method

a process used to design and perform experiments that minimizes experimental errors and bias

- Make observations

- Think of interesting questions

- Formulate hypotheses

- Develop Testable Predictions

- Perform experiment to test predictions

- Develop general theories

Hypothesis

a tentative, testable, and falsifiable explanation for an observed phenomenon in nature

Prediction

A forecast

Observational Study

No manipulation by experimenter

- Response variable

- Explanatory variable

Response variable

the outcome

Explanatory variable

the variable which may cause differences in the response

Controlled experiment

Manipulated by experimenter

- Independent variable

- Dependent variable

- Controlled variables

independent variable

what is being manipulated

dependent variable

the response that is being measured

controlled variables

everything else that is controlled

Why don't scientists always conduct controlled experiments?

1. Some controlled experiments violate ethical standards. (could be dangerous or can't force people to do things)

2. a randomized experiment may be impractical (not practical)

Correlation vs. Causation

Correlation: relationship between two variables

Causation: when one event or circumstance causes another event or circumstance to happen

Correlation does not cause causation, ex. obesitity is found open poorer people who cannot buy healthy food

placebo effect

the phenomenon in which the expectations of the participants in a study can influence their behavior

double-blind experiment

an experiment in which neither the experimenter nor the participants know which participants received which treatment

Elements

Building blocks of matter

- can't be broken down

- 92 naturally occurring ones

Which elements make up the human body?

carbon, hydrogen, oxygen, nitrogen

Atom

Smallest unit of an element

- Protons (+ positively charged particles), neutrons (0) in nucleus

- Electrons (-) in orbit

Atomic number

the number of protons in the nucleus of an atom and electrons

ex. atomic number 2 means 2 protons and electrons

atomic mass

number of protons and neutrons added together

Isotopes

Atoms of an element with different/unusual mass number

- different number of neutrons

Atom Stability

atoms become stable when their outermost shell is filled to capacity. Stable atoms tend not to react or combine with other atoms.

Atomic bonds

covalent, ionic, hydrogen

Ionic Bonds

An attraction between two oppositely charged ions

- Atoms give or take an electron

- Transfer of negatively charged electron changes charge of atom: "ion"

- WEAK BOND

Covalent Bonds

Atoms share electrons to become more stable

- sharing 1 electron: single bond

- sharing 2 electrons: double bond

- Max number of bonds per atom = # missing electrons

- STRONG BOND

- can be polar or nonpolar

nonpolar covalent bond

A type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity.

Hydrogen bond

An attraction between the slightly positively charged hydrogen atom of one molecule and the slightly negatively charged atom of another.

WEAK BOND

polar covalent bond

A covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.

LOOK FOR O and N, tend to grab electrons for themselves and are always polar

The Properties of Water

- Cohesion: molecules stick together

Adhesion: molecules stick to other polar molecules

- Surface tension: difficult to break surface

- High specific heat: takes a lot of energy/heat input to raise it's temperature

- High heat of vaporization: takes a lot of heat to cause it to evaporate

- Low density when frozen; ex. ice

- Ability to dissolve polar/ionic solutes

Hydrophilic

molecules with polar bonds are water-loving (mixes well)

Hydrophobic

molecules with nonpolar bonds are water-fearing (dont mix well)

pH

potential of hydrogen, how much hydrogen in a certain solution

- Acid: chemicals that add H+; low pH #

- Base/alkaline: chemicals that remove H+; high pH #

- pH scale: 1-14; 7 is neutral, each number is 10x change in H+ concentration

ex. lemon juice - 2 pH

tomato juice - 4 pH

There is 100x more hydrogen in lemon juice than tomato

- pH in living cells is near 7

pH buffers

compounds that help keep or prevent pH from changing drastically

- pH in living cells is near 7; they cannot survive pH changes so buffers help

Organic Molecules

molecules that contain carbon

Large form: polymer (many)

Individual subunits: monomer (one)

- Carbohydrates, Lipids, Proteins, and Nucleic acids

Carbon

essential for life because of its structure that has many vacancies allowing it to form many different bonds.

- makes up your "organic molecules"

- diverse: can make up to 4 bonds

Hydrocarbon

Organic molecules with carbon + hydrogen

- Simple carbon chain

- Nonpolar and hydrophobic

Functional groups

Addition of Functional groups changes a molecule's function.

- hydroxyl

- carbonyl

- carboxyl

- amino

- phosphate

- methyl

dehydration reaction (synthesis)

Chemical reaction that covalently bonds monomers together to build longer polymers with the loss of a water molecule

hydrolysis reaction

A chemical reaction that breaks apart a polymer by adding a molecule of water

When are organic molecules water soluble?

When they are polar (has N or O) because polar likes polar and water is polar

Carbohydrates

the primary fuel source for cellular mechanisms

- monosaccharide

- Disaccharide

- polysaccharide

struture: composed of primarily carbon, hydrogen, and oxygen

Monosaccharides

monomers of carbohydrates that provide cellular energy and are the building blocks for other organics

- fructose

-glucose

-galactose

Disaccharide

A double sugar molecule made of two monosaccharides bonded together through dehydration synthesis.

- provide cellular energy

- ex. maltose, sucrose, lactose

Polysaccharides

polymer of carbohydrates

- aka complex carbs

- made by dehydration synthesis

- stores energy in cells, structural

-ex. Starch, glycogen, cellulose, chitin

Good vs. Bad Carbohydrates

Mono and disaccharides - easy for body to use so give burst of energy but "bad"

Polysaccharides - complex for body to digest (complex carbs) so gives slow release of energy but "good"

Lipids

- Nonpolar hydrocarbons

- Consist of fats/oils (provide and store energy), steroids (signaling), and phospholipids (membranes)

Fats (solid) and oils (liquid)

- structure: Glycerol + triglyceride (3 fatty acid chains)

- There are Saturated Fats, Unsaturated fats, and Olestra

Olestra

a non-absorbable fat substitute made by attaching fatty acids to a sucrose backbone

- "fake fat"

- tastes like fat but can't be digested

Steroids

Lipids made of 4 rings of carbon

- Cholesterol: found in cell membranes

- Testosterone: male sex hormone

- Estrogen: female sex hormone

Phospholipids

Makes up cell membranes

- Phosphate + glycerol + 2 fatty acid chains

- Hydrophilic phosphate head (polar)

- Hydrophobic fatty acid tail (nonpolar)

Proteins

Nutrients the body uses to build and maintain its cells and tissues. Proteins are structural, regulatory, contractile, or protective.

- amino acids

- polypeptides

Amino acids

basic monomer of a protein

- 20 types and they differ in their side chain

- humans require 9 from food

- Made up of a central carbon atom+ hydrogen+ amino group + carboxyl group + side chain

Polypeptide

Polymer of a protein

- made up of many amino acids strung together

- infinite variety

Protein structures (conformation)

- Proteins fold to 3D structure

primary structure-chain of amino acids secondary structure- fold into helix tertiary structure-3D quaternary structure - protein consists of more than one amino acid chain