BI108 test 1

spilios BU

comparative experiments

look for differences between samples that may differ in multiple unknown ways. compares manipulated data from different groups

controlled experiments

manipulate one or more factors being tested. control group and experimental group are the same besides one variable of interest

What does an experiment consist of?

1. **O**bservation
2. **Q**uestion
3. **H**ypothesis
4. **P**rediction
5. **D**esign

The P value must be less than what number to safely reject the null hypothesis?

.05

Levels of biological organization (descending order)

1. Biosphere
2. Ecosystem
3. Community 
4. Population
5. Organism
6. Organ Systems
7. Tissue
8. Cell
9. Organelle 
10. Molecule

what is within the nucleus : what surrounds the nucleus

protons and neutrons : electrons

what is a chemical reaction

change in the distributions of electrons between atoms

how do van der waal interactions work?

temporary dipoles are formed as electrons move around the nucleus. Temporary partial positive and negative charges can cause a temporary interaction.

how is internal temp maintained

because of the large amounts of water in living tissues. it takes a large amount of energy to change the form of water.

what do acids do in water

release hydrogen ions H+ → resulting molecule is negatively charged

What do bases do in water

release hydroxide ions OH-, can accept H+ → resulting molecule is positively charged

what do functional groups do

influence the properties and behavior of macromolecules

state the name and polarity of this functional group

methyl: nonpolar

state the name and polarity of this functional group

hydroxyl: polar

state the name and polarity of this functional group

sulfhydryl: polar

state the name and polarity of this functional group

aldehyde: polar

state the name and polarity of this functional group

keto: polar

state the name and polarity of this functional group

carboxyl: charged acidic

state the name and polarity of this functional group

amino: charged basic

state the name and polarity of this functional group

phosphate: charged acidic

why aren’t lipids a “true” polymer?

because their individual monomers are not covalently bonded to eachother

describe the structure of a triglyceride

three fatty acid chains + glycerol backbone. connected through ester bonds formed by condensation reactions

describe the structure of a phospholipid

two fatty acid chains + glycerol backbone + a phosphate group. hydrophilic head with the charged phosphate group and hydrophobic tails made of the hydrocarbon fatty acids

amphipathic

a molecule with opposing chemical properties

where does a phospholipid bilayer form

in aqueous solutions

how are phospholipid molecules joined together in the bilayer

through non covalent forces

what are the uses of carbohydrates

1. a form of energy storage (within chemical bonds)
2. Used to transport stored energy 
3. carbon skeletons for the production of other molecules 
4. Extracellular structures

Monosaccharides

simple sugars. can have 5 carbons (pentose) or 6 carbons (hexose) within.

describe the structure of hexoses

six carbon sugars can exist in a ring form or straight chain form. ring forms are favored in aqueous solutions

What differentiates alpha and beta glucose

In Alpha, the hydroxyl group is out of plane. In Beta, the hydroxyl group is in plane

Dissacharides

2 monosaccharides joined together through glycosidic linkages

alpha glycosidic linkages

found in starch and glycogen molecules. bent branched easy to break.

beta glycosidic linkages

found in cellulose which humans can’t digest. linear bonds hard to break.

Oliigosaccharides

3-20 monosaccharides joined by glycosidic linkages. often see additional functional groups attached

where are oligosaccharides commonly found

bonded to proteins and lipids on cell surfaces acting as recognition signals

Polysaccharides

giant polymers of monosaccharides

examples of polysaccharides

1. starch (glucose storage in plants)
2. glycogen (glucose storage in animals)
3. cellulose (strong. found in plants)

integral proteins (location)

hydrophobic portion embedded within the lipid bilayer (amphipathic

anchored proteins (location)

covalently attached to lipids which insert into the lipid bilayer

peripheral proteins (location)

not embedded within the lipid bilayer, but may interact with integral proteins or phospholipid heads (likely polar/charged)

Selective permeability

some substances can pass through while others cannot

diffusion

the net process of random movement toward equilibrium. net movement remains directional until equilibrium is reached

Osmosis

the diffusion of water across membranes from a region of lower solute concentration to higher solute concentration

aquaporins

category of pores that increase the permeability of water

relative concentration of solutes

* Hypertonic: higher solute concentration outside of the cell
* Isotonic: equal solute concentrations
* Hypotonic: lower solute concentration outside of the cell

two categories which describe the movement of solutes across a membrane

passive transport + active transport

simple diffusion (passive)

many small, nonpolar, uncharged, or hydrophobic molecules can simply pass through the membrane. (remember there are no covalent bonds in the bilayer. They’re just hanging out close together)

mechanisms of facilitated diffusion (passive)

1. carrier proteins: Integral transmembrane proteins that **temporarily bind** to substances and move them through the bilayer
2. channel proteins: Integral transmembrane proteins that form a channel without binding

ion channel (channel protein)

Integral transmembrane protein - spans the entire length of the bilayer. most are gated: either by a ligand or chemical signal.

what is a ligand

any molecule/ion that binds to a protein by noncovalent bonds

active transport

moves substances against a concentration/electrical gradient and requires an input of energy (often ATP)

sodium potassium pump (primary active transport)

found in all animal cells. cells break a bond in ATP to release enough free energy to move ions against the concentration gradient. (1ATP = 3 Na out 2 K in)

exocytosis

material in vesicles is **expelled** from a cell

endocytosis

material is **brought into** a cell

components of a prokaryotic cell (bacteria and archaea):

* Most have a plasma membrane and cell wall
* no membrane bound nucleus or other compartments

components of a eukaryotic cell (plants, animals, protists, fungi)

* nucleus and other organelles are membrane-bound
* some have cell walls (not animals)

what are the internal and external structures of the cell?

1. extracellular support
2. the cytoskeleton
3. organelle structure

Where is the cell wall (extracellular support) found?

Plants, archaea, bacteria, fungi, and some protists have cell walls exterior to the cell membrane

What is the purpose of the cell wall

provides support. It can provide protection and structural integrity

What do animals have rather than a cell wall?

An extracellular matrix (complicated structure outside of the cell membrane)

what is the extracellular matrix made up of?

large assemblages of proteins and proteoglycan (protein and sugar molecules covalently bonded to proteins)

what are the functions of the extracellular matrix?

1. holds cells in tissues
2. orients cell movement
3. can have filtering properties
4. can have recognition properties
5. contributes to physical properties of cartilage, skin, etc.

what is the cytoskeleton?

a network of protein filaments and tubules in the cytoplasm, giving cells shape and coherence

nucleoid

region that contains the bacterial chromosome

nucleus

largest organelle, surrounded by nuclear envelope

cytoplasm

liquid component of a cell and all the material within it (besides the nucleus)

Prokaryotes relation to membrane

prokaryotes do not have membrane-bound organelles

the three components within eukaryotic cells:

Microfilaments, microtubules, intermediate filaments

functions of the cytoskeleton

1. Supports and maintains cell shape 
2. Holds organelles in position 
3. Moves organelles


1. Interacts with extracellular structures to hold the cell in place

Nucleus in eukaryotic cells

usually the largest organelle, membrane-bound, site of DNA replication and expression

what is the name of the membrane surrounding the nucleus

the nuclear envelope

Function of nuclear envelope

controls movement of molecules into or out of the nucleus (ex: RNA molecules are transported out of the nucleus as genes are expresssed)

Eukaryotic cells membrane system

Endomembrane system (within the membrane).

network of interconnected membranes in the cytoplasm

Movement through vesicles

what is within the Eukaryotic cells’ membrane system

1. Nuclear envelope
2. Endoplasmic reticulum 


1. Smooth and rough
2. Golgi apparatus

Rough endoplasmic reticulum (RER)

rough due to ribosomes attached

newly made proteins enter the RER where they are modified, folded, and transported to other regions

Smooth endoplasmic reticulum (SER)

More tubular than RER, no ribosomes

chemically modifies small molecules

modifies proteins

Golgi Apparatus

made of flattened sacs and small membrane-enclosed vesicles

receives protein from the RER and can further modify them

concentrates, packages, and sorts proteins

Ribosomes

site of protein synthesis

not membrane-bound. similar structure in both prokaryotic and eukaryotic cells

ribosomes in eukaryotic cells

in eukaryotic cells, there are free ribosomes as well as ribosomes bound to the RER

Mitochondria

the powerhouse of the cell.

energy in fuel molecules is transformed into the bonds of energy-rich atp

cells that require lots of energy can have many mitochindria

molecules with a double membrane system

mitochondria, chloroplast

chloroplast

unique to plant cells, site of photosynthesis (light energy is converted to the energy of chemical bonds)

what is this

the base structure of an amino acid

Which amino acid group are these a part of

positively charged polar amino acids

Which amino acid group are these a part of

negatively charged polar amino acids

Which amino acid group are these a part of

uncharged polar amino acids

Which amino acid group are these a part of

nonpolar amino acids

special cases

Which amino acid group are these a part of

cysteine

Terminal sulfhydryl group which can form disulfide bridges

glycine

Can greatly impact the 3 dimensional structure of a larger protein because its tiny

Proline

Really bulky which prohibits bending

how are amino acids bonded together

with covalent peptide bonds in condensation reactions

where is the bond in a protein

peptide bond between the amino group and the carboxyl group

Primary structure of a protein

basic sequence of amino acids

solely maintained by covalent bonds between amino acids

\

how many different amino acids exists

20

secondary structure of a protein

introduces fold and bends into the shape

alpha helices and beta pleated sheets

how are alpha helices and beta pleated sheets maintained

hydrogen bonds between the chains

Tertiary structure of a protein

larger bent 3-dimensional structure

dictated by interactions between the side chains

how are tertiary structures formed

any category of interaction between amino acids (mostly noncovalent with some covalent bonds - disulfide bridges)

Tertiary structure is determined by interactions between…

R groups (side chains attached to the alpha carbon of an amino acid)

* Hydrogen bonds
* Disulfide bridges 
* Van der Waals interactions
* Ionic interactions