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bio 107 unit 1 > unit chapters 2+3, 4+5, 6, 7 > Flashcards

unit chapters 2+3, 4+5, 6, 7 Flashcards

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1
Q

what is an element?

A

A substance that cannot be broken to another substance by a chemical rxn

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2
Q

What is matter?

A

is anthing that has a mass or takes up space, and is madde up of diff chemical compounds which are made up of elememts.
All orgainisms are made of of matter

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3
Q

What is a compound

A

a substance consiting of 2 or more elements in a fixed ratio

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4
Q

what are the 4 componets that make up 96% of biological mass?
Hint: CHNO

A

charbon, hydrogen, nitrogen, oxygen

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5
Q

what is an atom?

A

is the smallest unit of matter that still retains the same properties of an element

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6
Q

what forms a cloud around the nucleus?

A

electrons in shells

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7
Q

What do protons and neutrons form?

A

An atomic nucleus

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8
Q

protons and electrons

A

both are elctrically charged. Eact proton has a positive charge and Each electron has a negatve charge

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9
Q

3 kinds of particle of relevence

A

Protons, neutrons and electrons

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10
Q

what is the atomic number?

A

of protons in the nucleaus
Since all atoms of a particlucar eleemnt have the same # of protons in the nuclei. The # of protons is uqine to that element

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11
Q

atomic mass

A

of protons - # of neutrons
the atoms tottal mass can be approximated by the mass #

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12
Q

Isotopes

A

When atoms have more neutrons than other atoms of the same element causing greater mass

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13
Q

valence electrons

A

The electrons outermost shell
group 1 has 1 electron, group 2 have 2 electronts ect.

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14
Q

incomplete valence electrons

A

atoms with incomplete valence electrons share or transfer valnce electrons with other atoms

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15
Q

what is hybridization?

A

bonding of 2 atoms involves mixing to form chemical bonds

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16
Q

Orbitals

A

The three dimensional shape where an electron is found 90% of the time, each electron shell consists of a specific number of orbitals.

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17
Q

4 main types of Orbitals ( s,p, d and f)

A

they depend on the sub level, thurs carying more or less electronns

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18
Q

How many orbitals can an electron have?

A

they can have 2 orbitals max

ex). the p sublevel has 3 orbitals therefore 6 electrons max,
the d sublevel has 5 sublevels therefore 10 electrons max

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19
Q

what is a covalent bond?

A

The sharing of a pair of valence elecrons by 2 or more atioms
the structursl formula H-H
involves sharing valcne electrons between diff atoms

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20
Q

Polar bond

A

one atom attracts more than the other
ie). Water is a polar bond because the electrons spend more time with the oxygen atom because it has a stronger pull than hydrogen

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21
Q

non-polar

A

bonded atoms shared evenly

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22
Q

bonding capactity

A

the valence usually equals the # of unpaired electrons required to complete the atom’s outermost shell

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23
Q

Three bonding capacity

A

A single covalent bond (Single Bond) involves sharing one pair of valence electrons ( made up of only sigma bonds)

A double covalent bond (Double Bond) is sharing two pairs of valence electrons ( 1 sigma + 1 pie bonds)

Triple covalent bonds shares three pair of valence electrons ( sigma + 2 pie bonds )

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24
Q

Electronegativity

A

Measure of an atom’s attraction for the electrons in a covalent bond
Their numbers go from bottom left : is the lowest and the top right : is the highest
The more electronegative an atom, the more strongly its pulls share electrons toward itself ie). -oxygen is electronegative( pulls electrons towards itself)

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25
Q

Stable bonds

A

Stable isotopes are naturally occurring forms of chemical elements. These stable isotopes can occur naturally in atomic form or in combination with other atoms.

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26
Q

unstable bonds

A

Unstable isotopes undergo radioactive decay until they get a stable state. These isotopes are known as radio topes

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27
Q

ionic bonds

A

Atoms sometimes strip electrons from their bonding partners
After the transfer of an electron, both atoms gain chargers
Compounds formed with ionic bonds are ionic compounds ( salts like sodium chloride)

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28
Q

intramolecular forces

A

Forces of attraction between molecules (solubility, boiling points, density, state of matter and melting points are affected between molecules)
Neutral molecules are attracted to one another :
Hydrogen bonding, dipole-dipole interactions and dispersion forces

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29
Q

4 weak forces

A

Electrostatic interactions
Hydrogen bonds
Van Der waals force
Hydrophobic effects

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30
Q

what is Electrostatic interactions?

A

Forces between non covalent and charged ions
charge - charge interactions eg forms crystals structure of NaCl
Water disrupts the electrostatic interactions to dissolve many salts

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31
Q

hydrogen bonds

A

The hydrogen atom covalently bonded to an electronegative atom is also attracted to another electronegative atom. The hydrogen atom has a particle positive charge that allows it to be attracted to different electronegative nearby
The bonds are weaker than covalent bonds but are one of the strongest non-covalent bonds.
Hydrogen bonds require less energy to break.
Hydrogen bonds will be positioned into tetrahedral arrangements.

Water acts as a solvent to dissolve polar and ionized solutes into aqueous solutions

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32
Q

Van Der waals force

A

Individually weak and occur only when atoms and molecules are very close together.
Weak forces between nonpolar due to random fluctuations in electron charge
Every time the electrons vibrate they quickie becomes unevenly charged
ie) Van Der Waals theory explains how geckos can climb up a wall!

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33
Q

Hydrophobic effects

A

weak repulsive force that drives non polar to separate from poplar molecules. Drives a separation of Hydrophobic and Hydrophilic molecules ie). Water and oil

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34
Q

what are the 4 properties of water?

A

coheisive behaviour, temperature moderator,expansoion upond freezing, excellent solvent

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34
Q

coshesion and adhesion

A

Cohesion : is the hydrogen bonds holding substanced together
-helps transport water against gravity in plants

Adhesion : attraction between different substances ie) the plant separating the water

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34
Q

all bio moleculea are carbon-based

A

4 valence elctrons = can form 4 bonds
bonds easily with O,N,H
high enegry storage with c-c or c-h bondd

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35
Q

what is a polymer

A

A polymer is a long molecule consisting of many similar or identical buildings linked by covalent bonds.

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36
Q

what is a monomer

A

The repeating units that serve as building blocks of a polymer are similar molecules

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37
Q

carbohydrates

A

monosaccrides ( one ) to ploysaccrides

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38
Q

proteins

A

amino acids to polypeptieds

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39
Q

nucleodties

A

nucleice acids ( DNA RNA )

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40
Q

what is the dehydration reaction ( polymerization)

A

: a reaction in which two molecules are covalently bonded to each other with the loss of water molecules.
each monomer contributes part of the water molecule that is released during the rxn: One monomer provides a Hydroxyl group (OH-), while the other provides a Hydrogen (H).
this reaction builds a polymer chain

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41
Q

what is hydrolysis

A

process that essentially the reverse of dehydration rxn.
The bond between monomers is broken by the addition of a water molecule, with a hydrogen from water attaching to one monomer and hydroxyl group attaching to the other. An example of hydrolysis in our bodies is digestion

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42
Q

monoaaccrides

A

one or a smiple sugar

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43
Q

disaccrides

A

2 and are double sugar consitiong of two mactomoleus joined by a covalent bond

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44
Q

polysaccrides

A

more than two suagrs

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45
Q

most common monosacchirdes are

A

Glucose - 6C aldose sugar used for energy storage
Fructose- 6C ketose sugar used for energy by plants
Ribose- 5C aldose sugar used in nucleotides (DNA/RNA)
Ribulose-5C ketose sugar used for metabolism and photosynthesis
Glyceraldehyde - 3C aldose sugar initial breakdown product of glucose
Dihydroxyacetone - 3C Ketose sugar also is an initial breakdown product of glucose

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46
Q

monosachrides either have:

A

aldehyde (aldose) or ketone (ketose) functionality

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47
Q

Disaccharides :

A

consists of two monosaccharides joined by a Glycosidic linkage , a covalent bond formed between two monosaccharide by a dehydration reaction

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48
Q

Polysaccharides:

A

are macromolecules, polymers
with a few hundred to a few thousand monosaccharides joined
by Glycosidic linkage.

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49
Q

storage for polysacchrides

A

for engery and starchs, glycogen

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50
Q

strucual polymers

A

provide mechanical stregth (cellulose, chitin)

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51
Q

what are the amnio acids core structure?

A

Amino and carboxy functional groups, variable side groups

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52
Q

how do polypeptides form?

A

by dehydration (condensation) of amino acids and carboxly groups to form a poly pepetide

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53
Q

what are polypeptides

A

have the same peptide backbone with a wide variety of side groups/chains. Extending from the backbone are the different side chains (R groups) of the amino acid. Each specific polypeptide has a unique linear sequence of amino acids. Note that one end of the polypeptide chain has a free amino group,

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54
Q

acidic amino acids

A

those with side chains that are generally negative in charge due to the precise of the carboxyl group, which usually dislocates at cellular PH

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55
Q

basic amino acids

A

have amino groups in their side chain that are generally positive in charge, Because they are charged acidic and basic side chains are also hydrophilic

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56
Q

peptide bonds

A

polypeptides are formed by condensation ( dehydration ration with the removal of a water molecule) of one amino group and one carboxy group to form a Peptide bond ( amide).

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57
Q

primary structure of amino acids

A

is the linear sequence of amino acids ( N→ C ).

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58
Q

secondairy structure

A

is the result of hydrogen bonds between the repeating constituents of the polypeptide backbone (not the amino acids).

59
Q

The tertiary structure

A

is the overall shape of a polypeptide resulting from interactions between the si

60
Q

what detremines a protein structure?

A

A polypeptide chain of a given amino acid sequence can be arranged
into three- dimentail shape determined by the interactions responsible
for secondary and tertiary structure.
This folding normally occurs as
the protein is being synthesized in the crowded environment within
the cell, aided by other proteins.

61
Q

protein folding

A

Quaternary structures include assembling multiple polypeptides
( identical or different subunits) into one final protein.

62
Q

misfolindg proteins

A

Changing the primary sequence or other changes can cause a protein to misfold. ex siclkle cell

63
Q

compimentary strands

A

– each can serve as a
template for the reciprocal strand, but they are not identical

64
Q

DNA

A

DNA provides directions for its own relocation. DNA is the genetic material that organisms inherit from their parents.

65
Q

each chromosome contains how much DNA?

A

one long strand

66
Q

RNA

A

each gene along a DNA molecule directs synthesis of a type of RNA called messenger RNA (MRNA). The MRNA molecule interacts with the cell’s protein synthesizing machinery to direct the product of a polypeptide

67
Q

Gene flow

A

DNA→RNA→ Protein.

68
Q

where is the site of protein synthesis

A

in the ribosome

69
Q

what does MRNA do

A

messenger template for protein synthesis

70
Q

what is composed of a nucleotide?

A

composed of three parts: nitrogen containing (nitrogenous) base, a five carbon sugar ( a pentose) and one or more phosphate group

71
Q

Pyramid family of DNA

A

cytosin, thymine, adenine, guanine

72
Q

pyramid family of RNA

A

cytosin, uracil , adenine, guanine

73
Q

complimentary bases

A

the specific pairing of A-T and C-G ( or if RNA = A-U )

74
Q

can RNa be compimentary to DNA

A

Yes. RNA can also be complementary to DNA – we can generate RNA
from a DNA template (& vice versa)

75
Q

what do nuclotides have

A

have a ribose/deoxyribose sugar, a variable nucleoside base, and 1-3
phosphate residues
› Nucleotides are common in the cell as an energy currency due to the high energy of phosphoanhydride bonds

76
Q

polynucleotide

A

has a built in directionality along its sugar-phosphate backbone from 5’to 3’, somewhat a one-way street.

77
Q

what is the “two free ends”

A

of the polymer are distantly different from each other. One end has a phosphate attached to a 5’ carbon, and the other end has a hydroxyl group on a 3’ carbon –referred as the 5’ end and the 3’ en

78
Q

DNA structure

A

DNA (double stranded) base pairs with a second complementary strand
- forms an antiparallel double helix structure with a sugar phosphate backbone and complementary nucleotide base pairs at the center.

79
Q

RNA

A

Rna has a less defined structure and can form many different shapes. Complementary base pairings can occur, however, between two regions of RNA molecules or even between two stretches of nucleotides in the SAME RNA molecule.

80
Q

where is RNA produced from?

A

is produced from a DNA template and can hybridize (base pairs between RNA-DNA)

81
Q

tRNA

A

transfers amino acids during protein synthesis

82
Q

rRNA

A

ribosomal structure and function.

83
Q

Lipids

A

they form from large assemblies rather than polymers they are also amphipathic simalr to biomonmers but are not covalnelty linked

84
Q

amphipathic

A

having both hydrophilic and hydrophobic parts

85
Q

fatty acids

A

long carbon skeleton usually 16 or 18 carbon atoms in length.The carbon at one end of the skeleton is part of the carboxyl group. The rest of the skeleton consists of a hydrocarbon chain.
they are also no-polar thats why they are hydrophobic

86
Q

Saturated fats

A

straight hydrocarbon chains, tightly packed, at room temp the molecules in saturated fat such as lard or butter are packed closely together forming a solid.Also found in mammals
- If there are no double bond between carbon atoms composing a chain= saturated fat because the chain is saturated in hydrogen bonds

87
Q

unsaturated fats

A

kinked, packed loosely, fats of plants and fishes are built with one or more types of unsaturated fatty acids. Usually liquid at room temp. Usually referred to as oils.

-If there are one or more double bonds, with one fewer hydrogen atom on each double bonded carbon.= unsaturated fat

88
Q

phospholipids

A

Two fatty acids attached to glycerol phosphate rather than three. The third group of glycerol is joined to a phosphate group, which has a negative charge in the cell

89
Q

mammels typically have how many saturated and unsatureated fats?

A

Major lipids found in cell membranes. In mammals typically one saturated and one unsaturated fatty acyl group.

90
Q

lipid assembles

A

spontaneously form assemblies driven from hydrophobic forces. ( water interacts favorably with head groups, repels fatty tails). Have emergent properties like biopolymers but not covalently linked, does not require energy to assemble.
Assemblies are impermeable to other polar molecules

91
Q

Cholesterol

A

is the parent compound of sterols and steroids. All share a ridged fused ring structure. Highly hydrophobic with minimal hydrophilic -OH headgroup.
which is wedge between phospholipid molecules in the plasma membrane of animal cells, has different effects on membrane fluidity at different temperatures.
Cholesterol can be thought of as a Fluidity buffer.

92
Q

cell membranes

A

stable strcutures formed from assembly of amphipathic lipids

93
Q

lipid biylayers

A

are semi-permeable–most polar molecules cannot cross

94
Q

membrane proteins

A

Protein with hydrophobic amino acids can be amphipathic and span bilayers.

facilitate transport, signal transduction, cell-cell recognition, intercellular contact,enzyme functions and attachment to cytoskeleton and extracellular matrix.

95
Q

membrane fluidity

A

is regulated to maintain a constant viscosity

96
Q

increase in fluidity

A

with temperature, unsaturated fatty acids, cholesterol

97
Q

decrease in fluidity

A

with saturated fatty acids

98
Q

fluid mosaic modle

A

proteins are embended within the lipid bilayer
Lipids and proteins are mobile within the plane of the membrane (lateral).
Lipids and proteins cannot readily move across the plane of the membrane (transverse).

99
Q

lipid fluidity

A

Lipids with unsaturated fatty acids do not pack well together
lipids with saturated fatty acids pack well togther

100
Q

how do we meaure membrane fluidity?

A

melting when transiting from less fluid gel phase to a fluid phase
Saturated fatty acids give bilayers a higher melting point than unsaturated fatty acids.
-Cells regulate fatty acid content to maintain the same fluidity at different temps.

101
Q

intergal proteins

A

They penetrate the hydrophobic interior of the lipid bilayer. The majority are transmembrane proteins which span the membrane. The other integral proteins extend only partway into the hydrophobic interior.

102
Q

Peripheral proteins

A

are not embedded in the lipid bilayer at all ; they are appendages loosely bound to the surface of the membrane. signaling enxymes

103
Q

passive transport

A

Requires no energy expenditure but only moves substances down a concentration gradient. The concentration gradient itself represents potential energy and drives diffusion
-Simple diffusion (Osmosis)
- Facilitated diffusion

104
Q

Active transport:

A

requires energy to move substances up a concentration gradient
-Transport ATPasses (uniporters)

105
Q

Simple Diffusion ( Osmosis )

A

The cell membrane is semi-permeable
Allows free passage of H20, O2, CO2
Blocks polar molecules (glucose)
In a semi permeable membrane water moves to equilibrate solute concentrations
This movement of water can build pressure across a membrane

106
Q

Osmotic pressure:

A

movement of water across the cell membrane and the balance of water between the cell and its environment are crucial to organisms.

107
Q

Indirect active transport- co-transport (symport or antiport)

A

couples active transport of ions (Na+/H+) to drive other solutes
up a concentration gradient (cells establish membrane potential)

108
Q

Transport- Diffusion

A

Solutes diffuse from high to low concentration
-Gases ( O2, CO2) and hydrophobic compounds can freely diffuse across bilayers
Transport proteins can provide specific (Facilitated) passage for Polar molecules across the membrane.

109
Q

transfer protein 1 Channel proteins:

A

simply provide corridors that allow specific molecules or ions to cross the membrane

110
Q

transfer protein 2 Carrier proteins

A

such as glucose transporter, seem to undergo a subtle change in shape and somehow translocates the solute-binding sit across the membrane.
-Glucose transport into cells is passive

111
Q

Glucose transport

A

Glucose transport is a specific form of facilitated diffusion
Glucose only travels from high to low concentration BUT only glucose can pass through the GLUT transport protein

112
Q

Na+ / K+ Active transport

A

Na+ / K+ ATPase is a transporter in every (animal) cell
ATP hydrolysis provides energy to transport both ions up a concentration gradient.
ATP can power active transport by transferring its terminal phosphate group directly to the transport protein. This can introduce the protein to change its shape in a manner that translocates a solute bound to the protein across the membrane.
One transport system that works this way is the Sodium and potassium pump : which exchanges Na+ for K+ across the plasma membrane of an animal cell.
3 Na+ are exported
2K+ are imported per ATP hydrolyzed

113
Q

Membrane potential

A

Mostly used for indirect active transport
Cells maintain ions at an imbalance across the plasma membrane
-Na+ /K+ in animal cells
- 3 Na+ per 2K+ transport creates a charge imbalance
This creates a differential charge across the membrane→ Membrane potential : is used to drive indirect active transport.

114
Q

Human heath- Cystic Fibrosis

A

Lung Mucus is regulated partly by
active transport of Cl-
Cystic fibrosis is caused by a mutation in a
lung Cl- transporter (CFTR- cystic fibrosis
transmembrane conductance regulator)
CF leaves an individual susceptible to lung
infections and damage

115
Q

Bulk transport

A

Macromolecules are too large to move through transport proteins and
require bulk transport routes
Like active transport, these processes require energy.

116
Q

Exocytosis ( exit)

A

The cell secrets certain molecules by the fusion of vesicles with the plasma membrane.

117
Q

Endocytosis (enter)

A

The cell takes in molecules and particles matter by forming new vesicles from the plasma membrane

118
Q

Phagocytosis (cellular eating)

A

very large particles

119
Q

Pinocytosis ( Cellular drinking)

A

bulk fluid uptake

120
Q

Receptor- mediated endocytosis-

A

specific particle uptake (L.D.L

121
Q

Low density Lipoproteins

A

The Uptake of LDL is receptor mediated and driven by forming a clathrin coat.
There can be defects in the LDL receptor that causes heart disease. ie) clogged arteries from cholesterol will result in a heart attack.

122
Q

prokayotes

A

– lack internal organelles, circular DNA organized into nucleoid
– lack all membrane-bound organelles, equivalent functions occur
across the plasma membrane (e.g. in-folds of PM form thylakoids)

123
Q

Eukaryotes

A

internal membrane-bound organelles, linear DNA organized within the nucleus

124
Q

Eukarya origins

A

originated with endosymbiotic capture of aerobic bacteria (mitochondria) and later cyanobacteria (chloroplasts)

125
Q

organells

A

increase the internal membrane surface area allowing for
larger cells and specialization of functions

126
Q

organelle membranes

A

lipid bilayers ( plasma membranes)

127
Q

Nucleus

A

double membrane (envelope) with large nuclear pores for transport

128
Q

Endoplasmic reticulum

A

continuous membrane with nuclear envelope

129
Q

Rough ER

A

studded with ribosomes for protein synthesis

130
Q

Smooth ER

A

lacks ribosomes, lipid and carbohydrate synthesis

131
Q

Golgi apparatus

A

–receives newly synthesized protein from ER, packages and ‘matures’ for export or delivery to the plasma membrane

132
Q

Lysosomes

A

contain digestive enzymes for breaking down organelles (autophagy) or
ingested material (phagocytosis/phagosomes)

133
Q

Endomembrane system

A

responsible to export newly synthesized material ( Anterograde), mport nutrients, food, other material (Retrograde)

134
Q

Anterograde flow

A

[Nuclear membrane] —> Endoplasmic reticulum—> Golgi —> Lysosomes—>Plasma membrane

134
Q

Retrograde flow

A

Plasma membrane—>Lysosomes —> Golgi —>Endoplasmic reticulum —> [nuclear membrane]

135
Q

Vacuole

A

various fluid-filled organelles (e.g. plant central vacuole – turgor)

136
Q

Mitochondria

A

site of respiration (produces ATP from sugar)
› Respiration occurs across the highly folded inner membrane
power house of the cell

137
Q

Chloroplasts

A

site of photosynthesis (produces ATP from light + CO2
fixation)
› Occurs across the inner membrane – highly folded into thylakoid stacks

138
Q

Peroxisomes

A

contains reactions that produce peroxides and enzymes to break
down peroxides

139
Q

Cytoskeleton

A

internal cellular structure, support, shape, movement

140
Q

Microtubules

A

largest, tubular, rigidity, transport, axoneme motility (the central strand of a cilium or flagellum. It is composed of an array of microtubules, typically in nine pairs around two single central ones.)

141
Q

Microfilaments

A

smallest, fibrous, tension, transport, amoeboid motility and muscle contractility

142
Q

Intermediate filaments

A

intermediate size, cell structure, external structures (hair, nails)

143
Q

Cell wall / extracellular matrix

A

external support, rigidity or flexibility, bioactive

144
Q

Rigid cellulose walls

A

support plants, contain turgor pressure
» Low permeability – cells form plasmodesmata to overcome barrier

145
Q

Flexible collagen ECM

A

supports animal cells, highly porous
» Hydrated, solutes move freely, identify and support tissues and biologically active

146
Q

functional groups

A

hydroxyl and carboxly, amino acids phospate methyl conboxyl

bio 107 unit 1 (1 decks)

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