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cell structure and function > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

biomolecules

A

The molecules of living organisms
organic molecules
(carbon-containing compounds

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2
Q

Urey and Miller
the first cells had to arise from

A

the first cells had to arise from
nonliving chemicals, inorganic substances

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3
Q

Earth’s age

A

The Earth came into being about
4.54 billion years ago

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4
Q

4 stages of the Origin of life

A
  1. organic monomers
  2. Organic polymers
  3. Protocells or protobionts
  4. Protobionts acquire ability to self-replicate
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5
Q

explain Stage 1: Evolution of monomers
whatr the hypothesis for how monomers evolved?

A

Several hypothesis for how monomers evolved
1. monomers came from outer space
2. monomers came from reactions in the atmosphere
- molecules could be formed in the presence of outside energy sources using atmospheric gases
3. monomers came from reactions at hydrothermal vents

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6
Q

Miller and Urey Experiment

A

Stanley Miller and Harold Urey
conducted an experiment to test the
Oparin-Haldane hypothesis:
 Showed that gases (methane,
ammonia, hydrogen, and water) can
react with one another to produce
small organic molecules (amino
acids, organic acids)
 Strong energy sources
 Rainfall would have washed organic
compounds from the atmosphere
into the ocean.
 They would have accumulated in the
ocean, making it an organic soup.

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7
Q

Chemical Evolution at hydrothermal vents

A

Hydrothermal vents are chemical hot springs found
in seafloors.

  • They might have seeded life on Earth about 4 billion
    years ago.
  • Conditions including a 158°F (70°C) temperature
    are just right for chemical reactions responsible for
    the formation of amino acids and primitive
    membranes.
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8
Q

Explain stage 2: evolution of polymers
describe how polymers form and the 3 hypotheses

A

In cells, monomers join to form
polymers in the presence of enzymes.
A process known as polymerization.

Iron–Sulfur World Hypothesis:
 It suggests organic molecules reacted with amino
acids to form peptides in the presence of iron-nickel
sulfides.

Protein-First Hypothesis
 It assumes that protein enzymes arose first.
 DNA genes came afterwards.

RNA-First Hypothesis
 It suggests only RNA was needed to progress
toward the formation of the first cell or cells.
 Some viruses have only RNA genes.
 DNA genes would have come afterward.

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9
Q

Stage 3 evolution of Protocells

define proteinoids
define protocells
describe strucutre of protocells

A

Before the first true cell arose, there
would have been a protocell or
protobiont, the hypothesized
precursor to the first true cells

A protocell would have an outer
membrane and carry on energy
metabolism

Proteinoids are small polypeptides
with catalytic properties

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10
Q

Define and describe proteinoid and liposomes

A

When proteinoids are placed in
water, they form microspheres,
structures made of proteins with
many properties of a cell

If lipids are made available to
microspheres, lipids become
associated with microspheres,
producing a lipid-protein membrane

Lipids placed into water form cell-
sized double-layered bubbles called
liposomes

They may have provided the first
membranous boundary

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11
Q

liposomes

A

Lipids placed into water form cell-
sized double-layered bubbles called
liposomes

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12
Q

stage 4 : evolution of a self-replication system
Describethe 2 main hypotheses

A

2 main hypothesis
RNA - first
The first cell would have had an RNA gene that
directed protein synthesis.
 Reverse transcription could have led to DNA.
 RNA was responsible for both DNA and protein
formation

RNA - DNA -RNA - Protein

Protein First
The protocell would have developed a plasma
membrane and enzymes.
 Then, DNA and RNA synthesis would have been
possible.
 After DNA evolved, protein synthesis would have been
carried out according to the central dogma.
After DNA formed, the genetic code had to
evolve

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13
Q

cell

A

basic unit of biology

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14
Q

what 3 sciences converged to make cell bio

A

cytology
genetics
biochem

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15
Q
A
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16
Q

who named cells “cells”

A

Robert Hooke - 1665

he observed compartments formed by cell walls of dead plant tissue

he called these compartments cells

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17
Q

what two factors restricted progress in early cell biology

A

Microscopes had limited resolution, or
resolving power (ability to see fine detail)

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18
Q

compound microscope

A

1830s
had two lenses
improved magnification and resolution
could see structures 1um clearly

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19
Q

Robert Brown

A

identified the nucleus inside plants cells using the compound microscope

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20
Q

Mathias Schleiden

A

concluded that all plant
tissues are composed of cells

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21
Q

thomas Schwann

A

concluded that all ANIMALS
tissues are composed of cells

postulated the cell theory

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22
Q

Cell theory

A

Postulated the cell theory in 1839
1. All organisms consist of one or more cells.
2. The cell is the basic unit of structure for all
organisms

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23
Q

Rudolf Virchow
what year?

A

added to the cell theory in 1855
3. all cells arise only from preexisting cells

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24
Q

cytology

A

focuses mainly on cellular structure and
emphasizes optical techniques

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25
Q

biochemistry

A

focuses on cellular structure and
function

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26
Q

Genetics

A

focuses on information flow and heredity
and includes sequencing of the entire genome (all
of the DNA) in numerous organisms

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27
Q

Microscopy

A

crucial in helping cell
biologists deal with the
problem of small size of
cells and their
components

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28
Q

Micrometer

A

(μm), also called the micron, is
one millionth of a meter (10 -6 m

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29
Q

Size of bacterial cells vs plants vs animal

A

Bacterial cells are a few μm in diameter, whereas
cells of plants and animals are 10–20 times larger

Organelles are comparable to bacterial cells in size.

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30
Q

nanometer

A

The nanometer (nm) is used for molecules and
subcellular structures too small to be seen in the
light microscope
 The nanometer is one-billionth of a meter
(10-9 m)

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31
Q

angstrom (Å)

A

The angstrom (Å), which is 0.1 nm, equals about
the size of a hydrogen atom
It is used in cell biology to measure dimensions
within proteins and DNA molecules

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32
Q

light microscope

A

earliest tool of
cytologists

allowed identification of nuclei, mitochondria, and
chloroplasts within cells

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33
Q

light microscopy is also called

A

brightfield
microscopy because white light is passed directly
through a specimen

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34
Q

improvements in Microscopy

A

microtome -mid-1800s) allowed
preparation of very thin slices of
samples

dyes - A variety of dyes for staining cells
began to be used around the same
time

These improved the limit of resolution (how far apart objects
must be to appear as distinct)

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35
Q

the smaller the microscope’s limit of resolution, the…

A

greater its
resolving power (ability to see fine details)

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36
Q

Specialized Light Microscopy ( list the types)

A

Phase-contrast (PC) microscopy

 Differential interference contrast (DIC) microscopy

 Fluorescence microscopy

 Confocal microscope

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37
Q

Contrast Microscopy

A

Phase contrast and
differential interference
contrast microscopy
make it possible to see
living cells clearly

The phase of transmitted
light changes as it passes
through a structure with a
different density from the
surrounding medium

These types of microscopy
enhance and amplify these
slight changes

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38
Q

Fluorescence Microscopy

A

allows
detection of proteins, DNA sequences, or
molecules that have been made
fluorescent by binding to antibodies
( see slides for more)

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39
Q

antibody

A

protein that binds a particular
target molecule, called an antigen

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40
Q

GFP

A

Green fluorescent protein (GFP) can be
used to study the temporal and spatial
distribution of proteins in a living cell

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41
Q

Confocal microscopy

A

uses a
laser beam to illuminate a
single plane of a fluorescently
labeled specimen

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42
Q

Digital video microscopy

A

Digital video microscopy uses
video cameras to collect digital
images Microtubules in cultured cells (M. Engelke)

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43
Q

limit of resolution

A

refers to how far apart
objects must be to appear as distinct

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44
Q

resolving power

A

ability to see fine details

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45
Q

The resolution for a light microscope is related to

A

the physical nature of light

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46
Q

for visible light, the limit of resolution is about

A

200-350 nm

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47
Q

Electron Microscopy

A

The electron microscope, which
uses a beam of electrons rather
than light, was a major
breakthrough for cell biology

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48
Q

limit of resolution of electron microscope

A

about 100 times
better than light microscopes

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49
Q

electron microscopy magnification is

A

is much higher
than light microscopes—up to
100,000×

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50
Q

TEM

A

transmission electron microscopy - electrons are transmitted through the specimen

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51
Q

SEM

A

scanning electron microscopy (SEM), the
surface of a specimen is scanned by detecting
electrons deflected from the outer surface

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52
Q

Friedrich Wöhler

A

1828
showed that a compound made
in a living organism could be synthesized in the lab

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53
Q

Louis Pasteur

A

(1860s)
showed that yeasts could
ferment sugar into alcohol

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54
Q

The Buchners

A

1897) showed that fermentation could occur with yeast
extracts

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55
Q

enzyme

A

biological catalyst

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56
Q

Early biochem

A

fermentation pathways early 1920-1940s
Glycolysis - mulitple ppl
Krebs - hans krebs
ATP - Fritz lipmann
Calvin Cycle - Melvin Calvin

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57
Q

Subcellular fractionation

A

uses centrifugation to
separate/isolate different structures and macromolecules

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58
Q

Ultracentrifuges

A

are capable of very high speeds (over
100,000 revolutions per minute; rpm

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59
Q

Chromatography

A

techniques to separate molecules
from a solution based on size, charge, or chemical affinity

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60
Q

Electrophoresis

A

uses an electrical field to move
proteins, DN A, or RN A molecules through a medium
based on size/charge

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61
Q

Mass spectrometry

A

is used to determine the size and
composition of individual proteins

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62
Q

Genetics

A

Study of inheritance of characteristics from generation to generation

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63
Q

19th century =

A

discovery of the gene

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64
Q

Gregor Mendel

A

experimentation with peas which lead to the understanding of heredity factors from parents to offspring

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65
Q

Heredity factors are now known as

A

genes

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66
Q

mitosis

A

cell division
( knaned by walther Flemming

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67
Q

Who formulated the chromosome theory

A

Morgan, Bridges, Sturtevant

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68
Q

chromosome theory

A

proposing that Mendel’s hereditary factors are located
on chromosome

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69
Q

Friedrich Mischer

A

1869
first isolated DNA which he called nuclein

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70
Q

components of DNA

A

4 different nucleotides ( 1930s)

20 different amino acids = protein

DNA as the genetic material - 1940

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71
Q

one gene - one enzyme concept

A

Beadle and Tatum formulated the one gene–one enzyme
concept (each gene is responsible for the production of a single
protein)

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72
Q

who proposed the Double Helix model

A

Watson and Crick, with assistance from Rosalind Franklin, proposed the double helix model for DNA structure (1963)

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73
Q

who proposed the central dogma

A

Crick: central dogma of molecular bio

DNA ( transcription) - RNA ( translation) - protein

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74
Q

What are the three kinds of RNA molecules what what do they do?

A

mRNAs (messenger RNAs): translated to produce protein
rRNAs (ribosomal RNAs): components of ribosomes
tRNAs (transfer RNAs): bring the appropriate amino acid for protein synthesis

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75
Q

what are the exceptions to the central dogma

A

viruses with RNA genomes

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76
Q

reverse transcriptase

A

an enzyme that uses viral RNA to synthesize complementary DNA

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77
Q

recombinant DNA tech

A

restriction enzymes cut DNA at specific places, allowing scientists to create recomb. DNA molecules w/ DNA from different sources

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78
Q

DNA cloning

A

the generation of many copies of a specific DNA sequence

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79
Q

DNA transformation

A

process of introducing DNA into cells

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80
Q

sequencing DNA

A

DNA sequencing methods are used routinely for rapidly determining the base sequences of DNA molecules. It is now possible to sequence entire genomes (entire DNA content of a cell).

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81
Q

Bioinformatics

A

Comp sci & biology merged to interpret enormous amounts of sequencing and other data

Numerous bioinformatic tools are publicly available through NCBI (National Center for Biotechnology Information)

High-throughput methods allow for dramatic increases in the speed of molecular analysis

Expression levels of hundreds or thousands of genes can be monitored simultaneously
Ex: DNA Microarray Assay

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82
Q

CRISPR genome editing stands for

A

CRISPR = Clustered Regularly Interspaced Short Palindromic Repeats

see slide/come back to card

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83
Q

CRISPR is used as

A

a tool for genome editing

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83
Q

CRISPR was discovered as a

A

prokaryotic defense against
viral infection

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84
Q

Biological facts

A

Facts are provisional, dynamic and subject to change

a “fact” is an attempt to state our best current understanding of the world, based on observations and experiments

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85
Q

testing

A

Scientists seek to prove the null hypothesis, which is opposite to their hypothesis

The certainty of a particular hypothesis is strengthened when multiple attempts fail to confirm the null hypothesis

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86
Q

Experiments Test Specific Scientific Hypotheses
(idk how to make this a question)

A

First read peer reviewed sources, then formulate hypothesis
This may take the form of a model, which appears to be a reasonable explanation for the phenomenon

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87
Q

model organism

A

a species widely studied, well characterized, & easy to manipulate

Each has particular advantages, useful for experimental studies
Much of our knowledge is based on research using few organisms

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88
Q

cell cultures

A

Cell cultures are commonly used as model systems.
Cell cultures are used to study cancer, viruses, proteins, and cellular differentiation.
Some of what is learned from cultured cells may not reflect what happens within an intact organism

89
Q

In a typical experiment, one condition is varied, called the

A

independent

90
Q

The outcome is called the

A

dependent variable

91
Q

in vivo

A

experiments involve living organisms

92
Q

In vitro

A

experiments are done outside the living organisms
ex: in a test tube

93
Q

organic Chemistry

A

Study of carbon-containing compounds

94
Q

Biological chemistry

A

the study of
the chemistry of living systems

95
Q

the most important atom in
biological molecules

A

Carbon

96
Q

Carbon Atom

A

has a valence of 4, so it can form four
chemical bonds with other atoms

97
Q

Carbon is most likely to form what type of bonds

A

Covalent bonds

98
Q

Carbon atoms are most likely to form covalent bonds with

A

other carbon atoms and with oxygen (O), hydrogen (H),
nitrogen (N), and sulfur (S)

99
Q

Covalent Bonds

A

the sharing of a pair of electrons
between two atoms

100
Q

Hydrogen valence

A

Valence: 1

101
Q

Oxygen valence
(check)

A

Valence: 2?
shouldit not be 6

102
Q

Nitrogen valence

A

Valence: 3

103
Q

Single Bond

A

Sharing one pair of electrons
between two atoms forms a
single bond

104
Q

Double and Triple Bonds

A

Double bonds and triple
bonds involve two atoms
sharing two and three pairs of
electrons, respectively

105
Q

Whether carbon atoms form
single, double, or triple bonds
with other atoms, the total
number of covalent bonds
per carbon atom is

A

FOUR

106
Q

Stability is expressed as

A

Bond energy
aka the
amount of energy required to break 1 mole (~6 x
1023) of such bonds

107
Q

Bond energy is expressed as

A

calories per mole
(cal/mol)

 A calorie is the amount of energy needed to raise
the temperature of 1 g of water by 1ºC
 A kcal (kilocalorie) is equal to 1000 calories

108
Q

To break a covalent bond

A

energy is taken in

109
Q

are double bonds and triple bonds easy or harder to break

A

Double and triple bonds
are even harder to break

110
Q

solar radiation

A

slide page 3

111
Q

Hydrocarbons

A

are chains or
rings composed only of carbon
and hydrogen

ex. petroleum products, including
gasoline and natural gas, are
hydrocarbon

In biology, they are of limited
importance because they are
not soluble in water, except as
a component of biological

112
Q

Biological compounds normally contain…

A

These normally contain carbon, hydrogen, and one
or more atoms of oxygen, as well as nitrogen,
phosphorus, or sulfur

113
Q

functional
groups

A

These (O, N, P, S) are usually part of functional
groups, common arrangements of atoms that
confer specific chemical properties on a molecule

114
Q

important functional groups

A

Carboxyl and phosphate
groups (negatively
charged)

 Amino groups (positively
charged)

 Hydroxyl, sulfhydroxyl,
carbonyl, and aldehyde
groups (uncharged, but
polar

115
Q

Bond Polarity

A

In polar bonds, electrons are not shared equally
between two atoms
 Polar bonds result from a high electronegativity
(affinity for electrons) of oxygen and sulfur
compared to carbon and hydrogen
 Polar bonds have high water solubility compared to
C—C or C—H bonds, in which electrons are shared
equally

116
Q

WHat is carbon’s structure

A

tetrahedral structure

117
Q

When four atoms are
bonded to the four corners
of the tetrahedron, various
special configurations are
possible, called

A

sterioisomers

118
Q

Water has an indispensable role as

A

the universal solvent

119
Q

About x% of a cell by weight is water

A

About 75–85% of a cell by weight is water

120
Q

The high heat of vaporization makes water

A

an excellent coolant

121
Q

Osmosis

A

the process of water moving across cellular
membranes based on the concentration of solutes present

122
Q

Aquaporin (A QP)

A

a specialized channel protein that
allows for water to move more quickly than via osmosis

123
Q

 The most critical attribute of water is

A

its polarity,

124
Q

polarity,
which accounts for water’s:

A

Cohesiveness
 Temperature-stabilizing capacity
 Solvent properties

125
Q

what gives water its polarity

A

Unequal distribution of electrons
gives water its polarity

126
Q

water molecule shape

A

bent

127
Q

oxygen is highly….

A

The oxygen atom at one end of the
molecule is highly electronegative,
drawing the electrons toward it
 This results in a partial negative
charge at this end of the molecule,
and a partial positive charge around
the hydrogen atoms

128
Q

describe cohesion

A

Because of their polarity,
water molecules are attracted
to each other
 The electronegative oxygen
of one molecule is associated
with the electropositive
hydrogens of nearby
molecules

129
Q

Water is characterized by an extensive network of

A

hydrogen-bonded molecules, which make it
cohesive

130
Q

Cohesion is the result of

A

an extensive network of
hydrogen-bonded molecules,

131
Q

The combined effect of many hydrogen bonds
accounts for water’s high

A

Surface tension
 Boiling point
 Specific heat
 Heat of vaporization

132
Q

surface tension is the result of

A

s the result of the collective
strength of vast numbers of
hydrogen bonds
 Allows insects to walk along
the surface of water without
breaking the surface
 Allows water to move
upward through conducting
tissues of some plants

133
Q

Surface tension allows _____________ in some plants

A

Allows water to move
upward through conducting
tissues of some plants

134
Q

What gives water its its temperature-
stabilizing capacity?

A

High specific heat gives water its temperature-
stabilizing capacity
 Specific heat—the amount of heat a substance
must absorb to raise its temperature 1ºC
 The specific heat of water is 1.0 calorie per gram,
much higher than most liquids

135
Q

Describe Water’s temperature stabilizing capacity

A

Temperature-Stabilizing Capacity
 Heat that would raise the temperature of other
liquids is first used to break numerous hydrogen
bonds in water
 Water therefore changes temperature relatively
slowly, protecting living systems from extreme
temperature changes
 Without this characteristic of water, energy
released in cell metabolism would cause
overheating and death

136
Q

Describe heat of vaporization

A

Heat of vaporization is the amount of energy
required to convert 1 gram of liquid into vapor
 This value is high for water because of the many
hydrogen bonds that must be broken
 The high heat of vaporization makes water an
excellent coolant

137
Q

Why is water is able to dissolve a
large variety of substances?

A

Bc of its Polarity
Many of the molecules in cells are also polar and
so can form hydrogen bonds or ionic bonds with
water

138
Q

hydrophilic

A

Solutes that have an affinity for water and dissolve
in it easily are called hydrophilic (“water-loving”)

139
Q

Examples of hydrophilic molecules

A

Many small molecules—sugars, organic acids,
some amino acids—are hydrophilic

140
Q

hydrophobic def
ex. of hydrophobic molecules

A

Molecules not easily soluble in water—such as
lipids and proteins in membranes—are called
hydrophobic (“water-fearing”)

141
Q

NaCl in water

A

A salt, such as NaCl, exists as a
lattice of Na + cations (positively
charged) and Cl− anions (negatively
charged)
 For a salt to dissolve in a liquid, the
attraction of anions and cations in the
salt must be overcome
 In water, anions and cations take part
in electrostatic interactions with the
water molecules, causing the ions to
separate
 The polar water molecules form
spheres of hydration around the ions,
decreasing their chances of re-
association

142
Q

Solubility of Molecules with No Net Charge

A

Some molecules have no net charge at neutral pH
 Some of these are still hydrophilic because they
have some regions that are positively charged and
some that are negatively charged
 Water molecules will cluster around such regions
and prevent the solute molecules from interacting
with each other
 Hydrophobic molecules, such as hydrocarbons,
tend to disrupt the hydrogen bonding of water and
are therefore repelled by water molecules

143
Q

the importance of selectively permeable Membranes

A

Cells need a physical barrier between their contents
and the outside environment

 Such a barrier should be
 Impermeable to much of the cell contents
 Not completely impermeable, allowing some
materials into and out of the cell
 Insoluble in water to maintain the integrity of the
barrier
 Permeable to water to allow flow of water in and
out of the cell

144
Q

Membranes
whatare they and what are they composed of?

A

a hydrophobic
permeability barrier

 Consists of phospholipids, glycolipids, and
membrane proteins

Membranes of most organisms also contain sterols
—cholesterol (animals), ergosterols (fungi), or
phytosterols (plants)

145
Q

Glycolipids

A

sugars attached to lipids

146
Q

Membranes are also

A

amphipathic

147
Q

Amphipathic

A

they have both
hydrophobic and hydrophilic
regions

 Amphipathic phospholipids
have a polar head; the polarity
is due to a negatively charged
phosphate group linked to a
positively charged group
 They also have two nonpolar
hydrocarbon tails

148
Q

Polarity of the phospholipid head is due to

A

negatively charged group

149
Q

In water, amphipathic
molecules undergo

A

hydrophobic interactions

The polar heads of
membrane phospholipids
face outward toward the
aqueous environment
 The hydrophobic tails are
oriented inward
 The resulting structure is the
lipid bilayer

150
Q

A Membrane Is a Lipid Bilayer with

A

Proteins
Embedded in It

151
Q

Because of the hydrophobic
interior, a lipid bilayer is readily
permeable to

A

nonpolar molecules
However, it is quite impermeable
to most polar molecules and
highly impermeable to all ions

152
Q

What is the mebrane permeable and impermeable to ?

A

Permeable to nonpolar molecules

However, it is quite impermeable
to most polar molecules and
highly impermeable to all ions

Cellular constituents are mostly
polar or charged and are
prevented from entering or
leaving the cell
 However, very small molecules
diffuse

153
Q

How do ions pass through the membrane

A
154
Q

How does H20 and ethanol pass through the membrane

A

They are small uncharged polar molecules??

155
Q

How does O2 and Co2 pass through the membrane

A

Small nonpolar molecules so they diffuse

156
Q

How do cl-, and K+, Na+ pass through the membrane

A

Ion transport through transport proteins

157
Q

How are ions transported

A

Even the smallest ions are unable to diffuse across
a membrane

 This is due to both the charge on the ion and the
surrounding hydration shell

 Ions must be transported across a membrane by
specialized transport proteins

158
Q

Transport Proteins

A

Transport proteins act as either hydrophilic
channels or carriers

 Transport proteins of either type are specific for a
particular ion or molecule or class of closely related
molecules or ions

 Biological membranes are best described as
selectively permeable

159
Q

Most cellular structures are made of

A

ordered arrays
of linear polymers called macromolecules

160
Q

Important macromolecules in the cell

A

include
proteins, nucleic acids, and polysaccharides, and
( These three are built by polymerization)
and Lipids

161
Q

what is unique about lipids

A

share some features of macromolecules but
are synthesized somewhat differently

162
Q

Cellular Hierarchy

A

biological molecules and
structures are organized
into a series of levels,
each building on the
preceding one

Most cellular structures
are composed of small
water-soluble organic
molecules obtained from
other cells or synthesized
from nonbiological
molecules (CO 2 , NH 4 ,
PO 4 , etc.)

163
Q

Macromolecules Are Critical for

A

Cellular
Form and Function

164
Q

Hierarchical Assembly

A

The small organic
molecules then polymerize
to form biological
macromolecules

 Biological macromolecules
may function on their own
or assemble into a variety
of supramolecular
structures

 The supramolecular
structures are components
of organelles and other
subcellular structures that
make up the cell

165
Q

biological
macromolecules

A

The small organic
molecules then polymerize
to form biological
macromolecules

166
Q

supramolecular
structures

A

Biological macromolecules
may function on their own
or assemble into a variety

The supramolecular
structures are components
of organelles and other
subcellular structures that
make up the cell

167
Q

Lipids do not

A

go through the process of Polymerization

168
Q

How are macromolecules made

A

generated by the
polymerization of small
organic molecules

169
Q

Repeating units are called

A

Monomers

170
Q

Monomer of sugar or starch

A

Glucose

171
Q

Monomers of Proteins

A

amino acids

172
Q

Monomers of Nucleic acids

A

Nucleotides

173
Q

The major macromolecular polymers in the cell are

A

proteins, nucleic
acids, and polysaccharides

Nucleic acids and proteins have a variety of monomers that may be
arranged in nearly limitless ways; the order and type of monomer are
critical for function

 Polysaccharides, composed of one or two monomers, have relatively
few types

174
Q

exons

A

expressed

175
Q

introns

A

spliced out

176
Q

informational
macromolecules are

A

Nucleic acids are called informational
macromolecules because the order of the four
kinds of nucleotide monomers in each is non-
random and carries important information

 DNA and RNA serve a coding function, containing
the information needed to specify the precise amino
acid sequences of proteins

177
Q

Proteins

A

Proteins are composed of a nonrandom series of
amino acids

 Amino acid sequence determines the three-
dimensional structure, and thus the function, of a
protein
 With 20 different amino acids, a nearly infinite
variety of protein sequences is possible
 Proteins have a wide range of functions, including
structure, defense, transport, catalysis, and
signaling

178
Q

Proteins are composed of

A

nonrandom series of
amino acids

179
Q

Amino acid sequence determines

A

the three-
dimensional structure, and thus the function, of a
protein

180
Q

Protein functions

A

Proteins have a wide range of functions, including
structure, defense, transport, catalysis, and
signaling

181
Q

see table on page 14

A

go look at it

182
Q

Polysaccharides

A

Polysaccharides typically consist of single
repeating subunits or two alternating subunits
 The order of monomers carries no information and
is not essential for function
 Most polysaccharides are structural
macromolecules (e.g., cellulose or chitin) or storage
macromolecules (e.g., starch or glycogen)

183
Q

polysaccharides typically consist of

A

single
repeating subunits or two alternating subunits

184
Q

Polysaccharides
The order of monomers…

A

carries no information and
is not essential for function

185
Q

Most polysaccharides are

A

are structural
macromolecules (e.g., cellulose or chitin) or storage
macromolecules (e.g., starch or glycogen)

186
Q

Macromolecules Are Synthesized by

A

Stepwise Polymerization of Monomers

187
Q

production of most polymers follows basic
principles

A
  1. Macromolecules are always synthesized by the stepwise
    polymerization of monomers
  2. The addition of each monomer occurs by the removal of a water
    molecule (condensation reaction)
  3. The monomers must be present as activated monomers before
    condensation can occur
  4. To become activated, a monomer must be coupled to a carrier
    molecule
  5. The energy to couple a monomer to a carrier molecule is provided by
    adenosine triphosphate (ATP) or a related high-energy compound
  6. Macromolecules have directionality; the chemistry differs at each end
    of the polymer

( BE ABLE TO ORDER)

188
Q

primary protein strucutre

A

just a polypeptide no function
( 4 structures primary, secondary, tertiary, quaternary)

keratin - secondary structure

189
Q

Monomer activation

A

Monomers with available H and OH are activated by coupling them to appropriate carrier molecule, using energy from ATP or a similar high -energy compound

190
Q

Monomer Condensation

A

The first step in polymer synthesis involves the condensation of two activated monomers, with the release of one of the carrier molecules

191
Q

Polymerization

A

the nth step will add the next activated monomer to a polymer that already has n monomeric units

Elongation

192
Q

Carrier Molecules

A

A different kind of carrier molecule is used for each
kind of polymer

 For protein synthesis, amino acids are linked to
carriers called transfer RNA (tRNA)

 Sugars (often glucose) that form polysaccharides
are activated by linking them to ADP (adenosine
diphosphate), or UDP (uridine diphosphate)

 For nucleic acids, the nucleotides themselves
are high-energy molecules (ATP, GTP)

193
Q

Condensation

A

Activated monomers react with one another in a
condensation reaction, then release the carrier
molecule

The continued elongation of the polymer is a
sequential, stepwise process

194
Q

Hydrolysis

A

Degradation of polymers occurs via hydrolysis,
breaking the bond between monomers through
addition of one H + and one OH− (a water molecule)

195
Q

self-assembly

A

The principle of self-assembly states that
information needed to specify the folding of
macromolecules and their interactions to form
complex structures is inherent in the polymers
themselves

196
Q

molecular chaperones

A

Proteins called molecular chaperones are
sometimes needed to prevent incorrect folding

197
Q

Noncovalent Bonds and Interactions Are
Important in

A

the Folding of Macromolecules

198
Q

Many cellular structures are held together by what type of bonds

A

noncovalent bonds and interactions
 Hydrogen bonds
 Ionic bonds
 Van der Waals interactions
 Hydrophobic interactions

199
Q

Ionic Bonds

A

ionic bonds are strong noncovalent electrostatic
interactions between two oppositely charged ions
 They form between negatively charged and
positively charged functional groups
 Ionic bonds between functional groups on the same
protein play an important role in the structure of the
protein
 Ionic bonds may also influence the binding
between macromolecules

200
Q

Van der Waals Interactions

A

Van der Waals interactions (or forces) are weak attractions
between two atoms that occur only if the atoms are very
close to one another and oriented appropriately
 Atoms that are too close together will repel one another
 The van der Waals radius of an atom defines how close
other atoms can come to it, and it is the basis for space-
filling models of molecules

201
Q

Hydrophobic Interactions

A

Hydrophobic interactions describe the tendency of
nonpolar groups within a macromolecule to
associate with each other and minimize their
contact with water
 These interactions commonly cause nonpolar
groups to be found in the interior of a protein or
embedded in the nonpolar interior of a membran

202
Q

Many Proteins ____________ Fold into
Their Biologically Functional State

A

Spontaneously

203
Q

describe Spontaneous Folding

A

The immediate product of amino acid
polymerization is a polypeptide

 Once the polypeptide has assumed its correct
three-dimensional structure, or conformation, it is
called a protein

 The native (natural) conformation of a protein can
be altered by changing conditions, such as the pH
or temperature, or by treating with certain chemical
agents

204
Q

denaturation

A

The unfolding of polypeptides leads
to loss of biological activity (function)

205
Q

Renaturation

A

When denatured proteins are returned to conditions
in which the native conformation is stable, they may
undergo renaturation, a refolding into the correct
conformation
 In some cases, renaturation is associated with the
return of the protein function (e.g., ribonuclease)

206
Q

the spontaneity of polypeptide folding process

A

( Native molecule -> denatured -> renaturing -> renatured molecule)

Denaturation: First the folded polypeptide was exposed to denaturing conditions, resulting in a ribonuclease molecule with no fixed shape and no enzymatic activity

Renaturation- Then, renaturation conditions allowed the denatured polypeptide to return spontaneously to its native conformation, regaining enzymatic activity.

207
Q

molecular chaperones

A

Some proteins require molecular chaperones,
which assist the assembly process

 Molecular chaperones are not components of the
completed structures and they convey no
information

 They bind to exposed regions in the early stages of
assembly to inhibit unproductive assembly
pathways that would lead to incorrect structures

208
Q

self-assembly

A

The same principles of self-assembly that apply to
polypeptides also apply to the assembly of more
complex structures
 Ribosomes and membranes are capable of self-
assembly, for example

209
Q

prions

A

an infectious protein molecule, is a rare
example of self-assembly in proteins

210
Q

virus

A

A virus is a complex of nucleic
acids and proteins that uses living
cells to produce more copies of
itself via self-assembly

211
Q

what is a Tobacco Mosaic Virus

A

A good example is the tobacco
mosaic virus (TMV)
 It is a rodlike particle, with a single
RNA strand and about 2130
copies of a coat protein that form
a cylindrical covering for the RNA

212
Q

Self assembly of TMV

A

Self-Assembly of TMV Is Quite Complex
 The unit of assembly is a two-layered disc of coat
protein that changes conformation (from cylinder to
helix) as it interacts with the central RNA molecule
 This conformational change allows another disc to
bind and to interact with the RNA and thus to
change its conformation as well
 The process repeats until the end of the RNA
molecule is reached

213
Q

Spontaneity Self-Assembly of the Tobacco
Mosaic Virus (TMV)
steps

A

see slide 21

214
Q

Limits of Self-Assembly

A

Some assembly systems depend additionally on
information provided by a preexisting structure
 Examples
 Membranes
 Cell walls

215
Q

Hierarchical Assembly

A

Hierarchical assembly is the dependence on
subassemblies that act as intermediates of the
process of assembly of increasingly complex
structures

216
Q

Biological structures are almost always assembled

A

hierarchically

217
Q

Advantages of Hierarchical Assembly

A

Chemical simplicity—relatively few subunits are
used for a wide variety of structures
 Efficiency of assembly—a small number of kinds of
condensation reactions is needed
 Quality control—defective components can be
discarded prior to incorporation into higher-level
structure, reducing the waste of energy and
materials

218
Q

4 steps of CRISPR

A

C a s 9 protein is bound to the
targeted gene sequence with the help
of guide R N A

  • The targeted gene sequence is
    unwound and C a s 9 creates a
    double hyphen stranded break in it.
  • Repair without the addition of repair
    template results in gene disruption by
    deletions or insertions.
  • Recombination with the addition of
    repair template results in the
    correction or replacement of defective
    gene.
219
Q

If a piece of DNA called a repair template is
included

A

the cell can repair the break using a
process called homology‐directed repair

219
Q

When double stranded breaks are repaired,
the cell often introduces

A

erros

cell structure and function (8 decks)

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