Exam 2 Study Notes

Front 1

Cytosol

Back 1

Aqueous 'gel' of the Cell

Front 2

Biosynthetic Factory

Give example.

Back 2

Some that makes Biological molecules.

Example= Endoplasmic Reticulum

Front 3

Smooth ER

Back 3

Lipid Production....

Front 4

Rough ER

Back 4

Has Ribosomes and does Protein Production

Front 5

How does the protein 'know' to go into the ER?

Back 5

Signal Peptide= Cellular 'zip code'

Front 6

What happens to the protein in the ER?

Back 6

The protein folds through chaperones.

(if improper folding, the protein is destroyed)

Front 7

How can protein be Modified?

Back 7

Cleavage (cutting, slicing, dicing)
And
Attachment of Chemical Groups
Ex. Attach a polysaccharide= Glycoproteins

Front 8

Proteins and the Golgi apparatus.

Back 8

Shipping and receiving center...
Proteins leave the rough ER and travel to the Golgi apparatus.

Does the sorting/shipping.
Ships to the plasma membrane, to the outside of the cell (secreted),
Lysosome?

Front 9

Lysosome

Back 9

Digestive compartments/ Recycling Center.
Contains hydrolytic enzymes that break down macromolecules.
pH of compartment= around 5; optimum for hydrolytic enzymes.

Front 10

Lysosomal Storage Diseases

Back 10

Tay Sachs disease
Lysosomal enzyme normally breaks down lipid surrounding nerve cells.
Defective enzyme= lipid accumulates= nerve damage= death
Pompe's disease.
Mutation causing a non functional enzyme.
Glycogen builds up in muscle and liver cells= organ destroyed.

Front 11

Knock out mouse

Back 11

missing the defective enzyme== lives but muscle weakness.

Front 12

Cystic Fibrosis

Back 12

Mutation of the Cystic Fibrosis Transmembrane Regulator (CFTR)

Mislocalized, Misfolded, Misunderstood-- Protein doesn't go where its supposed to.

Pump doesn't work= sticky mucus.
DeltaF508 deletion= protein seen as abnormal and degraded in the ER

Front 13

Peroxisomes

Back 13

Break Down Molecules
ex. Fatty Acids (Cellular Mecromolecule)

!!!!!

Front 14

Mitochondria

Back 14

Chemical energy conversion--
Glucose + oxygen yields, water+ carbon dioxide+ ATP


The Powerhouse of the Cell

Front 15

Cellular respiration

Back 15

Energy extracted from chemical bonds in food, put into usable form (ATP)

Front 16

Chloroplasts

Back 16

Capture of light energy
Water + Carbon Dioxide + Light = Glucose + Oxygen

Front 17

Photosynthesis

Back 17

Conversion of solar energy to chemical energy.

Front 18

Cytoskeleton

Back 18

Functions= Structural Support, Motility, Cell division, regulation of cell activities.

Microfilaments= built up by Actin subunits
Intermediate Filament= ?
Microtubule= built up by Tubulin subunits

Front 19

Motor Proteins

Back 19

'Molecular motors' - Able to move along surface.
ATP causes shape change, allowing motor proteins to 'walk'

Front 20

Kinesin

Dynein

Back 20

Travel along microtubules between organelles

Front 21

Myosins

Back 21

travel along actin filaments (muscular system)

Front 22

Organic Molecules

Back 22

Carbon Containing-

ex. Carbohydrates
Proteins
Lipids
Nucleic Acids

Front 23

Nucleotides

Back 23

5-Carbon Sugar
Phosphate Group
Nitrogenous Base

Front 24

Nitrogenous Bases

Back 24

Cytosine
Adenine
Guanine
Uracil (in RNA)
Thymine (in RNA)

Front 25

DNA sugar/ # of strands
+
RNA sugar/ # of strands

Define.

Back 25

DNA= Deoxyribose, 2 strands
RNA= Ribose, 1 strands

Front 26

Name for many nucleotides added together..

Back 26

Polynucleotide

Front 27

What has directionality?

Back 27

Nucleic Acid

Front 28

-OH

Back 28

_OH?!?!?!?

what about it

Front 29

double-stranded helix?

Back 29

DNA

Front 30

DNA Strands are....

Back 30

Anti parallel -- meaning they run in opposite directions in accordance to its 3 prime and 5 prime ends

Front 31

Base pairings

Back 31

A to T
C to G
And vice versa...
Complementary base pairing (1 ring to 2 rings)... should have even width.

Front 32

Organization of DNA in Eukaryotic cells....

Back 32

Chromosomes= Long linear DNA molecules

Front 33

?!?!?

Back 33

?!!??!

Front 34

Basic Replication

Back 34

1. DNA strand is there.
2. Strands seperate.
3. New strands made- complementary to template strand.
4. Result: two DNA molecules identical to original.

Front 35

Replication Bubble

Back 35

?

Front 36

Replication Fork

Back 36

?

Front 37

Helicase

Back 37

Unwinds the double helix

Front 38

Topoisomerase

Back 38

Deals with the supercoiling of the helix.

Front 39

What stablizes the replication bubble?

Back 39

Single-stranded binding proteins.

Front 40

In what direction are new strands made for DNA

Back 40

5 prime to 3 prime.

Front 41

What will make a new complementary stand of DNA (to the template)?

Back 41

DNA Polymerase (III)

^ ^ ^ ^ ^ But^ ^ ^ ^ ^ ^ ^ ^ ^

Needs a 3 prime - OH to work.

Front 42

Primase

Back 42

Adds a short (about 100 nucleotides) to RNA primary. ====>> Single-stranded RNA complementary to DNA.

Front 43

Continuous Synthesis Leading Strand

Back 43

Starting at the DNA's 3 prime end.... The new RNA strand can run continuous towards the DNA's 5 prime end (thus, the RNA runs in the classic 5 prime to 3 prime direction).

Front 44

Discontinuous Synthesis Lagging Strand

Back 44

Where RNA still runs in the 5 prime to 3 prime direction, but in fragments since the DNA strand that it is on is split at the 5 prime end (see diagram).

Front 45

Okazaki Fragments

Back 45

Discontinuous Synthesis Lagging Strand.

Front 46

WHat remove the RNA primers

Back 46

DNA Polymerase (I)

^ ^ ^ ^ Also ^ ^ ^ ^ ^ ^

Fills in the gaps on the lagging strand created by the discontinuous fragments

Front 47

Ligase

Back 47

Connects the pieces of DNA at the end.

Front 48

Telomerase

Back 48

Elongates chromosomes ??

Front 49

Cell Senescence

Back 49

Death of the cell.

Limited to about 40 divisions/cell <= Then its too short after that.

Front 50

Why do cells die?

Back 50

1. Chromosomes too short
2. Loss of important genetic info?
3. With telomeres gone, chromosomes fuse/degrade.

Front 51

Telomerase

Back 51

Enzyme that can extend telomeres.

^ ^ ^ If a cell makes telomerase^ ^ ^
Then the chromosomes shorten.

Front 52

Where is Telemerase?

Back 52

Cells of Embryo's

Stem Cells

Front 53

Why isn't telemerase present in all cells?

Back 53

They could live forever

The fountain of youth!!

Front 54

Repairing mistakes in DNA synthesis?

Back 54

DNA polymerase has a proofreading function -- fixes most errors.

Front 55

If DNA polymerase misses mistakes....

Back 55

Mismatch Repair System.

For example, there is a mismatch amongst base pairs, That area gets chopped out by nucleases, then DNA polymerase rewrites, ligase closes it up?

Front 56

Excision Repair

Back 56

A thymine dimer distorts the DNA molecule

Fixes like Mismatch Repair System.

Front 57

Aeroderma Pigmentosum

Back 57

Skin Cancer

Caused by an accumulation of Thymine DImers

Front 58

Flow of information in the cell

Back 58

DNA gets transcribed, (RNA processing ensues), then turns into mRNA, mRNA exits the nuclear membrane, Translation occurs, now is a Polypeptide, which eventually turns into a functional protein.

Front 59

Transcription

Back 59

DNA into RNA.

Front 60

Types of RNA

Back 60

rRNA= Ribosomal RNA
tRNA= Transfer RNA
mRNA= Messenger RNA

Front 61

Does every one of your body cells contain your genome?

Back 61

Yes

About 30,000 genes in human genome

Front 62

What is a Gene?

Back 62

?!?

Front 63

How many genes are transcribed in any given cell type?

Back 63

A subset of genes

Front 64

Transcription (second notecard)

Back 64

DNA goes to mRNA

or

Gene goes to mRNA

Front 65

RNA Polymerase

Back 65

Enzyme that makes RNA molecule

Front 66

Regulatory proteins

Back 66

Influence rate of transcription

Front 67

Promotor

Back 67

Specific nucleotide sequence where RNA polymerase attaches and begins transcription

Front 68

Regulatory Sequence

Back 68

Site for binding of regulatory proteins

Front 69

Transcribed Region

Back 69

Information that specifies an amino acid.

Front 70

Terminator

Back 70

Signals end of transcription.

Front 71

Codon

Back 71

"word" that specifies which amino acid is put in polypeptide

Front 72

When is a tRNA considered "charged"?

Back 72

When an amino acid is attached to it.

Front 73

What will an anticodon bind with?

Back 73

A complementary Codon in mRNA

Front 74

Ribosomes

Back 74

Composed of proteins and rRNA's.
Made in the Nucleolus of the nucleus - cytosol.
Subunits join for protein synthesis.

Front 75

Cellular Respiration

Back 75

Glucose (C6 H12 O6) + 6 Oxygen (O2) yeilding 6 Carbon Dioxide (C O2) + 6 Water (H20) + ATP

Front 76

Phosphorylation

Back 76

Adding a phosphate to a protein.

Front 77

A protein is working when...

Back 77

It changes shape.

Front 78

Cristae

Back 78

Increase surface area of mitochondria

Front 79

Glycolysis (breakdown of sugars)

Back 79

Glucose converts to two pyruvate's (yields 2 ATPS)

Front 80

Pyruvate breakdown & Krebs cycle (Citric acid cycle)

Back 80

breakdown of pyruvates into Acetyl CoA

(basically yeilds 2 ATP)

Front 81

Substrate-level Phosophorylization

Back 81

Enzyme grabs Phosphate from a phosphorylated molecule and transfers it to ADP.


4 ATP's yielded.

Front 82

Electron Carriers

Back 82

Molecules that store electrons for later use

Front 83

Glycolysis/Krebs cycle

Back 83

Bonds broken/ new bonds formed

Electrons get shuffled (what happen to them????............oxidative phosphorylization)

Front 84

Two electron carriers

Back 84

NAD+ (ready to pick up electron)
NAD+ + electrons = NADH

FAD (ready to pick up electron)
FAD + electrons = FADH2

Front 85

During oxidative phosphorylization, the electrons carried by NADH and FADH2 are used....

Back 85

To make more ATP

Front 86

Study Mitochodrian, Oxydative Phoshorylization diagram

Back 86

On the back of lecture!!!

Front 87

players in the oxidative phosphorylation game

Back 87

1) The Mitochodrian
2) The Electron Transport Chain
Several Protein complexes in IMM.
All complexes accept/donate electrons.
3 complexes are also proton pumps.
3) Protons (H+, hydrogen ions)
4) Oxygen, the final electron acceptor.
5) ATP synthase.

Front 88

How many ATP's are made by OX PHOS?

Back 88

34

Front 89

How many ATP's are produced from an NADH? (per glucose molecule)

How many ATP's are produced from a FADH2? (per glucose molecule)

Back 89

NADH == 3 ATP/ glucose molecule

FADH2 = 2 ATP glucose per molecule

Overall= 30 ATP from all NADH's and 4 from all FADH2's.

Front 90

Anaerobic Respiration

Back 90

Lacking oxygen.
Single celled organisms can survive it.

Front 91

Cell cycle= regulated.....

where and what are the checkpoints for the cell?

Back 91

G1 checkpoint= Check cell size, DNA integrity.

G2 checkpoint= Check cell size, Completion of replication, DNA integrity.

Metaphase Checkpoint= Check that all chromosomes attached to kinetochores MT

Front 92

Proto-Oncogenes

Back 92

Genes that encode signals, receptors, signaling molecules, control proteins.

Front 93

If Proto-oncogenes are mutated

Back 93

Oncogenes= Cancer causing genes

Front 94

T/F= In a population, dominant alleles are more abundant.

Back 94

FALSE

Front 95

Huntington's Disease

Back 95

incurable, fatal neurological disease.

But, the allele for huntington's is dominant, BUT not common.

Front 96

Although a 2n individual can have only two alleles (at any one locus)...

Back 96

... There may be MULTIPLE alleles in a population.

ex. Blood Types.

Front 97

LOOK AT BLOOD TYPES

Back 97

DIFFERENT TYPES AND COMBINATIONS

Front 98

Pedigrees

Back 98

Family tree tracking through generations.

Genetic traits in humans can be tracked through this.

Front 99

T/F-- do dominant traits show up in every generation?

Back 99

TRUE

Front 100

How is the sex of an offspring determined?

Back 100

By the sex chromosome carried in the sperm.

Front 101

X Chromosome vs. Y chromosome

Back 101

X chromosome= lots of genes on the X chromosome.

Y chromosome= "genetic wasteland"

Front 102

Males are _______ for sex-linked genes.

Back 102

HEMIZYGOUS- (only one copy of that gene)

Front 103

If there is a mutation in an X-linked for a male....

Back 103

they will be affected fo sho.

Front 104

Females will be phenotypically normal if....

Back 104

...mutant allele is recessive.

Front 105

DO PUNANT SQUARE PROBLEMS
AND
PEDIGREES

Back 105

KNOW GENERAL RATIOS FOR PUNANT SQUARES

Front 106

Mutation

Back 106

Permanent change in DNA sequence

Front 107

Point mutation

Back 107

A single nucleotide base change in DNA

Front 108

Base pair mutation

Back 108

sometimes silent

Remember= Missense=different protein is added.

Effects depend on where the protein is changed.

Front 109

Sickle Cell Anemia

Back 109

Missense Mutation

Front 110

Prokaryotes reproduce by...

Back 110

Binary fission.

Front 111

Some eukaryotes reproduce by...

Back 111

mitosis/cytokinesis (asexual)

Front 112

Many eukaryotes consist of ...

Back 112

Two parents

Gamete production (through meosis)
Gamete meets gamete (mitosis?)

Front 113

Meosis's only use in eukaryote...

Back 113

Gamete production.

Front 114

In an animal... the female undergoes meosis to make...

Back 114

haploid egg.

Front 115

In an animal... the male undergoes meosis to make...

Back 115

haploid sperm.

Front 116

haploid egg + haploid sperm =

Back 116

Diploid zygote.

Front 117

T/F -- Daughter cells are not identical to parent?

Back 117

FALSE

Front 118

Nonsense

Back 118

Missense is which a stop message is in encoded.

Often very severe.

??

Front 119

Mitosis

Back 119

division of the nucleus

Front 120

Cytokinensis

Back 120

Division of cytoplasm and organelles

Front 121

Antibodies

Back 121

proteins that recognize and bind specific molecules

Front 122

What is epigenetics?

Back 122

The study of heritable changes in gene function without a change in the actual DNA.

Front 123

Based on the video and lecture, what types of chemical tag can modify gene
expression? Does this tag turn a gene on or off?

Back 123

?!?!?

Front 124

The video also talks about how DNA can become tightly wrapped
around histone proteins in the nucleus (see picture on right).
How could tightly wrapping DNA modify gene expression (genes
being transcribed into mRNA)?

Back 124

The piece of DNA doesn't get read???

Front 125

Typically, when agouti mice breed, most of the offspring are identical to the parents:
just as yellow, fat as pincushions, and susceptible to life-shortening disease. In a
fascinating experiment, scientists fed female agouti mice drugs that caused them to
methylate their DNA (the drug was given just before they mated with male agouti
mice).

What happened to the phenotypes of their offspring?

Back 125

They turned out norbal.

Front 126

Typically, when agouti mice breed, most of the offspring are identical to the parents:
just as yellow, fat as pincushions, and susceptible to life-shortening disease. In a
fascinating experiment, scientists fed female agouti mice drugs that caused them to
methylate their DNA (the drug was given just before they mated with male agouti
mice).

What did methylation do to the agouti gene that mothers passed to
their offspring?

Back 126

It "turn it off" the gene.

Front 127

It was originally thought that the pattern of an individual's epigenome was thought
to be firmly established during early fetal development. Although that is still seen as
a critical period, scientists have lately discovered that the epigenome can change in
response to the environment throughout an individual's lifetime.
What types of environmental factors are shown to be or could
potentially be important in shaping the epigenome?

Back 127

A drought that starved the individual or, on the other hand, a surplus of food.

Front 128

It was originally thought that the pattern of an individual's epigenome was thought
to be firmly established during early fetal development. Although that is still seen as
a critical period, scientists have lately discovered that the epigenome can change in
response to the environment throughout an individual's lifetime.

What happens to our epigenome when we age?

Back 128

?!?!?

Front 129

When scientists compared two types of mother rats - those that lick their offspring
after birth and those that neglect their newborns, they observed the following: The
licked newborns grew up to be relatively brave and calm (for rats). The neglected
newborns grew into the sort of rodents that nervously skitter into the darkest corner
when placed in a new environment. Further research has shown that licking
ultimately turns on genes that allow rats to deal with stress. These experiments
indicate that experience shapes behavior and experience shapes the epigenome.

What key experiment was carried out with these mice that indicated the epigenome,
unlike the genome, was changeable (how were non-licked mice made to act like mice
that had good parents)?

Back 129

?!?!?

Front 130

The critical period for epigenetic changes that are passed through several
generations appears to be during gamete formation. If your grandmother is passing
an epigenetic legacy to you, when is her critical period? What about your
grandfather? (When food supply available to grandparent affect future generations?)

Back 130

Grandmother= while she was in utero (an infant)-- the time when the grandmothers' eggs were forming.

Grandfather= Slow growth period, right before adolescence (when it's vital sperm making time).

Front 131

Effects of pesticide exposure have been seen through how many generations?

Back 131

3 generations (I believe)

Front 132

3 causes of genetic variation

Back 132

1) Crossing over. 2) Independent assortment. 3) Random Fertilization.

Front 133

Dominant allele

Back 133

fully expressed in the organisms appearance even if only 1 allele is present.

Front 134

Recessive allele

Back 134

No noticeable effect on phenotype if dominant allele is present.

Front 135

Mendel Genetics overview

Back 135

P(arent) generation : 1 purple x 1 white

F1 generation : 4 purples

F2 generation : 3 purples x 1 white

Front 136

Other reason animals eat...

Back 136

Raw material for cell structure- ATP
Essential Nutrients

Front 137

Ailmentary Canal

Back 137

Digestion System

Front 138

Four stages of food processing

Back 138

1) Ingestion (food enters body)
2) Digestion
3) Absorption
4) Elimination

Front 139

Mechanical digestion

Back 139

Physical breakdown of food (chewing)

Front 140

Chemical digestion

Back 140

Enzymatic breakdown of food molecules

Front 141

polymer's are introduced to enzyme's and create....

Back 141

Monomers

Front 142

Polysaccharides +/or disaccharides are introduced to enzymes in the stomach and turn into....

Back 142

Monosaccharide's

Front 143

Triglyceryl is introduced to enzymes in the stomach and turn into...

Back 143

Fatty acids + Glycerol

Front 144

Where does chemical digestion of carbohydrates begin?

Back 144

In the mouth

Front 145

Salivary amylase

Back 145

Breaks down starch

Front 146

What does Saliva consist of?

Back 146

1) Salivary Amylase
2) Mucin
3) Anti-microbial agents

Front 147

What does Mucin do?

Back 147

Lubricates food.

Front 148

What does antibacterial of the saliva do?

Back 148

It's our first line of defense.

Front 149

Bolus

Back 149

Food mixed with saliva

Front 150

Peristalsis

Back 150

Rhythmic movements of muscles that pushes food down to stomach.

Front 151

Bolus

Back 151

Food mixed with saliva

Front 152

What all does the stomach do?

Back 152

1) Churns Food.
2) Stores Food (although it isn't limitless)
3) Secretes Gastric Juice.

Front 153

When does chemical digestion in the stomach start?

Back 153

When Gastric Juice is secreted.

Front 154

Two gastric juices

Back 154

Hydrochloric Acid (HCL)

Pepsin
(Protease- Protein digesting enzyme).

Front 155

What do parietal cells secrete in the stomach (when food is present) that acts as a "inactive precursor"

Back 155

Pepsinogen (inactive form of pepsin)

Front 156

What do chief cells secrete (when food is present)?

Back 156

Hydrochloric Acid

Front 157

What is significant about the interaction between Pepsinogen and HCL?

Back 157

When HCL interacts with pepsinogen (the inactive form), it makes pepsinogen become active by turning into Pepsin.

Front 158

What is the purpose of mucus in the stomach?

Back 158

Protective layer for the stomach wall.

Front 159

What also happens in the stomach wall to protect it from pepsin destroying it?

Back 159

RAPID MITOSIS.

Front 160

3 : 1 ratio...

Back 160

Heterozygous x Heterozygous

Front 161

1 : 1 ratio...

Back 161

Heterozygous x Homozygous recessive.

Front 162

Chemotherapy

Back 162

Inserts chemicals into bloodstream. Prevents mitosis. Shorten MT- Stop replication.

Front 163

Radiation Therapy

Back 163

Energy particles end up destroying DNA- destroying the cell.

Front 164

Antibodies

Back 164

Proteins that bind onto receptors, blocks or shuts down cell response.

Front 165

Antisense Drug

Back 165

Single stranded nucleic acid.
Binds to mRNA strand which blocks translation (makes mRNA double stranded)

Front 166

Epigenetics Therapy

Back 166

Turns genes on/off (demethylization/ methylization)

Front 167

Angiogenesis Inhibitors

Back 167

Blocks formation of blood vessels.

Front 168

Thymine dimers

Back 168

bumps everything down..


what else?

Front 169

Endoplasmic reticulum

Back 169

Makes proteins and adds chemical groups (like carbohydrates) then sends them to golgi apparatus.