Bio2 Exam 1 From Notes

Front 1

Metabolism

Back 1

The sum of all chemical reaction occurring in a cell.

Front 2

Anabolism

Back 2

Synthesis of larger molecules from smaller (forming chemical bonds; protein/lipid/dehydration synthesis)

Front 3

Catabolism

Back 3

Breakdown of larger molecules to make smaller (hydrolysis)

Front 4

Endergonic

Back 4

(anabolic reactions) energy must be supplied

Front 5

Exergonic

Back 5

(catabolic reactions) Energy is released; most energy used to maintain our body temp.

Front 6

Energy

Back 6

The capacity to do work

Front 7

Kinectic Energy

Back 7

actively engaged in doing work now

Front 8

Potential Energy

Back 8

Stored energy

Front 9

Work

Back 9

Causing a change

Front 10

Thermodynamics

Back 10

Study of energy transformations;heat is produced

Front 11

1st Law (In energy and metabolism)

Back 11

Energy can be changed from one form to another, but it cannot be created or destroyed.

Front 12

2nd Law (in energy and metabolism)

Back 12

Energy is transformed from one form to another.
Some will be lost. (as heat)
Useful energy cannot be 100% recycled.
Spontaneously converts to other less organized forms.

Front 13

Heat

Back 13

Heat is the energy of random molecular motion.

Front 14

Responsible for the flow of energy in living things (Ameripress notes p.2)

Back 14

Kinetic chemical energy (Oxidation-Reduction Reactions)

Front 15

Oxidation-Reduction Reactions

Back 15

Electrons pass from one atom or molecule to another.

Front 16

Oxidation

Back 16

Loss of electrons

Front 17

Reduction

Back 17

Gain of electrons

Front 18

Enzymes

Back 18

Protein molecules that function as catalysts.
Lowers the energy of activation required by a reaction.

Front 19

Activation Energy

Back 19

Energy required to initiate a chemical reaction

Front 20

Identify three categories relative to determining a nation's needs and interests?

Back 20

In the book, Making Strategy--An Introduction to National Security Processes and Problems, Donald Nuechterlein provides a useful way of distinguishing between various interests. The three categories are how crucial is an interest to the United States, how vital is an interest to the United States, and which basic interest is at stake?

Front 21

Structure of Enzymes

Back 21

Large;
Globular;
One or more polypeptide chains;
Folded to create groove for active site

Front 22

Factors affecting enzyme activity (rate)

Back 22

Enzyme Concentration
Sub. Conc.
Temp.
pH.
Inhibitor Conc.

Front 23

Saturation Point

Back 23

The amount of enzyme(or sub.) in a solution the reaches a concentration enough that it will affect the reactions no longer.

Front 24

Inhibitor

Back 24

A molecule that decreases the rate of an enzymatic reaction.

Front 25

Competitive Inhibitor

Back 25

Another molecule is so close in shape to the substrate or a portion of the substrate that it competes with the substrate for the enzyme's active site

Front 26

Allosteric Inhibitor

Back 26

Molecule binds to enzyme at a site other than the active sire and changes the configuration of the enzyme enough so that it cannot bind to the substrate.

Front 27

Inhibition

Back 27

Common means by which cells regulate enzyme activity.

Front 28

Affinity (Preference)

Back 28

Enzymes are attracted to inhibitor rather than substrate.

Front 29

Feedback Inhibition

Back 29

A type of allosteric (changes enzyme) inhibition

Front 30

Cofactors

Back 30

Low molecular weight substances essential for enzyme function
(Ex. K+, Ca2+, Mg2+;mostly ions)

Front 31

CoFACTOR functions (2 of them)

Back 31

-Function in transporting electrons either donating or receiving them
-Function to change the shape of a substrate and/or enzyme

Front 32

Coenzymes

Back 32

Large, non-protein, organic molecules needed for enzyme function (not ions)
(Dependent on vitamin intake)

Front 33

CoENZYME functions (2 of them)

Back 33

-Transporting electrons; donating or receiving them
-Change shape of substrate and/or enzyme

Front 34

ATP

Back 34

Adenosine Triphosphate - Carrier of energy

Front 35

Functions of ATP (Chemical, Transport, Mechanical)

Back 35

Chemical Work - forms covalent bonds;usually synthesis
Transport Work - active trans; vesicle trans; pinocytosis; phagocytosis; receptor mediated endocytosis
Mechanical Work - movement; muscle contraction; flagella moving.

Front 36

Why ATP is a good carrier (3 reasons)

Back 36

1. Recognized throughout cell
2. Releases small amounts of energy (little water)
3. Energy is released in s step-wise manner, which again results in less waste.

Front 37

What is genetic Material? (4 requirements)

Back 37

1. Carry large amounts of info.
2. Be able to direct accurate replication
3. Chemically stable
4. Capable of mutation

Front 38

DNA (History)

Back 38

-1st Isolated by F. Miescher (1869)
-Called 'nuclein' since he found it in only the cell nuclei
-Then amended name to nucleic acid
-Then deoxyribonucleic acid
-5 C sugar that is missing an O

Front 39

R. Feulgen

Back 39

(1914)
-Discovered DNA has strong affinity for red-eye fuchsin (WTF is that?)
-Feulgen (fuchsin) staining revealed DNA was present in all cells' located in the chromosomes.

Front 40

Griffith Experiment

Back 40

Transforming factor; swapping of DNA; hereditary information was being changed. (The picture of the junkie rat that OD'ed)

Front 41

D.A Levene

Back 41

Showed that DNA could be broken down into:
1: 5 C Sugar
2. P Group
3. 4 Nitro Bases

Front 42

D.A Levene's correct assumption and the wrong one.

Back 42

Correct: Each Nitro Base is drawn to a sugar, which is drawn to a P group to form a Nucleotide.

Incorrect: The 4 nitro's are in equal amounts and clustered into groups of 4. (tetranucleotide) [Disproved by Chargaff]

Front 43

O. Avery (General)

Back 43

Exps. 16 years: 1st to use enzymes to purify specific compounds. Used DNA, RNA, Protein.

Front 44

O. Avery (5 step exp.)

Back 44

1. DNA caused bacteria to transform. DNA used was 99.98% pure.
2. Enz. that digest proteins had no effect on transformation, nor did RNase & enzyme that digests RNA
3. Enzymatic digestion of the transforming substance with DNase did prevent transformation.
4. The molecular weight of the trans. sub. contained ~1600 Nucleotides (allows variability)
5. Found DNA carries genetic info. and it has to be intact.

Front 45

Viruses

Back 45

small infectious agent that can replicate only inside the living cells of organisms.
Made of Protein and a Nucleic Acid.

Front 46

Bacteriophage

Back 46

parasites of bacteria hosts; most complicated shape for viruses.

Front 47

Virus Anatomy: 6 parts.

Back 47

1. Capsid - protein sheath
2. DNA
3. Neck
4. Tail - injection device
5. Base Plate
6. Tail FIber - allows virus to attach to specific host

Front 48

Hershey-Chase Experiment

Back 48

Experiment will all the radioactive stuff. P10 Ameripress.

Front 49

E. Chargaff (2 rules)

Back 49

Determined % composition of Nitro bases in diff. animals.
1. Proportions of the 4 bases are the same in all cells of a given species.
2. The proportion of purines equal that of pyrimidines.

Front 50

Rosalind Franklin & Maurice Wilkins

Back 50

Used x-ray diffraction (crystallography) data that showed giant double helix.
Found the structure/shape of DNA but didn't know what it was composed of. (Chargaff got that one).

Front 51

Watson & Crick

Back 51

Stole Franklin and Chargaff's info. and put it together to create the structure of the DNA molecule.

Front 52

DNA

Back 52

A double stranded polymer, more stable as a double helix; hydrogen bonds are stronger.

Front 53

DNA Structure (7 Specifics)

Back 53

1. 360' turn will be 3.4 nm in length; 10 base pairs in.
2. .34nm between each monomer (nucleotide) on each strand
3. right handed helix; rotates to the right
4. helix is 2nm wide
5. the P and sugar group of the nucleotides are on the outside of the strands
6. Acts as on acid
7. double-stranded polymer

Front 54

Phosphodiester Bond

Back 54

Bonds Nucleotides together; happening in the nucleus during the S phase.

Front 55

Ester Bond

Back 55

When an O single bonds to a carbon that is part of a sugar; made from dehydration synthesis.

Front 56

Anti-parallel

Back 56

The two strand s are in opposite orientation.

Front 57

Parental Duplex

Back 57

Original DNA

Front 58

Daughter Duplexes

Back 58

2 copies of original DNA
-Each daughter strand has a template and a new strand.

Front 59

Semi-Conservative Replication

Back 59

Only synthesizing one strand with the other using a template

Front 60

Polymerization

Back 60

Constructs the monomers by dehydration synthesis first before attaching them together; (p-s-base)

Front 61

Topoisomerase

Back 61

Family of enzymes that acts as one to change the structure of parental duplex
Sub: Super-coiled parental duplex
Product: relaxed (uncoiled) parental duplex

Front 62

Helicase

Back 62

Breaks the H bonds between the complimentary bases on the 2 strands; parental must be relaxed first
Sub: relaxed (uncoiled) parental duplex.
Product: 2 complimentary single strands (templates)

Front 63

Leading Strand

Back 63

Once 3' end is exposed the shape fit into RNA primase right away

Front 64

Continuous polymerization

Back 64

adding nucleotides one at a time to the 3' end of the new strand

Front 65

RNA Primase

Back 65

Enzyme that is the initial step in starting process of polymerizing from 5' to 3'
-polymerizes a short sequence of RNA nucleotides that are complimentary to the 3' end.

Front 66

RNA

Back 66

Nucleic Acid; A,C,G,U; single stranded; Ribose sugar (rather than deoxy);
Substrate: exposed 3' end of a template
Product: RNA Primer

Front 67

RNA Primer

Back 67

10-15 sequences of nucleotides that is complimentary to DNA Template.
This is the substrate for DNA polymerases.

Front 68

DNA Polymerase (What it is)

Back 68

Large Enzyme that attaches to the primer on the template (has RNA and DNA)

Front 69

DNA Polymerase Functions (4)

Back 69

1. Removes RNA primer 1 at a time,
2. Attaches DNA Nucleotides to the new strand. (From 5' to 3')
3. Proof Reads in reverse order (From 3' to 5')
4. Error Correction

Front 70

Lagging Strand

Back 70

Multi-Complicated; segments are 300-400 nucleotides long.
Goes from 5' to 3'

Front 71

Discontinuous Polymerization

Back 71

We are polymerizing the new strand in pieces (Lagging)

Front 72

Okazaki Fragments

Back 72

The pieces in a lagging strand that is polymerized separately.

Front 73

Lagging Strand steps (3)

Back 73

1. A 300 nucleotide area is exposed to the RNA primase, puts down the RNA primer, then pops off at end of segment.
2. DNA polymerase attaches laying down the DNA nucleotides then pops off at the end of the segment. This makes the Okazaki fragment
3. DNA Ligase forms last phospho-group that the DNA polymerase couldn't, connects the Okazaki fragments

Front 74

DNA Replication

Back 74

Bi-directional; Copying of DNA.

Front 75

Replication Bubble

Back 75

Where DNA is initiated in numerous origins in the middle of a DNA Strand.

Front 76

Keri Wallace

Back 76

Came up with the technique to use archeabacteria enzymes to replicate eukaryotic DNA

Front 77

Repetitive DNA

Back 77

Same Sequence repeated on same strand.
Large quantity in Eukaryotes
None in Pro's

Front 78

Highly Repetitive sequences (Satellite DNA)

Back 78

5-15 base pairs repeated 100k-1m times.
Too short to be copies of genes, maybe structural.
More of these; more centromeres and chroms. a cell has.

Front 79

Moderately repetitive sequences

Back 79

1k-1.5k base pairs repeated 1000's of times.
Likely multiple copies of same genes.

Front 80

Transposons

Back 80

"Jumping Genes"
Genes that move.
Barbara McClintock Nobel Prize 1983

Front 81

B-DNA (Wat/Crick Model)

Back 81

Thought to be a more dormant form of DNA. (See Z-DNA for Comparison)

Front 82

Z-DNA (Common Structural Isomer)

Back 82

Narrow (<2nm)
Contains 12bp per 360 degrees.
ZigZag Pattern
Left Handed Helix
Thought to be DNA in a more active form.

Front 83

Transcription

Back 83

Use part of DNA as template to produce strand of RNA (in nucleus)

Front 84

Translation

Back 84

Use RNA template to create protein (in cytosol)

Front 85

Promoter Region

Back 85

Sequence of DNA Nucleotides on the DNA strand that has a specific shape that provides "start" signal for transcription

Front 86

Terminator Region

Back 86

RNA polymerase encounters a specific sequence of nucleotides, with a specific shape, where it knows to jump off.

Front 87

RNA Polymerase

Back 87

Polymerizes in 5' to 3'
Breaks H bonds of base pairs on DNA strand
(Initial Substrate - promoter region)

Front 88

Exon

Back 88

Expressed sequence of DNA nucleotides at some time in the life of the organism.

Front 89

Intron

Back 89

In between sequence of DNA that are never expressed in ant cell, at any time.
(Pro's don't have these)

Front 90

mRNA Process 1
(2 steps)

Back 90

1. A GTP modifies the 5' end so it can fit through nuclear pores. When it goes through pores it used 2 P's for energy to open the pore, then becomes GMP
2. Poly Adenine Tail attaches to 3' so enzymes won't cut off useful info as it goes through nuclear pore. (1-300 adenines)

Front 91

mRNA Process 2
(2 steps)

Back 91

1. Splicesome - collection of enzymes to excise the introns and splice together the exons. Forms continuous exon.
2. Introns will then be recycled.

Front 92

2 Theories for Introns

Back 92

1. no function (used to be used till trait is no longer needed)
2. Increases physical distance among exons, providing a greater chance for crossing-over to occur, thus increasing frequencies of genetic recombination.

Front 93

Gene

Back 93

Nucleotide sequence that codes for 1 polypeptide chain.

Front 94

mRNA

Back 94

messenger RNA; are compliments of DNA sequence (transcripts). Dictates the sequence of amino acids in a polypeptide.

Front 95

rRNA

Back 95

ribosomal RNA; structural component together with proteins of ribosomes

Front 96

tRNA

Back 96

transfer RNA; 40 kinds, each carrying a specific amino acid and having an anti-codon comp. to mRNA codon

Front 97

Codon

Back 97

3 nucleotide sequence on mRNA

Front 98

Ribosomes

Back 98

Composed of small and larger concaved units.
mRNA goes through small space between the 2 subunits
Read the mRNA

Front 99

Ribosome subunits

Back 99

Small Subunit - one RNA molecule and 21 different proteins
Large Subunit - 2 RNA molecules and 34 different proteins

Front 100

Start Codon

Back 100

Initiates the translation; codes for only 2 amino acids

Front 101

Stop Codon

Back 101

Ends the Translation; doesn't code for any amino acid

Front 102

Polysome

Back 102

a collection of ribosomes reading a single mRNA strand.

Front 103

Translation

Back 103

Protein Synthesis.
Only occurs when 2 ribosomal subunits come together
(Pic on ameripress 20)

Front 104

Karyotope

Back 104

A photograph representation of chromosomes present in a single nucleus of a somatic cell. (Can be obtained from blood, etc)

Front 105

Aminocentesis

Back 105

Used to detect major genetic problems.
Collection of sloughed off fetal cells in amniotic fluid, used in conjunction with ultrasound.

Front 106

DNA Mutations

Back 106

Change in Base sequence
Caused by Mutagens (chemicals, UV, X-ray, etc.)

Front 107

Substitution (Mutation)

Back 107

Usually less severe in its effects; single nucleotide sub., usually no effect.

Front 108

Additions and Deletions

Back 108

Results in framseshifts, effects usually more severe due to more changes in amino acid sequence.
Entire sequence is effected.

Front 109

Germline Mutations

Back 109

phenotype effects are passed to next generation (Birth defects, happen during meiosis)

Front 110

Somatic Mutations

Back 110

Not passed to next generation, may have extreme phenotypic effects (ex. Cancer)

Front 111

Sex-influenced Traits

Back 111

Abnormal gene is located on an autosome, but its expression is influenced by hormone concentration.

Front 112

Enzyme Activity Tests

Back 112

Diagnosis; Detection of enzymes necessary for normal function.

Front 113

RFLP's

Back 113

Restriction Fragment Length Polymorphisms.
-Presence or Absence of specific nucleotide sequence for normal function.
-Involves use of restriction endonucleases which cut DNA at specific sites
-Separate fragments by gel electrophoreses
-Pattern of separated fragments indicates presence or absence of a nutrition