Bio Exam 4

Front 1

Allele

Back 1

Different gene sequences among all humans.

Front 2

Polymorphism

Back 2

Differences in DNA sequence. NOT a mutation.

Front 3

Mendel's Observations

Back 3

Bred pea plants.

Observation 1: some alleles are dominant over others.

Observation 2: Alleles Segregate

Front 4

How did Mendel Conduct His Experiment?

Back 4

Po = parental plants were True bred... meaning that the offspring produced from self-fertilization remained uniform from one generation to the next.

F1 = He bred purple x white sexually and found all to be purple.

F2 = He bred the purple x purple from end of F1 to find 75% P and 25% W

Front 5

Genotype

Back 5

Describes gene sequence

Front 6

Phenotype

Back 6

How gene sequence are interpreted physically.

Front 7

How do we get functions from genes?

Back 7

genes -> proteins -> function

unique genome -> unique proteome -> unique phenotype.

Front 8

Somatic vs Germline Mutation

Back 8

Somatic - not passed on (ie: UV radiation)

Germline - passed on (ie: X ray) and produces gametes (sperm and egg)

Front 9

Mendel Ratio

Back 9

Found that phenotypes exhibit a 3:1 ratio while genotypes are 1:2:1 (true breeding dominant, not true breeding dominant, true breeding recessive).

Front 10

Punnet Squares

Back 10

Predict patterns of inheritance

Front 11

Genetic Diseases

Back 11

Sickle Cell Anemia - recessive disease allele (carriers not affected)

Huntington's - dominant disease allele (carriers affected)

Hemophilia (recessive, X linked)

Front 12

Mitosis

Back 12

Division of the cell that results in generation of two, genetically identical daughter cells (identical to each other and parent cell)

Front 13

Haploid vs. Diploid

Back 13

Haploid: # of unique chromosomes (n=3)

Diploid: organisms that contain 2 copies of each chromosome (2n=6)

Front 14

Homologous

Back 14

Diploid cells are:

Homo - same type and same genes

Front 15

Chromosome Duplication

Back 15

Results in 1 chromosome consisting of 2 sister chromatids, sister chromatids will be separated during mitosis (which doesn't change ploidy).

Front 16

Ploidy

Back 16

The number of sets of chromosomes in a cell.

Front 17

All Cells Are Either In:

Back 17

M Phase: Mitosis and Cytokinesis

- division of genetic material and organelles to 2 new cells.

Interphase: The time of a cells life cycle between division (when its doing what its made for)

Front 18

Cell Cycle

Back 18

Go: subphase of G1 were cells don't divide for long time

G1: normal cell growth and function

S: synthesis (dna replication)

G2: preparation for division

Mitosis: Division of identical genetic material

Cytokinesis: cytoplasm, cell membrane and other organelles are divided between daughter cells.

Front 19

How does the cell cycle run?

Back 19

Most cells exist in function in G1, until given signal to replicate DNA.

Afters S phase, there are two identical sister chromatids for every chromosome.

Mitosis divides those identical chromatids into 2 new cells.

III (1 chromsome) -> XXX (duplication into s. chromatids) -> XXX (lineup in nucleus) -> III + III (divide into 2 cells)

Front 20

Difference between II II II II and XX XX XX XX

Back 20

First one shows diploid cells (they are paired but not duplicated)... second one (shows duplicated pairs).... Each X is split up into new cell

Front 21

Prophase

Back 21

C. condense and appear as two sister chromatids.

Cytoskeleton is dissambled and spindle begins to form

Front 22

Metaphase

Back 22

All C. are aligned at equator of cell called the metaphase plate, chromosomes are attached to opposite poles and are under tension.

Front 23

Anaphase

Back 23

sister chromatids are split and individual chromosomes are freed and pulled to opposite poles.

Spindle poles move apart

Front 24

Telophase

Back 24

C. clustered at opposite poles decondense and nuclear envelopes re-from around chromosomes.

Front 25

Phosphorylation

Back 25

Addition of a phosphate functional group to a protein that changes shape, function and charge of protein. Done by kinase enzymes, and phosphatase removes a phosphate group.

Front 26

Cyclin

Back 26

protein that is only made during specific times on substages in cell cycle

Front 27

Cdk

Back 27

Cyclin dependent kinase - only functions when in complex with cyclin. They phosphorylate a lot of other proteins and enzymes to advance cell cycle

Front 28

How does cell cycle advance?

Back 28

Cyclin is made during G2, which binds to Cdk to advance to M. It then degrades and the cycle repeats. High cyclin = high Cdk phosphorylation = high division rate.

Front 29

Stopping the cell cycle?

Back 29

Cell can't go in "reverse", checkpoints, are signals in c.c. where cells wait for signals to proceed

Front 30

3 major checkpoints

Back 30

G1/S checkpoint: growth factors, nutrition state, size of cell

G2/S checkpoint: replication completed, DNA integrity is okay

Spindle checkpoint: chromosomes attached to metaphase plate

Front 31

Cancer

Back 31

Regulation of cell cycle is disrupted that begins with a tumor (mass of cells with uncontrolled cell division). The proteins that act as checkpoint don't work properly, usually due to mutation in genes that make protein.

Front 32

2 types of proteins

Back 32

tumor suppressing: STOP. Prevent cell division by acting at checkpoints.

proto-oncogene: START. promote cell division by failing to act checkpoints.

Front 33

Mutations of those proteins

Back 33

P.O. - produces oncogenes that cause cancer by stimulating cell division where it shouldn't occur. (its always going).

T.S. - cause cancer by failing to block cell division in cells taht are damaged or are in no condition to divide (its always going).

Front 34

p53

Back 34

Tumor suppressing

- dna damage causes p53 to become phosphorylated and prevents its (degradation)... which causes a build up of p53.

- accumulation of p53 int he nucleus produces cell division inhibitors. (could act on protein that stops cyclin/cdk binding

Front 35

What can pass through membrane and what can't?

Back 35

Small hydrophobic molecules can pass directed through.

Proteins have to be secreted by exocytosis (done w/ vesicles). which fuses with the plasma membrane.

Front 36

Why does cell signaling happen?

Back 36

Allows us to have multicellularity and organize to form tissues, etc..

Front 37

5 Cell signaling outputs

Back 37

1. change cell shape.

2. change cell migration

3. change cell division/proliferation/growth

4. change cell function

5. change gene expression, which changes proteins made... DNA -> RNA -> protein

Front 38

Direct Contact

Back 38

Tight junction, adhesive junction, or a gap junction

Front 39

Gap Junction

Back 39

When cells are in close contact with each other they have perfectly lined up pores that are able to transport things right to them.

Front 40

Paracrine & Autocrine Signaling

Back 40

short range signaling

Paracrine (next door)

Autocrine (to itself)

ie: growth factors

Produce short lived, local effects.

Front 41

Endocrine Signaling

Back 41

Long - range signaling

ie: through blood, hormones

Live longer and produce effects elsewhere.

Front 42

Synaptic Signaling

Back 42

A kind of paracrine signaling

ie: neurotransmitters

Transports through a small synaptic gap to the target cell.

Front 43

LIgand

Back 43

small molecules or protein that transports a signal that binds to the receptor

Front 44

Amino Acids and Phosphorylation

Back 44

Only 3 AA can be phosphorylated (ser, thr, tyr) and it causes a protein conformational change.

Front 45

Nuclear Hormone Signaling

Back 45

Intercellular signaling

Small, hydrophobic molecules go right through membrane to cause cellular response... it binds to a n. hormone receptor (causes conformational change) that bind to dna to help rna pol. transcribe, make it not transcribe, or know how much to transcribe.

Front 46

N.H.S. Receptor

Back 46

Has 3 domains:

ligand bind domain

activation domain (inhibitor or no inhibitor)

dna binding domain

Front 47

Extracellular Receptors

Back 47

All integral membrane proteins (permanently attached to membrane).

Ligand does not enter cell to change signal

Ligand binding causes conformational change, which changes activity of receptor.

Front 48

Channel Linked Receptor

Back 48

AKA: Ligand - gated channel

Channel contains receptor specific ligand.

Ligand binding -> receptor -> conformational change (opens channel)

Amino acids on inside indicate whether + or - ions come through.

Front 49

Enzyematic Receptor

Back 49

phosphorylation and their substrates are found in the intercellular space (cytoplasm).

ie: insulin, growth factors

2 types (both kinases): RTK and Ser/Thr Kinase

Ligand binding causes receptors to dimerize which cause them to phosphorylate each other (auto-phosphorylation). Other proteins bind to P group on cytoplasmic domain of receptors and can become phosphorylated which causes a cellular response

Front 50

Secreted proteins

Back 50

Not phosphorylated

Front 51

Ras

Back 51

a small G protein if bound to GTP is active and GDP is inactive. Phosphorylation occurs by trading GDP for GTP. Which starts phosphorylation cascade, RAS - RAF - MEK - ERK - Transcription Factors (which go into nucleus and turn on genes)

Front 52

RTK

Back 52

receptor Tyr kinase pathway

Front 53

Shutting down RTK pathway

Back 53

1. activated Ras eventually hydrolyzes GTP to yield GDP.

2. active receptor (bound to ligand) is eventually endocytosed (expelled from cell), which makes a vesicle that contains the receptor that can be recycled or degraded.

Front 54

GPCR Signaling

Back 54

Gene Protein Coupled Receptor

Front 55

GPCR Structure

Back 55

7 transmembrane domains

extracellular ligand binding domain

intercellular domain that makes contact with LARGE G-protein

Front 56

GPCR Process

1. Ligand Binding to GPCR

Back 56

Causes a conformational change

Front 57

GPCR Process

2. Activation of G protein

Back 57

Heterotrimer - alpha - GDP, beta, gamma (made of three things).

Alpha binds to GTP and dissociates from beta and gamma and activates 2nd messengers (beta and gamma work together to do that too).

Front 58

GPCR pathway

Back 58

Ligand - GPCR - Alpha-GTP - adneyl cyclase - cAMP - PKA - glycogen - glucose

Front 59

Problem: Diverse outputs from 1 signal

Back 59

Different cells respond differently to same signal because different cells have different signaling specific pathway member present. Also, not all cells have same proteins present so some of the options some cells have some cells don't even have.

Front 60

Operator

Back 60

Binding sit for other proteins called (repressors and inducers) before the promoter region that inhibit RNA pol to binding site. And help with make sure not all cells are transcribing same genes.

Front 61

How do you make intermediate amount of protein

Back 61

Regulate frequency of transcription

Front 62

Bacteria in Low and High Trp

Back 62

Low Trp - bacteria make their own (encoded enyzmes make Amino acids)

High Trp - bacteria don't make their own

Front 63

Operon

Back 63

Cluster of co-regulated genes (includes operator and promoter) that all have same promoter/operator.

Front 64

How does Trp operon work?

Back 64

It encodes Trp synthesis pathway components (that synthesizes Trp together).

Trp turns Trp operon off so it won't produce it. Uses a TRp repressor which conformationally changes and binds to operon to inhibit RNA pol. binding.

No Trp -> Trp operon turns on (bacteria must synthesize own Trp)

Can change as soon as there isn't any Trp left

Front 65

Lac Operon

Back 65

encodes lactose catabolism pathaway components. Includes a CAP binding domain (CAP-Operator- Promoter - Genes in that order)

Front 66

Lac Operon On/Off

Back 66

On: Lactose is used (catabolism breaks it down)

Off: Lactose is not used (it is ignored)

Front 67

Lac Presence/Not

Back 67

If lac is present, lac operon is expressed so lac can be broken down

Front 68

Glucose Presence

Back 68

Lac operon is repressed. CAP is an inducer that is active when bound to cAMP... it binds to the CAP region and is necessary for lac operon expression. When glucose is present, cAMP levels go down which makes CAP not active and causes it not to bind which turns lac operon off.

Front 69

Cell Fate

Back 69

It changes and is driven by different combinations of transcription factors.

Front 70

RNA Splicing

Back 70

Alternative splicing causes multiple gene products from different variations of mRNA and proteins

Front 71

Enhancers

Back 71

Each gene has multiple enhancers located close to promoter or far away, or even are in introns.

Each enhancer contains TF binding sequence.

Front 72

2 kinds of TF

Back 72

general (all cells, help RNA pol. work) - assemble to promoter

Activators/repressors - cell type specific, bind to enhancers, produce combos that lead to differences in different cell types.

Front 73

How can enhancers far away affect gene sequence?

Back 73

a loop like figures forms with one specific TF from RNA pol. holoenzyme to activate transcription

Front 74

Nucleosomes

Back 74

organize dna and regulate genes by having histone proteins that can bind tightly to dna and this can limit access of ran pol to promoters and TF to enhancers.

Dense nucleosomes -> repressive to transcription

Front 75

2 major kinds of post translational modificiation

Back 75

acetylation (-) makes it looser due to negative phosphates in dna/increase gene expression

methlyation (+) makes it tighter and decreases gene expression.

Both changes charge of protein that interacts with DNA.