BIO 311C Final Map

Protein

Binds to operator

Positive Regulation

Activator

Operon Gene Regulation On

Negative Regulation

Repressor

Operon Gene Regulation Off

Specific Transcription Factor

Last gene that enters the nucleus

Turns gene regulation on or off

Far Away from the Gene

Activator binds to enhancer

DNA bending brings activator
closer to promotion site

Activators bind to mediator proteins

Brings the activator closer to
the promotion site

Gene Organization

Structural genes

Genes whose expression is controlled together

Lac A

Structural Gene for B-Galactoside transacetylase

Lac Y

Structural Gene for B-Galactoside permease

Lac Z

Structural Gene for B-Galactosidase

Regulatory gene

Lac I

Codes for repressor protein

Regulatory regions

Promoter

Occurs structural and regulatory gene/s

Operator

“Switch” is a segment of DNA

Location where protein binds

Proteins are called activators/repressors

The binding causes positive/negative regulation

Turn on gene expression

Turn off gene expression

Regulation Through Operons

Occurs at level of transcription

Positive regulation= gene expression ON

expression at high level

With activator, transcription occurs

Without activator, no transcription occurs

Negative regulation= gene expression OFF

Repressor protein bond to operator sequence

With repressor, no transcription occurs

Without repressor, transcription occurs

Lac Operon

Example of negative and positive regulation

Regulation needs both repressor and operator

Lac= Lactose

Disaccharide made of glucose and galactose

Inducer of the lac operon

Lactose absent, repressor active, operon off

Transcription of structural genes is blocked

Negative regulation of operon

Lactose present, glucose scarce (cAMP level high)

Abundant lac mRNA synthesized

Operon ON: Induced/ high expression

Activator protein CAP is activated by cAMP

CAP helps RNAP to bind promoter

Facilitates transcription

Lactose present, repressor inactive, operon on

No glucose= operon ON

Inducible operon

All structural genes are transcribed

Forms a long mRNA

mRNA translates= B-Galactosidase, Permease, Transacetylase

Takes in more Lactose from outside

Break it down to glucose and galactose

Uses sugars as needed

Lactose present, glucose present (cAMP level low)

Little lac mRNA synthesized

Presence of Glucose operon OFF

Blocks Adenylyl Cyclase

Prevents production of cAMP

CAP cannot be activated

CAP can't help RNAP to bind promoter

Transcription factors

Proteins that help turn specific genes "on" or "off"

Help increase or decrease level of transcription

General

Low levels of transcriptions

Background/basal

Bind to promoter and regions near

Specific

Change levels of transcription

Increase levels of transcription

Done by activators

High levels of transcription are reduced by repressors

Bind to distal control elements called enhancers

Present near or far from gene they are controlling

Control elements in DNA

Proximal

Sequences in DNA close to promoter

Bind general transcription factors

Distal

Enhancers

Sequences in DNA upstream or downstream of gene

Can be close or far from gene they are controlling

Bind to specific transcription factors

Operons

Helps with regulation with an on-off switch

"Switch"

Segment of DNA known as an "operator"

Positioned within promoter

Proteins bind to operators to turn on gene expression for multiple genes

OR to turn off expression

Postive regulation

Negative regulation

Gene Organization

Proximal

basal (general) expression

specific to eukaryotes
(ex. humans)

Distal

enhancers

bind activator proteins

activator bound to receptor is brought
to promoter via DNA bending proteins

transcription increased via
RNA polymerase II

Regulation through Operons

operons do not occur in eukaryotic cells
- made in mRNA w/ individual promoter

Transcription Factors
(instead of operons)

activators

repressors

Other Destinations

Endomembrane system

Secretory pathway (Polypeptide synthesis)

Cell Communications

Membrane receptors

Signal molecule and GDP = Inactive

G-Protein alters shape, so GTP can bind to it

Now active, G-protein can activate enzyme (Adenylyl Cyclase)

Enzyme is activated at reception

Polypeptides function as a Kinase

Kinase adds phosphates to other kinase through ATP

Tyrosine Kinase Receptor is activated

Cellular Respiration

Location-
Cytoplasm/cytosol of the cell

Input-
2 ATP
1 Glucose

Output-
4 ATP
2 NADH
2 pyruvate

Net-
2 pyruvate
2 ATP
2 NADH

Substrate level oxidation-
ATP made

Location-
Matrix of the mitochondria

Input-
2 Pyruvate

Output-
2 CoA
2 NADH

Net-
2 CoA
2 NADH

NO Substrate level oxidation-
ATP not made

Location-
Matrix of the mitochondria

Input-
2 CoA

Output-
6 NADH
2 FADH2
2 ATP

Net-
6 NADH
2 FADH2
2 ATP

Substrate level oxidation-
ATP made

Location-
Inner mitochondrial membrane

Input-
O2
2 FADH2
10 NADH

Output-
H2O
28 ATP

Net-
H2O
28 ATP

Electron transport chain and chemiosmosis-
ATP made

Subtopic

Multi-step pathway that
helps amplify a signal

More coordination

More regulation

Second messenger

Small, nonprotein, water-soluble molecules or ions

Used in signal transduction to
relay a signal within the cell

cyclic AMP

Formed from ATP

Synthesized using the enzyme Adenylyl Cyclase

Once used for the relay, cAMP is
converted into AMP by an enzyme
called phosphodiesterase

Cell Structures and Functions

fimbriae

allows for surface adhesion

nucleoid

non-enclosed region for DNA

ribosomes

synthesize proteins

plasma membrane

structure; enclose

cell wall

rigid wall; provides structure

glycocalyx

capsule or slime layer outer coating

flagella

allows locomotion of organelles

bacterial chromosome

single, coiled chromosome

centrosome

site for initiation of microtubules

lysosome

makes macromolecules

flagellum

allows for movement

cytoplasm

gel-like substance; contains cell consistency

golgi apparatus

secretion of cell products & active in synthesis

peroxisome

metabolic functions

mitochondrion

regulates cellular respiration & produces majority of ATP

ribosomes

synthesize proteins

rough er

produce proteins

smooth er

synthesize proteins

plasma membrane

structure; enclose

cytoskeleton

support shape

nucleus

contains genetic material

central vacuole

storage and hydrolysis

cell wall

cell shape and protection

chloroplast

photosynthetic organelle

plasmodesmata

connects cytoplasms

Part of an amino acid

Electrically charged on basic and acidic groups

Polar

Tryptophan can function

Contains – OH, SH or NH groups

All contain polar covalent bonds

Hydrogen bonding

Non-Polar

Contains – H, CH or a carbon ring

Hydrophobic

All contain nonpolar covalent bonds

Van der waals forces

Basic

Hydrophilic

Positively charged

Acidic

Negatively charged

Ionic bonding

The only covalent bond

Forms protein structures

Tertiary structure

Quaternary structure

Primary structure

Covalent peptide bonds

Secondary structure

Hydrogen bonds

Tertiary structure

Electrostatic interactions/disulfide bridges

Low to high concentration

Energy required

High to low concentration

Diffusion

Facilitated Diffusion

Osmosis

No energy required

Hydrophilic heads and hydrophobic tails

Filter unwanted particles

Membrane fluidity

Saturated Fat

Less fluid membrane

Unsaturated Fat

More fluid membrane