BISC 101 Test 1

What are cells?

What are cells?

• make up living organisms

• different characteristics

• Mostly surrounded by membrane

• transform energy

What are unique features in eukaryotic cells?

• Nucleus

• Membrane-bound compartments with specific functions

The 3 Domains of life

• Bacteria

• Archaea

• Eukarya

Function of a nucleus

Stores DNA and determines which products to create

Functions of ER

Production of lipids and membrane protein

Functions of the Golgi Appartus

Receives material from ER, modifies, sends to appropriate location

Functions of Chloropast

Contains chlorophyll which gives out its colour + solar energy used to make glucose

Functions of Mitochondria

Produces ATP and breaks down carbs, proteins, fats

Functions of cell membrane

Controls what goes in and out

Functions of Lysosome

Digestion/ disassembly of macromolecules into monomers for reuse

Functions of Cytoskeleton

Provides base and support of the cell + tracks for vesicles and organelles

4 types of cellular macromolecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic Acids

Polymer

Molecule consisting of many similar or identical building blocks linked together by covalent bonds

Lipids Characterisitcs

• Hydrophobic biological molecules

• Many non-polar bonds (C-H)

• The out lyre (add one)

• Ex: Fats, Sterols, Phospholipids

Fatty Acids

Phospholipids and fats contain this and have similar traits for both phospholipids and fats. They have a larger hydrophilic portion

Differences in fats = different fatty acids

• different tail length (short vs long)

• different # and position of double bonds

Saturated fatty acids

• No double bonds (saturated with hydrogen)

• Straight

• Solid at room temp (butter)

• Rigid and tight together

Unsaturated fatty acids

• Contain 1 or more double bond

• Bent

• Liquid at room temp (olive oil)

• Loose and not packed together

• Loses 1 H

Phospholipids are amphipathic

They have hydrophobic and hydrophilic portions as well form membrane bilayers in water

Plasma/ cell membrane

• Separates cell from its surrounding

• Controls movement of molecules in and out of the cell

• Composes of phospholipids, proteins, carbohydrates, may contain sterol

• A fluid mosaic model

Factors affecting membrane fluidity

• Temperature: increase of temperature = increase of fluidity, the opposite will be the same. Can’t be too fluid or rigid; needs to be perfect fluidity

• Type of phospholipids: Unsaturated fatty acids more fluid than saturated ones. Shorter fatty acids more fluid than longer fatty acids

The phospholipid bilayer is semi-permeable

• Permeability depends on chemical properties of substances

• Transport allow passage of important substances that can’t cross on their own.

• Large, uncharged polar molecules and ions can’t cross

Passive Transport (energy)

Does not require an input of energy

Active Transport (energy)

Requires an input of energy

Diffusion

The tendency of molecules to move down a concentration gradient. Releases energy

Passive Transport

Each substance diffuses independently

Facilitated Transport

• Diffusion that is “helped” by transport protein

• No energy required

Hypotonic solution

Contains higher solute concentration → burst

Hypertonic solution

Contains lower solute concentration → shrivel

Isotonic solution

Equal solute concentrations + water is still moving but has no net movement → stays the same

Osmosis and Cells

Water passes through membrane by osmosis via channel proteins. Plasma membrane restricts solute flow

Active Transport

• Causes substance to move against its concentration gradient

• Builds up concentration and membrane potentials

• Requires energy

ATP equals to

Cellular source of energy

ATP hydrolysis

allows transport to change shape

Na K Pump

• Transport 3 Na ion out of the cell

• Transport 2 K ion into the cell

• Both against their concentration gradients

• Uses energy in the form of ATP

Primary Active Transport

energy from ATP

Secondary Active Transport

energy from concentration gradient

Potential energy

Stored energy due to position or composition

Na Glucose Cotransporter 1

• Transport 1 glucose molecule into the cell

• Transport 3 Na ions into the cell

• Uses energy from NA concentration gradient

Bulk Transport

• Some cargos too big for individual transport proteins

• Transported within membrane-bound vesicles

Export

Exocytosis

Import

Endocytosis

Exocytosis

• Secretion of cargoes through fusion of vesicles with the plasma membrane

• Cargos released to cell exterior

• Membrane become part of plasma membrane

Pinocytosis

• Internalization of liquids and dissolved solutes (takes in the solutes inside the water)

• Vesicle is produced from plasma membrane

Receptor-mediated

• Internalization of specific molecules (cargos)

• Receptor-cargo complex internalized in vesicle

Phagocytosis

• Internalization of cells or molecular aggregates

• Used for eating and defence

• Cellular eating

DNA

genetic information of the cell

RNA

• diverse functions

• Carries genetic information from DNA to sites of protein synthesis

• Enzymatic activity

Nucleic Acids Monomer: nucleotides

• Pentose sugar (deoxyribose)

• Phosphate group

• Purine or pyrimidine base

Pentose sugar

5 carbon sugar as a ring

Phosphate group

• Confers -ve charge

• Linked to 5’ carbon on sugar

Nitrogenous base

• defines nucleotide identity

• Purines (2 ring structure) and Pyrimidines (1 ring)

Polymer

nucleotides joined by phosphodiester bond (DNA bond). 3’ OH of one nucleotide is covalently bonded to the 5’ phosphate of the next

Nucleic Acids

• directional molecules

• New nucleotides are always added to 3’ end

Double Helix

• 2 strands of DNA twist around each other to form double helix

• All pairs have same geometry

• 2 strands are antiparallel (run in opposite directions)

• Purine-pyrimidine pair

Base pairs of DNA

• A=T

• C=G

Deoxyribonucleotide

DNA: has thymine and missing O2

Ribonucleotide

RNA: has uracil and has an extra hydroxyl

RNA 3D structure

• Exists as a single strand

• Unique shapes due to internal base-pairing

DNA replication

• semi conservative

• Each daughter helix composed of: one strand of parental molecule and one newly synthesized strand

DNA polymerase

• The enzyme that joins nucleotides to synthesize DNA

• Synthesis has to go from 3’ to 5’

• Reads the next base to match the nucleotide and DNA polymerase creates a new phosphate linkage

Primase

• DNA polymerase cannot synthesize DNA de novo

• Creates short (10-12 nucleotide) RNA primer → reads the template of DNA prime & use base pairing to match the nucleotide to create a new RNA sequence

• Extended by the DNA polymerase

DNA replication - How it begins

• DNA strands at origin of replication = specific DNA sequence

• Creates 2 replication forks = site of DNA replication

DNA helicase

• Unwinds DNA duplex at each replication fork

• Exposes more single stranded template

Leading strand

one new DNA strand is made continuously 5’→3’

Lagging strand

DNA synthesis occurs in small pieces (Okazaki fragments) 5’→3’, later joined by DNA ligase

Central Dogma of Molecular Biology

Using DNA as a template to create RNA → Using mRNA as a template to create a polypeptide

Transcription

Synthesis of RNA using DNA as a template. Nucleic acid → nucleic acid. Occurs one gene at a time

Translation

Synthesis of polypeptide using mRNA sequence as a template. Nucleic acid → polypeptide

Gene

• Unit of heredity

• Sequence of DNA encoding a protein

DNA-dependant synthesis of RNA

• Strands of DNA are separated (break apart base pairs)

• One strand acts as the template to synthesize a strand of complementary RNA (template strand)

• RNA is complementary to DNA template.

RNA polymerase

• The enzyme that joins nucleotides to synthesize RNA

• 3→5 transcribed ti 5→3 which becomes template and the opposite is the same. Strands are always written 5→3

Promoter

Specific DNA sequence where transcription begins

Coding Sequence

DNA sequence is transcribed

Terminator

Specific DNA sequence where transcription ends

Initiation

RNA polymerase binds promoter

Elongation

Template strand of DNA read to synthesize RNA

Termination

RNA polymerase dissociates from template at terminator

mRNA processing in Eukaryotes

• Eukaryotes modify transcripts before translation

• Does not occur in prokaryotes

Pre-mRNA

Transcribed sequence

mRNA

Mature, processed sequence

5’ cap

• Modified G nucleotide

• Attached by 5’-5’ linkage

polyA tail

• String of A nucleotides at 3’ end of mRNA

Introns

• Non-coding or intervening sequences (removes)

• Don’t encode protein

Exons

• Coding or expressed sequence (left behind to code)

• Encode protein

Splicing

Introns are removed, exons ligated together to make mature mRNA

How is protein sequence encoded?

• Nucleic acid “language” is translated to that of proteins 3 letters at a time, read 5’→3’

• One Codon = 3 nucleotides = one amino acid

• Amino acids linked together via peptide bonds

Genetic Code

• 3 nucleotide codons of RNA = 64 combinations

• 61 of 64 codons encode amino acids

AUG = start codon

• Tells translation where to start

• Encodes a methionine (Met)

• All proteins start with Met

3 STOP codons

UAA, UGA, UAG:

• Tells translation where to stop

• Do not encode an amino code

Ingredients for translation:

• mRNA carries information (order of amino acids)

• tRNA delivers the amino acids

• Ribosome (contains RNA) uses information mRNA to attach amino acids in the correct order

tRNA

delivers amino acid to the ribosome during translation

Translation mechanism - tRNA

• Bridge between amino acid and mRNA

• Anticodon is complementary to the codon

• Different tRNA for each amino acid

Ribosome for Translation

• RNA-protein complex

• Consists of a small and a large subunit

• Catalyzes peptide bond formation (between amino acids)

Translation Summary

• Start codon initiates translation

• tRNA delivers amino acids to the ribosomes by base pairing to codons in mRNA

• Ribosome (rRNA) creates peptide bonds between incoming amino acids

• Recognition of stop codon terminates translation

Polyribosomes

• mRNA is translated by many ribosomes at the same time

What effects do mutations have on a gene expression for a promoter?

mRNA & polypeptide: gene won’t be transcribed so mRNA can’t be transcribed to create a polypeptide which slows down production

What effects do mutations have on a gene expression for a start codon?

polypeptide only: When genes is transcribed, 3’→5’ is the template, It starts the translation machinery but the transcription won’t care about the mutation. The mRNA will be mutated & produced so the translation machine will continue to find a AUG to start which creates a completely different polypeptide.

Gene Expression in Eukaryotes

• Transcription and Translation are separated in eukaryotes.

• Occur in different cellular compartments: Transcription = nucleus, Translation = cytoplasm

• Transcription (and mRNA processing) are complete before translation

Gene Expression in Prokaryotes

• Transcription and translation are coupled in prokaryotes

• Occur in the same cellular compartment

• Translation begins before transcription is finished