Biology Midterm

Amino Acid

Monomers of proteins, 20 amino acids. Can be acidic or basic, hydrophilic or hydrophobic.

R Group

Part of an amino acid that differs and gives amino acid different properties

Peptide Linkage

Covalent bond between carboxyl group and amino group of 2 amino acids. Formed through condensation.

Tripeptide

Three amino acids bonded together

Nutrient

A chemical substance found in food used by the body

Essential Amino Acids

Cannot be synthesized by the body

Non-essential Amino Acids

Can also be through metabolism if necessary. This process is called transamination

Denaturation

When a protein folds incorrectly because of a change in temperature of pH

Primary structure

Linear sequence of amino acids

Secondary structure

Protein folds open itself through hydrogen bonds in backbone, no interaction between R groups (ex: alpha helices and beta sheets)

Tertiary structure

Interactions between R groups

Quaternary structure

2+ polypeptide chains come together to form a complex bioactive molecule

Integral proteins

Proteins attached to membrane

Conjugated protein

Has a non-protein prosthetic group.

Non-conjugated structure

Has no non-protein group.

Insulin

Hormone made in the pancreas that promotes the synthesis and storage of glycogen in the liver and muscle cells

Hemoglobin

Protein in red blood cells that carries oxygen

Collagen

A non-conjugated protein

-Three polypeptide molecules, triple helix

-Every third amino acid is glycine

-Stacks of the triple helices form fibers

Cell Theory

1. Cells can only arise from preexisting cells

2. Living organisms are comprised of cells, the smallest unit of life

3. Unicellular organisms carry out all functions of life in one cell

Unicellular

Single cell organisms

Multicellular

Organisms made of many cells

Protists

Single cell eukaryotes

Prokaryote

Unicellular, no nucleus or membrane bound organelles

• Very small

• Nucleoid instead of nucleus

• 70s ribosomes

• 2 types: Eubacteria and archaea

Bacteria

Unicellular organisms with a cell wall (made of peptidoglycan), plasma membrane, cytoplasm, naked DNA (sans histones) , 70s ribosomes

Sometimes have pilli and/or flagella

Pilli

Little ‘hairs’ on some bacteria that enable attachment to other bacteria

Flagella

A tail that allows bacteria to move around

Gram positive bacteria

thick cell wall, stains red/pink

Gram negative bacteria

thin cell wall, stains purple

Differentiation

Process by which cells become specialized, some genes/proteins are expressed more than others

Eukaryotes

Cells with membrane bound organelles and a nucleus, 80S ribosomes

Organelles

‘Little organs’ with specialized functions in cells

Cytoplasm

Fluid in cells, contained by plasma membrane

Plasma membrane

semi permeable membrane made of lipids and proteins

Nucleus

Control center where DNA is stored

Nuclear envelope

Double layered membrane that surrounds nucleus

Nuclear pores

Small holes in nuclear envelope that allow materials (such as RNA and proteins) in/out of nucleus

Chromosome

Length of DNA that carries specific genes

Condensed during mitosis and meiosis

Contained within nucleus

Chromatin

Nuclear material made of DNA and histone proteins, contained in nucleus

Nucleolus

Sited of ribosome synthesis, in nucleus

Mitochondria

Organelle, site of Krebs Cycle and Electron Transport Chain

Produces ATP, number depends on cell type/activity

Endoplasmic reticulum

Network of folded tubes, sacs and sheets

• Transports stuff throughout cell

• Made up of proteins, connected to nuclear envelope

• Can have ribosomes (Rough ER) or not (smooth ER)

Golgi Apparatus

Modifies, sorts, and packs proteins for shipment

• Stack of flattened membranous sacs (‘pancakes’)

Lysosomes

Spherical vesicles surrounded by a single membrane

• Hydrolytic enzymes break down waste and foreign materials

• Involved in autolysis and apoptosis (cell suicide)

Gene mutation

Change in the sequence of bases of a gene, more likely to occur in areas with less accessory proteins

Substitution

Swapping one base for another

Insertion

Adding a base to the DNA sequence

Deletion

Removing a base from the DNA sequence

Frameshift

Mutation (insertion or deletion) that ‘messes up’ (shifts) 3 base pair codons

Every codon is affected by mutation

Degeneracy

AKA redundancy

Different codons can encode for same amino acid

Means that mutations sometimes have no impact

Mutagen

Agent that causes a genetic mutation

• Can cause cancer (ex: radiation, bacterial infection, carcinogens, hpv)

• Not all mutations are caused by mutagens

Transition

A substitution with a base of the same shape (Ex: Purine —> purine), less likely to change amino acid

Transversion

A substitution with a different shape of base, (ex: purine —> pyrimidine)

Germaine mutations

Occur in germ (reproductive) cells, passed down to offspring

Somatic mutations

Occur in somatic (non-reproductive) cells, passed down as cells divide in body

Genetic knockout

Deactivation or removal of a specific gene

Mutant

A genetically modified organism with 2 knockout alleles

Model Organisms

Non-human species that scientists use in the lab to investigate and understand biological processes

CRISPR

Clustered regularly interspaced short palindromic repeats, used as microbial immune system to remember and fight viruses

Used for gene editing

Cas

CRISPR associated protein

CRISPR Cas9

Gene-editing technology derived from bacterial CRISPR system. Cuts specific DNA then DNA repair mechanisms fix it in a way that modifies genetic sequence.

Cas9

Endonuclease that cuts strands of DNA at a specific site

Protospacer adjacent motif (PAM)

DNA sequence where Cas9 binds, downstream of target sequence

Non-homologous end joining (NHEJ)

Repair stage of CRISPR Cas9. Enzymes reconnect ends of broken DNA

Risky and can lead to mutations

Homology directed repair

Repair stage of CRISPR Cas9

Researchers design an RNA template to patch the breaK. A complementary DNA strand is created during repair.

Transcription

Synthesis of mRNA from DNA template, carried out by RNA polymerase

Promoter

A DNA sequence that is recognized by RNA polymerase to promote transcription

Template strand

Used to transcribe mRNA

AKA antisense/non-coding strand

3’-5’

Non-template strand

AKA coding/sense strand

5’-3’

Enhancer regions

Areas of DNA that increase transcription rates when a protein binds to them

Repressor regions

Areas of DNA that decrease transcription rates when a protein binds to them

Transcription initiation complex

Proteins and enzyme (RNA polymerase) that start transcription

Transcription factors

Factors that help initiate transcription, different factors can activate different genes

Gene expression

How the information is a gene directs protein synthesis

Ex: Housekeeping genes (always expressed), developmentally expressed, expressed in mature cells, signal based expression

Reverse transcription

RNA is converted to DNA, carried out by reverse transcriptase

RT-PCR

reverse transcriptase PCR

Introns

Non-coding sequences that interrupt coding sequences, transcribed but not translated

Exons

Coding sequences, transcribed and translated

Telomeres

Found at the ends of chromosomes, prevent degradation, attaching to other chromosomes, and apoptosis (programmed apoptosis)

VNTRs

Variable number tandem tandem repeats— short sequences of repeating bases, used in genetic profiling

Post transcriptional

Changes to newly transcribed mRNA, occurs in eukaryotic cells before translation

Transcription Steps

Initiation, elongation, termination

5’ capping

Modified guanine nucleotide added to 5’ end of mRN to prevent nuclear transport and degradation as well as promote translation

3’ polyA tail

100-250 bp chain of adenines added to 3’ end to increase stability

Intron splicing

Introns cut out

Alternative splicing

Splicing to create different combinations of exons

Translation

Synthesis of mRNA to protein, occurs on ribosomes in cytoplasm

Ribosome

Macromolecules used for translation, made of protein and RNA

Have a large and small subunit that come together around RNA

tRNA binding sites

Sites on ribosome where tRNA binds

• A site: 1st site, where tRNA and mRNA bind

• P site: Peptide strand is transferred on to amino acid

• E site: Exit site

tRNA activation

An enzyme facilitated process that produces charged tRNA (tRNA with an amino acid attached)

1. Enzyme binds to ATP+amino acid

2. Amino acid/AMP complex forms and specific tRNA molecule is recruited

3. Amino acid and tRNA bind, AMP released

Translation Initiation

1. mRNA binds with small ribosomal subunit on 5’ end

2. Initiator tRNA (w/ methionine) binds to AUG sequence

3. Moves to P site

4. peptide linkage

Translation elongation

1. New activated tRNA moves to A site

2. Old tRNA leaves E site

3. Peptide linkage forms in A site

4. Ribosome advances one codon, tRNAs shift down the line

5. Process repeats

Post-translational modification

Modification of proteins, ex: glycosilation to create glycoprotein

Ubiquitination

Post translational modification that involves the addition of the protein ubiquitin, prevents degradation

Proteolysis

Breakdown of proteins by hydrolysis, enzyme catalyzed, occurs in proteosomes

Translation termination

When a stop codon (UAA, UAG, UGA) is reached the polypeptide is released from the ribosome

DNA replication

Process by which DNA is copied. Occurs during synthesis phase of interphase.

Semi-conservative replication

Results in two DNA molecules with one original strand and one new strand

Helicase

1st step of replication, peels apart DNA and creates replication fork

Polymerase III

Reads primers and then synthesizes nucleotides

Polymerase I

Removes primers and switches them with nucleotides