BY-110 Cellular and Molecular Bio EXAM #2

Know in General how a polypeptide is structured

a polypeptide is a chain of amino acids linked together by peptide bonds.

POLPEPTIDE: PRIMARY STRUCTURE

sequence of amino acids in the polypeptide chain. Each amino acid in the sequence is connected by a peptide bond (a COVALENT BOND) between carboxyl group of one amino acid and amino group of next.

POLYPEPTIDE: SECONDARY STRUCUTURE

polypeptide chain folds into regular structures due to hydrogen bonding between backbone atoms.

ALPHA HELIXES: coiled structure where the peptide chain twists into a spiral.

BETA SHEETS: peptide chain folds into sheet-like structure with strands running alongside each other, stabilized by hydrogen bonds.

POLYPEPTIDE: TERTIARY STRUCTURE

over-all 3 dimensional shape of the polypeptide formed by interactions between (R-groups) of amino acids (hydrophobic, hydrogen, ionic, disulfide, and van der waals)

POLYPEPTIDE: QUATERNARY STRUCUTRE

multiple peptides come together to form multi-sub unit (functioning) proteins. (4-sub units) (interactions: hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bonds)

Know the different kinds of amino acids.

NON-POLAR: hydrophobic (water fearing) side chains (R-group)

POLAR: side chains that are hydrophilic (water loving)

ACIDIC: negatively charged

BASIC: positively charged

Be able to explain denaturation, why it happens and the implications of it for protein.

DENATURATION: process in which a protein loses it’s native 3 dimensional structure due to the disruption of the forces that maintain it’s shape such as hydrogen bonds, ionic bonds, and disulfide bonds. Leads to the unfolding or mis-folding of the protein causing it to loose it’s functional shape.

WHY IT HAPPENS: alterations in pH, salt concentration, temperature, and other environmental factors that cause a protein to unravel.

IMPLICATIONS: loss of biological function proteins function is very dependent on the shape of it.

IREVERSIBILITY: denaturation is irreversible especially when protein structure is completely disrupted.

Explain the general structure, type, and roles of nucleic acid.

Nucleic acids are polymers made up of nucleotides.

PHOSPHATE GROUP: phosphorous atom bonded to 4 Oxygen atoms

SUGAR MOLECULE: five carbon sugar (DNA: deoxyribose and RNA: ribose)

NITROGENOUS BASE:

• Purines: Adenine, and Guanine

• Pyrimidines: Cytosine, Thymine (DNA) and Uracil (RNA)

Nucleotides are linked together by ____________ which are between the phosphate group of one nucleotide and the sugar of the next.

PHOSPHODIESTER BONDS

TYPES OF NUCLEIC ACIDS:

DNA:

• double stranded forming a double helix, two strands of nuclotides are coiled together.

• ADENINE pairs with THYMINE

• GUANINE pairs with CYTOSINE

• they pair through hydrogen bonds

RNA:

• single stranded though it can fold into secondary strucutres. Sugar is ribose and URCAIL REPLACES THYMINE

• ADENINE pairs with URACIL

• GUANINE pairs with CYTOSINE

• mRNA: messenger (carries genetic information from DNA to ribosome)

• tRNA: transfer ( brings amino acids to ribosome)

• rRNA: ribosomal (component of ribosome)

Roles of DNA and RNA:

DNA: stores and transmits genetic information

RNA: plays a central role in protein synthesis

BOTH: work together in translation and transcription to ensure cell functioning and inheritance.

Compare and contrast components of nucleic acids.

DNA:

• Sugar: deoxyribose

• BASES:

  • Adenine - Thymine

  • Guanine - Cytosine

• Double stranded

• role; genetic information storage

• stability: more stable with long term storage

• location: nucleus (nucleoid region)

RNA:

• Sugar: ribose

• BASES:

  • Adenine - Uracil

  • Guanine - Cytosine

• Single stranded

• roles: protein synthesis and gene regulation

• stability: less stable, and short lived

• location: nucleus and cytoplasm

Know complementary base-pairing and be able to identify complementary sequences.

DNA:

• Adenine and Thymine (2 hydrogen bonds)

• Guanine and Cytosine (3 hydrogen bonds)

• EXAMPLE:

  • 5’ - ATGCCGTA - 3’

  • 3’ - TACGGCAT - 5’

RNA:

• Adenine and Uracil

• Guanine and Cytosine

• EXAMPLE:

  • DNA: 5’ - ATGCCGTA - 3’

  • RNA: 3’ - UACGGCAU - 5’

Know the importance of bioinformatics

• uses software and other computational tools to deal with the data resulting from sequencing many genomes.

• GENOME: the full set of genes and genetic material present in an organism

• Many genomes have been sequences, generating large sets of data.

• Analyzing large sets of genes or even comparing whole genomes of different species is called GENOMICS.

• Analyzing the sets of genes expressed (RNA) is referred to as TRANSCRIPTOMICS

• A similar analysis of large sets of proteins including their sequences is called PROTEOMICS.