In this paper, we investigate the structural properties of trees and bipartite graphs through the lens of topological indices and combinatorial graph theory. We focus on the First and Second Hyper-Zagreb indices, $HM_1(G)$ and $HM_2(G)$, for trees $T \in T(n, Δ)$ with $n$ vertices and maximum degree $Δ$. Key propositions demonstrate that the presence of end-support or support vertices of degree at least three, distinct from a vertex of maximum degree, implies the existence of another tree $T' \in T(n, Δ)$ with strictly smaller Hyper-Zagreb indices. These results are extended to exponential forms, highlighting the influence of high-degree vertices. Additionally, we explore structural characterizations of trees via degree sequence majorization and $S$-order, establishing conditions for the first and last trees in specific classes. For bipartite graphs, we examine equitable coloring, cycle lengths, and $k$-redundant tree embeddings, supported by theorems on connectivity and minimum degree constraints. The paper also addresses the independence number of bipartite graphs, exterior covers, and competition numbers of complete $r$-partite graphs, providing bounds and structural insights. Finally, we discuss Markov-chain algorithms for generating bipartite graphs and tournaments with prescribed degree sequences, analyzing their mixing times and convergence properties. These results contribute to the understanding of extremal properties and combinatorial structures in graph theory, with applications in chemical graph theory and network analysis.